title: Lung, Hgf mutant, P21

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

description: Library name: Hgf_mut

data_processing:
We used STAR version 2.7.10a to generate a reference genome index for GRCm39, with Gencode annotations vM33.
FASTQ reads were mapped against the reference genome index using STAR with the settings “ --soloType CB_UMI_Complex --soloUMIlen 8 --soloCellFilter None --outSAMtype BAM SortedByCoordinate --soloFeatures GeneFull_Ex50pAS --runRNGseed 1 --soloMultiMappers EM --readFilesCommand zcat --outSAMattributes NH HI AS nM NM MD jM jI MC ch CB UB GX GN sS CR CY UR UY”.
Libraries using standard BD Rhapsody beads were mapped using the adapter parameters “--soloAdapterSequence NNNNNNNNNACTGGCCTGCGANNNNNNNNNGGTAGCGGTGACA --soloCBposition 2_0_2_8 2_21_2_29 3_1_3_9 --soloUMIposition 3_10_3_17 --soloCBwhitelist BD_CLS1.txt BD_CLS2.txt BD_CLS3.txt”, libraries with BD Rhapsody enhanced beads with --soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA --soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 --soloUMIposition 3_10_3_17 --soloCBwhitelist BD_CLS1_v2_draft.txt BD_CLS2_v2_draft.txt BD_CLS3_v2_draft.txt”
Assembly: mm39
Supplementary files format and content: Tab-separated values and MatrixMarket format counts

source_name: Lung

extract_protocol:
Lung lobes were dissected, finely minced using sharp scissors and transferred into enzymatic digestion solution containing 40U/ml collagenase I (Gibco, 170100-017), 40U/ml Collagenase IV (Gibco, 170100-019), 4U/ml Dispase II (Thermo Fisher, 17105041) and 2 U/µl DNase I (Worthington, LK003170) prepared in DMEM (Gibco, 31053028) medium. Digestion was performed in a water bath, at 37°C for 30 min. During this time, the tissue was also mechanically dissociated by passing it through a needle-syringe for several times.  Enzymatic digestion was stopped by addition of FACS buffer (2% FBS in DMEM) and the lysate was passed through 70 µm cell strainer (Falcon, 352350). The filtrate was centrifuged for 5 min at 4°C and the pellet was resuspended in RBC lysis solution (eBioscience, 00-4333-57) and further incubated for 10 min on ice. Post resuspension in FACS buffer, the cell lysis was pass through a 50 um Cell Trics filter (Sysmex, 04-0042-2317). Cells were centrifuged for 5 min at 4°C and the pellet was resuspended in cold MACS depletion buffer (autoMACS Running Buffer-MACS Separation Buffer, Miltenyi Biotec, 130-091-221). To proceed with magnetic separation and depletion of CD45+ cells and erythrocytes from the cell suspension, CD45 microbeads (Miltenyi Biotec, 130-052-301) and Ter119 microbeads (Miltenyi Biotec, 130-049-901) were added to the cells resuspended in MACS depletion buffer and incubated for 20 min at 4°C. After washing, the cell solutions were passed through MACS MS column (Miltenyi Biotec, 130-042-201) attached to a MACS separator placed on a magnetic Multistand. Filtrate solution consisting of CD45-/Ter119- cells was collected and cell number was counted using Luna Automated Cell Counter (L10001). For each mouse genotype, 40000 cells were prepared for further sequencing from the two mouse littermates, using equal cell number of cells per sample. For the single cell sequencing of postnatal cerebral cortex, two P12 Nodal lox/lox  control and two Nodal iPCKO mice were anesthetized by intraperitoneal injection of Xylazine (16mg/Kg) and Ketamine (100mg/Kg) and transcardially perfused with 10 mL of ice-cold PBS supplemented with Heparin (25 U/mL). Brains were collected and the meningeal layers removed. Next, the cerebral cortex of each hemisphere was dissected and transferred to ice-cold DMEM supplemented with Penicillin/Streptomycin, Glutamine (GlutaMAX, Gibco) and 25 mM HEPES (PAA, Cat. No. S11-001), hereafter dissection media. The cortices belonging to mice from the same genotype were pooled together and minced using scalpels. The resulting paste was resuspended in 1 mL of enzyme blend containing Papain (25 U/mL, Worthington Cat. No. LK003176), DNAseI (113 U/mL, Worthington Cat. No. LK003170), and Liberase DH (100 µg/mL, Roche Cat. No. 5401054) dissolved in pre-warmed dissection media and incubated 30 min at 37oC. During this time, the tissue was further homogenized by repeatedly pipetting the solution up and down every 10 minutes using filtered 1mL tips. After the first 15 min of incubation, 0.5 mL of the described enzyme blend were further added. Next, the tissue homogenate was filtered through a 70µm nylon mesh into a 50mL Falcon tube, the filter was washed with 1 mL of pre-warmed dissection media and the final volume obtained was measured. In order to remove debris and myelin, the cell suspension was mixed with 1.7x volume 22% BSA (Carl Roth Cat. No. 8076.2) dissolved in PBS and centrifuged at 1000 g for 12 min and RT. The supernatant was aspirated and the remaining cell pellet resuspended in 1mL of the described enzyme blend for a final 20min incubation step at 37oC with pipetting every 5min. The resulting single-cell suspension was filtered through a 40µm cell strainer and diluted by addition of 8mL of pre-warmed dissection media. After centrifugation at 300 g for 5min, the supernatant was discarded and the cell pellet resuspended in 1ml of Red Blood Cell Lysis Buffer (Sigma Cat. No. R7757). After a 1 min incubation at RT, 20ml of ice-cold PBS supplemented with 2% fetal calf serum were added and the whole suspension centrifuged at 300 g for 5 min at 4oC. Next, the supernatant was discarded and the cell pellet resuspended in 1ml of filter-sterilized endothelial cell buffer (15 mM HEPES, 153 mM NaCl, 5.6 mM KCl, 1.7 mM CaCl2, 1.2 mM MgCl2 and 10% BSA, pH 7.4) (PMID: 30637296). Cell concentration was assessed using an automated cell counter and 4 x 104 cells from each genotype were loaded into BD Rhapsody Cartridge (BD Biosciences Cat. No. 633733) for cell capture.
Cells were loaded into a BD Rhapsody Cartridge (BD Bioscience, 633733) and captured on the BD Rhapsody Express Single-Cell Analysis System (BD Bioscience). Single-cell mRNA whole transcriptome (WTA) libraries were created using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit (BD Bioscience, 633801) and DNA sequencing was performed on a NextSeq500 (Illumina) using 2 x 75 bp paired end reads with an 8 bp single index.

treatment_protocol: Cre activity was induced by three consecutive intraperitoneal injection of 50 μg tamoxifen (T5648, Sigma) in ethanol-peanut oil (P52144, Sigma) from P1 to P3.

value: Lung

value: Lung cells (CD45+ cells and erythrocytes were depleted!)

value: Hgf iPCKO


title: AD3-STAT

status: Public on Mar 19 2026

type: SRA

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

description: Library name: C002M9M

library_source: transcriptomic

data_processing:
Quality control of sequencing data was performed with FastQC (v0.11.9). Reads were mapped on the GRCm39 (mm39) mouse genome assembly with STAR (v2.7.9a) and quantified with RSEM (v1.3.3). We selected samples that passed quality control filters based on the number of detected genes (> 15% expressed coding genes; threshold at 1 transcript per million, TPM) and the number of uniquely mapped reads (> 60%). This excluded nine samples, probably due to the small number of input cells. The final number of samples per group was N=5, 2, 2 for STAT3+, NF-kB+ and STAT3+/NF-kB+ astrocytes in APP and N=4, 2, 3 in WT mice. Differential gene expression analysis was performed with DESeq2 (v1.32.0) Bioconductor (v3.13) package on R (v4.1.1). Only genes with a raw count number greater than or equal to 10, in at least one sample in each of the two compared groups were analyzed. Results were considered statistically significant for an adjusted p value smaller than or equal to 0.05 and a |log2(fold-change)| greater than or equal to 1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Prefrontal cortex

extract_protocol:
Twelve-month-old WT and APP mice were killed and their PFC rapidly collected in Hank's Balanced Salt Solution without Ca2+ and Mg2+ (HBSS; Sigma). The PFC of three mice were pooled, resulting in N=5 independent PFC samples from APP mice. Cells were mechanically and enzymatically dissociated with fire-polished Pasteur pipettes and the neural tissue dissociation kit with papain (Miltenyi Biotec), following manufacturer's instructions. Myelin removal beads II (Miltenyi Biotec) were used to deplete myelin from cell suspensions using MS columns. Cells were centrifuged at 300 g for 5 min at 4°C, resuspended in 400 µl HBSS with Ca2+ and Mg2+ and sorted on a BD Influx cell sorter. GFP was detected at 530/40 nm (488 nm excitation), CFP at 450/50 nm (408 nm excitation).
The complete protocol is described in Ceyzériat et al. 2018 (PMID 30322407). Sorted cells were placed 5 min at RT and chloroform was added to TRIzol for 3 min. Samples were centrifuged at 12,000 g for 15 min at RT. Aqueous phase was collected and 1 volume of 70% ethanol was added. Samples were transferred onto an RNeasyMin Elute spin column and RNA was purified according to manufacturer’s instructions, with on-column DNAse treatment (RNeasy micro kit, Qiagen, Hilden, Germany). RNA was eluted with 14 µl of RNAse-free deionized water and stored at - 80 °C until transcriptomic analysis. The lower number of astrocytes sorted per sample was not compatible with RNA quality assessment, and full length double strand cDNA libraries were amplified with 18 LD-PCR cycles.

treatment_protocol: Astrocyte-specific lentiviral reporters (LV) were generated to monitor the activity of the transcription factors STAT3 and NF-kB (p65). Six copies of the cis-acting enhancer element recognized by STAT3 or NF-kB were placed upstream of a minimal TA promoter with the TATA box from the Herpes simplex virus thymidine kinase promoter. The STAT3-responsive promoter (P-STAT3) controls the expression of the fluorescent protein eGFP, while the NF-kB-responsive promoter (P-NF-kB) drives the expression of eCerulean with a nuclear localization sequence (CFPnuc).

tag: tissue

value: Prefrontal cortex

tag: cell type

value: Astrocytes

tag: genotype

tag: subpopulation

value: STAT


title: WT_CT_P1O_H3K27ac_rep2

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

country: USA

institute: UC Davis

library_source: genomic

data_processing:
For CUT&Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads were trimmed by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10)
Trimmed reads were aligned with the mouse genome (GRCm38/mm10) using Bowtie2 83 (version 2.4.5) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates from all mapped bam files were removed using the ‘MarkDuplicates’ command in Picard tools (version 3.0.0) (https://broadinstitute.github.io/picard/ ).
To compare replicates, Pearson correlation coefficients were calculated and plotted by ‘multiBamSummary bins’ and ‘plot correlation’ commands from deepTools 84 (version 3.5.5). Biological replicates were pooled using the ‘merge’ command in samtools for visualization and other analyses after confirming reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10,000 / aligned spike-in reads).
Spike-in normalized genome coverage tracks with 1 bp resolution in BigWig format were generated using ‘bamCoverage’ from deepTools with the parameters ‘--binSize 1 --extendReads --samFlagInclude 64 --normalizeUsing RPKM --scaleFactor $scale_factor’. Track views were visualized and exported from Integrative Genomics Viewer 85 (version 2.14.1).
Assembly: mm10
Supplementary files format and content: bigWig, spike-in normalized tracks
Supplementary files format and content: bed, peaks
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: ovary

extract_protocol:
CUT&Tag libraries of oocytes were prepared as previously described32,33 with some modifications (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 2000 S2 cells to 1000 mouse oocytes) at the beginning of each reaction.
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

value: ovary

tag: cell line

value: primary cells

value: P1 oocytes

value: WT

tag: antibody

tag: reads length


title: Diabetic mesenteric artery intima 4 replicate 2

city: DUARTE

first: Naseeb

middle: Kaur

last: Malhi

email: naseebmalhi@gmail.com, nmalhi@coh.org

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

description:
Library name: T2D-4_2
Single-cell RNA sequencing assay

library_source: transcriptomic single cell

data_processing:
10X Genomics cellranger (v6.1.1) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Assembly: GRCh38-2020-A
Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood Vessel

