title: PDI BIOL REP 3 STROMAL

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

description: Library name: Str_n3_P4HB_B3

data_processing:
RNA paired-end sequencing quality control was assessed through FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) and multiQC (Ewels et al., 2016). Both adapters and low quality bases (QV < 20) were trimmed from reads’ extremities using Trimmomatic (Bolger et al., 2014) with a minimum read length of 30 bp. An average of 53.6 million reads per sample were kept post-trimming for downstream analyses. All libraries were mapped against the bovine ARS-UCD1.3 release-114 reference genome (retrieved from https://ftp.ensembl.org/pub/release-113/fasta/bos_taurus.ARS-UCD1.3.dna.toplevel.fa.gz) through STAR aligner (Dobin et al., 2013) with default parameters. STAR-generated sorted BAM output files were used for assigned read counts to gene features with featureCounts (Liao et al., 2014) with the following parameters: -p -B -C -M -O --fraction. We relied on Bos_taurus.ARS-UCD1.3.113.gtf annotation file downloaded from https://ftp.ensembl.org/pub/release-113/gtf/bos_taurus.ARS-UCD1.3.113.gtf.gz.
Assembly: Bos_taurus.ARS-UCD1.3.113.gtf
Supplementary files format and content: gene_counts.txt

organism: Bos taurus

source_name: Endometrium

growth_protocol: Primary bovine endometrial cells cultured within endometrium on a chip device

extract_protocol:
Qiagen miRNeasy Micro kit with on-column Qiagen Dnase digestion
RNA libraries were prepared and sequenced by Novogene (Cambridge) as per their standard protocols which are described here based on information provided. Due to the small amount of RNA recovered, a SMARTer amplification process was performed using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Clontech) to synthesise the double-stranded cDNA libraries. Briefly, first strand cDNA synthesis was performed, followed by template switching and extension, then cDNA amplified by PCR to produce double stranded cDNA. The amplified cDNA samples were purified with AMPure XP beads and quantified with a Qubit 2.0 fluorometer (Life Technologies). Library prep was then carried out using the Novogene NGS RNA library prep set (PT042). Briefly, the cDNA samples were sheared by the Covaris system, then sheared fragments underwent end-repair, A-tailed, and ligated to sequencing adaptors. During this process a 200 bp size selection was used. The resulting libraries was then checked with Qubit 2.0 fluorometer (Life Technologies), diluted to 2 ng/mL, insert size checked on an Agilent 2100 bioanalyser and quantified to greater accuracy by qPCR.

treatment_protocol: Vehicle control, recombinant bovine CAPG 1ug/mL, or recombinant bovine PDI 1ug/mL for 24 hours

value: Endometrium

value: Primary

value: Stromal

value: Recombinant bovine PDI 1ug/mL


title: CES17

status: Public on May 19 2025

type: SRA

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

country: USA

institute: University of Pittsburgh

description: Library name: A1763

library_source: transcriptomic

data_processing:
Quality filtered and trimmed raw fastq files were aligned to the rat genome using STAR aligner (version 2.7.9a) and counted by Feature Counts (v.1.5.0-p3). Differential expression was performed using DESeq2 in R 4.2.0 and the resulting differentially expressed genes (DEGs) were determined using the design matrix of the different factors such as timepoints, condition and sex, at a defined cut-off criteria of |log2 fold-change|≥ 0.25 and p- value <0.1 adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. DEGs were subjected to REACTOME pathway analyses to determine the significantly enriched pathways. To extract further biological insight from the samples, we implemented gene set enrichment analysis (GSEA)which assesses the statistical enrichment of gene ontologies, and pathways, at a 5% significance, and data were visualized using Cluster profiler v4.8.1.
Assembly: mRatBN7.2
Supplementary files format and content: Count_Data.csv

molecule: total RNA

organism: Rattus norvegicus

source_name: Bone

extract_protocol:
RNA was extracted using miRneasy mini kit (QIAgen) and quantified using Qubit Flurometer
Samples had RNA integrity numbers of 5.5 – 9.6. RNA was shipped to Novogene Co. Ltd. (USA) for library preparation and sequencing. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and stranded mRNA-seq libraries were generated and individually barcoded using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.  Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) ring, the second-strand synthesis in the NEBNext Ultra II Directional RNA Library prep protocol, the reaction uses a buffer containing dUTP, which allows the incorporation of dUTP in place of dTTP. This process is facilitated by the NEBNext Second Strand Synthesis Reaction Buffer with dUTP mix and the NEBNext Second Strand Synthesis Enzyme Mix. The incorporation of dUTP is essential for strand specificity, as it renders the second-strand cDNA uracil-containing, making it susceptible to degradation during subsequent PCR steps. This selective degradation ensures that only the first-strand cDNA is amplified, preserving strand orientation in the final library. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer and PCR products were purified (AMPure XP system). Library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced by NovaSeq6000 on an S4 flow cell (PE150 read length).

treatment_protocol:
Rats were housed in 12-hour light/dark conditions with ad libitum access to a standard rodent chow (Lab diets, Prolab RMH1800, St. Louis. MO) and water.  Timed pregnant Sprague-Dawley rats (Charles River, Wilmington, MA) were delivered to the vivarium on gestational day 18.  Dams delivered pups without intervention on PND 0. On PND 2, the dams were randomly transferred to cages containing a standard plexiglass cage with ample sawdust and 3 paper towels to use as nesting material (STD), or an impoverished cage (CES) which had limited sawdust which was inaccessible to the dam by a wire mesh platform which sat 2cm above the cage floor and one half of one paper towel was provided as nesting material (Figure 1). Pups were randomly distributed to dams until each litter contained 12 pups with equal male: female ratio. These cages then remained undisturbed for 7 days. On  PND 10, all litters were transferred to and maintained in standard cages until offspring were weaned on PND 21. On PND 10, 21 and 35, equal numbers of offspring were anesthetized with isoflurane and euthanized by decapitation. The bilateral tibia and lumbar vertebra were collected and stored at -80°C until analyses.
gene expression profiles of the lumbar vertebrae in male and female offspring at PND 10, 21, and 35 and comprehensively evaluated their bone health parameters

tag: tissue

value: Bone

tag: Sex

value: M

tag: time point

tag: strain

value: Sprague Dawley

tag: treatment

value: CES


title: c7

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: d4c7 oogonia-like cells

library_source: genomic

data_processing:
All reads were processed with Trim_Galore! v0.6.3 with default settings to remove adapter and low-quality sequences.  Processed reads were mapped on the mouse genome, GRCm38.p6, using Bismark v0.22.1 and bowtie2 v2.3.4.1 with the “-X 2000” option.  The resulting BAM files were then processed with the script deduplicate_bismark to remove PCR duplicates, and methylation levels per CpG were calculated using the bismark_methylation_extractor script included in the Bismark package.
Assembly: GRCm38.p6
Supplementary files format and content: biskark report text

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Genomic DNAs were purified from 500 (c34 oocyte-like cells ≥ 60 μm in diameter) to 15,000 cells (c7 oogonia-like cells, c13 fetal oocyte-like cells) by using Nucleospin Tissue XS (Macherey-Nagel, 740901) and eluted in 10 μl elution buffer.  The DNA concentration was quantitated by using a Qubit dsDNA HS Assay Kit (Thermo Fisher, Q32854) and 20–140 ng of genomic DNAs were mixed with 1 pg of pUC19 DNA and 20 pg of unmethylated lambda DNA for a total volume of 50 μl.  The DNAs were then fragmented by sonication using an E220 focused-sonicator from Covaris (peak incident power: 140W; duty factor: 10%; cycles per burst: 200; and treatment time: 130 ms).  The fragmented DNA samples were purified by two rounds of Axygen beadspurification (0.7×volumes and then 0.9×volumes).
All fragments were applied to library construction using a NEBNext Enzymatic Methy-seq Kit (New England Biolabs, E7120) according to the manufacturer’s instructions.  Library concentrations and fragment sizes were evaluated with KAPA Library Quantification Kits (Nippon Genetics, KK4828) and a Labchip GX Touch HT nucleic acid analyzer (Perkin Elmer).  The sequencing was performed using an Illumina Novaseq sequencer (Illumina).

tag: cell line

tag: cell type

value: Oocyte-like cell

tag: transgene

value: ovarian soma-free culture

tag: time

value: day 7


title: E198K_corrected, DIV14 neurons 02

city: Boston

first: Randee

last: Young

state: MA

address: 4 Blackfan st

institute: Boston Children's Hospital

data_processing:
Sequence reads were mapped to GRCh38 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Homo sapiens

source_name: E198K corrected iPSCs

growth_protocol: E198K patient derived and corrected control iPSCs were maintained in mTeSR Plus medium.

extract_protocol:
RNA was harvested from iPSC-derived neurons at 14 days in vitro using a standard TRIzol RNA extraction protocol and purified using the Zymo RNA-concentrator kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: iPSCs were induced into neural stem cells (NSCs) in Gibco Neural Induction Media and expanded in Gibco Neural Expansion Media. After four passages, NSCs were differentiated into neurons and plated on poly-D-lysine and laminin coated plates in Gibco Neurobasal media supplemented with B27, 10 µm ascorbic acid, 1X GlutaMAX supplement, and CultureOne supplement. After 3 to 5 days, or once neural progenitors adopted a neuronal-like morphology with clear projections, B27 Plus supplement was substituted for B27.

