title: Hyaloid blood vessels, control, SORT-seq, rep2

description: Library name: IAC-MV-s008


title: adr-mto2J mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep1

status: Public on Apr 27 2026

type: SRA

city: Rochester

first: Matthew

middle: Thomas

last: Sipple

state: New York

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

description: Library name: P18ADR1

library_source: other

data_processing:
Initial processing of circular-consensus sequences (ccs), quality control, and demultiplexing was completed with the SMRT Link software package (Pacific Biosciences).
Q20 reads were then processed with the pbBioconda (Pacific Biosciences) distribution using the lima package to remove overhangs and Isoseq to refine reads.
Reads then entered the FLAIR analysis pipeline to align reads to chromosome 6 (mm39), define transcript isoforms present, and quantify isoform utilization (PMID: 32188845).
Assembly: mm39
Supplementary files format and content: Transcript_isoform_counts.txt, Isoform counts file, the first column represents unique transcript isoform IDs, remaining columns represent each sample, rows represent counts for each unique transcript isoform, tab-delimited text file.
Supplementary files format and content: Transcript_isoform_sequence_key.txt, Transcript isoform identities key, text file that contains uniuque transcript sequences for each unique identifier.

molecule: other

organism: Mus musculus

source_name: Quadriceps muscle

growth_protocol: Mice of the above genotypes were housed in accordance with UCAR policy at University of Rochester Medical Center. Mice were sacrificed at P7 and P18 timepoints with UCAR approved methods.

extract_protocol:
Total RNA was isolated from murine quadriceps tissue with Rneasy kit (Qiagen).
Total RNA was reverse transcribed using SuperScript II (Invitrogen) with Rnase H treatment. Sequencing libraries were generated based on the PacBio protocol for multiplexing with barcoded universal primers designed to amplify Clcn1 transcripts from exon 1 to exon 23 (final exon). The remainder of library prep was completed per SMRTbell Express Template Prep Kit 2.0. The pooled libraries were diluted and submitted for sequencing on the PacBio Sequel system at the Molecular Biology and Genomics Core (Washington State University, Pullman, WA).

tag: tissue

value: Quadriceps muscle

tag: genotype


title: adr-mto2J mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P18ADR3


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P18Mbnl1KOClcn1deltaE7a3

value: Mbnl1 knockout; Clcn1 e7a deletion


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P18Mbnl1KOClcn1deltaE7a1


title: adr-mto2J mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P18ADR2


title: Mbnl1 knockout mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P18Mbnl1KO3

value: Mbnl1 knockout


title: Mbnl1 knockout mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P18Mbnl1KO2


title: AVM1

city: Luzhou

first: zhenghong

last: peng

address: No. 25, Taiping Street, Jiangyang District

country: China

institute: The Affiliated Hospital of Southwest Medical University

description:
Library name: AVM1
Brain arteriovenous malformation

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count and fpkm value for each Sample

molecule: total RNA

source_name: brain

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: brain

tag: treatment

value: Brain arteriovenous malformation


title: Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P18Clcn1deltaE7a3

value: Clcn1 e7a deletion


title: Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P18Clcn1deltaE7a2


title: Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P18Clcn1deltaE7a1


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P18Mbnl1KOClcn1deltaE7a2


title: WT mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P18WT3

value: WT


title: Pcgf5_siRNA_RNA-seq_L2C_rep1

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

country: Japan

institute: Kyoto University

description: Library name: Sample3

data_processing:
For RNA-seq, the sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.a). Gene expression levels were calculated using RSEM (ver. 1.3.3). For ChIP-seq, the sequencing reads were mapped to the mouse genome (mm10) using Bowtie2 (ver. 2.4.5) and converted to bigwig (BW) files using counts per million (CPM) normalization by bamCoverage in deepTools.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.3.3) for RNA-seq. Bigwig files generated by banCoverage for ChIP-seq.

molecule: polyA RNA

source_name: Late 2-cell stage embryo

growth_protocol: Superovulated mouse oocytes were in vitro fertilized and resulting embryos were cultured in KSOM up to apropriate stage (late two-cell, 36 hpi; four-cell, 48hpi; morula, 72 hpi).

extract_protocol:
RNA-seq library was generated from ten embryos per each group, by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual. ChIP-seq library were generated from morula-stage embryos at 72 hpi were collected as approximately 40 embryos per biological replicate. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The morulae were freed from the zona pellucida by using pronaseK before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was processed for ChIP using anti-H2AK119ub1 antibody (8240; Cell Signaling Technology). The ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer. Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.
SMART-Seq v4 PLUS Kit (Takara Bio USA) and Low Cell ChIP-Seq Kit (Active Motif) was used according to the manufacturer’s manual.

treatment_protocol: For KD experiment, One-cell stage embryos at 3 hpi were electroporated with non-targeting or Pcgf5-targeting siRNAs.

value: Late 2-cell stage embryo

value: in vitro produced, siPcgf5 treated from the one-cell stage

tag: batch


title: Mbnl1 knockout mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P18Mbnl1KO1


title: WT mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P18WT2


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P7Mbnl1KOClcn1deltaE7a1


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P7Mbnl1KOClcn1deltaE7a2


title: WT mouse, P18, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P18WT1


title: Mbnl1 knockout mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P7Mbnl1KO3


title: Mbnl1 knockout; Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P7Mbnl1KOClcn1deltaE7a3


title: Mbnl1 knockout mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P7Mbnl1KO1


title: Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P7Clcn1deltaE7a3


title: Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P7Clcn1deltaE7a2


title: WT mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P7WT1


title: Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep1

description: Library name: P7Clcn1deltaE7a1


title: WT mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep3

description: Library name: P7WT3


title: WT mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P7WT2


title: Primary canine osteosarcoma dog 11

city: Gainesville

first: Rebecca

last: Nance

state: FL

address: 2015 SW 16th Ave

department: Small Animal Clinical Sciences

institute: University of Florida

description:
Library name: OSA11
Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw sequence data was aligned to canFam4 reference genome and reads counted using 10x Genomics SpaceRanger (v2.1.0) with the tif image to generate barcodes, features, and matrix files.
Assembly: canFam4/UU_Cfam_GSD_1.0
Supplementary files format and content: barcodes.tsv.gz = list of spatial barcodes (tab-separated gzipped)
Supplementary files format and content: features.tsv.gz = list of gene IDs (tab-separated gzipped)
Supplementary files format and content: matrix.mtx.gz = gene expression count data (matrix market exchange format gzipped)
Supplementary files format and content: tif = scanned H&E image
Library strategy: Spatial Transcriptomics