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3.0 gene expression

treatment_protocol: Primary endothelial cells were freshly isolated from human mesenteric arteries

value: Blood Vessel

value: Intima cells isolated from human mesenteric arteries


title: WT_CT_P1O_H3K27ac_rep1


title: Female, Astrocyte, Uninjured, Trap Sample 1

city: Palo Alto

first: Vivianne

middle: L

last: Tawfik

address: 3174 Porter Drive

department: Anesthesiology, Perioperative and Pain Medicine

institute: Stanford University

description:
Library name: Female_Uninjured_ Trap_1
Column D

data_processing:
FASTQ files were passed through the nf-core RNAseq (v3.12.0) pipeline which performed quality control (FastQC), trimming (Trim Galore), alignment to genome reference (STAR; GRCm38), and transcript quantification (RSEM). Genes with ≥ 25 counts in at least 90% of samples were included for analysis.
Assembly: GENCODE GRCm38
Supplementary files format and content: comma-separated values files report raw gene counts for each sample

source_name: Homogenized lumbar spinal cord

extract_protocol:
RNA was isolated by Azenta Life Sciences (formerly GeneWiz) using a routine protocol.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences (formerly GeneWiz) using a standard poly-A selection protocol for mRNA species (eukaryotic).

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

tag: treatment

value: No fracture


title: Lung, Hgf control, P21

country: Germany

description: Library name: Hgf_ctrl

value: Hgf  lox/lox


title: AD1-DOUBLE

description: Library name: C002M9I

value: DOUBLE


title: Diabetic mesenteric artery intima 4 replicate 1

description:
Library name: T2D-4_1
Single-cell RNA sequencing assay


title: Brain, Nodal mutant, P12

description: Library name: Nodal_mut

source_name: Brain, cerebral cortex

value: Brain, cerebral cortex

value: brain cells (myelin debris was removed!)

value: Nodal iPCKO


title: Diabetic mesenteric artery intima 3

description:
Library name: T2D-3
Single-cell RNA sequencing assay


title: Non-Diabetic mesenteric artery intima 1 replicate 2

description:
Library name: ND-1_2
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729233


title: Non-Diabetic mesenteric artery intima 1 replicate 1

description:
Library name: ND-1_1
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729232


title: Lung, Bdnf mutant, P21

description: Library name: Bdnf_cKO

value: Lung

value: Lung cells (CD45+ cells and erythrocytes were depleted!)

value: Bdnf iPCKO


title: Brain, Nodal control, P12

description: Library name: Nodal_ctrl

value: Nodal lox/lox


title: AD4-STAT

description: Library name: C002M9P

value: Prefrontal cortex

value: Astrocytes

value: STAT


title: Non-Diabetic mesenteric artery intima 4

description:
Library name: ND-4
Single-cell RNA sequencing assay

value: Blood Vessel


title: AD2-STAT

description: Library name: C002M9J


title: Diabetic mesenteric artery 6 section 4

description:
Library name: T2D-6_LibD
Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw fastq files were processed using 10X Genomics spaceranger (v1.2.0) pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: Nine processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample; one high resolution and one low resolution image of the tissue to align to transcripts (.png); one image showing the fiducial alignment of the capture area (.jpg); one image with the detected tissue region overlaid (.jpg); a json file with scaling factors for mapping between pixel coordinates and spot positions (.json); a csv file containing spatial coordinates of each capture spot along with whether it was detected as part of the tissue (.csv).
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh froxen tissue was embedded in OCT. 10μm sections were cut via cryostat onto 10X Visium slides
Spatial transcriptomics sequencing libraries were prepared using 10X Genomics Visium Spatial Gene expression slides and reagents using the manufacturers instructions


title: AD1-NFKB

description: Library name: C002M9H

value: NFKB


title: NMO-24h-Brain CD45+, scRNAseq

city: Xi'an

first: Zhe

last: Feng

address: No.620 West Chang'an Street

country: China

institute: Shaanxi Normal University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Brain tissue was minced and centrifuged at 300g for 5 min at 4°C. The supernatant was discarded. Add enzyme I mixture, resuspend and then add enzyme II mixture, incubate at 37°C, 90 rpm, 3 times for 10 min each time, filter through a 70 μm filter. Then centrifuge and discard the supernatant, add pre-cooled D-PBS and resuspend, and afterwards add debris remover, mix well and slowly add pre-cooled D-PBS, thoroughly remove the upper two layers, add pre-cooled D-PBS, resuspended and centrifuge for 10 min. Centrifuge for 10 min, completely remove the upper two layers, add pre-cooled D-PBS and resuspend, centrifuge and discard the supernatant, and resuspend the cells in PBS containing 0.1% BSA and pass through a 30 μm sterile cell strainer.
Library was performd accordiing to the manufacter's instructions（10×Genomics Chromium Single Cell 3’ Reagent Guidelines v3 Chemistry; https://support.10×genomics.com/single-cell-gene-expression）.Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion（GEM）.The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier（UMI）and the 10× Barcode. The pooled barcode cDNA was then cleaned up with Silane DynaBeads, amplifiled by PCR and the apropiated sized fragments were selected for subsequent library construction. Read 2 is used for downstream analysis in Cell ranger, which is added during library construction by end repair, adenine tailing, junction ligation and PCR.

value: brain cells

tag: cell subset

value: brain

tag: strain

tag: age


title: Non-Diabetic mesenteric artery intima 2

description:
Library name: ND-2
Single-cell RNA sequencing assay

value: Intima cells isolated from human mesenteric arteries


title: Diabetic mesenteric artery 6 section 3

description:
Library name: T2D-6_LibC
Fresh frozen spatial transcriptomic sequencing


title: zebrafish general cell population- control, replicate2

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description:
Library name: P3.3.10.1
Column name in P2_P3_readCountMatrix.txt: P3.3.10.1

data_processing:
Data was analyzed with the UTAP pipeline (v1.10.2, Kohen R et. al. BMC Bioinformatics. 2019 Mar 25;20(1):154. doi: 10.1186/s12859-019-2728-2.) . The pipeline steps included fastq trimming using Cutadapt (DOI: 10.14806/ej.17.1.200) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” --times 2 -u 3 -u -3 -q 20 -m 25. The trimmed reads were then mapped to the danRer11 genome using STAR (v2.5.2b).
Quantification of raw read counts per gene was performed using the UCSC  gene annotation. The quantification process involved marking read duplicates with an in-house UTAP script, followed by quantification using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode. As MARseq is a 3’ protocol, the quantification was applied to a region that includes the 3’ 1000 bp of each transcript and 100 bases downstream of the 3’ end was used for quantification.
Read count normalization and differential expression analysis were performed using DESeq2 (v1.36.1) (DOI: 10.1186/s13059-014-0550-8), with the betaPrior parameter set to TRUE. Genes with a log2 fold change (log2FC) > 1, an adjusted p-value (p.adj) < 0.05, and > 10 normalized read count in at least one of the compared conditions were considered differentially expressed.
Assembly: danRer11
Supplementary files format and content: P2_P3_readCountMatrix.txt, crude read count in text format

organism: Danio rerio

source_name: FACS sorted  general cell population- control

growth_protocol: Zebrafish (Danio rerio) were housed at ∼28 °C, 14 hour light:10 hour dark and fed with Artemia and flake food. Fish were maintained and fed following the standard protocols. Crosses were performed with at least 3 old adults. Embryos were kept in E3 zebrafish embryo medium at 28 °C until reaching the desired developmental stage.

extract_protocol:
RNA isolation. Purification of RNA from sorted cells (~20,000 iridophores or general cell population) was done using Dynabeads® mRNA DIRECT™ Purification Kit (Ambion, 61012) according to manufacturer protocol. The purified RNA samples were frozen at -80°C until the step of RNA-seq library preparation.
Bulk MARS-Seq preparation. RNA-seq libraries were prepared at the Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. A bulk adaptation of the MARS-Seq (Jaitin, D. A. et al.  Science 343, 776-779 (2014) and  Keren-Shaul, H. et al. Nat Protoc 14, 1841-1862 (2019)  protocol was used to generate RNA-Seq libraries for expression profiling of iridophores and general control cell population. Briefly, RNA (all RNA amount purified from ~20,000 sorted cells) from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second-strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR as previously described (Jaitin, D. A. et al.  Science 343, 776-779 (2014) and  Keren-Shaul, H. et al. Nat Protoc 14, 1841-1862 (2019)  For Danio rerio, the housekeeping gene actinb1 was selected for its relatively high and uniform expression and was specifically calibrated for the MARS-Seq protocol. Sequencing was done on a NextSeq 500 using NextSeq High Output, 75 cycles, allocating 400M reads in total (Illumina).

treatment_protocol: Tg(pnp4a:PALM-mCherry) positive 5dpf larvae were anesthetized with Tricaine (0.1% MS-222 (Sigma)) and immersed in TrypLE Express (Invitrogen, 12604039). Fish were incubated at 37°C and shaken at 200 rpm for 2 hr, followed by mechanical disruption with vortex and pestels to further dissociate the cells. Cells were then strained through a 40 µM cell strainer with cold HL-15 buffer with 1mM EDTA and centrifuged at 3000 RCF for 5 min at 4°C (HL-15 Buffer: Hank’s Balanced salt solution 40% (Sigma H8264) and 60% Leibovitz's L-15 Medium (Gibco 21083-027)). The pelleted cells were then resuspended in 10 ml of fresh cold HL-15 with 1mM EDTA and then were incubated with Hoechst (H3570, Invitrogen)) to mark the nuclei for 30 min before FACS. FACs Sorting. Cell isolation was carried out by customizing a protocol described previously36,37 (zhoar). Cells were isolated from Tg(pnp4a:PALM-mCherry) positive fish larvae and sorted via Fluorescence-Activated Cell Sorting (FACS). Cells were analyzed and sorted using a BD FACSAria™ III or V Cell Sorter with a 100 µM nozzle. Cells were illuminated using a both 405 and 561 nm lasers. Cells were gated based on attributes to separate cells from each other as well as from cellular debris. Cellular debris were detected using forward, side scatter and Hoescht signals to select against the smallest particles (1 mm or less). Cells were additionally sorted and enriched based on detection using 561 nm filters, corresponding to the pnp4a:PALM-mCherry signal. Cells (~20,000 cells per sample) were collected directly into lysis buffer (Dynabeads® mRNA DIRECT™ Purification Kit (Ambion, 61012)). After reaching ~20,000 cells each sample was vortexed, spinned down and placed immediately on dry ice. The cell collection was performed in three biological replicates and stored in -80°C before proceeding to next steps of sample preparation.