value: E198K corrected iPSCs

value: iPSCs

tag: genotype

value: cortical neuron differentiation


title: CES20

description: Library name: A1709


title: PDI BIOL REP 2 STROMAL

country: United Kingdom

description: Library name: Str_n2_P4HB_A3

molecule: polyA RNA


title: STD16

description: Library name: A1752

value: F

value: STD


title: MEF_caMEK1_Dox_d2_1

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

institute: Kyoto University

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome and reporter sequences (mCherry, EGFP, Xenopus MEK1SDSE and human MKK6EE) using STAR v.2. 6.0.c with the GENCODE vM25 annotation gtf file after trimming adaptor sequences and low-quality bases with cutadapt-1.12. The uniquely mapped reads were summarized at the gene level using HTSeqcount v.0.11.2, with the GENCODE vM25 annotation file.
Expression values were calculated as FPKM.
Assembly: mm10
Supplementary files format and content: tsv file include raw counts or FPKM values

source_name: MEF

growth_protocol: MEF; Embryos were harvested at E13.5, and MEFs were derived from the eviscerated and decapitated embryos with 0.25% trypsin. MEFs were maintained in high glucose DMEM (Nacalai Tesque) supplemented with 2 mM L-glutamine (Nacalai Tesque), 1× NEAA (Nacalai Tesque), 100 U/mL penicillin, 100 μg/mL streptomycin (Nacalai Tesque), 10% foetal bovine serum (Gibco), and 0.11 mM mercaptoethanol. MEFs were plated into 12-well culture plates at a density of 2 × 104 cells/well. Dox was added at a concentration of 2 μg/mL. Passages were performed every three or four days for MEFs not treated with Dox.

extract_protocol:
Hepatocyte;The liver was perfused with EGTA solution (calcium-free Hank’s balanced salt solution (HBSS) (Wako) containing 0.5 mM EGTA (Sigma) and 10 mM HEPES (Nacalai Tesque)), followed by a second perfusion with HBSS containing collagenase D (SIGMA) for bulk RNA-seq or Liberase TM Research Grade (Roche) for scRNA-seq and 10 mM HEPES. After passage through a 70 µm cell strainer, the cells were centrifuged at 50 g for 2 minutes three times to enrich for hepatocytes.  Colonic epithelial cells; The colon was dissected, cut open longitudinally and rinsed with ice-cold HBSS three times. The total colon without the caecum was used. The tissue was incubated for 30 min at 37 °C in isolation buffer (HBSS containing 10 mM HEPES (Nacalai Tesque), 5 mM EDTA (GIBCO) and 1 mM DTT (Sigma)) and then shaken vigorously for 30 sec to separate the crypt from the stromal tissues. After passage through a 70 µm cell strainer, the crypt suspension was centrifuged at 800 rpm for 3 min. The supernatant was decanted, and the crypt pellet was subsequently resuspended in 0.25% trypsin/1 mM EDTA and incubated for 15 min at 37 °C. The cell suspension was centrifuged at 3000 rpm for 5 min. Dissociated hepatocytes and crypt cells were passed through a 40 µm cell strainer and sorted with a FACSAria II (BD Bioscience) machine using a 130 µm nozzle. Dead cells were gated out by DAPI incorporation (100 ng/mL for crypt cells and 500 ng/mL for hepatocytes). To enrich for hepatocytes, we used 2 FSC-neutral density (ND) filters and 10-SSC ND filters. Ccells were sorted into RNAprotect Cell Reagent (QIAGEN) and stored at -80 °C until RNA extraction.
Total RNA was extracted using the RNeasy plus Mini or Micro Kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified with a NanoDrop instrument (Thermo Scientific). Total RNA (in vitro sample; 100 ng, FACS-sorted samples; 50 ng) was prepared for library construction. High-quality RNA samples (RNA Integrity Number value > 8, as determined by Bioanalyzer) were used for library construction. RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were sequenced on a NextSeq 500 (Illumina) as 76-bp single-end reads.

treatment_protocol: Doxycycline (Sigma) was dissolved in drinking water at 0.2 mg/mL for caMEK1 mice and 2 mg/ml for caMKK6 and control mice; the drinking water was also supplemented with 10 mg/mL sucrose (Nacalai Tesque).

value: MEF

value: male

value: Dox

value: Day 2


title: ABDE3 TSCs, untreated 1

city: Oxford

first: Alexandra Maria

last: Bisia

address: S Parks Rd

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
Paired-end reads were aligned against the GRCm38/mm10 genome using STAR RNA-seq aligner package, with default parameters and –outSAMtype BAM SortedByCoordinate.
BAM file primary alignments with mapping quality of >254 were treated as RNA-seq data and imported into SeqMonk 1.48.0.
RNA-seq quantitation pipeline using DESeq2 was used to identify significantly differentially expressed genes (P<0.05).
Assembly: GRCm38/mm10
Supplementary files format and content: raw-counts.txt

growth_protocol: Cultured on Matrigel-coated plates in TX defined medium (Kubaczka et al., 2014)

extract_protocol:
Total RNA was harvested using a Quick-RNA MicroPrep kit (Zymo) per the manufacturer’s instructions.
Library preparation was carried out using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Addition to culture medium of 200nM dTAG-13 dissolved in DMSO, or 10uM BRM014 dissolved in DMSO, or DMSO only for control.

value: Trophoblast stem cell

value: Eomesdeg/deg

value: Untreated


title: E198K_corrected, DIV14 neurons 01


title: STD15

description: Library name: A1751

value: Bone

value: M

value: Sprague Dawley


title: GV_house_Input_1

data_processing:
Paired-end reads were processed using Trim-Galore! v0.4.1/cutadapt v1.9.1 (refs) to remove adaptor sequences.
The truncated reads were then aligned to (GRCm38.p3) using Bowtie2 v2.3.4.1 (refs) with the “-very-sensitive” option.  Reads aligned to chromosomes 1 to 19, X, and Y were converted to the BAM format by SAMtools v1.7 (refs).
In the samples sequenced in a paired-end manner, duplicated reads were removed using the MarkDuplicates command of Picard Tools v2.18.23 (https://broadinstitute.github.io/picard/).
BED files were obtained from the BAM format using the bamtobed command of BEDTools v2.29.2 (refs).
Assembly: mm10
Supplementary files format and content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 100” option of deepTools v3.5.0.The blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary files format and content: Due to the broad peak nature of epigenetic marks of H3K4m3, H3K27me3, and H3K36me3 in oocytes, the peaks enriched by these marks were identified using epic2 v0.0.41 (refs) with the “--bin-size” of 1kb for H3K4me3 and 10kb for H3K27me3 and H3K36me3. For H3K27ac peaks, MACS v2.1.1 (refs) was used with the “-q 0.01 --nomodel --keep-dup all --extsize 200” option.

extract_protocol:
Briefly, cells were pelleted and resuspended in nuclear isolation buffer (10 mM Tris-HCl, pH8.0, 140 mM NaCl, 5 mM MgCl2, 0.6% NP-40, 0.1% Triton X-100, 0.1% deoxycholate, 1 x EDTA-free proteinase inhibitor cocktail and 1 mM PMSF). Chromatin was then fragmented with MNase (2 U/μl at 37 °C for 7.5 min) and diluted in NChIP immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1 × EDTA-free protease inhibitor cocktail and 0.1 mM PMSF). Carrier DNA (30 ng) was added into the fragmented chromatin to reduce DNA loss during immunoprecipitation. The fragmented chromatin was then pre-cleared with 5 μl of Dynabeads Protein A/Protein G (ThermoFisher) and immunoprecipitated overnight at 4 °C with the pre-prepared antibody-beads complex, which contains 700 ng H3K4me3 antibody (Digagenode, 15410003) or H3K27me3 antibody (Merk, 07‐449), H3K36me3 (Active motif, 61101) and 5 μl Dynabeads Protein A/Protein G. After immunoprecipitation, beads were washed twice with 150 μl of low salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF, and 0.2 ng/μl carrier DNA) and twice with 150 μl of high salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF, and 0.2 ng/μl carrier DNA). Protein-DNA complexes were eluted from beads in 100 μl ChIP elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 65 °C. Immunoprecipitated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
Adaptor ligation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, New England Biolabs), and library pre-amplification was performed by 9 cycles of PCR. The pre-amplified library was digested by I-SceI (5 U/μl; 2 h incubation at 37 °C followed by 20 min heat inactivation at 65 °C). Barcoded final libraries were generated by further amplification of the carrier-DNA-removed pre-amplification products.

value: GV Oocyte

value: WT


title: CAPG BIOL REP 3 STROMAL

description: Library name: Str_n3_CAPG_G2

value: Endometrium

value: Primary

value: Stromal

value: Recombinant bovine CAPG 1ug/mL


title: E198K_patient, DIV 14 neurons 03

source_name: E198K patient iPSCs

value: E198K patient iPSCs

value: iPSCs

value: cortical neuron differentiation


title: CAPG BIOL REP 2 STROMAL

description: Library name: Str_n2_CAPG_F2


title: CES16

description: Library name: A1740

value: F

value: CES


title: CES15

description: Library name: A1739


title: E198K_patient, DIV 14 neurons 02


title: GV_house_K36me3_2


title: MEF_caMEK1_NoDox_d2_1

value: MEF

value: male

value: No Dox

value: Day 2


title: CES18

description: Library name: A1764

value: Bone


title: E198K_corrected, DIV14 neurons 03

value: E198K corrected iPSCs


title: CES14

description: Library name: A1738

value: M

value: Sprague Dawley


title: GV_house_K27me3_1

value: GV Oocyte

value: WT


title: VC BIOL REP 3 STROMAL

description: Library name: Str_n3_VC_D2

value: Endometrium

value: Primary

value: Stromal

value: PBS vehicle control


title: CUT&RUN_Ser5P_U1AMO3

first: Ana

last: Fiszbein

address: 24 Cummington Mall, LSE(Life Science and Engineering) Building

department: Biology

institute: Boston University

description: Ser5-P enrichment after U1 AMO - replicate 3

data_processing:
The initial reads were trimmed to a length of 50bp to remove mapping bias towards the longer fragments, and adapter sequences and low-quality 3’ bases were removed using trimmomatic. Trimmed reads were aligned to the reference genome GRCh38.99 using STAR v2.7.9a. E.coli spike-in reads were aligned to E.coli K12 MG1655 reference genome for normalization. The resulting BAM files were merged and converted to bigwig files using a custom script.
Assembly: Ensembl reference genome GRCh38.99
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) under standard cell culture conditions at 37°C in a humidified atmosphere with 5% CO2. The DMEM medium was supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotics.