organism: Canis lupus familiaris

source_name: tumor

extract_protocol:
Fresh frozen tissue was embedded in OCT and 10μm sections were sectioned onto 10x Genomics Visium spatial transcriptomic slides using cryostat (Manual CG000239 Rev F, Visium, 10X Genomics)
Spatial transcriptomic libraries were prepared for 10x Genomics Visium v1 spatial transcriptomics platform following manufacturer's instructions (Manual CG000239 Rev F, Visium, 10X Genomics)

value: tumor


title: Recurrent canine osteosarcoma dog 9

description:
Library name: OSA9b
Fresh frozen spatial transcriptomic sequencing


title: Mbnl1 knockout mouse, P7, Quad tissue, Clcn1 amp from E1-E23, rep2

description: Library name: P7Mbnl1KO2


title: Primary canine osteosarcoma dog 7

description:
Library name: OSA7
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 8

description:
Library name: OSA8
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 9

description:
Library name: OSA9
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 5

description:
Library name: OSA5
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 10

description:
Library name: OSA10
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 6

description:
Library name: OSA6
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 3

description:
Library name: OSA3
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 2

description:
Library name: OSA2
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 4

description:
Library name: OSA4
Fresh frozen spatial transcriptomic sequencing


title: Metastatic canine osteosarcoma dog 1

description:
Library name: OSA1b
Fresh frozen spatial transcriptomic sequencing


title: Primary canine osteosarcoma dog 1

description:
Library name: OSA1
Fresh frozen spatial transcriptomic sequencing


title: ints11_2_biorep2

city: Oxford

first: Luke

last: Slade

address: Sherrington Rd, Oxford

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Library name: ints11_2
Column name in G22ReadsAll.txt: ints11_2

data_processing:
Fastq files were clipped to remove adaptors using fastx_clipper from the Fastx Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Reads were then aligned to the C. elegans genome using bowtie with the following parameters: bowtie –f –v 0 –k 1 –S and resultant sam files were converted to bam files using samtools version 1.9 and to bed files using bedtools
Reads were annotated to specific loci using the annotation provided by TinyRNA
scripts in R were used to classify reads as microRNAs or 22G-RNAs and to quantify the number of reads.  DESeq2 was used for normalization of the 22G-RNAs and the miRNAs were normalized relative to total read count
Assembly: WBCel235 v113
Supplementary files format and content: G22ReadsAll.txt - list of all 22G RNAs mapped and their target mRNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were grown on standard NGM plates seeded with OP50 from eggs to L4 larval stage. At L4, animals were shifted to RNAi NGM plates seeded with either control (empty vector; L4440) or ints-11 dsRNA bacteria. Transferred every 2-days onto fresh plates.

extract_protocol:
Total RNA was extracted using the TRIzol method. Approximately 2,000 worms collected in 1000uL of TRIzol were freeze/thawed five times with vortexing. Phase separating tubes were utilised to obtain aqueous phases, precipitated with isopropanol overnight and cleaned up/washed with 75% ethanol and air dried. ~3ug of RNA per sample was DNAse treated, then incubated with 2uL of 5´ Pyrophosphohydrolase (RppH; NEB, M0356S) to leave 5´ monophosphate RNA.
3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing with SE50

treatment_protocol: RNAi plates contained Carbenicillin (100ug/mL) and IPTG (1mM) for dsRNA induction. Empty vector vs ints-11 RNAi

value: whole animal

tag: cell line

tag: cell type

value: wild type

value: ints11 RNAi

tag: time


title: Ev_3_biorep3

description:
Library name: Ev_3
Column name in G22ReadsAll.txt: Ev_3

value: empty vector RNAi


title: Ev_1_biorep1

description:
Library name: Ev_1
Column name in G22ReadsAll.txt: Ev_1


title: ints11_1_biorep1

description:
Library name: ints11_1
Column name in G22ReadsAll.txt: ints11_1


title: 28hpf

city: Ciudad Autonoma de Buenos Aires

first: Maria

middle: Ines

last: Perez Millan

state: Buenos Aires

address: Ciudad Universitaria

department: IFIBYNE

country: Argentina

institute: UBA-CONICET

description: Library name: sample 28hpf

library_source: transcriptomic single cell

data_processing:
The bioinformatic processing was performed in Python 3.10.16 using the scanpy package 1.11.0 (https://github.com/scverse/scanpy) (Wolf et al. 2018). Briefly, both samples, 28 hpf and 52 hpf, were concatenated, obtaining a total of 5827 cells (1899 cells and 3927 cells at 28 hpf y 52 hpf respectively). Cells with less than 100 transcripts, as well as transcripts detected in less than 3 cells were eliminated. Cells with mitochondrial transcript percentages above 5% and scrublet (https://github.com/swolock/scrublet) doublet prediction scores higher than 0.2 were also eliminated. After filtering 1785 cells and 3784 cells remained at 28 hpf y 52 hpf, respectively. Normalization was performed using bbknn (https://github.com/Teichlab/bbknn) batch correction and UMAP dimensionality reduction was performed using the 2500 most highly variable genes.
Assembly: GRCZ11
Supplementary files format and content: matrix files

organism: Danio rerio

source_name: pituitary

extract_protocol:
Female prop1:GAL4;UAS:mScarlet-CAAX zebrafish were crossed with wild-type (AB) male zebrafish on consecutive days (24 hours difference), using separators to control mating times. At 28 hpf and 52 hpf embryos were placed on ice to stop their development and Tricaine was used as anaesthetic. Dissection was carried out manually, using insulin needles and a glass plate under a fluorescence microscope (Nikon SMZ18). The dissection for 28 hpf embryos consisted of removing most of the torso, while dissection of embryos at 52 hpf consisted in separating the head. Samples were collected and conserved in chilled 1X PBS until their disaggregation.    The single cell suspension was filtered through a Cell Strainer Snap Cap (Corning) and kept on ice. Before FACS, 1 uL of 1 mg/ml DAPI was added. Dissected sibling embryos that did not exhibit fluorescence were used as a negative sorting control. FACS sorting was performed on a Bigfoot spectral cell sorter (Thermo Fisher) and cells were captured in a minimal volume (20 µL) of PBS with 5% FBS in a 1.5 mL eppendorf tube, previously coated with PBS + 20% FBS. The collected cells were kept on ice until sequencing.
ScRNA libraries were prepared using two lanes in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the standardized protocol and the sequencing was performed on a NextSeq 2000 sequencer (Illumina). Raw reads were aligned using Cellranger 9.0.1 against the GRCZ11 reference. DNA from the transgenic lines bns714 and bns681 was added using the mkref package from CellRanger (10x Genomics).