value: WT


title: NMO-24h-Brain CD45-, scRNAseq

description: 10x Genomics


title: Diabetic mesenteric artery 6 section 2

description:
Library name: T2D-6_LibB
Fresh frozen spatial transcriptomic sequencing


title: zebrafish general cell population- control, replicate3

description:
Library name: P3.3.10.2
Column name in P2_P3_readCountMatrix.txt: P3.3.10.2

value: FACS sorted  general cell population- control


title: Multidose7

city: Rochester

first: Nkechi

middle: M

last: Odogwu

state: MN

address: 200 First Street SW

department: Cardiovascular Medicine

institute: Mayo Clinic

description:
Library name: M915_R
column name in MDProcessedCountsData.csv

data_processing:
Raw reads were summarized with FastQC version 0.11.7
Sequence read was  trimmed with Trimmomatic version 0.33 . After trimming, the cleaned reads are re-assessed with FastQC to summarize read length, quality, and duplication. Trimmed reads were aligned to the Sus scrofa 11.1 reference genome with HISAT2 version 2.1.0
Alignments were summarized with RNASeQC to estimate library complexity and exon profiling efficiency. Processed alignments were filtered of reads that have a mapping quality of less than 60 and sorted by read name with Samtools version 1.7. ) from the Subread package version 1.6.2 to produce an expression counts matrix.
Fragments were counted in a strand-specific manner, requiring that both mates of a read pair map to a feature to be counted.  normalization, and differential expression testing.
To filter the matrix to only expressed genes, only genes with a normalized relative expression of 0.5 reads per million in at least five samples.
Assembly: Sscrofa11.1
Supplementary files format and content: CSV files includes FKMP value of each sample

organism: Sus scrofa

source_name: Cardiac Tissue

extract_protocol:
RNA was isolated using the TRIzol/phenol–chloroform
The libraries were sequenced following Illumina's standard protocol for the Illumina NextSeq 2000.

value: Cardiac Tissue


title: Multiome, PDX, Neratinib and Fulvestrant Treatments, GEX

city: Madison

first: Parth

middle: H

last: Khatri

state: WI

address: 1111 Highland Ave

department: Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

description: Library name: HCI032-FVNER_RNA

data_processing:
10X Multiome data was processed using cellranger-arc count
Assembly: hg38
Supplementary files format and content: Control cellranger-arc output files: HCI032-CON_barcodes.tsv.gz, HCI032-CON_features.tsv.gz, HCI032-CON_matrix.mtx.gz, HCI032-CON_atac_fragments.tsv.gz
Supplementary files format and content: Neratinib cellranger-arc output files: HCI032-NER_barcodes.tsv.gz, HCI032-NER_features.tsv.gz, HCI032-NER_matrix.mtx.gz, HCI032-NER_atac_fragments.tsv.gz
Supplementary files format and content: Fulvestrant cellranger-arc output files: HCI032-FV_barcodes.tsv.gz, HCI032-FV_features.tsv.gz, HCI032-FV_matrix.mtx.gz, HCI032-FV_atac_fragments.tsv.gz
Supplementary files format and content: Neratinib+Fulvestrant cellranger-arc output files: HCI032-FVNER_barcodes.tsv.gz, HCI032-FVNER_features.tsv.gz, HCI032-FVNER_matrix.mtx.gz, HCI032-FVNER_atac_fragments.tsv.gz

source_name: breast cancer xenograft

growth_protocol: Fresh human breast tumor fragments were implanted into the cleared inguinal mammary fat pads. Tumor volume was measured every 3-4 days using a Vernier caliper, and tumor volume was estimated using the following formula: V = (length × width × height × 0.5) mm3.

extract_protocol:
Nuclear dissociation was performed based on the 10X Genomics' Nuclei Isolation Guide (CG000366). HCI032 tumors were cut into <2 mm pieces, homogenized using a Dounce homogenizer in 1ml of ice-cold lysis buffer until the solution was uniform, and incubated on ice for 5 minutes with an additional 0.5 ml of lysis buffer. The suspension was filtered through a 70 μm Flowmi Cell Strainer, followed by a 40 μm strainer and centrifuged at 500 x g for 5 min at 4°C. The pellet was washed twice with 1 ml of cold wash buffer and twice with 1ml of cold dilution buffer, with a 5-minute incubation, and centrifugation at 500 x g for 5 min at 4°C after each wash. The pellet was then resuspended with 1ml of sort buffer (2.5% BSA in DPBS with DTT and RNAse inhibitor) and 5 μl 7-ADD stain solution and incubated at room temperature for 10 minutes, followed by a 20-minute incubation on ice. Following centrifugation, the nuclei were washed twice with 500 μl sort buffer and filtered through a 40 μm Flowmi Cell Strainer after each wash. Nuclei were then centrifuged at 500 x g for 5 min at 4°C and resuspend in diluted Nuclei Buffer (10× Genomics, PN-2000153, add 0.1% RNase inhibitor). FACS sorted, and counted using a Countess® II Automated Cell Counter.
The multi-omics snRNA-seq and snATAC-seq libraries were constructed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle Kit (Cat# 1000283, 10x Genomics) according to the manufacturer’s guidelines. Libraries were sequenced on Illumina NovaSeq 6000 instruments using 50 bp paired-end sequencing targeting 6000 cells per sample with a depth of 60000 reads per cell according to the manufacturer's recommendations (10x Genomics).

treatment_protocol: When tumors reached ~100 mm3, mice were randomized into four groups, and treated with either vehicle, fulvestrant (5 mg/mouse/week s.c.), neratinib (40 mg/kg P.O.) or a combination of fulvestrant and neratinib for four to five weeks.

value: breast cancer xenograft

value: breast cancer cells

value: Neratinib+Fulvestrant


title: Diabetic mesenteric artery 7 section 1

description:
Library name: T2D-7_LibC
Fresh frozen spatial transcriptomic sequencing


title: zebrafish general cell population- control, replicate1

description:
Library name: P3.25.10
Column name in P2_P3_readCountMatrix.txt: P3.25.10


title: Lung, Bdnf control, P21

description: Library name: Bdnf_ctrl

value: Lung

value: Lung cells (CD45+ cells and erythrocytes were depleted!)

value: Bdnf lox/lox


title: Multiome, PDX, Neratinib and Fulvestrant Treatment, ATAC

description: Library name: HCI032-FVNER_ATAC

library_source: genomic single cell


title: Single5

description:
Library name: M924_R
column name in MDProcessedCountsData.csv


title: Multiome, PDX, Fulvestrant Treatment, ATAC

description: Library name: HCI032-FV_ATAC

value: Fulvestrant


title: zebrafish iridiphores, replicate2

description:
Library name: P2.3.10.1
Column name in P2_P3_readCountMatrix.txt: P2.3.10.1

source_name: FACS sorted  iridiphores

value: FACS sorted  iridiphores


title: Hela cell,100k,pol2,rep2

city: chongqing,china

first: xipeng

last: shen

address: yixueyuan road NO.1

department: basic medicine

institute: CQMU

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome (or human hg19 for datasets generated from Hela cell) using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9 or hg19
Supplementary files format and content: All attached processed data were in .bed format.

source_name: Hela cell

growth_protocol: PWK&PhJ male mouses (6-8weeks) were mated with C57BL/6N female mouses (6-8weeks) and the time when the vaginal plug was observed the next day was considered E0.5. The embyos were disserted at E6.5 and E7.5, respectively. Germ layers were seperated using enzyme digestion coupled with mechanical separation.

extract_protocol:
ChIP-seq was performed with minor adjustments to the STAR ChIP-seq protocol. Samples were lysed in a buffer containing 0.5% Tween-20, 0.5% NP-40, and 0.1% SDS, and gently pipetted to release genomic DNA. The mixture was then digested with MNase (Sigma) at 37°C for 5 minutes. Primary antibodies-anti-Pol II RBP1 (BioLegend), anti-Phospho-POLR2A CTD-S2 (Abclonal), anti-SP1(Proteintech), anti-H3K4me3 (Millipore) or anti-H3K27me3 (Abclonal)-were added, followed by incubation at 4°C overnight. Protein A Dynabeads (Thermo Fisher Scientific) were added to the solution and incubated for 3-4 hours. Beads were washed five times with RIPA buffer containing 0.1% protease inhibitor and once with LiCl wash buffer. Elution of DNA fragments was achieved with proteinase K treatment.
The library was constructed using NEB Next® UltraTM II DNA Library Prep Kit according to the operation instruction.

treatment_protocol: C57BL/6N female mouses(5 weeks) were superovulated with PMSG following hCG 48h later. After mating with PWK mouses, PN3 zygotes were colleted in M2 medium the next day. The CRISPR-ZEN methods were used to deliver Cas9-sgRNA complex into zygotes for gene editing. Zygotes were cultured to 2-cell stage in vitro and transferred to E0.5 pseudopregnancy foster mice. Germ layers were seperated as described above. The ExVE of embryos was collected for genotyping.

value: Hela cell


title: Hela cell,10k,pol2,rep2


title: zebrafish iridiphores, replicate3

description:
Library name: P2.3.10.2
Column name in P2_P3_readCountMatrix.txt: P2.3.10.2


title: Control4

description:
Library name: M913_R
column name in MDProcessedCountsData.csv


title: Control5

description:
Library name: M914_R
column name in MDProcessedCountsData.csv


title: Multiome, PDX, Neratinib Treatment, GEX

description: Library name: HCI032-NER_RNA

value: Neratinib


title: Control3

description:
Library name: M876
column name in MDProcessedCountsData.csv


title: AD1-STAT

description: Library name: C002M9G

value: Prefrontal cortex

value: Astrocytes

value: STAT


title: Diabetic mesenteric artery 6 section 1

description:
Library name: T2D-6_LibA
Fresh frozen spatial transcriptomic sequencing

value: Blood Vessel


title: Hela cell,10k,pol2,rep1


title: Non-Diabetic mesenteric artery 1

description:
Library name: ND-8
Single-cell RNA sequencing assay

value: Artery cells isolated from human mesenteric arteries


title: CAF+DEX_3

city: hirakata

first: Yuko

last: Emoto

country: Japan

institute: Kansai Medical University

description: Library name: Sample12

data_processing:
The libraries were sequenced on a NextSeq 2000 sequencer (Illumina, Inc., California, USA) to generate 75-nt single reads. Duplicate reads were removed from the raw reads using Seqkit (ver. 2.0.0), and adapter sequence was trimmed with Cutadapt (ver. 3.7). The trimmed reads were mapped to rat genome assembly (rn7) using STAR (ver. 2.7.11b) with the following parameters: --alignEndsType EndToEnd -- outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outReadsUnmapped None --outSAMtype BAM Unsorted --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 -- outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1. Reads mapped to miRNA genes were quantified using featureCounts in the Subread package (ver. 2.0.6) with the following parameters: -s 1 -O -M -p -C -B -T. Differential gene expression analysis was performed using the RNA-seq Analysis Portal (ver. 5.1, Qiagen). miRBase (https://www.mirbase.org/) was used as the reference database.
Assembly: Rnor_6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Rattus norvegicus

source_name: liver

growth_protocol: Six-week-old male Sprague-Dawley rats (Jcl:SD) were purchased from CLEA Japan, Inc. (Tokyo, Japan). They were housed in plastic cages with paper-chip bedding in an air-conditioned room at 22 ± 2°C and 60 ± 10% relative humidity under a 12-h light/dark cycle. The animals had free access to food and water (CLEA Rodent Diet CE-2 for Mice, Rats, and Hamsters; CLEA Japan, Inc.).