extract_protocol:
CUT&RUN assays were performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher, #14-1048) following the manufacturer's instructions.
Libraries were generated using the CUT&RUN Library Prep Kit (EpiCypher, #14-1002) following the manufacturer's instructions.

value: HeLa

value: U1 AMO


title: c0

description: day 4 PGCLC

value: PGCLC

value: ovarian soma-free culture

value: day 3


title: PDI BIOL REP 1 STROMAL

description: Library name: Str_n1_P4HB_H2

value: Recombinant bovine PDI 1ug/mL


title: GV_house_K36me3_1


title: STD14

description: Library name: A1728

value: F

value: STD


title: STD13

description: Library name: A1727

value: Bone


title: CUT&RUN_Ser5P_U1AMO2

description: Ser5-P enrichment after U1 AMO - replicate 2


title: VC BIOL REP 1 STROMAL

description: Library name: Str_n1_VC_B2


title: E18_house_K4me3_2

source_name: Prdm1-mVenus; Dppa3-ECFP reporter

value: Prdm1-mVenus; Dppa3-ECFP reporter

value: Oocyte (E18.5)


title: STD12

description: Library name: A1726

value: M

value: Sprague Dawley


title: E18_house_K4me3_1

value: WT


title: PDI BIOL REP 3 EPITHELIAL

description: Library name: Epi_n3_P4HB_A2

value: Endometrium

value: Primary

value: Epithelial


title: CUT&RUN_Ser5P_U1AMO1

description: Ser5-P enrichment after U1 AMO - replicate 1

value: HeLa


title: GV_house_K4me3_1

value: GV Oocyte


title: PDI BIOL REP 2 EPITHELIAL

description: Library name: Epi_n2_P4HB_H1


title: CUT&RUN_Ser5P_Ctrl2

description: Ser5-P enrichment after Control AMO - replicate 2

value: Control AMO


title: E198K_patient, DIV 14 neurons 01

value: E198K patient iPSCs

value: iPSCs

value: cortical neuron differentiation


title: CAPG BIOL REP 1 STROMAL

description: Library name: Str_n1_CAPG_E2

value: Stromal

value: Recombinant bovine CAPG 1ug/mL


title: PDI BIOL REP 1 EPITHELIAL

description: Library name: Epi_n1_P4HB_G1

value: Recombinant bovine PDI 1ug/mL


title: STD10

description: Library name: A1715

value: Bone

value: F

value: STD


title: CUT&RUN_Ser5P_Ctrl1

description: Ser5-P enrichment after Control AMO - replicate 1


title: E18_house_K36me3_2

value: Prdm1-mVenus; Dppa3-ECFP reporter

value: Oocyte (E18.5)


title: E18_house_K27me3_2

value: WT


title: CAPG BIOL REP 3 EPITHELIAL

description: Library name: Epi_n3_CAPG_F1

value: Endometrium

value: Primary


title: E18_house_K36me3_1


title: CUT&RUN_Ser2P_U1AMO3

description: Ser2-P enrichment after U1 AMO - replicate 3

value: HeLa

value: U1 AMO


title: CES12

description: Library name: A1703

value: Sprague Dawley

value: CES


title: CES13

description: Library name: A1704


title: VC BIOL REP 2 STROMAL

description: Library name: Str_n2_VC_C2

value: PBS vehicle control


title: STD11

description: Library name: A1716


title: CUT&RUN_Ser2P_U1AMO2

description: Ser2-P enrichment after U1 AMO - replicate 2


title: E18_house_K27me3_1


title: CES11

description: Library name: A1702

value: M


title: CAPG BIOL REP 2 EPITHELIAL

description: Library name: Epi_n2_CAPG_E1

value: Epithelial


title: CUT&RUN_Ser2P_U1AMO1

description: Ser2-P enrichment after U1 AMO - replicate 1


title: CES10

description: Library name: A1786


title: E18_house_Input_1


title: CUT&RUN_Ser2P_Ctrl3

description: Ser2-P enrichment after Control AMO - replicate 3

value: Control AMO


title: CUT&RUN_Ser5P_Ctrl3

description: Ser5-P enrichment after Control AMO - replicate 3


title: CAPG BIOL REP 1 EPITHELIAL

description: Library name: Epi_n1_CAPG_D1

value: Recombinant bovine CAPG 1ug/mL


title: c34_H18_Input_2

source_name: H18 Prdm1-mVenus; Dppa3-ECFP reporter

value: H18 Prdm1-mVenus; Dppa3-ECFP reporter

value: d4c34 oocyte-like cell


title: VC BIOL REP 3 EPITHELIAL

description: Library name: Epi_n3_VC_C1


title: c34_H18_Input_1


title: CES9

description: Library name: A1785

value: Bone


title: CUT&RUN_Ser2P_Ctrl2

description: Ser2-P enrichment after Control AMO - replicate 2


title: CES8

description: Library name: A1784


title: VC BIOL REP 2 EPITHELIAL

description: Library name: Epi_n2_VC_B1


title: CUT&RUN_Ser2P_Ctrl1

description: Ser2-P enrichment after Control AMO - replicate 1


title: VC BIOL REP 1 EPITHELIAL

description: Library name: Epi_n1_VC_A1


title: STD9

description: Library name: A1774

value: F

value: STD


title: c34_H18_K36me3_2

value: WT


title: c34_H18_K4me3_2


title: CUT&RUN_RNAPII_U1AMO3

description: Total RNAPII enrichment after U1 AMO - replicate 3


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep3

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

data_processing:
As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: hg38
Supplementary files format and content: Processed data files were obtained with above data processing steps. The methylexport data includes chromosome number, cytosine position in CpG, strand, methylated C reads, total C reads in each columns.

source_name: Colon

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Genomic DNA was isolated using the DNeasy Tissue & Blood kit (Qiagen) according to the manufacturer's protocol.
The library preparation for WGBS was performed with the tPBAT protocol described previously (Miura F, Nucleic Acids Res, 2012; Miura F, Nucleic Acids Res, 2019). One hundred nanograms of genomic DNA spiked with 1% (w/w) of unmethylated lambda DNA (Promega) was used for the library preparation.

treatment_protocol: To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.

value: Colon

value: Colorectal cancer cell

value: Auxin

value: 8 days


title: STD8

description: Library name: A1772

value: Sprague Dawley


title: c34_H18_K36me3_1


title: CES7

description: Library name: A1762

value: CES


title: CUT&RUN_RNAPII_U1AMO2

description: Total RNAPII enrichment after U1 AMO - replicate 2

value: HeLa

value: U1 AMO


title: c34_H18_K27me3_2


title: CUT&RUN_RNAPII_U1AMO1

description: Total RNAPII enrichment after U1 AMO - replicate 1


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep1


title: CES5

description: Library name: A1760

value: M


title: c34_H18_K27me3_1


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep2


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep3

value: 6 days


title: c13_H18_Input_2

value: d4c13oocyte-like cells


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep2


title: CUT&RUN_RNAPII_Ctrl2

description: Total RNAPII enrichment after Control AMO - replicate 2

value: Control AMO


title: STD6

description: Library name: A1749


title: c13_H18_Input_1

value: H18 Prdm1-mVenus; Dppa3-ECFP reporter


title: CUT&RUN_RNAPII_Ctrl1

description: Total RNAPII enrichment after Control AMO - replicate 1


title: STD7

description: Library name: A1750

value: Bone


title: c13_H18_K4me3_4


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep1


title: DNMT1-AID_WGBS_Day8_Rep3


title: STD5

description: Library name: A1748


title: c13_H18_K4me3_3


title: CUT&RUN_H3K4me3_U1AMO3

description: H3K4me3 enrichment after U1 AMO - replicate 3


title: DNMT1-AID_WGBS_Day8_Rep2


title: CES4

description: Library name: A1737

value: F


title: c13_H18_K4me3_2


title: CES6

description: Library name: A1761


title: DNMT1-AID_WGBS_Day8_Rep1


title: CUT&RUN_H3K4me3_U1AMO2

description: H3K4me3 enrichment after U1 AMO - replicate 2


title: CES3

description: Library name: A1736


title: c13_H18_K4me3_1


title: DNMT1-AID_WGBS_Day6_Rep3


title: CUT&RUN_RNAPII_Ctrl3

description: Total RNAPII enrichment after Control AMO - replicate 3


title: CUT&RUN_H3K4me3_Ctrl3

description: H3K4me3 enrichment after Control AMO - replicate 3


title: c13_H18_K36me3_2


title: CUT&RUN_H3K4me3_Ctrl2

description: H3K4me3 enrichment after Control AMO - replicate 2


title: STD4

description: Library name: A1725

value: STD


title: c13_H18_K36me3_1

value: WT


title: STD3

description: Library name: A1724


title: DNMT1-AID_WGBS_Day6_Rep1

value: Colon


title: DNMT1-AID_WGBS_Day6_Rep2

value: Colorectal cancer cell


title: UHRF1-AID_WGBS_Day8_Rep3

value: Auxin


title: c13_H18_K27me3_2


title: c13_H18_K27me3_1


title: UHRF1-AID_WGBS_Day8_Rep2

value: 8 days


title: U373B3

city: Hong Kong SAR

first: Kwong Lam

last: Fung

address: L7-55 Paediatrics, Lab Block, Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence then mapped to hg38 whole genome using two-pass STAR.
Transcript per million (TPM) were quantified using RSEM and normalized by median normalization method for differential expression analysis.
Assembly: hg38