value: pituitary

value: wt


title: 52hpf

description: Library name: sample 52hpf


title: ints11_3_biorep3

description:
Library name: ints11_3
Column name in G22ReadsAll.txt: ints11_3


title: Ev_2_biorep2

description:
Library name: Ev_2
Column name in G22ReadsAll.txt: Ev_2


title: ESCs after in vitro decidualzaiton_3

city: Shanghai

first: Yifei

last: Sang

address: 910 Hengshan Rd

institute: Shanghai Jiao Tong University

description:
Library name: positive_3
positive_3

data_processing:
The raw data was filtered with SOAPnuke (v1.4.0) by 1) Removing readscontaining adapters (adapter contamination); 2) Removing reads whose unknown base('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio(Base quality less than or equal to 15) is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format.
Trinity (v2.0.6) was used to assemble the clean reads and BUSCO to assess theassembly quality.
Clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) and the expression level of genes was calculated by RSEM (v1.2.8).
The candidate coding regions in Unigene were identified by the softwareTransdecoder (v3.0.1), the regions were aligned to SwissProt by BLAST. Thehomologous sequences of the Pfam protein and the coding regions were respectivelysearched and predicted by Hmmscan. Unigene was detected with MISA was used forUnigene detection (v1.0) and Primer3 (v2.2.2) designed primer for SSRdetection.
Assembly: NCBI
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Homo sapiens

source_name: endometrial stromal cells

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: endometrial stromal cells


title: ESCs after in vitro decidualzaiton_2

description:
Library name: positive_2
positive_2


title: ESCs before in vitro decidualzaiton_3

description:
Library name: control_3
control_3


title: TSPOKO+CLP8

city: Minami-ku

first: Kazuya

last: Kikutani

state: Hiroshima

address: 1-2-3 Kasumi

department: Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences

institute: Hiroshima Univeristy

description:
Library name: K8
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.

data_processing:
Raw sequencing reads were quality-checked prior to downstream analysis. Gene expression analysis was performed using R (version 4.4.2). Normalization was conducted using DESeq2 (version 1.46.0) with size-factor normalization and variance stabilizing transformation. Differentially expressed genes were identified using the Benjamini–Hochberg method for multiple testing correction. Principal component analysis was performed using prcomp, and heatmaps were generated using pheatmap.
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: Processed data files include gene expression matrices generated from RNA-seq analysis, including normalized expression values.

source_name: Spleen

growth_protocol: Mice were maintained under standard laboratory conditions with free access to food and water.

extract_protocol:
Total ribonucleic acid (RNA) was extracted from spleen tissue samples using the NucleoSpin RNA XS (TAKARA Bio, Japan).
mRNA was enriched using oligo-dT beads, followed by reverse transcription to synthesize cDNA. The synthesized cDNA was subjected to end repair and adapter ligation. Libraries were amplified by PCR, quality-checked using a Bioanalyzer 2100 system, and sequenced on the BGISEQ-500 platform.

treatment_protocol: Sepsis was induced by cecal ligation and puncture (CLP). Sham-operated mice underwent the same procedure without ligation or puncture.

value: Spleen

tag: strain

tag: Sex

value: male

value: TSPO knockout


title: TSPOKO+CLP7

description:
Library name: K7
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: ESCs before in vitro decidualzaiton_1

description:
Library name: control_1
control 1


title: ESCs before in vitro decidualzaiton_2

description:
Library name: control_2
control_2


title: Metastatic canine osteosarcoma dog 2

description:
Library name: OSA2b
Fresh frozen spatial transcriptomic sequencing


title: TSPOKO+CLP6

description:
Library name: K6
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: L1a1 RNA rep3

status: Public on Apr 28 2026

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

description: Library name: L1a1 RNA rep3

data_processing:
Each sample R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20. We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA.
Assembly: GRCh37
Supplementary files format and content: oligos_to_barcodes.txt file contains pairs of oligo-barcode associations. activity_and_differential_activity.txt file contains for each oligo the RNA read count, DNA read count, activity (classification, estimate and FDR), and differential activity for each pair of alleles (logFC and FDR).

source_name: Fetal chondrocytes

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen).
For DNA/RNA barcode sequencing, mRNA was treated with Turbo DNase to remove contaminating DNA, and reverse transcribed with SuperScript IV (Invitrogen) using a primer containing unique molecular identifiers (UMIs). Resulting cDNA and genomic DNA was split into multiple reactions to reduce PCR jack-potting effects and barcode amplification performed with NEBNext high-fidelity polymerase for three cycles using a forward primer containing P5 adaptor and a sample index and a reverse primer containing P7 adaptor and UMIs. PCR products were purified with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification using P5 and P7 primers. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA-barcode association, CRE-barcode fragment is amplified with a forward primer upstream from CRE and a reverse primer downstream from barcode, using a plasmid library as a template, followed by AMPure XP beads purification and sequencing.

value: Fetal chondrocytes


title: TSPOKO+CLP4

description:
Library name: K4
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: TSPOKO+CLP5

description:
Library name: K5
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: TSPOKO+CLP1

description:
Library name: K1
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP7

description:
Library name: B7
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: ESCs after in vitro decidualzaiton_1

description:
Library name: positive_1
positive 1


title: WT+CLP8

description:
Library name: B8
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP5

description:
Library name: B5
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: TSPOKO+CLP3

description:
Library name: K3
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP1

description:
Library name: B1
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham7

description:
Library name: A7
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.

value: Sham


title: WT+CLP2

description:
Library name: B2
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: TSPOKO+CLP2

description:
Library name: K2
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP4

description:
Library name: B4
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham4

description:
Library name: A4
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP6

description:
Library name: B6
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham5

description:
Library name: A5
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham6

description:
Library name: A6
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham3

description:
Library name: A3
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+CLP3

description:
Library name: B3
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham1

description:
Library name: A1
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: WT+Sham8

description:
Library name: A8
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.


title: S2-HAGrh_100uM_aHA_INPUT_B_R1

city: Madison

first: Melissa

middle: M

last: Harrison

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description: Library name: ChIPseq_23

library_source: genomic

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using Bowtie2 (v2.4.4). Unmapped reads, reads aligning to the mitochondrial genome or unplaced scaffolds, reads aligning more than once or low-quality reads (MAPQ<30) were removed.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Schneider 2 cells

growth_protocol: Drosophila S2 cells were cultured in Schneider's medium with supplemented antibiotic/antimycotic and 10% FBS at 27˚C.