extract_protocol:
At dissection, a piece of liver tissue was cut into small pieces, placed in Ambion RNAlater solution (Thermo Fisher Scientific Inc., Massachusetts, USA), and stored overnight at 4 °C. The following day, the samples were transferred to -20 °C until use. Total RNA, including the small RNA fraction, was isolated from 10–20 mg of liver tissue using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.
The miRNA-seq library was prepared using the QIAseq miRNA Library Kit (Qiagen), following the manufacturer’s instructions. In brief, a pre-adenylated DNA adapter was ligated to the 3' ends of all miRNAs, followed by ligation of an RNA adapter to the 5' ends of mature miRNAs. Reverse-transcription (RT) was then performed using an RT primer containing Unique Molecular Indices (UMIs). Finally, the library was amplified with sample-specific index primers.

treatment_protocol: fter the acclimatization period, the 7-week-old rats were divided into four groups: control, caffeine, dextromethorphan, and caffeine plus dextromethorphan (n = 5 per group). The rats were orally administered the drugs for 5 consecutive days, as described below. The caffeine group (CAF) received 120 mg/kg caffeine, the dextromethorphan group (DEX) received 100 mg/kg dextromethorphan hydrobromide monohydrate, and the combination group (CAF + DEX) received 120 mg/kg caffeine and 100 mg/kg dextromethorphan hydrobromide monohydrate. All drugs were dissolved in sterile distilled water. Age-matched control groups (control) were treated with vehicle (sterile distilled water) only.

value: liver

value: Caffeine and Dextromethorphan administration


title: CAF+DEX_2

description: Library name: Sample11


title: Control2

description:
Library name: M872_R
column name in MDProcessedCountsData.csv

value: Cardiac Tissue


title: Multidose6

description:
Library name: M873_R
column name in MDProcessedCountsData.csv


title: Multiome, PDX, DMSO Treatment, GEX

description: Library name: HCI032-CON_RNA

value: breast cancer xenograft

value: breast cancer cells

value: DMSO


title: zebrafish iridiphores, replicate1

description:
Library name: P2.25.10
Column name in P2_P3_readCountMatrix.txt: P2.25.10

value: WT


title: DEX_3

description: Library name: Sample9

value: Dextromethorpan administration


title: Diabetic mesenteric artery intima 2 replicate 2

description:
Library name: T2D-2_2
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729241

value: Intima cells isolated from human mesenteric arteries


title: Diabetic mesenteric artery intima 1 replicate 2

description:
Library name: T2D-1_2
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729239


title: CAF+DEX_1

description: Library name: Sample10


title: Diabetic mesenteric artery intima 1 replicate 1

description:
Library name: T2D-1_1
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729238


title: Single3

description:
Library name: M862_R
column name in MDProcessedCountsData.csv


title: Diabetic mesenteric artery 7 section 2

description:
Library name: T2D-7_LibD
Fresh frozen spatial transcriptomic sequencing


title: Single2

description:
Library name: M859_R
column name in MDProcessedCountsData.csv


title: Multiome, PDX, DMSO Treatment, ATAC

description: Library name: HCI032-CON_ATAC


title: Multidose5

description:
Library name: M823
column name in MDProcessedCountsData.csv


title: U87-MG cells, control rep2

city: Dalian

first: Jianxin

last: Wang

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: All_gene_counts.txt, All_gene_fpkm.txt

growth_protocol: Human glioblastoma cell lines U87-MG were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with MEM (Gibco), 100 unit/mL penicillin and 100 mg/mL streptomycin.

extract_protocol:
1. Freeze 2ml Eppendorf microcentrifuge tube with tissue sample and glass ball at -80°C and then grind the sample in the MM300 Mixer Mill at 30Hz for two minutes.2. Add 1 ml fresh TRIzol Reagent to the mechanically disrupted tissue sample, vortex well, and incubate the sample at room temperature for 5 minutes.3. Add 0.2 ml of chloroform to the microcentrifuge tube for homogenization. Vortex well, and incubate the sample at room temperature for 3 minutes.4. Centrifugate the sample at maximum speed on table microcentrifuge at 4°C for 5 minutes.5. Transfer the aqueous phase to a fresh 2 ml microcentrifuge tube. Add an equal volume of chloroform to the fresh microcentrifuge tube, vortex well. Spin at maximum speed on table microcentrifuge for 5 minutes.6. Transfer the aqueous phase to a fresh 2 ml microcentrifuge tube. Add an equal volume of isopropanol to the fresh microcentrifuge tube, vortex well. Spin at maximum speed on table microcentrifuge at 4°C for 10 minutes.7. Wash the pellet with 1.5 ml 70% ethanol. Spin at maximum speed on table microcentrifuge for 5 minutes.8. Dissolve the pellet in 400 μl 1xTE at 55°С well with vortex. Add an equal volume of 10 M LiCl to the solution and chill it at -20°C for several hours (or overnight).9. Spin the tube at maximum speed on table microcentrifuge at 4°C for 10 minutes. Carefully remove and discard the supernatant (contains DNA and small RNA < 200 nt).10. Wash pellet with 1.5 ml 70% ethanol, vortex well. Spin the tube at maximum speed on table microcentrifuge at 4°C for 10 minutes. Discard the ethanol, do not dry the pellet.11. Dissolve the pellet in 200-400 μl fresh RNase-free ddH2O or 1xTE.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting ZDHHC15 and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

value: Glioblastoma

value: Negative Control


title: U87-MG cells, MAGED2 knockdown rep2

value: Knockdown MAGED2 gene


title: Non-Diabetic mesenteric artery intima 3

description:
Library name: ND-3
Single-cell RNA sequencing assay


title: Multiome, PDX, Fulvestrant Treatment, GEX

description: Library name: HCI032-FV_RNA

value: Fulvestrant


title: U87-MG cells, control rep1


title: CAF_3

description: Library name: Sample6

value: Caffeine administration


title: Hela cell,100k,pol2,rep1

value: Hela cell


title: Non-Diabetic mesenteric artery 7 section 2

description:
Library name: ND-7_LibD
Fresh frozen spatial transcriptomic sequencing

value: Blood Vessel


title: Multidose4

description:
Library name: M121_R
column name in MDProcessedCountsData.csv


title: Diabetic mesenteric artery intima 2 replicate 1

description:
Library name: T2D-2_1
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO sample GSM4729240


title: DEX_2

description: Library name: Sample8


title: Non-Diabetic mesenteric artery 7 section 1

description:
Library name: ND-7_LibC
Fresh frozen spatial transcriptomic sequencing


title: U87-MG cells, MAGED2 knockdown rep1


title: Single4

description:
Library name: M870_R
column name in MDProcessedCountsData.csv


title: Multiome, PDX, Neratinib Treatment, ATAC

description: Library name: HCI032-NER_ATAC

value: Neratinib


title: Non-Diabetic mesenteric artery 6 section 2

description:
Library name: ND-6_LibB
Fresh frozen spatial transcriptomic sequencing


title: 2-F: Fulvestrant treated BT474 cells

first: Huy

last: Dinh

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: scRNA- seq was performed by the UW- Madison Biotechnology Center Gene Expression Center.  For the single cell preparation, BT474 cells were treated with DMSO as control, fulvestrant (100 nM), neratinib (200nM) or both (fulvestrant plus neratinib) for 4h, then cells were digested with trypsin into single cells and resuspended with buffer 1x PBS (Ca++/Mg++-free) + w/v 0.04% BSA (non-acetylated) + 1U/ml RNase Inhibitor for cell number counting and cell viability measurement using Countess® II Automated Cell Counter. The scRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3’ v3 Reagent Kit according to the manufacturer’s guidelines (10x Genomics). cDNA libraries were uniquely sample indexed and pooled for sequencing. A MiSeq (Illumina) sequencing run was used to sample balance on a NovaSeq SP flowcell (Illumina) using a 28×72bp sequencing reaction targeting 3000 cells per sample with a depth of 60000 reads per cell according to the manufacturer's recommendations (10x Genomics).

data_processing:
Raw reads from all samples were aligned to the hg19 reference genome, UMI (unique molecular identifier) counting was performed using Cell Ranger v.3.1.0 (10X Genomics)
The barcodes can be separated by sample using the last character of the barcode, which corresponds to the sample number at the start of each sample name.
Assembly: hg19
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: A sparse gene expression matrix for all samples with rows indexed by features and columns by cell barcodes

source_name: Cell line

growth_protocol: BT474 cells were maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (VWR) and 1% Penicillin-Streptomycin (P/S) (Gibco).

treatment_protocol: BT474 cells were treated with DMSO as control, fulvestrant (100 nM), neratinib (200nM) or both (fulvestrant plus neratinib) for 4h.

value: Fulvestrant treated


title: Multidose1

description:
Library name: M114
column name in MDProcessedCountsData.csv


title: Control1

description:
Library name: M840_R
column name in MDProcessedCountsData.csv


title: Non-Diabetic mesenteric artery intima 5

description:
Library name: ND-5
Single-cell RNA sequencing assay
Raw data previously uploaded in GEO samples GSM4729234-GSM4729237


title: Non-Diabetic mesenteric artery 6 section 1

description:
Library name: ND-6_LibA
Fresh frozen spatial transcriptomic sequencing


title: Non-Diabetic mesenteric artery 6 section 3

description:
Library name: ND-6_LibD
Fresh frozen spatial transcriptomic sequencing


title: DupC, rep2

status: Public on Mar 18 2026

city: Heidelberg

first: Maarten

last: van den Hoogenhof

address: Eppelheimer Str. 8,

institute: Institute of Experimental Cardiology

description: Library name: DupC2

data_processing:
https://galaxyproject.org
Assembly: GENCODE GRCh38 reference genome (release 45, Ensembl 111)
Supplementary files format and content: csv file includes raw counts of each sample

source_name: Human IPSCs

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer's protocol. 1 μg of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the SMART-Seq Total RNA Pico Input kit following manufacturer's protocol.

value: Human IPSCs

value: DupCmutant


title: DEX_1

description: Library name: Sample7

value: liver


title: Wildtype, rep2

description: Library name: WT2

value: Wildtype


title: 1-D: DMSO treated BT474 cells

extract_protocol:
The scRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3’ v3 Reagent Kit according to the manufacturer’s guidelines (10x Genomics). cDNA libraries were uniquely sample indexed and pooled for sequencing.
A MiSeq (Illumina) sequencing run was used to sample balance on a NovaSeq SP flowcell (Illumina) using a 28×72bp sequencing reaction targeting 3000 cells per sample with a depth of 60000 reads per cell according to the manufacturer's recommendations (10x Genomics).