growth_protocol: DMEM (high glucose) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted using Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS control

value: Glioblastoma

value: wild-type

value: 1U/ml BCT-100


title: FL3-Flag_IP2

city: Shanghai

first: Desheng

last: Zeng

address: 300 Feng Lin Road

country: China

institute: CAS Center for Excellence in Molecular Plant Science

description: IP

data_processing:
Samples underwent sequencing, producing image files converted by Illumina platform software into raw FASTQ data (Raw Data), or off-machine data.
Reference genome and gene model annotation files were downloaded directly from genome websites. BWA (0.7.17-r1188) was used to construct a reference genome index, followed by alignment of filtered reads to the reference genome.
MACS3 (3.0.0a7) Peak Calling software was employed, using the "narrow" parameter and filtering for qvalue < 0.05 to generate narrow peaks.
Deeptools (3.5.1) calculated signals for specific genomic regions, generating signal heatmaps and profiles using plotHeatmap (3.5.1) and plotProfile (3.5.1) functions.
RIdeogram (0.2.2) visualized peak distribution on chromosomes.
Peak annotation was conducted using ChIPseeker (v1.34.1).
Assembly: TAIR10.1_NCBI
Supplementary files format and content: The bigwig files represent the depth of sequence coverage (include the peak files with quantitative data, and tag density files) except for input samples.
Supplementary files format and content: Tab-delimited text files show the merge peaks except for input samples.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium for 10 days.

extract_protocol:
ChIP experiments were performed as described previously (Yang et al, 2018) with slightly modification. Histone-DNA complexes were isolated with anti-Flag affinity beads.
The ChIP-seq library was generated using the TruSeq Nano DNA High Throughput Library Prep Kit  according to manufacturer instructions.

treatment_protocol: Plant materials (1 g) underwent pretreatment with 1.5 mM EGS for 30 minutes to cross-link proteins contributing to FLs’ chromatin associating ability.

value: seedlings

tag: antibody

value: anti-flag


title: CUT&RUN_H3K4me3_Ctrl1

description: H3K4me3 enrichment after Control AMO - replicate 1

value: HeLa


title: U373B2


title: FL3-Flag_IP1

description: IP


title: c7_H18_Input_3

value: d4c7oogonia-like cells


title: CUT&RUN_H3K4me3_U1AMO1

description: H3K4me3 enrichment after U1 AMO - replicate 1

value: U1 AMO


title: U373B1


title: UHRF1-AID_WGBS_Day6_Rep3

value: 6 days


title: c7_H18_Input_2

value: H18 Prdm1-mVenus; Dppa3-ECFP reporter


title: WT_IP2

description: IP


title: c7_H18_K27me3_2


title: UHRF1-AID_WGBS_Day6_Rep2


title: WT_IP3

description: IP


title: U373P2

value: PBS


title: UHRF1-AID_WGBS_Day8_Rep1


title: c7_H18_K27me3_1


title: U373P3


title: WT_IP1

description: IP


title: U373P1


title: FL3-Flag_IP3

description: IP


title: FL3-Flag_INPUT3

description: Input


title: scRNA_intestine_LPL_nippo_day7

city: Beijing

first: Xiaohuan

last: Guo

address: Hai Dian

department: Institute for Immunology

institute: Tsinghua University

description:
Naive_Nb_LPL_barcodes.tsv
Naive_Nb_LPL_genes.tsv
Naive_Nb_LPL_matrix.mtx

library_source: transcriptomic single cell

data_processing:
bulk RNA-seq: aligned to mm10 with Bowtie2(v2.2.5) with default parameters
bulk RNA-seq: gene expression profiles were harvested with RSEM(V1.2.8, p 8, forward prob 0.5, paired end)
scRNA-seq: Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (SingleronBiotechnologies) with default parameters.
sc-RNA-seq: Trimmed reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b).
sc-RNA-seq: Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1).
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq data: tab-delimited text files include TPM values for each sample.
Supplementary files format and content: For scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: For scRNA-seq data: barcodes.tsv, cell names (colname names of the count matrix)
Supplementary files format and content: For scRNA-seq data: genes.tsv, gene names (row names of the count matrix)

source_name: Intestinal LPL

growth_protocol: For bulk RNA-seq, intestinal organoids were cultured in ENR medium with or without 4-OHT(1 μM) for 3 days, Then the passaged organoids were treated with 20ng/ml IL-13 and with or without 50ng/ml RANKL for 4 days.

extract_protocol:
Single-cell suspensions were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits.

value: Intestinal LPL

value: N.brasiliensis infection for 7 days in vivo


title: UHRF1-AID_WGBS_Day6_Rep1

value: Colon


title: FL3-Flag_INPUT2

description: Input


title: U87B3


title: U87B2


title: scRNA_intestine_LPL_naive

value: WT

value: non-infected


title: FL3-Flag_INPUT1

description: Input


title: KO4

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
After sequencing, generated reads were filtered and mapped to the reference genome using HISAT2 (v2.0.4)and assembled using StringTie (v1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (v0.9.8) and the expression levels of all transcripts were calculated by Stringtie and ballgown.
Differential gene analysis was performed by DESeq2 software and then subjected to enrichment analysis of GO functions.
Assembly: Mus_musclus.GRCm38 V99
Supplementary files format and content: FPKM, count values for each Sample

source_name: cortical bone tissue

extract_protocol:
Total cortical bone RNA from 4 weeks WT and UbcCre/ERT2 Ripk4fl/fl mice was extracted using Trizol reagent (Thermofisher), quantified and purified using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent).
Following purification, mRNA library was constructed, fragmented, amplified and loaded into the nanoarray and sequencing was performed on Illumina Novaseq™ 6000 platform following the vendor’s recommender protocol.

value: cortical bone tissue

value: UbcCre/ERT2 Ripk4fl/fl

tag: stain background


title: U87B1

value: Glioblastoma

value: wild-type


title: KO3


title: IGF2BP3_input_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of PAIP1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from PAIP1-RNA complexes and another for the western blotting assay for PAIP1 immunoprecipitation.The PAIP1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: genotype/variation

value: expressing vector with IGF2BP3-FLAG


title: WT_INPUT3

description: Input

value: seedlings


title: IGF2BP3_IP_2

value: HeLa

value: anti-FLAG  sigma, F7425


title: IGF2BP3_input_2


title: IGF2BP3_IP_1


title: KO2


title: U87P3


title: WT_INPUT1

description: Input


title: KO1


title: WT_INPUT2

description: Input


title: U87P1


title: HeLa_IGF2BP3_2nd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Pvalue <= 0.01
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). IGF2BP3 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: OE_RNA against human IGF2BP3 transfection of HeLa cells was performed using lipofectAMINE 2000

value: IGF2BP3 overexpression


title: HeLa_IGF2BP3_1st


title: flΔ4_Dark 3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: TAIR10.1_NCBI
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

growth_protocol: Seedlings were grown on 1/2 MS medium for 4 days.

extract_protocol:
Total RNA was extracted from the seedlings using TRIzol® Reagent according the manufacturer’s instructions.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol:
For "dark" group, the seedlings were grown in continious darkness.
For "blue" group, the seedlings were moved from darkness to blue light (30 μmol·m-2·s-1) for 30 min.

value: fkd1 fl1-2 fl2 fl3


title: U87P2


title: HeLa_control_2nd

value: control


title: WT_Ctrl4


title: WT_Ctrl3


title: HeLa_control_1st


title: HUVEC siFUS_2

data_processing:
Illumina bcl2fastq software used for basecalling. Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the GRch38 genome by HISAT (Kim, Pertea et al. 2013) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)(Trapnell et al. 2010).
The R Bioconductor package DESeq2 was utilized to screen out the (DEGs). P value <0.01 and fold change>1.5 or < 2/3 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as described previously (Xia et al. 2017).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVEC cells

growth_protocol: The HUVECs line (Angio-Proteomie, Boston, MA, USA) were cultured at 37℃ with 5% CO2 in Ham's F-12K with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
Total RNAs were extracted from HUVECs using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al. DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
Two μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: siRNA transfection of the cells was performed using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and Western blotting analysis.