extract_protocol:
ChIP was performed as previously described (Gibson et al. 2024). 25x106 cells were fixed in 0.8% formaldehyde for 7 min and quenched with 125 mM gylcine. Fixed chromatin was sonicated on a Covaris S220 for five 120s rounds with 60s delay, peak power at 170, a duty factor of 10%, and 200 cycles per burst.  IPs were incubated with anti-Grh or anti-HA antibody at 4˚C overnight. Samples were purified using Dynabeads Protein A for Grh (20 uL; Thermo Fisher Scientific) or M-280 Sheep Anti-Mouse IgG for HA (60 uL; Thermo Fisher Scientific). The beads were washed, and chromatin was eluted. IPs and inputs were treated with 90ug RNaseA for 30 mins at 37˚C, and crosslinks were reversed by adding proteinase K overnight at 65˚C. DNA was isolated by phenol:chloroform extraction and concentrated overnight by ethanol precipitation.
Libraries were constructed using the NEB Next Ultra II kit.

treatment_protocol: S2 cells were treated with respective amounts of CuSO4 to induce expression for 48 hours.

value: Schneider 2 cells

value: 100 uM CuSO4

tag: antibody


title: S2-HAGrh_100uM_aHA_INPUT_A_R2

description: Library name: ChIPseq_20


title: S2-HAGrh_100uM_aHA_IP_B_R2

description: Library name: ChIPseq_22

value: HA


title: S2-HAGrh_100uM_aHA_IP_B_R1

description: Library name: ChIPseq_21


title: S2-HAGrh_100uM_aHA_INPUT_A_R1

description: Library name: ChIPseq_19


title: S2-HAGrh_100uM_aGrh_INPUT_R2

description: Library name: ChIPseq_18


title: S2-HAGrh_100uM_aHA_IP_A_R1

description: Library name: ChIPseq_15


title: WT+Sham2

description:
Library name: A2
Spleen tissue collected 17 days after sham or CLP surgery. RNA extracted and sequenced using BGISEQ-500 platform.

value: WT


title: S2-HAGrh_100uM_aGrh_INPUT_R1

description: Library name: ChIPseq_17


title: S2-HAGrh_100uM_aHA_INPUT_B_R2

description: Library name: ChIPseq_24


title: S2-HAGrh_100uM_aHA_IP_A_R2

description: Library name: ChIPseq_16


title: S2-HAGrh_100uM_aGrh_IP_R2

description: Library name: ChIPseq_14

value: Grh


title: E. coli single biofilm 48h in urine 3

city: South Bend

first: Ellsa

last: Wongso

address: 809 Lindenwood Dr S

institute: University of Notre Dame

description: Library name: EC3

data_processing:
Sequence reads were trimmed for adapter sequence/low quality sequence using Trimmomatic on UseGalaxy (E. faecalis and E. coli) and by GeneWiz for C. albicans
HISAT2 and htseq-count were used to mapped reads to reference genome. Deseq2 was used to normalized and analyzed counts
Assembly: GCF_000013265.1 (E. coli UTI89), GCF_000172575.2 (E. faecalis OG1RF), GCF_000182965.3 (C. albicans SC5314)
Supplementary files format and content: tab delimited text files includes raw counts for each file provided by GeneWiz

organism: Escherichia coli

source_name: bacteria

growth_protocol: Bacteria and/or fungi were grown in human sterilized urine in a fibrinogen-coated flasks for 48 hours at 37℃

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep kit from Zymo Research. 500 ng of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by GeneWiz

value: bacteria

value: urine 48h


title: E. coli single biofilm 48h in urine 1

description: Library name: EC1


title: S2-HAGrh_100uM_aGrh_IP_R1

description: Library name: ChIPseq_13


title: Yeast transcriptome after lectin treatment4

city: Dalian

first: Changqing

last: Tong

state: Liaoning

address: Heishijiao Str.

department: College of Food science and Engineering

institute: Dalian Ocean University

description: Library name: ZK_r9_YL4

data_processing:
Raw sequencing reads were filtered using fastp to remove adaptors and low-quality sequences.
Clean reads were aligned to the Saccharomyces cerevisiae reference genome using HISAT2
Gene expression quantification was performed using featureCounts.
Assembly: Saccharomyces cerevisiae reference genome (SGD R64-1-1)
Supplementary files format and content: Gene-level read count matrix in tab-delimited text format, containing raw count values.

organism: Saccharomyces cerevisiae

source_name: yeast cell (treated)

growth_protocol: Saccharomyces cerevisiae cells were cultured in YPD medium at 30 °C with shaking at 200 rpm until mid-logarithmic phase.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions, followed by quality assessment with Agilent 2100.
mRNA was enriched using oligo(dT) beads, fragmented, and reverse transcribed to cDNA. Libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Cells in the treatment group were incubated with Cyclina sinensis lectin (CSL) under defined conditions, while control groups received no treatment.

value: yeast cell (treated)

value: wild-type

value: lectin


title: E. coli single biofilm 48h in urine 2

description: Library name: EC2


title: Yeast transcriptome after lectin treatment5

description: Library name: ZK_r10_YL5


title: Yeast control transcriptome8

description: Library name: ZK_r6_Y8

source_name: yeast cell (control)

value: yeast cell (control)


title: Yeast control transcriptome7

description: Library name: ZK_r5_Y7


title: Yeast control transcriptome4

description: Library name: ZK_r3_Y4


title: Yeast control transcriptome6

description: Library name: ZK_r4_Y6


title: Yeast control transcriptome2

description: Library name: ZK_r1_Y2


title: Yeast transcriptome after lectin treatmen8

description: Library name: ZK_r12_YL8


title: Yeast transcriptome after lectin treatment6

description: Library name: ZK_r11_YL6


title: Yeast transcriptome after lectin treatment3

description: Library name: ZK_r8_YL3


title: hypothalamus_WT_4

city: Göteborg

first: Yiwen

last: Jiang

address: Vita Stråket 11, Klinfarmlab

country: Sweden

institute: University of Gothenburg

description: Library name: Pool8

data_processing:
Raw sequencing reads were assessed for quality using FastQC (v0.12.1).
Transcript-level quantification was performed using Salmon (v1.10) with selective alignment.
Reads were mapped against the GENCODE mouse reference transcriptome (vM32).
Transcript-level abundances were summarized to gene-level counts using the tximport package (v1.28) in R (v4.4).
Differential expression analysis was performed using DESeq2 (v1.40).
Multiple testing correction was applied using the Benjamini-Hochberg method, and genes with false discovery rate (FDR) ≤ 0.05 were considered significant.
Assembly: Mus musculus GRCm39 (GENCODE vM32)
Supplementary files format and content: csv file with raw counts for each sample and the mean counts for each group with adjusted p values

source_name: hypothalamus

extract_protocol:
Total RNA was isolated from hypothalamus using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA quality was assessed using Agilent 4200 TapeStation. Libraries were prepared using the Illumina Stranded mRNA Library Preparation Kit with poly(A) selection.