value: DMSO treated


title: 4-F-N: Fulvestrant + neratinib treated BT474 cells

value: Fulvestrant + neratinib treated


title: DupC, rep1

description: Library name: DupC1


title: Wildtype, rep3

description: Library name: WT3


title: Multidose3

description:
Library name: M120
column name in MDProcessedCountsData.csv

value: Cardiac Tissue


title: 3-N: Neratinib treated BT474 cells

value: Neratinib treated


title: Control_1

description: Library name: Sample1


title: PANS_4_post

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description: Library name: PANS_4_post

data_processing:
HIVE™ scRNAseq libraries were sequenced using specific primers contained in the kit on an Illumina NovaSeq X sequencer (AGRF Ltd., Melbourne). Data was analysed using the Seurat package.
Assembly: Human hg38, build 104
Supplementary files format and content: tab separated values and qc files

source_name: RBC depleted leukocytes

extract_protocol:
Venous blood was collected into acid-citrate-dextrose (ACD) tubes, and red blood cells (RBCs) were removed following the EasySep™ RBC Depletion protocol from STEMCELL Technologies (catalogue #18170) using the EasySep™ Magnet (catalogue #18000, Stemcell Technologies).The resulting cell suspension was then loaded into the HIVE™ collectors following the manufacturer’s protocol (Honeycomb Biotechnologies, Inc., USA) and stored at -80°C until library preparation and sequencing by AGRF Ltd. Samples were always loaded into a HIVE™ collector within 1 hour of collection to reduce neutrophil activation.
Following a standard protocol (Honeycomb Biotechnologies, Inc., USA), cell-loaded HIVE™ devices were sealed with a semi-permeable membrane, allowing for a strong lysis solution and a hybridisation solution. After collection, beads with captured transcripts were extracted from the HIVE™ by centrifugation and transferred to a 96-well plate (AGRF Ltd., Westmead). The size profiles of the final libraries were determined on a TapeStation platform using a D5000 ScreenTape System (Agilent Technologies, Santa Clara, CA, USA), and the concentration of final pooled libraries was determined by qPCR

treatment_protocol: venous blood was collected prior to starting NTI164 (baseline) as well as after 12 weeks of receiving the drug

value: RBC depleted leukocytes

tag: condition

value: PANS


title: Control_3

description: Library name: Sample3


title: Control_2

description: Library name: Sample2


title: PANS_5_post

description: Library name: PANS_5_post


title: Single1

description:
Library name: M118
column name in MDProcessedCountsData.csv


title: CAF_2

description: Library name: Sample5


title: PANS_3_post

description: Library name: PANS_3_post


title: PANS_2_post

description: Library name: PANS_2_post


title: Multidose2

description:
Library name: M117
column name in MDProcessedCountsData.csv


title: CAF_1

description: Library name: Sample4


title: PANS_2_pre

description: Library name: PANS_2_pre


title: Wildtype, rep1

description: Library name: WT1


title: PANS_3_pre

description: Library name: PANS_3_pre


title: DupC, rep3

description: Library name: DupC3


title: PANS_4_pre

description: Library name: PANS_4_pre


title: control_1

description: Library name: control_1

value: control


title: control_3

description: Library name: control_3


title: MECP2_media

description:
Library name: MECP2_media
HIVEseq

data_processing:
Fastqs were processed into gene and transcript counts ising beenet v1.1 (Honeycomb Biotechnologies, Inc)
Assembly: Human hg38
Supplementary files format and content: ensembl build 104
Supplementary files format and content: tab separated values and qc files

growth_protocol: Venous blood from the participants was collected in Vacutainer ACD tubes (BD Biosciences, BD367756) after gaining written consent. Peripheral blood mononuclear cells (PBMCs) were isolated and stored, as previously described10. Frozen PBMC aliquots were thawed rapidly in a 37°C water bath, followed by washing with thawing medium consisting of RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX™, and 1% HEPES. The cells were then incubated in culture medium (RPMI 1640 supplemented with 10% FBS and 1% GlutaMAX™) at 37°C in a 5% CO2 atmosphere for 3 hours.

extract_protocol:
cells were harvested from the wells by scraping with 1mL pipette tip, washed and stained with DAPI (1:100). The live cells (DAPI-negative) were sorted by the Westmead Institute for Medical Research (WIMR) using the BD FACSAriaTM III Cell Sorter and subsequently loaded into the HIVETM devices, following the manufacturer’s instructions (Honeycomb Biotechnologies, Inc). 12 HIVETM devices were loaded with approximately 30,000 cells from each sample (individual butyrate-treated and untreated samples from 4 patients and 2 controls) in 1 mL of DPBS + 1% FBS followed by 3 mL of cell media (DPBS + 1% FBS). HIVEsTM were then placed onto a spin plate and spun at 30 x g for 3 minutes to allow the single-cells to settle into the picowells containing 3’ transcript-capture beads. The solution was removed from the HIVETM devices, and 2mL sample wash solution (provided in kit) was added to each. The sample wash solution was removed, and the cell-loaded HIVEs™ were frozen at -80°C after the addition of 2mL cell preservation solution
Following standard protocol, cell-loaded HIVETM devices were sealed with a semi-permeable membrane, allowing for the use of the strong lysis solution followed by the addition of hybridization solution. After collection with or without storage, beads with captured transcripts were extracted from the HIVETM device by centrifugation. The remaining HIVETM library preparation steps were conducted in a 96-well plate format (https://honeycombbio.zendesk.com/hc/en-us/articles/15173667166491-HIVE-CLX-Transcriptome-Recovery-Library-Preparation-User-Protocol). The size distribution and quality of the final libraries were determined on a TapeStation 2150 platform with HSD5000 ScreenTape System (Agilent Technologies, Santa Clara, CA, USA). The concentration of final pooled libraries was determined by qPCR. HIVETM scRNAseq libraries were sequenced using specific primers contained in the kit on an Illumina® NovaSeq® X sequencer.

treatment_protocol: Following the incubation, the cells were treated with 5mM butyrate in culture media or control culture media (untreated) for 24 hours at 37oC in a 5% CO2 atmosphere. A dose of 5mM butyrate was chosen based on the ideal blood ketone ranges in pediatric epilepsy of ~2.5-5 mM beta-hydroxybutyrate on ketogenic diet 18 and butyrate has epigenetic effects at this concentration10

value: media


title: control_nonmonogenic_butyrate

description:
Library name: control_nonmonogenic_butyrate
HIVEseq

value: WT

value: butyrate


title: MECP2_butyrate

description:
Library name: MECP2_butyrate
HIVEseq


title: control_nonmonogenic_media

description:
Library name: control_nonmonogenic_media
HIVEseq


title: control_4

description: Library name: control_4


title: CHD7_media

description:
Library name: CHD7_media
HIVEseq


title: PANS_5_pre

description: Library name: PANS_5_pre


title: control_8

description: Library name: control_8


title: CHD7_butyrate

description:
Library name: CHD7_butyrate
HIVEseq


title: nonmonogenic_butyrate

description:
Library name: nonmonogenic_butyrate
HIVEseq

value: Monogenic


title: DNA from pediatric low-grade glioma 1

type: genomic

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Restored DNA was assayed on Infinium MethylationEPIC kit (Illumina, USA), according to the Infinium HD FFPE Methylation Assay protocol (Illumina, USA).

scan_protocol: Prepared BeadChips were scanned on the NextSeq-550 (Illumina, USA). On-Chip quality metrics of each sample were carefully monitored including minimal CpG detection limits (>95% at p<0.05). Output of raw signal intensities were obtained via iDAT files as output from the NextSeq-550.

data_processing: Raw methylation (.idat) files were imported, pre-processed, and normalized (ssNoob method) using minfi46 (v1.44.0). Probes that failed to hybridize (detection P value > 0.01) in one or more samples were removed, as well as cross-reactive probes, those that overlapped with known single nucleotide polymorphisms (SNPs), and those targeting the X and Y chromosomes.

label: Cy3 and Cy5

source_name: formalin-fixed paraffin embedded

label_protocol: Standard Illumina Protocol.

extract_protocol: FFPE tissue had a minimum of 200 ng of genomic DNA bisulfite-converted (EZ DNA Methylation Kit, Zymo Research D5001) under the manufacturer’s specifications. Bisulfite-converted DNA was then subjected to the Infinium FFPE DNA Restore kit (Illumina, USA).

value: formalin-fixed paraffin embedded


title: DNA from pediatric low-grade glioma 23


title: DNA from pediatric low-grade glioma 82


title: DNA from pediatric low-grade glioma 20


title: control_monogenic_media

description:
Library name: control_monogenic_media
HIVEseq


title: DNA from pediatric low-grade glioma 76


title: DNA from pediatric low-grade glioma 22


title: DNA from pediatric low-grade glioma 19


title: DNA from pediatric low-grade glioma 83


title: control_monogenic_butyrate

description:
Library name: control_monogenic_butyrate
HIVEseq


title: DNA from pediatric low-grade glioma 84


title: DNA from pediatric low-grade glioma 42


title: DNA from pediatric low-grade glioma 6


title: DNA from pediatric low-grade glioma 21


title: DNA from pediatric low-grade glioma 17


title: DNA from pediatric low-grade glioma 18


title: DNA from pediatric low-grade glioma 12


title: DNA from pediatric low-grade glioma 7


title: DNA from pediatric low-grade glioma 43


title: DNA from pediatric low-grade glioma 14


title: DNA from pediatric low-grade glioma 15


title: DNA from pediatric low-grade glioma 81


title: KMT2D_media

description:
Library name: KMT2D_media
HIVEseq


title: KMT2D_butyrate

description:
Library name: KMT2D_butyrate
HIVEseq


title: DNA from pediatric low-grade glioma 80


title: nonmonogenic_media

description:
Library name: nonmonogenic_media
HIVEseq


title: DNA from pediatric low-grade glioma 8


title: DNA from pediatric low-grade glioma 13


title: DNA from pediatric low-grade glioma 16


title: DNA from pediatric low-grade glioma 10


title: DNA from pediatric low-grade glioma 11


title: DNA from pediatric low-grade glioma 9


title: DNA from pediatric low-grade glioma 45


title: DNA from pediatric low-grade glioma 75


title: DNA from pediatric low-grade glioma 87


title: DNA from pediatric low-grade glioma 79


title: DNA from pediatric low-grade glioma 92


title: DNA from pediatric low-grade glioma 74


title: DNA from pediatric low-grade glioma 85


title: DNA from pediatric low-grade glioma 40


title: DNA from pediatric low-grade glioma 78


title: DNA from pediatric low-grade glioma 77


title: DNA from pediatric low-grade glioma 91


title: DNA from pediatric low-grade glioma 73


title: DNA from pediatric low-grade glioma 41


title: DNA from pediatric low-grade glioma 44


title: DNA from pediatric low-grade glioma 49


title: DNA from pediatric low-grade glioma 90


title: DNA from pediatric low-grade glioma 35


title: DNA from pediatric low-grade glioma 48


title: DNA from pediatric low-grade glioma 93


title: DNA from pediatric low-grade glioma 34


title: DNA from pediatric low-grade glioma 37


title: DNA from pediatric low-grade glioma 94


title: DNA from pediatric low-grade glioma 38


title: DNA from pediatric low-grade glioma 60


title: DNA from pediatric low-grade glioma 39


title: DNA from pediatric low-grade glioma 36


title: DNA from pediatric low-grade glioma 89


title: DNA from pediatric low-grade glioma 86


title: DNA from pediatric low-grade glioma 96


title: DNA from pediatric low-grade glioma 62


title: DNA from pediatric low-grade glioma 95


title: DNA from pediatric low-grade glioma 97


title: DNA from pediatric low-grade glioma 69


title: DNA from pediatric low-grade glioma 88


title: DNA from pediatric low-grade glioma 64


title: DNA from pediatric low-grade glioma 30


title: DNA from pediatric low-grade glioma 29


title: DNA from pediatric low-grade glioma 66


title: DNA from pediatric low-grade glioma 33


title: DNA from pediatric low-grade glioma 63


title: DNA from pediatric low-grade glioma 57


title: hepatopancreas, 18°C, 0 hours, sample 5

city: Gangneung-city

first: Young Chang

last: Sohn

address: Jukheon-gil 7

country: South Korea

institute: Gangneung-Wonju National University

description: Library name: M0_Hep5

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to xgHalRufe1.0.p(NCBI) whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: xgHalRufe1.0.p
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