value: HUVEC cells

value: FUS  knockdown in HUVEC cell


title: flΔ4_Dark 2


title: flΔ4_Dark 1


title: WT_Ctrl2


title: HUVEC siFUS_1


title: WT_Ctrl1


title: HUVEC NC_3

value: HUVEC  cell (control plasmid)


title: WT_Dark 5


title: HUVEC NC_2


title: ChIP-Seq_HEK293T_3__HA_GATAD2A_WT

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19

source_name: Human embryonic kidney 293T cells

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
For ChIP assays, cells were fixed with 1% formaldehyde (Sigma) for 15 mins at room temperature (RT) (for RNA Pol II (Bethyl Laboratory A300-653A) ChIP) or fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 15 mins at RT (for HA-tagged proteins (Abcam, ab9110), CHD4 (Abcam, ab70469), MBD3 (Abcam, ab45027), HDAC2 (Santa Cruz Biotechnology,  sc7899), GATAD2A (Abcam, ab87663 or Proteintech, 12294-1-AP), KDM1A (Bethyl Laboratory, A300-215A) and H3R17me2a (Abcam, ab8284)). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 2 hrs. After washing and elution, the cross-linked protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Normal condition

tag: chip antibody


title: 8-T2

first: Koichi

last: Yuki

address: 300 Longwood Avenue

description:
Library name: Sample 10
mRNA profiles

data_processing:
CLC genomic benchwork
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner v.2.5.2b
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Ch38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

extract_protocol:
RNA was purified using Trizol
Illumina Nextera XT library was used for sequencing library preparation

value: Blood

value: Neutrophils


title: ChIP-Seq_HEK293T_3__HA_GATAD2A_7R/K


title: WT_Dark 4


title: 8-T0

description:
Library name: Sample 9
mRNA profiles


title: HUVEC NC_1


title: cry2_Blue 3


title: HUVEC siFUS_3


title: 6-T2

description:
Library name: Sample 8
mRNA profiles


title: 6-T0

description:
Library name: Sample 7
mRNA profiles


title: cry2_Blue 1


title: Oligo/barcode pairings

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: Oligo/barcode pairings

library_source: other

data_processing:
Paired-end reads were merged into single amplicons using Flash to identify oligo/barcode pairings. Genomic DNA sequences and barcodes were extracted and mapped back to the oligo design file using minimap2. Alignments with more than a 5% error rate were discarded, retaining only high-quality alignments, which were compiled into a lookup table with their matching barcodes. After sequencing the RNA and plasmid libraries, 19 bp barcode tags were assigned to oligos from the lookup table, and oligo counts were aggregated by summing across all barcodes. Variants with fewer than 20 DNA counts or with zero RNA counts in oligos for either allele were excluded from further analysis.
We normalized the MPRA samples using MPRAmodel, where the library counts for DNA plasmid replicates with RNA Jurkat cells (3 replicates) and separately with primary T cells (7 replicates) were normalized across samples using the "summit-shift" method, which shifts the log2(fold change) density peak to line up with 0 and centers the RNA/DNA ratio distribution of each sample around 1, effectively assuming that most genomic elements in the MPRA are minimally active (which we anticipate is true for this library because most variants included for each association are not causal).
To define active elements, significant differences in counts between plasmid (DNA) and Jurkat and primary T cell-types (RNA) were determined using a negative binomial generalized linear model (GLM) within DESeq2. This model incorporated independent dispersion estimates for each cell-type and library. Activity of genomic elements was quantified in log2(fold-change) units comparing counts from RNA versus DNA, using a contrast in DESeq2's design matrix to compare treatment conditions and Wald's test to assess significance.
Assembly: GRCh38
Supplementary files format and content: processed data files contain data library, counts and normalized counts in .gz and .out file format

molecule: other

source_name: plasmid library

growth_protocol: CD4 T cells were magnetically isolated (BioLegend #480130) and activated in T cell media (TCM), constituting either 1) X-VIVO 15 (Lonza #04-418Q) supplemented with 25 mM HEPES, 1 mM Sodium Pyruvate, 0.5% Non-essential amino acids, 1% Penicillin Streptomycin, 0.5% L-Glutamine, 5% FBS, 55 mM 2-mercaptoethanol or 2) CTS OpTmizer T cell Expansion medium (ThermoFisher #A1048501) supplemented with 5% FBS, 1% glutamine, 100U/mL PenStrep, 55 mM 2-mercaptoethanol. Cells were activated with human T cell activation beads (Miltenyi #130-091-441) and recombinant human IL-2 (final concentration 100 U/mL; NCI Biological Resources Branch). Lenti-X 293T cells were maintained in DMEM, supplemented with 10% FBS, 1% glutamine, 100U/mL PenStrep, 1 mM sodium pyruvate, 1x MEM non-essential amino acids, and 10 mM HEPES. Cells were passaged every two-three days using trypsin-EDTA for dissociation and kept at a confluency of less than 60%.

extract_protocol:
Total RNA was extracted from cells using QIAGEN Maxi RNeasy (QIAGEN, 75162) following the manufacturer’s protocol including the on-column DNase digestion. A second DNase treatment was performed on the purified RNA using 5 μL of Turbo DNase (Life Technologies, AM2238) with buffer, in 750 μL of total volume for 1 h at 37 °C. The digestion was stopped with the addition of 7.5 μL 10% SDS and 75 μL of 0.5 M EDTA followed by a 5-min incubation at 70 °C. The total reaction was then used for pulldown of GFP mRNA.
First-strand cDNA was synthesized from the DNase-treated GFP mRNA with SuperScript III. Single-stranded cDNA was purified by SPRI and eluted in 30 μL EB. To minimize amplification bias during the creation of cDNA tag sequencing libraries, samples were amplified by qPCR to estimate relative concentrations of GFP cDNA using 1 μL of sample in a 10 μL PCR reaction containing 5 μL Q5 NEBNext master mix, 1.7 μL SYBR Green I diluted 1:10,000 (Life Technologies, S-7567) and 0.5 μM of TruSeq_Universal_Adapter and MPRA_Illumina_GFP_F primers. Samples were amplified with the following qPCR conditions: 95 °C for 20 s, 40 cycles (95 °C for 20 s, 65 °C for 20 s, 72 °C for 30 s), 72 °C for 2 min. The number of cycles for sample amplification was 1−n (the number of cycles it took for each sample to pass the threshold) from the qPCR. To add Illumina sequencing adapters, 10 μL of cDNA samples and mpra:minP:gfp plasmid control (diluted to the qPCR cycle range of the samples) were amplified using the reaction conditions from the qPCR scaled to 50 μL, excluding SYBR Green I. Amplified cDNA was SPRI purified and eluted in 40 μL of EB. To determine oligo/barcode combinations within the MPRA pool, Illumina libraries were prepared from the plasmid library by performing five separate amplifications with 200 ng of plasmid in a 100 μL Q5 NEBNext PCR reaction.  Amplified material was SPRI purified using a 0.6 × bead/sample ratio and eluted with 30 μL of EB. Sequencing indexes were then attached using 20 μL of the eluted product and the same reaction conditions as for the tag-seq protocol, except the number of enrichment cycles was lowered to 5. Samples were molar pooled and sequenced using 2 × 150 bp chemistry.

value: plasmid library


title: MPRA plasmid rep 5

description: Library name: MPRA plasmid rep 5


title: cry2_Blue 2


title: 3-T2

description:
Library name: Sample 6
mRNA profiles


title: MPRA plasmid rep 4

description: Library name: MPRA plasmid rep 4


title: WT_Blue 3


title: 3-T0

description:
Library name: Sample 5
mRNA profiles


title: WT_Dark 6


title: MPRA plasmid rep 3

description: Library name: MPRA plasmid rep 3


title: ChIP-Seq_HEK293T_CHD4

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
For ChIP assays, cells were fixed with 1% formaldehyde (Sigma) for 15 mins at room temperature (RT) (for RNA Pol II (Bethyl Laboratory A300-653A) ChIP) or fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 15 mins at RT (for HA-tagged proteins (Abcam, ab9110), CHD4 (Abcam, ab70469), HDAC2 (Santa Cruz Biotechnology,  sc7899), GATAD2A (Abcam, ab87663 or Proteintech, 12294-1-AP), KDM1A (Bethyl Laboratory, A300-215A) and H3R17me2a (Abcam, ab8284)). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 2 hrs. After washing and elution, the cross-linked protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.


title: WT_Blue 2


title: WT_Blue 1


title: 2-T0

description:
Library name: Sample 3
mRNA profiles


title: MPRA plasmid rep 1

description: Library name: MPRA plasmid rep 1


title: Primary T MPRA mRNA rep 7

description: Library name: Primary T MPRA mRNA rep 7

source_name: blood

value: blood

value: CD3+CD4+T cells


title: cry2_Dark 3


title: MPRA plasmid rep 2

description: Library name: MPRA plasmid rep 2


title: 1-T2

description:
Library name: Sample 2
mRNA profiles


title: cry2_Dark 2


title: Primary T MPRA mRNA rep 6

description: Library name: Primary T MPRA mRNA rep 6


title: RNA-Seq_HEK293T_siHDAC2

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.