value: hypothalamus

tag: age

value: female

value: wildtype


title: hypothalamus_WT_2

description: Library name: Pool4


title: hypothalamus_WT_3

description: Library name: Pool6


title: hypothalamus_KO_2

description: Library name: Pool3


title: Yeast control transcriptome3

description: Library name: ZK_r2_Y3


title: hypothalamus_WT_1

description: Library name: Pool2


title: hypothalamus_KO_1

description: Library name: Pool1


title: APOE3_DC_Cortex_DSP-1001660014839-B-H06

city: Washington

first: Christopher

last: Albanese

address: 3800 Reservoir Road NW

institute: Georgetown university

description:
Library name: DSP-1001660014839-B-H06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

data_processing:
Raw FASTQ files were processed using the NanoString GeoMx DSP analysis pipeline. Sequencing reads were demultiplexed and aligned to probe sequences to generate digital count matrices for each ROI/AOI. Quality control was performed using NanoString GeoMx DSP QC metrics, including sequencing saturation, alignment rate, and negative control probe assessment. Data were normalized using upper quartile (Q3) normalization to account for technical variability across ROIs. Downstream analyses were performed using normalized counts
Assembly: mm10
Supplementary files format and content: Processed gene expression count matrix from NanoString GeoMx DSP WTA platform for mouse brain ROIs.
Library strategy: Spatial Transcriptomics

source_name: Cortex

extract_protocol:
Tissue sections were processed directly for NanoString GeoMx DSP analysis, where RNA targets were hybridized in situ with oligonucleotide probes. Regions of interest (ROIs/AOIs) were selected, and target-specific oligonucleotide tags were released via UV photocleavage for downstream quantification.”
Tissue sections were processed using the NanoString GeoMx DSP RNA assay according to the manufacturer’s slide preparation protocol. After ROI/AOI selection and UV-photocleavage of oligo tags, NGS libraries were generated following the NanoString GeoMx DSP NGS readout/library preparation workflow and sequenced on an Illumina Novaseq 6000 platform.

treatment_protocol: Treatments were administered via intraperitoneal injection in fractionated doses, twice weekly over a two-week period with one of the following regimens: (1) doxorubicin (3 mg/kg/week, Abcam, Waltham, MA) plus docetaxel (10 mg/kg/week, Abcam), referred to as DD; (2) doxorubicin (3 mg/kg/week) plus cyclophosphamide (40 mg/kg/week, Abcam), referred to as DC, or (3) vehicle control (V; 50% Dimethyl Sulfoxide (Fisher Scientific, Pittsburgh, PA):50% Phosphate Buffered Saline (PBS, Fisher Scientific).

value: Cortex

value: DC


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-H12

description:
Library name: DSP-1001660014839-B-H12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

source_name: Hippocampus

value: Hippocampus


title: APOE3_DC_Cortex_DSP-1001660014839-B-H05

description:
Library name: DSP-1001660014839-B-H05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Yeast transcriptome after lectin treatment2

description: Library name: ZK_r7_YL2


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-H11

description:
Library name: DSP-1001660014839-B-H11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-H03

description:
Library name: DSP-1001660014839-B-H03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DD


title: hypothalamus_KO_3

description: Library name: Pool5


title: hypothalamus_KO_4

description: Library name: Pool7


title: APOE3_veh_Cortex_DSP-1001660014839-B-G01

description:
Library name: DSP-1001660014839-B-G01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: veh


title: APOE3_veh_Cortex_DSP-1001660014839-B-G02

description:
Library name: DSP-1001660014839-B-G02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-G09

description:
Library name: DSP-1001660014839-B-G09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-F12

description:
Library name: DSP-1001660014839-B-F12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-F11

description:
Library name: DSP-1001660014839-B-F11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-H04

description:
Library name: DSP-1001660014839-B-H04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Cortex_DSP-1001660014839-B-F05

description:
Library name: DSP-1001660014839-B-F05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-F04

description:
Library name: DSP-1001660014839-B-F04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Cortex_DSP-1001660014839-B-F06

description:
Library name: DSP-1001660014839-B-F06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-E08

description:
Library name: DSP-1001660014839-B-E08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-F03

description:
Library name: DSP-1001660014839-B-F03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-G10

description:
Library name: DSP-1001660014839-B-G10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-E07

description:
Library name: DSP-1001660014839-B-E07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-E10

description:
Library name: DSP-1001660014839-B-E10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-G08

description:
Library name: DSP-1001660014839-B-G08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-D12

description:
Library name: DSP-1001660014839-B-D12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-G07

description:
Library name: DSP-1001660014839-B-G07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Cortex_DSP-1001660014839-B-E02

description:
Library name: DSP-1001660014839-B-E02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-E09

description:
Library name: DSP-1001660014839-B-E09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-D05

description:
Library name: DSP-1001660014839-B-D05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Cortex_DSP-1001660014839-B-E01

description:
Library name: DSP-1001660014839-B-E01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-B12

description:
Library name: DSP-1001660014839-B-B12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_veh_Cortex_DSP-1001660014839-B-B07

description:
Library name: DSP-1001660014839-B-B07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_Veh_Cortex_DSP-1001660014839-B-C02

description:
Library name: DSP-1001660014839-B-C02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Veh


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-D11

description:
Library name: DSP-1001660014839-B-D11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Cortex_DSP-1001660014839-B-D07

description:
Library name: DSP-1001660014839-B-D07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Cortex_DSP-1001660014839-B-D06

description:
Library name: DSP-1001660014839-B-D06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_C_2

type: other

city: Cambridge

first: Gabriel

last: Ferreras-Garrucho

state: Cambridgeshire

address: 93 Lawrence Weaver Rd

department: Crop Science Centre, Department of Plant Sciences

institute: University of Cambridge

description: transcript

hyb_protocol: At Resolve BioSciences, sections were washed twice in 1 × phosphate buffered saline (PBS) for 2 min, followed by 1 min washing in 50 % and 70 % ethanol at room temperature. Ethanol was removed by aspiration and DST1™ buffer was added, followed by tissue priming for 30 min at 37 °C and by a 48h hybridization using probes specific for the target genes. Samples were washed to remove excess probes and fluorescently tagged in a two-step colour development process. Fluorescent signals were removed after imaging in a decolourization step. Colourization, imaging, and decolourization were iterated for multiple cycles to generate a unique combinatorial code for each target gene.

scan_protocol: Samples were imaged by Resolve BioSciences using a Zeiss Celldiscoverer 7 with a 50 × Plan Apochromat water immersion objective having a numerical aperture (NA) of 1.2 and a 0.5 × magnification changer, resulting in a final magnification of 25 × (Glenn et al., 2023). To visualize fungal structures, sections from experiment 1 were stained with WGA-AF633 (Invitrogen), although staining was suboptimal. In experiment 2, WGA-AF488 was used to improve fungal structure visibility. All sections were counterstained with DAPI to visualize both plant and fungal nuclei.