organism: Haliotis discus hannai

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

value: hepatopancreas


title: DNA from pediatric low-grade glioma 59


title: tentacle, 18°C, 0 hours, sample 5

description: Library name: M0_Ten5

value: tentacle


title: DNA from pediatric low-grade glioma 70


title: eye, 18°C, 0 hours, sample 5

description: Library name: M0_Eye5

value: eye


title: DNA from pediatric low-grade glioma 32


title: DNA from pediatric low-grade glioma 61


title: eye, 18°C, 0 hours, sample 2

description: Library name: M0_Eye2


title: tentacle, 18°C, 0 hours, sample 2

description: Library name: M0_Ten2


title: DNA from pediatric low-grade glioma 27


title: DNA from pediatric low-grade glioma 26


title: DNA from pediatric low-grade glioma 58


title: gill, 18°C, 0 hours, sample 2

description: Library name: M0_Gil2

value: gill


title: gill, 18°C, 0 hours, sample 5

description: Library name: M0_Gil5


title: DNA from pediatric low-grade glioma 55


title: DNA from pediatric low-grade glioma 31


title: DNA from pediatric low-grade glioma 3


title: DNA from pediatric low-grade glioma 4


title: DNA from pediatric low-grade glioma 68


title: DNA from pediatric low-grade glioma 53


title: DNA from pediatric low-grade glioma 2


title: tentacle, 27°C, 6 hours, sample 4

description: Library name: H6_Ten4


title: tentacle, 27°C, 24 hours, sample 3

description: Library name: H24_Ten3


title: DNA from pediatric low-grade glioma 25


title: hepatopancreas, 27°C, 6 hours, sample 2

description: Library name: H6_Hep2


title: hepatopancreas, 18°C, 0 hours, sample 2

description: Library name: M0_Hep2


title: DNA from pediatric low-grade glioma 24


title: tentacle, 27°C, 6 hours, sample 2

description: Library name: H6_Ten2


title: DNA from pediatric low-grade glioma 46


title: gill, 27°C, 24 hours, sample 3

description: Library name: H24_Gil3


title: DNA from pediatric low-grade glioma 52


title: hepatopancreas, 27°C, 6 hours, sample 4

description: Library name: H6_Hep4


title: DNA from pediatric low-grade glioma 67


title: DNA from pediatric low-grade glioma 28


title: gill, 27°C, 6 hours, sample 4

description: Library name: H6_Gil4


title: eye, 27°C, 6 hours, sample 2

description: Library name: H6_Eye2


title: eye, 27°C, 6 hours, sample 4

description: Library name: H6_Eye4


title: gill, 27°C, 6 hours, sample 2

description: Library name: H6_Gil2


title: DNA from pediatric low-grade glioma 47


title: DNA from pediatric low-grade glioma 72


title: DNA from pediatric low-grade glioma 50


title: DNA from pediatric low-grade glioma 56


title: DNA from pediatric low-grade glioma 5


title: hepatopancreas, 27°C, 24 hours, sample 3

description: Library name: H24_Hep3


title: DNA from pediatric low-grade glioma 54


title: eye, 27°C, 24 hours, sample 3

description: Library name: H24_Eye3


title: hepatopancreas, 27°C, 24 hours, sample 2

description: Library name: H24_Hep2


title: DNA from pediatric low-grade glioma 71


title: DNA from pediatric low-grade glioma 51


title: hepatopancreas, 9°C, 6 hours, sample 3

description: Library name: C6_Hep3


title: tentacle, 27°C, 24 hours, sample 1

description: Library name: H24_Ten1


title: tentacle, 9°C, 6 hours, sample 3

description: Library name: C6_Ten3


title: gill, 27°C, 24 hours, sample 2

description: Library name: H24_Gil2


title: scn_WT_DMSO_2

city: New Haven

first: Priyanka

last: Jamadagni

state: CT

address: 333 Cedar Street

department: School of Medicine

institute: Yale University

description:
Library name: Sample 20
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx

data_processing:
The downstream data was processed using DESeq2 software package
Assembly: The reads were mapped to GRCz10 genome for zebrafish and GRCh38 for the hPSC derived iGLUT cells.
Supplementary files format and content: Excel spreadsheets include raw counts for both cells and zebrafish samples, and DESeq2 processed files for zebrafish samples, for each treatment group vs control group.

growth_protocol: Larval zebrafish were raised in fish media upto 6 days post fertilization. iGluts were raised to D60.

extract_protocol:
RNA was extracted from fish at 6 days post fertilization and from cells at D60. RNA was extracted using Qiagen Rneasy Plus Micro Kit.
For fish, NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina was used. For cells, Kapa mRNA Hyper Prep Kit Cat# KR1352 was used.

treatment_protocol: Larval zebrafish were treated with Levocarnitine or DMSO for 24 hours from 5 to 6 days post fertilization. iGluts were treated with Levocarnitine or DMSO for 48 hours.

value: brain

value: scn1lab WT

value: DMSO


title: scn_WT_LEVO_2

description:
Library name: Sample 23
gene_count_matrix_all samples.csv
scn_WT_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx

value: 10 µM Levocarnitine 24hrs


title: DNA from pediatric low-grade glioma 65


title: scn_WT_DMSO_3

description:
Library name: Sample 21
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: gill, 9°C, 6 hours, sample 2

description: Library name: C6_Gil2


title: scn_WT_LEVO_3

description:
Library name: Sample 24
gene_count_matrix_all samples.csv
scn_WT_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: eye, 9°C, 6 hours, sample2

description: Library name: C6_Eye2


title: tentacle, 9°C, 24 hours, sample 3

description: Library name: C24_Ten3


title: tentacle, 9°C, 6 hours, sample 2

description: Library name: C6_Ten2


title: gill, 9°C, 6 hours, sample 3

description: Library name: C6_Gil3


title: scn_HOM_DMSO_4

description:
Library name: Sample 15
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx

value: scn1lab homozygous mutant


title: scn_WT_LEVO_1

description:
Library name: Sample 22
gene_count_matrix_all samples.csv
scn_WT_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: scn_HOM_LEVO_1

description:
Library name: Sample 16
gene_count_matrix_all samples.csv
scn_HOM_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: hepatopancreas, 9°C, 24 hours, sample 3

description: Library name: C24_Hep3


title: scn_WT_DMSO_1

description:
Library name: Sample 19
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: eye, 9°C, 6 hours, sample3

description: Library name: C6_Eye3


title: eye, 27°C, 24 hours, sample 2

description: Library name: H24_Eye2


title: gill, 9°C, 24 hours, sample 1

description: Library name: C24_Gil1


title: scn_HOM_LEVO_3

description:
Library name: Sample 17
gene_count_matrix_all samples.csv
scn_HOM_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: scn_HOM_LEVO_4

description:
Library name: Sample 18
gene_count_matrix_all samples.csv
scn_HOM_LEVO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: eye, 9°C, 24 hours, sample 3

description: Library name: C24_Eye3


title: hepatopancreas, 9°C, 6 hours, sample 2

description: Library name: C6_Hep2


title: dyrk_WT_LEVO_4

description:
Library name: Sample 12
gene_count_matrix_all samples.csv
dyrk_WT_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx

value: dyrk1a WT


title: scn_HOM_DMSO_1

description:
Library name: Sample 13
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: tentacle, 9°C, 24 hours, sample 2

description: Library name: C24_Ten2


title: dyrk_WT_DMSO_4

description:
Library name: Sample 9
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: dyrk_WT_LEVO_2

description:
Library name: Sample 10
gene_count_matrix_all samples.csv
dyrk_WT_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: hepatopancreas, 9°C, 24 hours, sample 2

description: Library name: C24_Hep2


title: liver, control lineage, female, f2 generation, biol rep2

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: Control lineage, f2 generation, female liver 2

data_processing:
The “nf-core/methylseq” (v1.6.1) automated bioinformatic pipeline for Methylation (Bisulfite) sequencing data was used to analyze all the samples. In particular, the “nf-core/methylseq” pipeline's "Bismark workflow" was used to align the reads on the medaka genome (assembly ASM223467v1).
The Bismark coverage files of each individual sample, which describe the methylation percentages and overall coverages of methylated and unmethylated cytosines at each CpG location, were collected for further downstream analyses using methylKit R package. The samples of all the generations (f0, f1 and f2) were processed in the same way.
Assembly: ASM223467v1
Supplementary files format and content: Bismark Coverage file (*.bismark.cov.gz) for each sample

organism: Oryzias latipes

extract_protocol:
DNA was extracted by using Quick-DNA Microprep Kit following manufacturer's protocol
DNA library was prepared by using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina following manufacturer's protocol

value: liver

tag: generation

tag: Sex

value: female


title: scn_HOM_DMSO_2

description:
Library name: Sample 14
gene_count_matrix_all samples.csv
scn_HOM_DMSO_vs_scn_WT_DMSO_DESeq2_fulltable.xlsx


title: dyrk_HOM_LEVO_1

description:
Library name: Sample 4
gene_count_matrix_dyrk_hom_levo_1.csv
dyrk_HOM_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx

value: dyrk1a  homozygous mutant


title: liver, BPA lineage, female, f2 generation, biol rep1

description: Library name: BPA lineage, f2 generation, female liver 1

value: with BPA in f0 generation


title: liver, control lineage, female, f2 generation, biol rep3

description: Library name: Control lineage, f2 generation, female liver 3

value: control


title: dyrk_HOM_LEVO_2

description:
Library name: Sample 5
gene_count_matrix_all samples.csv
dyrk_HOM_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: dyrk_HOM_DMSO_2

description:
Library name: Sample 2
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: dyrk_WT_DMSO_3

description:
Library name: Sample 8
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: dyrk_WT_DMSO_1

description:
Library name: Sample 7
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: liver, BPA lineage, female, f2 generation, biol rep2

description: Library name: BPA lineage, f2 generation, female liver 2


title: liver, BPA lineage, male, f2 generation, biol rep2

description: Library name: BPA lineage, f2 generation, male liver 2

value: male


title: Gt time(dpi):4 rep:D

city: Harpenden

first: Erika

last: Kroll

address: West Common

country: United Kingdom

institute: Rothamsted Research

description:
Library name: Gt_PDB_D
150bp paired reads

data_processing:
Read mapping with HISATv2.1.0; transcript abundance quantified with StringTie v2.1.1; gene count matrix generated with prepDE.py
Assembly: GCA_051938715.1 (Gt-19d1) and GCA_051938805.1 (Gh-2C17)
Supplementary files format and content: Raw gene count matrix csv files

organism: Gaeumannomyces tritici

source_name: Mycelium

growth_protocol: Fungal mycelium was grown up in 200 ml conical flasks containing 50 ml Potato Dextrose Broth (PDB; Formedium, UK) supplemented with 50 μg/ml kanamycin. Flasks were inoculated with 3 x mycelial plugs taken from the leading edge of a two-week old fungal colony growing on Potato Dextrose Agar (PDA; Formedium, UK) using a no.2 cork borer (5 mm). Plugs were cut up into small pieces to ensure even mycelial growth. Five flasks were set up for each fungus to provide five treatment replicates. Inoculated flasks were placed in a New Brunswick™ Innova® 44 orbital shaker (New Brunswick Scientific, UK) at 20 °C, 160 RPM for four days. Cultures were filtered through sterile Miracloth (Merck, USA) by vacuum filtration, followed by three washes with sterile water.