title: Primary T MPRA mRNA rep 5

description: Library name: Primary T MPRA mRNA rep 5


title: cry2_Dark 1


title: RNA-Seq_HEK293T_siKDM1A


title: WT_Dark 3


title: Colon_HFD

type: RNA

city: Fujisawa

first: Yoko

last: Yokoyama

address: 5322 Endo

institute: Keio University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Colon_High fat diet_13weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using theRneasy Mini kit (Qiagen, Hilden, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: male

value: High fat diet (60% fat)

value: Colon


title: Colon_CD

source_name: Colon_Control diet_13weeks

value: Control diet (10% fat)


title: Ileum_HFD

source_name: Ileum_High fat diet_13weeks

value: Ileum


title: Bat_HFD+Ex

source_name: Bat_High fat diet+Ex_13weeks

value: High fat plus 2% nori extract

value: Brown adipose tissue


title: Primary T MPRA mRNA rep 4

description: Library name: Primary T MPRA mRNA rep 4


title: Ileum_HFD+PP

source_name: Ileum_High fat diet+PP_13weeks

value: High fat plus 2% porphyran


title: Ileum_HFD+Ex

source_name: Ileum_High fat diet+Ex_13weeks


title: 2-T2

description:
Library name: Sample 4
mRNA profiles


title: Colon_HFD+Ex

source_name: Colon_High fat diet+Ex_13weeks


title: Bat_HFD

source_name: Bat_High fat diet_13weeks


title: Colon_HFD+PP

source_name: Colon_High fat diet+PP_13weeks


title: WT_Dark 2

source_name: seedlings

value: seedlings


title: RNA-Seq_HEK293T_siCHD4


title: Primary T MPRA mRNA rep 3

description: Library name: Primary T MPRA mRNA rep 3


title: STD2

description: Library name: A1713

data_processing:
Quality filtered and trimmed raw fastq files were aligned to the rat genome using STAR aligner (version 2.7.9a) and counted by Feature Counts (v.1.5.0-p3). Differential expression was performed using DESeq2 in R 4.2.0 and the resulting differentially expressed genes (DEGs) were determined using the design matrix of the different factors such as timepoints, condition and sex, at a defined cut-off criteria of |log2 fold-change|≥ 0.25 and p- value <0.1 adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. DEGs were subjected to REACTOME pathway analyses to determine the significantly enriched pathways. To extract further biological insight from the samples, we implemented gene set enrichment analysis (GSEA)which assesses the statistical enrichment of gene ontologies, and pathways, at a 5% significance, and data were visualized using Cluster profiler v4.8.1.
Assembly: mRatBN7.2
Supplementary files format and content: Count_Data.csv

source_name: Bone

extract_protocol:
RNA was extracted using miRneasy mini kit (QIAgen) and quantified using Qubit Flurometer
Samples had RNA integrity numbers of 5.5 – 9.6. RNA was shipped to Novogene Co. Ltd. (USA) for library preparation and sequencing. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and stranded mRNA-seq libraries were generated and individually barcoded using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.  Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) ring, the second-strand synthesis in the NEBNext Ultra II Directional RNA Library prep protocol, the reaction uses a buffer containing dUTP, which allows the incorporation of dUTP in place of dTTP. This process is facilitated by the NEBNext Second Strand Synthesis Reaction Buffer with dUTP mix and the NEBNext Second Strand Synthesis Enzyme Mix. The incorporation of dUTP is essential for strand specificity, as it renders the second-strand cDNA uracil-containing, making it susceptible to degradation during subsequent PCR steps. This selective degradation ensures that only the first-strand cDNA is amplified, preserving strand orientation in the final library. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer and PCR products were purified (AMPure XP system). Library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced by NovaSeq6000 on an S4 flow cell (PE150 read length).

value: Bone

value: F

value: Sprague Dawley

value: STD


title: RNA-Seq_HEK293T_siGATAD2A


title: WT_Dark 1


title: Primary T MPRA mRNA rep 2

description: Library name: Primary T MPRA mRNA rep 2


title: RNA-Seq_HEK293T_siCARM1_rep2


title: STD1

description: Library name: A1712

value: M


title: Bat_CD

source_name: Bat_Control diet_13weeks


title: RNA-Seq_HEK293T_siCTL_rep2

value: siCTL


title: Parse sequencing, PC3docetaxel sublibrary8 (contains all samples)

city: Baltimore

first: Sarah

middle: R

last: Amend

state: MD

address: 600 N Wolfe St

department: Brady Urological Institute

institute: Johns Hopkins University

description: Library name: PD_sublibrary8

data_processing:
RNA barcodes were filtered on Total UMI Count ( > 500 UMIs), feature count ( > 350 features), and percentage of mitochondrial genes ( < 25%). Seurat v4.3.057 was used for handling of normalization, identification of variable genes, scaling, principal component analysis, UMAP dimensional reduction, and SNN generation followed by Leiden clustering.
Assembly: Human GRCh38/hg38
Supplementary files format and content: matrix files

growth_protocol: RPMI medium supplemented with 10%FBS and 1% penicilin/streptomycin

extract_protocol:
Cells were collected on timepoint day using tubes pre-coated with bovine serum albumin (BSA). Cell fixation was performed on timepoint day using Parse Biosciences Fixation kit (Parse Biosciences) according to manufacturer protocol, except for no cell filtering steps were performed. No cell filtering steps were performed during barcoding and library prep to prevent loss of the large cells surviving chemotherapy.
Barcoding and library prep for PC3 cells untreated and surviving cisplatin was done using the Evercode Whole Transcriptome Mega kit according to manufacturer protocol (V2, Parse Biosciences). Sequencing was performed on an Illumina NovaSeq 6000 and alignment done using v0.7.2p alignment pipeline (Parse Biosciences). Barcoding and library prep for PC3 cells untreated and surviving docetaxel was done using the Evercode Whole Transcriptome Mega kit according to manufacturer protocol (V2, Parse Biosciences). Sequencing was performed on an Illumina NovaSeq X and alignment done using v1.0.6p alignment pipeline (Parse Biosciences).

value: untreated, 1, 5, and 10 DPT


title: Ileum_CD

source_name: Ileum_Control diet_13weeks


title: CES2

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

description: Library name: A1701

value: CES


title: RNA-Seq_HEK293T_siCARM1_rep1

source_name: Human embryonic kidney 293T cells


title: Primary T MPRA mRNA rep 1

description: Library name: Primary T MPRA mRNA rep 1

value: blood

value: CD3+CD4+T cells


title: Parse sequencing, PC3docetaxel sublibrary7 (contains all samples)

description: Library name: PD_sublibrary7


title: RNA-Seq_HEK293T_siCTL_rep1


title: CES1

description: Library name: A1700


title: Parse sequencing, PC3docetaxel sublibrary6 (contains all samples)

description: Library name: PD_sublibrary6


title: Mwat_HFD

source_name: Mwat_High fat diet_13weeks

value: male

value: High fat diet (60% fat)

value: Mesenteric white adipose issue


title: rat, SCI, rep3

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

description: Library name: samples6

data_processing:
After obtaining raw FASTQ files, the first step is to perform quality control using FastQC to assess read quality, adapter contamination, and sequence length distribution, followed by MultiQC to aggregate results across samples. Next, adapter sequences (e.g., TruSeq small RNA adapters) and low-quality bases (Q < 20) are trimmed using Cutadapt or fastp, retaining reads between 18–30 nt to focus on mature miRNAs. The cleaned reads are then aligned to a reference genome  using Bowtie2 or STAR with stringent parameters (–very-sensitive-local) to account for short miRNA sequences, and non-uniquely mapped reads are filtered out to reduce noise. For quantification, aligned reads are counted against miRNA annotations  using miRDeep2 or featureCounts to generate a raw count matrix. Downstream analysis involves normalization  and differential expression testing with multiple testing correction (FDR < 0.05). Finally, biological interpretation includes target prediction (TargetScan, miRDB), pathway enrichment (KEGG, GO), and visualization (PCA, heatmaps), with optional batch effect correction (limma or sva) if needed. Processed data should be deposited in public repositories (GEO, ENA) following MIAME standards. This pipeline ensures robust miRNA profiling while accounting for technical variability and biological relevance.
Assembly: Rnor_6.0
Supplementary files format and content: Raw counts were converted to CPM using edgeR (v3.40.2) with default parameters

source_name: spinal cord segment

extract_protocol:
The total RNA was extracted using Trizol (Invitrogen, CA, USA).The TRIzol extraction protocol begins by lysing samples with TRIzol reagent (1 mL per 50-100 mg tissue or 5-10×10⁶ cells), homogenizing tissues in liquid nitrogen or directly lysing adherent/suspension cells without washing. After 5-minute room temperature incubation for complete nucleoprotein dissociation, add 0.2 mL chloroform per 1 mL TRIzol, vortex vigorously for 15 sec, incubate 3 min, then centrifuge at 12,000×g (4°C, 15 min) to separate phases. Transfer the upper aqueous phase (60% of initial TRIzol volume) to a new tube, mix with 0.5 mL isopropanol per 1 mL TRIzol, incubate 10 min at RT, and pellet RNA by centrifugation (12,000×g, 10 min, 4°C). Wash the pellet twice with 75% ethanol (1 mL per initial TRIzol volume) using 5-min 12,000×g spins, air-dry briefly (5-10 min), then resuspend RNA in 25-50 μL DEPC-treated water. Assess purity via A260/A280 ratio (1.8-2.0) and integrity by electrophoresis, with immediate use or storage at -80°C to avoid degradation. For challenging samples (high fat/protein), include an initial 10-min 12,000×g clarification spin before phase separation.
18–30 nt small RNAs enriched by 15% denaturing PAGE gel electrophoresis. Gel slice corresponding to miRNA size range excised under UV shadowing, RNA eluted in 0.3 M NaCl overnight at 4°C, and purified by ethanol precipitation.3′ and 5′ adapters (NEBNext Multiplex Small RNA adapters) ligated using T4 RNA Ligase 2  at 22°C for 1 hour (3′) and 16°C overnight (5′).cDNA synthesized using SuperScript III Reverse Transcriptase , followed by 15 cycles of PCR with indexed primers.Amplified libraries purified using Agencourt AMPure XP beads  at 1.8× ratio to remove adapter dimers.Library fragment size distribution analyzed by Agilent Bioanalyzer (peak at ~140 bp, reflecting 50 bp miRNA + adapters).