data_processing: Probes yielding fewer than 20 transcript counts per section across both -Ri and +Ri conditions were excluded from downstream analyses. Additionally, root sections with significant tissue damage or low overall transcript abundance were omitted from further analysis. Additionally, root sections with significant tissue damage or low overall transcript abundance were excluded from downstream analyses. Image analyses, including generation of image-transcript overlays and manual cell-boundary segmentation was performed in Fiji under ImageJ software license (Schindelin et al., 2012). Transcript colocalization analysis was carried out using the Polylux plugin (Resolve Biosciences). Default settings were used for transcript colocalization analyses (xy-step size = 1, z-step size = 3.5, search radius = 50, and distance penalty = 4). To account for section-to-section variability, we calculated the median transcript colocalization score separately for all transcripts within mock and mycorrhizal samples. Single-cell clustering analysis was performed using the Seurat package in R. Cell cluster identities were then mapped back to their original spatial context in ImageJ using the Polylux plugin (Resolve Biosciences).

label: fluorescence

organism:
Oryza sativa
Rhizophagus irregularis

source_name: Root

label_protocol: Resolve Biosciences’ Molecular Cartography instructions

growth_protocol: Seeds of Oryza sativa cv. Japonica, Nipponbare were surface-sterilized briefly in 70% (v/v) ethanol, then for 20 min in 3% (v/v) sodium hypochlorite. Imbibed seeds were germinated on 0.9% (w/v) bactoagar at 30°C for 7 d. Pre-germinated seedlings were transferred into pots (11 x 8 cm) containing sterile quartz sand in walk-in growth chambers at 12-h:12-h, light:dark cycle at 28:20°C and 60% relative humidity. Plants were inoculated with 900 spores of R. irregularis DAOM197198 (Mycorise® ASP, Premier Tech Biotechnologies, Rivière-du-loup, Canada). Plants were watered three times weekly for the ﬁrst two weeks post-inoculation (wpi), thereafter fertilized twice a week with half Hoagland solution (25 µM Pi) and 0.01% (w/v) Sequestren Rapid (Syngenta), as previously described by (Gutjahr et al., 2008). Plants plants were harvested at six wpi.

extract_protocol: Root segments were fixed in paraformaldehyde (PFA) and embedded in paraffin according to Resolve Biosciences’ standard plant tissue preparation protocol, adapted from (Zöllner et al., 2021). Semi-thin sections (10 µm) were made using a Leica HistoCore Autocut R microtome and adhered to the Molecular Cartography slides. Sections underwent deparaffinization, permeabilization and refixation according to Resolve BioSciences’ user guide. Samples were mounted in SlowFade Diamond Antifade Mountant (Thermo Fisher Scientific) and shipped to Resolve Biosciences for Molecular Cartography analysis.

value: Root

tag: experiment

tag: root type

value: LLR

tag: inoculation

value: myc


title: APOE3_Veh_Hippocampus_DSP-1001660014839-B-C09

description:
Library name: DSP-1001660014839-B-C09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-C10

description:
Library name: DSP-1001660014839-B-C10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-B05

description:
Library name: DSP-1001660014839-B-B05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-D04

description:
Library name: DSP-1001660014839-B-D04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_Veh_Cortex_DSP-1001660014839-B-C03

description:
Library name: DSP-1001660014839-B-C03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Cortex_DSP-1001660014839-B-C11

description:
Library name: DSP-1001660014839-B-C11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-B02

description:
Library name: DSP-1001660014839-B-B02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_Veh_Hippocampus_DSP-1001660014839-B-C08

description:
Library name: DSP-1001660014839-B-C08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-A09

description:
Library name: DSP-1001660014839-B-A09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_B_2

description: transcript


title: APOE3_DD_Cortex_DSP-1001660014839-B-A11

description:
Library name: DSP-1001660014839-B-A11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DD_Hippocampus_DSP-1001660014839-B-B04

description:
Library name: DSP-1001660014839-B-B04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_D_2

description: transcript


title: APOE3_veh_Cortex_DSP-1001660014839-B-B06

description:
Library name: DSP-1001660014839-B-B06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_C_1

description: transcript


title: APOE3_veh_Hippocampus_DSP-1001660014839-B-C01

description:
Library name: DSP-1001660014839-B-C01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_B_1

description: transcript


title: LLR_myc_A_2

description: transcript


title: APOE3_DD_Cortex_DSP-1001660014839-B-A10

description:
Library name: DSP-1001660014839-B-A10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Hippocampus_DSP-1001660014839-B-A08

description:
Library name: DSP-1001660014839-B-A08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE3_DC_Cortex_DSP-1001660014839-B-A03

description:
Library name: DSP-1001660014839-B-A03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: CR_myc_D_2

description: transcript

value: CR


title: APOE3_DC_Cortex_DSP-1001660014839-B-A02

description:
Library name: DSP-1001660014839-B-A02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_myc_A_1

description: transcript


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-H12

description:
Library name: DSP-1001660022855-A-H12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: CR_myc_A_2

description: transcript


title: CR_myc_B_1

description: transcript


title: APOE4_DC_Cortex_DSP-1001660022855-A-H06

description:
Library name: DSP-1001660022855-A-H06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-H11

description:
Library name: DSP-1001660022855-A-H11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: CR_myc_C_2

description: transcript


title: CR_myc_B_2

description: transcript


title: APOE4_DC_Cortex_DSP-1001660022855-A-H05

description:
Library name: DSP-1001660022855-A-H05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: LLR_mock_D_2

description: transcript

organism: Oryza sativa

value: mock


title: HGrC1 cells, 1 µM PFOS, 12 weeks, biol rep 2

city: Novi Sad

first: Tamara

middle: Miroslav

last: Tomanic

address: Trg Dositeja Obradovica 2

country: Serbia

institute: Faculty of Sciences University of Novi Sad

description: Library name: Sample_30

data_processing:
Raw sequencing reads were filtered using SOAPnuke (v2.3) to remove low-quality and contaminating reads. Filtering criteria included removal of reads containing adapter sequences, reads with >1% ambiguous bases (N), and low-quality reads defined as those in which >40% of bases had a Phred quality score ≤20. Clean reads passing all filters were retained in FASTQ format for downstream analysis. Parameters: -l 20 -q 0.4 -n 0.01
Clean reads were aligned to the human reference genome using HISAT2 (v2.0.4). Parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Bowtie2 (v2.2.5) was used to map the clean reads to the reference gene sequence (transcriptome). Parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM (v1.2.8) was used to calculate the gene expression level of each sample. Parameters: -p 8 --forward-prob 0 --paired-end
Assembly: Species: Homo_sapiens Source: NCBI Reference Genome Version: GCF_000001405.40_GRCh38.p14
Supplementary files format and content: TPM_all_samples.txt - TPM values for all genes and samples
Supplementary files format and content: FPKM_all_samples.txt - FPKM values for all genes and samples
Supplementary files format and content: Read_count_all_samples.txt - read counts for all genes and samples
Supplementary files format and content: Normalized_read_count_all_samples.txt - normalized read counts for all genes and samples

growth_protocol: HGrC1 human granulosa cells were maintained in DMEM/F12 supplemented with 100,000 U/L penicillin, 100 mg/L streptomycin, 1.4 g/L sodium bicarbonate, 2 mM L-glutamine, and 10% fetal bovine serum (FBS), pH 7.4, at 37 °C in a humidified atmosphere with 5% CO₂. Subculturing was performed twice a week.