extract_protocol:
Samples were ground to a fine powder using a pre-cooled sterile mortar and pestle under liquid nitrogen. Samples were not allowed to thaw prior to RNA extraction. When the amount of tissue was limited (as in chapter 5), samples were ground in an RNAse-free 1.5 ml Eppendorf tube containing liquid nitrogen, using a pre-cooled RNAse-free disposable pestle (Thermo Scientific™, USA). RNA extractions were carried out using the E.Z.N.A.® Plant RNA Kit with the associated RNase-free DNase I Set (Omega-Biotek, USA) following the standard protocol provided. RNA was eluted in 30 μl RNAse free water and stored at -80 °C.
mRNA library preparation was carried out by Novogene (China) using the Novogene RNA Library Prep Set (PT042) for polyA enrichment.

value: Mycelium

value: Treatment=Gt. Time=4d. Replicate:D


title: eye, 9°C, 24 hours, sample 1

description: Library name: C24_Eye1


title: liver, BPA lineage, female, f2 generation, biol rep3

description: Library name: BPA lineage, f2 generation, female liver 3


title: Gt time(dpi):4 rep:C

description:
Library name: Gt_PDB_C
150bp paired reads

value: Treatment=Gt. Time=4d. Replicate:C


title: liver, control lineage, female, f2 generation, biol rep1

description: Library name: Control lineage, f2 generation, female liver 1


title: liver, control lineage, male, f2 generation, biol rep2

description: Library name: Control lineage, f2 generation, male liver 2


title: dyrk_HOM_DMSO_1

description:
Library name: Sample 1
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: liver, BPA lineage, male, f2 generation, biol rep3

description: Library name: BPA lineage, f2 generation, male liver 3


title: liver, control lineage, male, f2 generation, biol rep3

description: Library name: Control lineage, f2 generation, male liver 3


title: dyrk_HOM_DMSO_4

description:
Library name: Sample 3
gene_count_matrix_all samples.csv
dyrk_HOM_DMSO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: gill, 9°C, 24 hours, sample 3

description: Library name: C24_Gil3


title: dyrk_HOM_LEVO_3

description:
Library name: Sample 6
gene_count_matrix_all samples.csv
dyrk_HOM_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx


title: Gt time(dpi):4 rep:A

description:
Library name: Gt_PDB_A
150bp paired reads

value: Treatment=Gt. Time=4d. Replicate:A


title: Gt time(dpi):4 rep:B

description:
Library name: Gt_PDB_B
150bp paired reads

value: Treatment=Gt. Time=4d. Replicate:B


title: dyrk_WT_LEVO_3

description:
Library name: Sample 11
gene_count_matrix_all samples.csv
dyrk_WT_LEVO_vs_dyrk_WT_DMSO_DESeq2_fulltable.xlsx

value: brain


title: T2R1

city: Amherst

first: Han

last: Jiang

state: MA

address: 240 Thatcher Rd, N572 SUN Lab, LIFE SCIENCE LAB

department: Mechanical Engineering

institute: University of Massachusetts Amherst

description: Library name: SAMPLES 10

data_processing:
Raw sequencing reads were first processed with fastp (version 0.23.4) to remove adapters and perform quality trimming (default parameters, with --detect_adapter_for_pe).
The cleaned reads were then aligned to the Canis familiaris reference genome (ROS_Cfam_1.0, Ensembl release 108) using STAR (version 2.7.10b) with default parameters and --quantMode TranscriptomeSAM to generate transcriptome-aligned BAM files.
Gene and isoform expression levels were quantified using RSEM (version 1.3.3) in paired-end mode with default settings.
The resulting gene-level expected counts were used to generate the raw count matrix (dog_count_matrix.csv), and TPM values were calculated for the normalized expression matrix (dog_tpm_matrix.csv).
Assembly: Canis familiaris, ROS_Cfam_1.0 (Ensembl release 108)
Supplementary files format and content: dog_count_matrix.csv: A comma-separated values (CSV) file containing the raw expected counts for each gene across all samples. Rows represent genes (identified by Ensembl gene IDs, e.g., ENSCAFG00845007406), and columns represent individual samples (named according to the GEO metadata sample names). This file was generated directly by RSEM and serves as the input for differential expression analysis.
Supplementary files format and content: dog_tpm_matrix.csv: A comma-separated values (CSV) file containing the Transcripts Per Million (TPM) normalized expression values for each gene across all samples. The row and column structure is identical to the count matrix. TPM values are suitable for comparing expression levels between samples and genes.

organism: Canis lupus familiaris

source_name: kidney

growth_protocol: MDCK cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humdified atmosphere with 5% CO2 at 37C

extract_protocol:
Bio-rad Aurum™ Total RNA Mini Kit
Poly(A) mRNA enrichment was performed from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Stranded RNA-seq libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs) following the manufacturer's instructions. The libraries were sequenced on an Illumina NovaSeq X Plus platform with 101 bp paired-end chemistry.

treatment_protocol: 25 um Yoda1 treat for 12hr and 24 hr

value: kidney

value: MDCK

value: Epithelial cell of kidney

value: 25 um Yoda1 treat for 24 hr


title: sperm, control lineage, male, f1 generation, biol rep3

description: Library name: Control lineage, f1 generation, sperm 3

source_name: sperm

value: sperm


title: sperm, control lineage, male, f1 generation, biol rep1

description: Library name: Control lineage, f1 generation, sperm 1


title: sperm, control lineage, male, f1 generation, biol rep2

description: Library name: Control lineage, f1 generation, sperm 2


title: T1R2

description: Library name: SAMPLES 8

value: 25 um Yoda1 treat for 12hr


title: C57BL/6J Male gWAT 5 nicotine

city: Irvine

first: Raquel

last: Chamorro-Garcia

address: 4351 Natural Sciences 2

institute: University of California Irvine

description: Library name: Sample 40

data_processing:
Galaxy Project platform
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequences were mapped to mm10 using RNA STAR
Read count extraction, normalization and determination of differentially expressed genes was performed using DESeq2
Assembly: mm10
Supplementary files format and content: Tables are txt format and they include normalized counts per sample for all genes with more than 10 counts in total

source_name: gonadal white adipose tissue

extract_protocol:
RNA was extracted using Zymo Direct-zol RNA Miniprep Kits.
RNA libraries for 3' tag were prepared using Illumina library prep kit following manufacturer's protocol

value: gonadal white adipose tissue

value: Nicotine

tag: batch


title: T1R1

description: Library name: SAMPLES 7


title: C57BL/6J Male gWAT 4 nicotine

description: Library name: Sample 39


title: C1R3

description: Library name: SAMPLES 3


title: C2R2

description: Library name: SAMPLES 5


title: C57BL/6J Male gWAT 3 nicotine

description: Library name: Sample 38


title: T1R3

description: Library name: SAMPLES 9


title: C57BL/6J Male gWAT 1 nicotine

description: Library name: Sample 36


title: C57BL/6J Male gWAT 5 control

description: Library name: Sample 35

value: Control


title: T2R2

description: Library name: SAMPLES 11


title: sperm, BPA lineage, male, f1 generation, biol rep3

description: Library name: BPA lineage, f1 generation, sperm 3

value: with BPA in f0 generation


title: C2R1

description: Library name: SAMPLES 4


title: C1R2

description: Library name: SAMPLES 2


title: C57BL/6J Male gWAT 3 control

description: Library name: Sample 33


title: C57BL/6J Male gWAT 2 control

description: Library name: Sample 32


title: Gt time(dpi):4 rep:E

description:
Library name: Gt_PDB_E
150bp paired reads

value: Treatment=Gt. Time=4d. Replicate:E


title: liver, BPA lineage, male, f2 generation, biol rep1

description: Library name: BPA lineage, f2 generation, male liver 1

value: liver

value: male


title: sperm, BPA lineage, male, f1 generation, biol rep1

description: Library name: BPA lineage, f1 generation, sperm 1


title: T2R3

description: Library name: SAMPLES 12


title: C57BL/6J Male gWAT 4 control

description: Library name: Sample 34


title: C57BL/6J Male liver 4 nicotine

description: Library name: Sample 29

source_name: Liver

value: Liver


title: C1R1

description: Library name: SAMPLES 1


title: Female flower week1 rep2

first: Leor

last: Eshed-Williams

address: Herzl 229

institute: Hebrew University of Jerusalem

description: Library name: F1c

data_processing:
Raw reads were filtered and cleaned, with Illumina adapter sequences removed using Trimmomati
The FASTX Toolkit version 0.0.13.2 was used to trim read-end nucleotides with quality scores <30 using the FASTQ Quality Trimmer
Reads with less than 70% high-quality bases (quality score ≥ 30) were filtered out using the FASTQ Quality Filter
Assembly: Cannabis sativa 'Pink Pepper' reference genome (NCBI assembly GCA_029168945.1)
Supplementary files format and content: Excel file includes the chromosomes on which the genes are located, normalized FPKM values for each sample and averages, logFC values and homology to Arabidopsis (TAIR database)

organism: Cannabis sativa

source_name: shoot apex

extract_protocol:
Total RNA from apical shoot tips was extracted using the RNeasy Mini Plant Kit (Qiagen, Netherlands) following the manufacturer's instructions, including treatment with RNase-free DNase (Qiagen). Each RNA sample was loaded on agarose gel for integrity validation and quantified using NanoDrop.
RNA libraries were constructed by Macrogen Europe B.V. according to Illumina's protocol

value: shoot apex

value: female flower induction


title: sperm, BPA lineage, male, f1 generation, biol rep2

description: Library name: BPA lineage, f1 generation, sperm 2


title: C57BL/6J Male gWAT 2 nicotine

description: Library name: Sample 37


title: C57BL/6J Male liver 1 nicotine

description: Library name: Sample 26


title: C57BL/6J Male liver 4 control

description: Library name: Sample 24


title: Male flower week3 rep2

description: Library name: M3c

value: male flower induction (STS)


title: C2R3

description: Library name: SAMPLES 6

value: kidney


title: liver, control lineage, male, f2 generation, biol rep1

description: Library name: Control lineage, f2 generation, male liver 1

value: control


title: Vegetative rep1

description: Library name: V2b

value: vegetative


title: C57BL/6J Male liver 3 control

description: Library name: Sample 23


title: C57BL/6J Male liver 2 control

description: Library name: Sample 22


title: Female flower week3 rep2

description: Library name: F3c


title: C57BL/6J Male gWAT 1 control

description: Library name: Sample 31


title: Control-4

city: Paris

first: Manvendra

last: Singh

address: 160 Rue de Vaugirard,

department: Systems Biology

institute: Institut Necker

description:
Library name: S7
Normalized TPM

data_processing:
FASTX-Toolkit and Trimmomatic were used to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases.
Salmon was used to build index and align the reads
Quantified data was checked for GC content and gene length biases using R package NOISeq. Mean variance and PCA were computed between biological replicates using the tximport package The differential expression analysis was conducted using the DESeq2 package
The transcriptome of 6 RNA samples were prepared with the stranded mRNA library kit and sequenced on the ‘DNBseq’ platform at BGI Group.
Assembly: hg19
Supplementary files format and content: The transcriptome of 6 RNA samples were prepared with the stranded mRNA library kit and sequenced on the ‘DNBseq’ platform at BGI Group.