value: spinal cord segment

value: SCI


title: Mwat_HFD+Ex

source_name: Mwat_High fat diet+Ex_13weeks

value: High fat plus 2% nori extract


title: Bat_HFD+PP

source_name: Bat_High fat diet+PP_13weeks

value: High fat plus 2% porphyran

value: Brown adipose tissue


title: 1-T0

description:
Library name: Sample 1
mRNA profiles

source_name: Blood

value: Blood

value: Neutrophils


title: rat, SCI, rep2

description: Library name: samples5


title: ChIP-Seq_HEK293T_KDM1A


title: Liver_HFD+PP

source_name: Liver_High fat diet+PP_13weeks

value: Liver


title: Mwat_HFD+PP

source_name: Mwat_High fat diet+PP_13weeks


title: ChIP-Seq_HEK293T_3__HA_CARM1_rep2


title: ChIP-Seq_HEK293T_HDAC2

value: Santa Cruz;sc7899


title: Liver_HFD+Ex

source_name: Liver_High fat diet+Ex_13weeks


title: Parse sequencing, PC3docetaxel sublibrary5 (contains all samples)

description: Library name: PD_sublibrary5


title: rat, SCI, rep1

description: Library name: samples4


title: Parse sequencing, PC3docetaxel sublibrary4 (contains all samples)

description: Library name: PD_sublibrary4


title: Mwat_CD

source_name: Mwat_Control diet_13weeks

value: Control diet (10% fat)


title: rat, seven days post-tDCS, rep3

description: Library name: samples3

value: seven days post-tDCS


title: rat, seven days post-tDCS, rep1

description: Library name: samples1


title: rat, seven days post-tDCS, rep2

description: Library name: samples2


title: IMR5 - siXPO1-10_rep3

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

data_processing:
Illumina RTA v3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.7.3a built in Partek Flow
DESeq2 package was used to normalize counts using the Partek E/M model
Genome_build: hg19

source_name: IMR5, MYCN-amplified

growth_protocol: IMR5 cells are grown in RPMI media supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine. They are split every 3-4 days.

extract_protocol:
Total mRNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per the manufacturer’s protocol.
Strand-specific whole transcriptome sequencing libraries were prepared using the TruSeq® Stranded Total RNA LT Library Prep Kit (Illumina) by following the manufacturer’s procedure.

treatment_protocol: Selinexor treated cells were grown in media with 100nM of selinexor for 24 hours prior to RNA extraction. Control cells were growin media supplemented with DMSO. In the XPO1 knockdown cells, IMR5 cells were nucleofected with #10 ON-TARGETplus siRNAs targeting XPO1. Negative control siRNAs were obtained from Horizon (Cat. # LQ-003030-00-000) and transiently transfected into IMR-5 cells using the Nucleofector with solution L and program C-005 (Amaxa Biosystems). RNA was extracted from the transfected cells after 72 hours

value: Neuroblastoma cell line


title: IMR5 - siXPO1-10_rep2


title: IMR5 - siXPO1-10_rep1


title: ChIP-Seq_HEK293T_3__HA_CARM1_rep1


title: Parse sequencing, PC3docetaxel sublibrary1 (contains all samples)

description: Library name: PD_sublibrary1

value: untreated, 1, 5, and 10 DPT


title: AorticValve, Control, 7 weeks, Rep 2

city: Athens

first: Nikolaos

last: Anousakis-Vlachochristou

address: Vas Sofias 114 Ave

department: First Department of Cardiology, Athens Medical School

country: Greece

institute: National and Kapodistrian University of Athens

data_processing:
SmallRNA-Seq lane FASTQ files were merged through concatenation. Data processing was performed using DIANA-mAP (v1.0), a fully automated computational pipeline with an emphasis on preprocessing, allowing for miRNA NGS data analysis from the raw data for quantification and differential expression. Preprocessing was performed with the external tools FastQC (v0.11.7), DNApi (v1.1), and Cutadapt (v1.16). The raw datasets were quality checked, allowing a minimum Phred score of 10, while adapters were provided by the NEBNext manuals and trimmed using a 10 bp minimum allowed read length after trimming. Reads were subsequently aligned to the Oryctolagus Cuniculus GCF_009806435.1 genome assembly from RefSeq using Bowtie (v1.1.1), allowing up to five multiple maps per read. Aligned reads were quantified through miRDeep2 (v0.0.8) using the miRBase v22 hairpin and mature Oryctolagus Cuniculus miRNA forms, allowing one mismatch on the precursor during alignment. Finally, differential expression analysis between the various time points was performed based on the negative binomial distribution using DESeq2 (v1.30.1). The parameters of the remaining DIANA-mAP and external tools were set to their default values.
Assembly: Oryctolagus Cuniculus GCF_009806435.1
Supplementary files format and content: tab-delimited text file with raw counts per Sample

organism: Oryctolagus cuniculus

source_name: Aortic Valve

extract_protocol:
small RNA was extracted using Trizol
small RNA-Seq libraries were prepared using the NEBNext Multiplex Small RNA Library Prep kit for Illumina. NGS Sequencing was performed on a Nova-Seq 6000 System (Illumina), which produced an average sequencing depth of 2.2 million 68 bp single-end reads for the sRNA-Seq data.

treatment_protocol: At sacrifice, one aortic valve cusp was dissected, separated from most of the surrounding fat using magnifying lenses, cleaned from blood in normal saline buffered heparin solution and immersed in RNAlater. All procedures was done in a glass bench using sterilized forceps and scissors, all material was thoroughly cleaned from RNAses using RNAse OFF (Takara Bio) and excessive detergent removed with water for injection. The RNAlater-preserved samples were stored at 4 C for 24 hours and then transferred at - 75 C for long-term storage.

value: Aortic Valve

value: WT

value: normal chaw


title: Parse sequencing, PC3docetaxel sublibrary2 (contains all samples)

description: Library name: PD_sublibrary2


title: eWAT_cdna_cold_16

city: Odense

first: Jan-Wilhelm

last: Kornfeld

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

description: Library name: Sample 6

data_processing:
basecalling using Guppy
Quality trimming using NanoFilt (-q 7)
mapping to the transcriptome (GENCODE M22) using minimap2 (-ax map-ont –secondary=no)
quantification using GenomicAlignments
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw transcript counts for every transcript

source_name: epididymal white adipose tissue

growth_protocol: Mice were kept at 22°C to 24°C on a regular 12 h light cycle with ad libitum access to food (Altromin 1324) and water.

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Whole frozen eWAT samples were homogenised in 1 ml TRIsure (Bioline) per animal using a tabletop homogeniser (FastPrep-24 5G, MP Biomedicals). Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250). Poly-A+ RNA was iolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) following the manufacturer's protocol.
Libraries were prepared from 100 ng poly-A+ RNA using the SQK-DCS109 direct cDNA sequencing kit and the EXP-NBD104 barcoding kit according to the manufacturer’s protocol.

treatment_protocol: 20 weeks old male wild type C57BL/6N mice were singly housed at 4 °C for a period of 24 h prior to harvesting adipose tissues.

value: epididymal white adipose tissue

value: male

value: cold

tag: mouse id


title: IMR5 - sicontrol_rep3

value: sicontrol


title: AorticValve, Control, 2 weeks, Rep 1


title: VeNx, replicate 1, scRNA-seq

city: Shenzhen

first: Fan

last: Qiu

address: 3025 Shennan Middle Road

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

data_processing:
The sequenced data were processed into expression matrices with the Cell Ranger Single-cell software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/what-is-cell-ranger).
Assembly: mRatBN7.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Tissue s were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, then pipetting 5-10 times with a Pasteur pipette。The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells  using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Lung

value: Lung cells

value: vehicle and normoxia


title: Parse sequencing, PC3docetaxel sublibrary3 (contains all samples)

description: Library name: PD_sublibrary3


title: VeNx, replicate 2, scRNA-seq


title: AorticValve, Control, 7 weeks, Rep 1


title: eWAT_cdna_cold_12

description: Library name: Sample 5


title: AorticValve, Control, 7 weeks, Rep 3


title: AorticValve, Exp, 2 weeks, Rep 4

value: 1% cholesterol + 3500 IUs ergocalciferol


title: IMR5 - sicontrol_rep2


title: Liver_CD

source_name: Liver_Control diet_13weeks

value: Liver


title: SuHx, replicate 3, scRNA-seq

value: sugen-5416 and hypoxia


title: IMR5 - sicontrol_rep1


title: eWAT_cdna_ctrl_10

description: Library name: Sample 4

value: ctrl


title: Liver_HFD

source_name: Liver_High fat diet_13weeks

value: High fat diet (60% fat)


title: SuHx, replicate 2, scRNA-seq


title: IMR5 - selinexor_rep3

value: Neuroblastoma cell line

value: selinexor


title: eWAT_cdna_cold_7

description: Library name: Sample 3


title: AorticValve, Exp, 2 weeks, Rep 3

value: Aortic Valve


title: SuHx, replicate 1, scRNA-seq


title: eWAT_cdna_ctrl_6

description: Library name: Sample 2


title: AorticValve, Exp, 2 weeks, Rep 2

value: WT


title: IMR5 - selinexor_rep2


title: scRNA-seq on PBMC from NSCLC patients prior to treatment with ICIs

city: Buk-gu

first: GyeongDae

last: Kim

state: Gwangju,

address: 123, Cheomdangwagi-ro

department: Life Science

country: South Korea

institute: gwangju institute of science and technology

description:
Library name: Raw expression matrix
10x Genomics

data_processing:
Raw base call (BCL) files were demultiplexed using mkfastq application (Cell Ranger v7.1.0) to make FASTQ files. Sequencing reads were mapped to the Ensembl genes (GRCh38) using count application (Cell Ranger v7.1.0) with default settings
Assembly: GRCh38
Supplementary files format and content: expression matrix from Seruat object
Supplementary files format and content: metadata of Seurat object containing UMAP coordinates, cell types, and patient stages etc.