extract_protocol:
RNA was extracted using TRIzol™ reagent (Invitrogen, Thermo Fisher Scientific), according to the manufacturers' protocol.RNA quantity and integrity were evaluated using the 4150 TapeStation System (Agilent Technologies), and all samples met library preparation criteria.
Stranded mRNA libraries were prepared using oligo(dT) beads to enrich mRNA with poly(A) tail. Purified mRNA was fragmented and reverse transcribed using random hexamer primers to generate first-strand cDNA, followed by second-strand synthesis incorporating dUTP in place of dTTP. Double-stranded cDNA underwent end repair, 3′ adenylation, and adapter ligation. Prior to PCR amplification, the dUTP-containing strand was selectively degraded using uracil-DNA glycosylase, preserving strand specificity. The remaining strand was PCR-amplified to generate sequencing libraries. PCR products were denatured, circularized using a splint oligonucleotide and DNA ligase, and converted into DNA nanoballs prior to sequencing on the DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Four independent vials of human granulosa cells HGrC1 were thawed and expanded into separate flasks (biological replicates). Cells from each flask were subsequently divided into four experimental groups and exposed to PFOS (0.01, 0.1, or 1 µM), or vehicle control (0.05% DMSO) for 6 or 12 weeks, with PFOS re-dosed at each passage. Cells were exposed in 10% FBS-supplemented medium with 100 nM estradiol.

value: granulosa cells

value: 1 µM PFOS

value: 12 weeks


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repC2

description:
Library name: TC072_TR_C2
Column name in gene_counts_matrix.csv: summed in pARK1_TRAP_TR_Myc_C

data_processing:
UMI deduplication, genome alignment (STAR), and count quantification were processed using the Lexogen NGS Kangaroo Data Analysis Platform. To address low read counts in AM-inducible TRAP samples, an additional library was constructed and sequenced from the original RNA extractions, with resulting counts combined at the count level. Subsequent data analysis, including differential gene expression, was carried out in R using the DESeq2 package.
Assembly: O. sativa Nipponbare reference transcriptome Os-Nipponbare-Reference-IRGSP- 1.0.58 (Kawahara et al., 2013)
Supplementary files format and content: comma-delimited matrix of raw gene counts

molecule: cytoplasmic RNA

source_name: Whole roots

growth_protocol: Seeds of Oryza sativa cv. Japonica, Nipponbare were surface-sterilized briefly in 70% (v/v) ethanol, then for 20 min in 3% (v/v) sodium hypochlorite. Imbibed seeds were germinated on 0.9% (w/v) bactoagar at 30°C for 7 d. Pre-germinated seedlings were transferred into pots (11 x 8 cm) containing sterile quartz sand in walk-in growth chambers at 12-h:12-h, light:dark cycle at 28:20°C and 60% relative humidity. Plants were inoculated with 900 spores of R. irregularis DAOM197198 (Mycorise® ASP, Premier Tech Biotechnologies, Rivière-du-loup, Canada). Plants were watered three times weekly for the ﬁrst two weeks post-inoculation (wpi), thereafter fertilized twice a week with half Hoagland solution (25 µM Pi) and 0.01% (w/v) Sequestren Rapid (Syngenta), as previously described by (Gutjahr et al., 2008). Six wpi wild-type plants were retained as “nurse plants” to enable rapid colonization of young test plants. Here, five pre-germinated seedlings were sown into pots, each already containing a colonized nurse plant. Test plants were harvested at three wpi.

extract_protocol:
Promoter:TRAP constructs were prepared with the TRAP destination vector pH7WG-OsTRAP which was engineered by modifying p35S:HF-OsRPL18 (Zhao et al., 2017). This vector contains a Gateway recombination site for promoter insertion upstream of a chimeric ribosomal protein fusion comprising a 6×His-FLAG-3×Gly tag, GFP, and OsRPL18/eL18 (Os03G0341100). Promoters listed in Table S6 were cloned into pENTR-D/TOPO (Invitrogen) and subsequently recombined into the TRAP vector via LR Clonase II enzyme mix (Invitrogen). All constructs were validated by Sanger sequencing. Resulting T-DNA plasmids were introduced into Oryza sativa japonica cv. Nipponbare embryogenic calli, derived from mature seed embryos, through Agrobacterium tumefaciens-mediated transformation (strain EHA105A). T2 generation plants were used for TRAP experiments. TRAP was performed as previously described (Mustroph et al., 2009; Reynoso et al., 2015) with modifications outlined by Reynoso et al. (2019). From each sample, both total RNA and TRAP RNA (following ribosome purification) were extracted using the RNeasy Micro Kit (Qiagen).
Libraries were prepared with the QuantSeq 3’ mRNA-seq kit (Lexogen) incorporating unique dual indices (UDIs) and unique molecular identifiers (UMIs) for three biological replicates per treatment. RNA samples were diluted to an equal concentration and sent for poliA library generation and sequencing to Novogene (Cambridge) with a sequencing depth of 3 Gb (10 million reads). Sequencing was performed on an Illumina NovaSeq 6000 platform generating 150 bp single-end reads.