source_name: BeWo

growth_protocol: BeWo cells were maintained in GlutaMAX™ DMEM/F-12 medium (#31331028, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin/streptomycin (P/S).

extract_protocol:
Total RNA was extracted with Direct-zolTM RNA MicroPrep plus kit (Zymo Research, Cat# R2062, Zymo Research) following the manufacturer’s instructions.
Stranded mRNA Library(oligo dT, stranded)

treatment_protocol: For LTR8BKO, wild type control and LTR8B KO BeWo cells were seeded in 6-well plate at the concentration 1 x 10^6 cells per well of 6-well plate. At 2nd day, cells were treated with 50 μM Forskolin for 48h. Then cells were harested for RNA extraction and downstream bulk RNA-seq. For PSG9 KD, BeWo cells were seeded in 6-well plate at the concentration 1 x 10^6 cells per well of 6-well plate. At 2nd day, cells were transfected with ~ 2,5 μg pLKO.1-scramble or ~ 2,5 μg pLKO-PSG9shRNA by the Lipofectamine 3000 reagent. At 24h post-transfection, transfected cells were screened with the fresh media containing 4 μg/ml Puro for 24h. Then transfected cells were washed and further treated with the mixture of 50 μM Forskolin and 4 μg/ml Puro for 48h. Cells were harvested for RNA-seq analysis. In the end, 3 representative replicates were selected for RNA-seq based on the RNA quality.

value: BeWo

value: human trophoblast cell line

value: WT

value: BeWo syncytialization


title: Male flower week3 rep1

description: Library name: M3b


title: LTR8BKO-3

description:
Library name: S6
Normalized TPM

value: LTR8B KO


title: C57BL/6J Male liver 2 nicotine

description: Library name: Sample 27

value: Nicotine


title: LTR8BKO-4

description:
Library name: S8
Normalized TPM


title: C57BL/6J Male liver 3 nicotine

description: Library name: Sample 28


title: Male flower week1 rep2

description: Library name: M1c


title: C57BL/6J Male liver 5 nicotine

description: Library name: Sample 30


title: Control-1

description:
Library name: S1
Normalized TPM


title: C57BL/6J Male liver 5 control

description: Library name: Sample 25

value: Control


title: Female flower week1 rep1

description: Library name: F1b


title: Male flower week1 rep1

description: Library name: M1b


title: Female flower week3 rep1

description: Library name: F3b


title: Vegetative rep2

description: Library name: V2c


title: LTR8BKO-1

description:
Library name: S2
Normalized TPM


title: C57BL/6J Male liver 1 control

description: Library name: Sample 21


title: C57BL/6J Female gWAT 4 nicotine

description: Library name: Sample 19

value: gonadal white adipose tissue


title: PT-S1 cells, 1000ng/ml, replicate 3

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

description: Library name: PTS11000-3

data_processing:
Reads aligned by STAR and transcript abundance estimation using RSEM
Assembly: hg38
Supplementary files format and content: tab delimited txt file includes raw counts for each samples

source_name: cell line

extract_protocol:
RNeasy Mini Kit (Qiaen)
TruSeq Stranded Total RNA LT Sample Prep Kit

value: Lymphoma

value: Brincidofovir treatment


title: C57BL/6J Female gWAT 1 nicotine

description: Library name: Sample 16


title: C57BL/6J Female gWAT 2 nicotine

description: Library name: Sample 17


title: C57BL/6J Female gWAT 5 control

description: Library name: Sample 15


title: PT-S1 cells, 1000ng/ml, replicate 1

description: Library name: PTS11000-1


title: C57BL/6J Female gWAT 3 nicotine

description: Library name: Sample 18


title: PT-S1 cells, 100ng/ml, replicate 3

description: Library name: PTS1100-3


title: PT-S1 cells, 100ng/ml, replicate 2

description: Library name: PTS1100-2


title: C57BL/6J Female liver 5 nicotine

description: Library name: Sample 10

value: Liver


title: C57BL/6J Female gWAT 1 control

description: Library name: Sample 11


title: PT-S1 cells, control, replicate 3

description: Library name: PTS1C3

value: Mock treatment


title: C57BL/6J Female gWAT 5 nicotine

description: Library name: Sample 20


title: Control-3

description:
Library name: S5
Normalized TPM


title: C57BL/6J Female gWAT 2 control

description: Library name: Sample 12


title: C57BL/6J Female liver 4 nicotine

description: Library name: Sample 9


title: PT-S1 cells, 100ng/ml, replicate 1

description: Library name: PTS1100-1


title: PT-S1 cells, control, replicate 2

description: Library name: PTS1C2


title: PT-S1 cells, control, replicate 1

description: Library name: PTS1C1


title: PT-S1 cells, 1000ng/ml, replicate 2

description: Library name: PTS11000-2


title: C57BL/6J Female liver 2 nicotine

description: Library name: Sample 7


title: C57BL/6J Female gWAT 4 control

description: Library name: Sample 14


title: C57BL/6J Female liver 1 nicotine

description: Library name: Sample 6


title: Chondrocytes from osteoarthritis patient OA3

city: guangzhou

first: cuicui

last: wang

state: guangdong

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

description: Library name: OA3

data_processing:
Raw sequencing reads were processed to generate gene expression matrices according to the manufacturer's pipeline.
Cells with low gene counts or high mitochondrial gene expression were filtered out prior to downstream analysis.
Quality control, normalization, and downstream analyses were performed using standard scRNA-seq analysis workflows in R with Seurat (version 3.0)
Raw scRNA-seq data have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1437490.
Assembly: GRCh38
Supplementary files format and content: Processed data include gene expression matrices, cell annotations, cluster marker genes, and differential expression results derived from scRNA-seq analysis

source_name: cartilage

growth_protocol: Human cartilage tissues were obtained from osteoarthritis patients and healthy controls. Chondrocytes were isolated from cartilage tissues and cultured in F12 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted from chondrocytes according to the manufacturer's instructions. RNA quality and quantity were assessed prior to library preparation.
scRNA-seq libraries were prepared according to the manufacturer's protocol. Libraries were constructed and sequenced on the Illumina NovaSeq 6000 platform.

treatment_protocol: No specific treatment was applied to the samples prior to RNA extraction

value: cartilage

value: chondrocytes

tag: subject status

value: osteoarthritis patient


title: C57BL/6J Female liver 5 control

description: Library name: Sample 5


title: C57BL/6J Female liver 4 control

description: Library name: Sample 4


title: Chondrocytes from osteoarthritis patient OA2

description: Library name: OA2


title: Chondrocytes from healthy control HC3

description: Library name: HC3

value: healthy control


title: Chondrocytes from healthy control HC2

description: Library name: HC2


title: C57BL/6J Female gWAT 3 control

description: Library name: Sample 13


title: Chondrocytes from osteoarthritis patient OA1

description: Library name: OA1


title: HEK293FT, RNA, Variant MPRA, Replicate 4

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: HEK_Variant_MPRA4_RNA
Column title in counts file rna_count_4

data_processing:
Count files were generated using MPRAsnakeflow with a min oligo threshold of 10.
The barcode association dictionary was generated using MPRAflow for each size present in the design (219bp, 218bp, 216bp, 214bp, 212bp, 210bp, 208bp) using ---mapq 0 and a cigar score flag for the length of the oligo to require an exact match (ex: --cigar 219M) dictionaries were converted to tsvs, combined, and repeat barcodes were removed.
Assembly: hg38
Supplementary files format and content: Count files are tsvs of total barcode counts for RNA and DNA.
Supplementary files format and content: The barcode association dictionary is a tsv file of barcodes and oligo names.
Supplementary files format and content: The design file is the fasta file sent to Twist biosciences to generate the oligo pool.

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: human embryonic kidney cells


title: C57BL/6J Female liver 3 control

description: Library name: Sample 3


title: HEK293FT, DNA, Variant MPRA, Replicate 4

description:
Library name: HEK_Variant_MPRA4_DNA
Column title in counts file dna_count_4


title: Chondrocytes from healthy control HC1

description: Library name: HC1


title: C57BL/6J Female liver 2 control

description: Library name: Sample 2


title: HEK293FT, RNA, Variant MPRA, Replicate 2

description:
Library name: HEK_Variant_MPRA2_RNA
Column title in counts file rna_count_2


title: HEK293FT, RNA, Variant MPRA, Replicate 3

description:
Library name: HEK_Variant_MPRA3_RNA
Column title in counts file rna_count_3


title: HEK293FT, DNA, Variant MPRA, Replicate 3

description:
Library name: HEK_Variant_MPRA3_DNA
Column title in counts file dna_count_3


title: IgG ChIP-seq negative control

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

description:
Library name: IgG_ChIP_control
IgG ChIP control

data_processing:
After initial quality assessment with FastQC, paired-end pT4 ChIP-seq reads from SCP1 or mutant treated samples were trimmed using cutadapt v.4.6 (paramters: -m 20 -q 20), and then mapped onto human reference genome, hg38, using bowtie2 v.2.5.2.
Assembly: hg38
Supplementary files format and content: Processed data files include broadPeak files containing enriched regions identified from ChIP-seq data and bigWig files containing normalized genome-wide coverage/signal tracks. Raw data files are paired-end FASTQ files.

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2.

extract_protocol:
Cells were fixed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorupter UCD-200, and then anti-pThr4 antibody (6D7) was used for immunoprecipitation (IP).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Kit for Illumina and sequenced as paired-end 150-bp reads on a Illumina NovaSeq 6000

value: kidney

value: epithelial cell

value: IgG ChIP control


title: pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 3

description:
Library name: pThr4_ChIP_SCP1_D96A_rep3
pThr4 ChIP-seq performed in HEK293 cells


title: C57BL/6J Female liver 3 nicotine

description: Library name: Sample 8


title: HEK293FT, DNA, Variant MPRA, Replicate 2

description:
Library name: HEK_Variant_MPRA2_DNA
Column title in counts file dna_count_2


title: pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 2

description:
Library name: pThr4_ChIP_SCP1_D96A_rep2
pThr4 ChIP-seq performed in HEK293 cells