source_name: PBMC

extract_protocol:
Peripheral blood samples were obtained from patients prior to ICI administration. Peripheral blood mononuclear cells (PBMCs) for single cell RNA sequencing analysis were separated from whole blood utilizing standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen until use. All samples showed a high viability of about 90% on average after thawing. Plasma excluding cells was obtained by centrifugation at 4000 rpm at 4°C for 10 minutes. The supernatant aliquot 1.5ml e-tube and store at -80°C until use. Frozen plasma was thawed and centrifuged at 13,000 rpm at 4°C for 5 minutes before use in the experiment.
Library preparation for single-cell RNA-seq was followed according to the Chromium Single Cell 3’ Reagent Kits User Guide (v3.1, 10X Genomics). Single-cell suspensions were filtered through a 40um Flowmi cell strainer (Bel-Art), counted using a CountessII automated cell counter (ThermoFisher), and then loaded onto a microfluidic chip. In the Chromium Controller, cells were separated into Gel Beads-in-emulsion (GEMs) where polyadenylated RNAs in individual cells were tagged with a UMI (unique molecular identifier) and cell barcode. As soon as GEM generation was finished, reverse transcription was performed to produce barcoded cDNAs. cDNAs were amplified through PCR and amplified cDNAs were used for sequencing library construction. Briefly, cDNA amplicons were enzymatically fragmented, end-repaired, dA-tailed, and ligated with a sequencing adaptor.

value: PBMC

tag: subject status

value: NSCLC patient


title: eWAT_cdna_ctrl_5

description: Library name: Sample 1

value: epididymal white adipose tissue

value: male


title: AorticValve, Exp, 2 weeks, Rep 1


title: IMR5 - selinexor_rep1


title: IMR5 - dmso_rep3

value: dmso


title: BatchB ethanol extract of Schisandrae Fructus (Low dose) rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

description: Library name: sample 9-3-6

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.6). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.9a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz's L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 0% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Leibovitz's L-15, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

value: Schisandrae Fructus ethanol extract 12.4 μg/mL

tag: batch

value: B


title: AorticValve, Exp, 4 weeks, Rep 3

tag: tissue


title: BatchB ethanol extract of Schisandrae Fructus (Medium dose) rep3

description: Library name: sample 9-3-5

value: Schisandrae Fructus ethanol extract 62 μg/mL


title: WT-GL261-9Gy-PMX-rep3

city: Irvine

first: Robert

middle: Paul

last: Krattli Jr

state: CA

address: 811 Health Sciences Road, MedSci B-120

department: Anatomy and Neurobiology

institute: University of California, Irvine

description: Total RNA isolated from fresh-frozen brain samples, no amplification of genetic material

hyb_protocol: For each 12-lane cartridge, 70 µl of Master Mix were combined with 42 µl of the fluorescent labeled Reporter CodeSet, flicked to mix, and briefly spun down before 8 µl of combined solution were added to each lane. 5 µl of total RNA (20 ng/µl) per sample was then added to individual lanes. Next, 2 µl of the biotin Capture ProbeSet was added to each lane. Then, loaded cartridges were placed in a thermocycler at 65 degrees Celsius for approximately 20 hours. Following hybridization, cartridges are loaded onto nCounter Prep Station (NanoString™) to perform liquid transfers, magnetic bead separations, and immobilization of molecular labels on the sample cartridge surface. Protocol as described per the manufacture’s instructions: NanoString™ (Seattle, WA).

scan_protocol: Scanning of hybridized cartridges was performed on an nCounter Digital Analyzer (NanoString™) per the manufacturer’s instructions: NanoString™ (Seattle, WA).

data_processing: The raw value data were normalized utilizing a two-step normalization process: an initial Positive Control Normalization, followed by a CodeSet Content Normalization using 13 internalized housekeeping genes that accompanied the Neuroinflammation Panel. Both processes were performed by the nSolver Analysis Software 4.0 (NanoString™).

label: Color-Coded Reporter Probe

source_name: fresh-frozen brain tissue

label_protocol: 5 µl of total RNA (20 ng/µl) per sample were labeled with a fluorescent Reporter ProbeSet per the manufacturer’s instructions: NanoString™ (Seattle, WA).

extract_protocol: Total RNA was isolated from 100 mg of fresh-frozen brain tissue per sample. Brain samples were first homogenized in QIAzol Lysis Reagent (Qiagen) and then underwent RNA isolation with RNeasy Plus Universal Mini Kit (Qiagen) to obtain a minimum of 100 ng of unreplicated RNA, whose purity was verified with both NanoDrop (ThermoFisher) and Bioanalyzer 2100 (Agilent Technologies).

value: fresh-frozen brain tissue

tag: Sex

tag: tumor induction

value: Yes

tag: tumor cell line

tag: radiation dose

value: 9 Gy

tag: pmx205 drug tx


title: IMR5 - dmso_rep2

tag: cell line

tag: treatment


title: AorticValve, Exp, 4 weeks, Rep 2

value: 1% cholesterol + 3500 IUs ergocalciferol


title: WT-GL261-9Gy-PMX-rep2

tag: strain


title: BatchB ethanol extract of Schisandrae Fructus (High dose) rep3

description: Library name: sample 9-3-4

tag: genotype

value: Schisandrae Fructus ethanol extract 310 μg/mL


title: BatchB ethanol extract of Schisandrae Fructus (Low dose) rep2

description: Library name: sample 9-2-6


title: WT-GL261-9Gy-PMX-rep1


title: Paclitaxel_MDAMB231_3

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description:
Library name: Paclitaxel_MDAMB231_3
DK24082_019

data_processing:
Adapter sequences were removed using Cutadapt, and the reads were subsequently mapped to the GRCH 38 genome using HISAT2 aligner. Read counts for each gene were collected by featureCounts. Differentially expressed genes were identified with DESeq2 using filtering thresholds of FDR < 0.05. Pathway enrichment analysis was perfored by DAVID.
Assembly: GRCH38
Supplementary files format and content: txt, csv

source_name: breast cancer

extract_protocol:
RNAs were purified by the RNeasy Mini Kit (Qiagen).
RNA-seq library preparation was conducted with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (LEXOGEN), and the libraries were sequenced on a NextSeq500.

value: breast cancer

tag: cell type

value: luminal


title: BatchB ethanol extract of Schisandrae Fructus (Medium dose) rep2

description: Library name: sample 9-2-5


title: AorticValve, Exp, 7 weeks, Rep 4

value: Aortic Valve


title: Paclitaxel_MDAMB231_2

description:
Library name: Paclitaxel_MDAMB231_2
DK24082_08


title: WT-GL261-9Gy-rep3

value: No


title: BatchB ethanol extract of Schisandrae Fructus (High dose) rep2

description: Library name: sample 9-2-4


title: AorticValve, Exp, 4 weeks, Rep 4

value: WT


title: WT-GL261-9Gy-rep2


title: AorticValve, Exp, 7 weeks, Rep 3


title: AorticValve, Exp, 7 weeks, Rep 2


title: CMPD1_MDAMB231_3

description:
Library name: CMPD1_MDAMB231_3
DK24082_06


title: Paclitaxel_MDAMB231_1

description:
Library name: Paclitaxel_MDAMB231_1
DK24082_07


title: BatchB ethanol extract of Schisandrae Fructus (Low dose) rep1

description: Library name: sample 9-1-6


title: WT-GL261-9Gy-rep1


title: BatchB ethanol extract of Schisandrae Fructus (Medium dose) rep1

description: Library name: sample 9-1-5


title: WT-GL261-0Gy-rep3

value: 0 Gy


title: CMPD1_MDAMB231_2

description:
Library name: CMPD1_MDAMB231_2
DK24082_05


title: Myocardium, Experimental, Replicate 3

description:
RNAseq_myocardium_raw_counts.txt
1062-MYO_S26

data_processing:
RNA-Seq lane FASTQ files were merged through concatenation. Data were preprocessed by utilizing FastQC (v0.11.9) for quality control with a minimum quality score of 10 and by removing the NEBNext adapters using TrimGalore (v0.6.6), introducing a minimum read length allowance of 20 bp. Using the Oryctolagus Cuniculus GCF_009806435.1 genome assembly and annotations from RefSeq, reads were subsequently aligned using STAR (v2.7.8a). Aligned reads were quantified through RSEM (v1.3.3) using RefSeq annotations. Finally, the R package edgeR (v3.42.4) was used for the assessment of DEGs between time points by fitting a quasilikelihood negative binomial generalized log-linear model to the count data (glmQLFit function), which was robust to potential outliers. Prior to the statistical analyses, expression measurements were normalized to account for library depth (counts per million, CPM), while between-library normalization scaling factors were calculated by implementing the trimmed mean of M-values method. Finally, genes with consistently low expression values among the majority of observed samples were filtered out (with the filterByExpr function).
Assembly: Oryctolagus Cuniculus GCF_009806435.1
Supplementary files format and content: tab-delimited text file with raw counts per Sample

source_name: Myocardium

extract_protocol:
RNA was extracted using Trizol
RNA sequencing libraries were prepared using the NEBNext Ultra II directional RNASeq kit. NGS Sequencing was performed on a Nova-Seq 6000 System (Illumina), which produced an average sequencing depth of 21.2 million 100 bp single-end reads for the RNA-Seq data.

value: Myocardium


title: AorticValve, Exp, 7 weeks, Rep 1