value: Whole roots

value: Myc (+Ri)


title: LLR_mock_C_2

description: transcript


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-H03

description:
Library name: DSP-1001660022855-A-H03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-H04

description:
Library name: DSP-1001660022855-A-H04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repB2

description:
Library name: TC070_TR_B2
Column name in gene_counts_matrix.csv: summed in pARK1_TRAP_TR_Myc_B


title: LLR_mock_B_2

description: transcript


title: HGrC1 cells, 1 µM PFOS, 12 weeks, biol rep 3

description: Library name: Sample_31


title: HGrC1 cells, 1 µM PFOS, 12 weeks, biol rep 4

description: Library name: Sample_32


title: LLR_mock_C_1

description: transcript


title: APOE4_DD_Cortex_DSP-1001660022855-A-G10

description:
Library name: DSP-1001660022855-A-G10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, 1 µM PFOS, 12 weeks, biol rep 1

description: Library name: Sample_29


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repA2

description:
Library name: TC068_TR_A2
Column name in gene_counts_matrix.csv: summed in pARK1_TRAP_TR_Myc_A


title: LLR_mock_A_2

description: transcript


title: APOE4_DD_Cortex_DSP-1001660022855-A-G09

description:
Library name: DSP-1001660022855-A-G09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: CR_mock_B_2

description: transcript


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repC2

description:
Library name: TC066_TR_C2
Column name in gene_counts_matrix.csv: summed in pPT11_TRAP_TR_Myc_C


title: CR_mock_A_2

description: transcript


title: CR_mock_B_1

description: transcript


title: HGrC1 cells, 0.1 µM PFOS, 12 weeks, biol rep 3

description: Library name: Sample_27

value: 0.1 µM PFOS


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-G08

description:
Library name: DSP-1001660022855-A-G08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: hsc_w326r_s4

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

institute: University of Edinburgh

description: Library name: hsc_w326r_s4

data_processing:
Sequencing quality was assessed with FASTQC (v0.11.4); low-quality reads and remaining adaptors removed using TrimGalore (v0.4.1, Settings: --adapter AGATCGGAAGAGC --adapter2 AAATCAAAAAAAC). PCR duplicates were identified and removed using Bismark’s deduplicate_bismark command. Aligned BAM files were processed to report coverage and the number of methylated reads for each CpG observed. Forward and reverse strands were combined using Bismark’s methylation extractor and bismark2bedgraph modules with custom Python and AWK scripts.
Processed EM-seq files were assessed for conversion efficiency based on the proportion of methylated reads mapping to the CpG-methylated pUC19 DNA (>96% in all cases) and lambda genome spike-ins (<0.5% in all cases).
BigWigs for visualisation of EM-seq data were generated using BEDtools (v2.30.0)99 and converted to bigWigs using UCSC tools bedGraphToBigWig (v369). Windows with a total coverage <5 were excluded before conversion to bigWigs.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: EM-seq

source_name: Bone marrow

extract_protocol:
Genomic DNA was extracted using QIAamp UCP DNA micro kit (QIAGEN).
Libraries were prepared from 0.5-1 ng of each sample using the NEBNext Enzymatic Methyl-seq Kit (NEB #E7120) according to manufacturer instructions for low input samples. Briefly, DNA controls were spiked in: unmethylated lambda DNA and CpG-methylated pUC19 DNA. Controls were diluted 1:500 and 1 mL of the relevant diluted controls were added to each DNA sample. Then, DNA samples were sheared to an average size of 240-290bp using Covaris E220 Evolution Focused Ultrasonicator (Covaris #3814). Sheared DNA samples were end-repaired, 5’ phosphorylated and 3’ dA-tailed. After adapter ligation, DNA fragments were purified with NEBNext Sample Purification Beads followed by Enzymatic Methyl-seq two-step conversion. Fragments were then purified with AMPure XP beads (1X volume) before PCR with unique dual index sequences to selectively enrich DNA fragments with adapter sequences and allow multiplex sequencing. Libraries were quantified by Qubit. Sequencing was performed on NextSeq 2000 (Illumina, #20038897) using P3 Reagents (#20040560).

value: Bone marrow

value: HSC

value: Dnmt3a W326R/+


title: HGrC1 cells, 0.1 µM PFOS, 12 weeks, biol rep 4

description: Library name: Sample_28


title: hsc_w326r_s6

description: Library name: hsc_w326r_s6


title: hsc_w326r_s2

description: Library name: hsc_w326r_s2


title: HGrC1 cells, 0.1 µM PFOS, 12 weeks, biol rep 2

description: Library name: Sample_26


title: HGrC1 cells, 0.1 µM PFOS, 12 weeks, biol rep 1

description: Library name: Sample_25


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-G07

description:
Library name: DSP-1001660022855-A-G07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Hippocampus


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repA2

description:
Library name: TC062_TR_A2
Column name in gene_counts_matrix.csv: summed in pPT11_TRAP_TR_Myc_A


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repB2

description:
Library name: TC064_TR_B2
Column name in gene_counts_matrix.csv: summed in pPT11_TRAP_TR_Myc_B


title: HGrC1 cells, 0.01 µM PFOS, 12 weeks, biol rep 3

description: Library name: Sample_23

value: 0.01 µM PFOS


title: hsc_wt_s3

description: Library name: hsc_wt_s3

value: Dnmt3a +/+


title: Rice whole roots 3 wpi, pAM1, TRAP mRNA, Myc(+Ri), repB2

description:
Library name: TC076_TR_B2
Column name in gene_counts_matrix.csv: summed in pAM1_TRAP_TR_Myc_B


title: HGrC1 cells, 0.01 µM PFOS, 12 weeks, biol rep 4

description: Library name: Sample_24


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-F12

description:
Library name: DSP-1001660022855-A-F12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DC


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-G01

description:
Library name: DSP-1001660022855-A-G01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repC

description:
Library name: TC072_TR_C
Column name in gene_counts_matrix.csv: pARK1_TRAP_TR_Myc_C


title: APOE4_veh_Cortex_DSP-1001660022855-A-G02

description:
Library name: DSP-1001660022855-A-G02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Cortex

value: veh


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repB

description:
Library name: TC070_TR_B
Column name in gene_counts_matrix.csv: pARK1_TRAP_TR_Myc_B


title: Rice whole roots 3 wpi, pARK1, total mRNA, Myc(+Ri), repC

description:
Library name: TC071_CR_C
Column name in gene_counts_matrix.csv: pARK1_TRAP_CR_Myc_C


title: hsc_wt_s1

description: Library name: hsc_wt_s1


title: APOE4_DC_Cortex_DSP-1001660022855-A-F07

description:
Library name: DSP-1001660022855-A-F07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: hsc_wt_s5

description: Library name: hsc_wt_s5


title: Rice whole roots 3 wpi, pAM1, TRAP mRNA, Myc(+Ri), repA2

description:
Library name: TC074_TR_A2
Column name in gene_counts_matrix.csv: summed in pAM1_TRAP_TR_Myc_A


title: Ddx3x CM-KO E10.5 Female RPF-Seq Rep 3

city: Chapel Hill

first: Kayla

middle: K

last: Mason

state: NC

address: 133 N Medical Drive

institute: University of North Carolina Chapel Hill

description:
Library name: KO Female RPF-Seq Rep 3
RPF-seq

data_processing:
Libraries were run on a NextSeq 200 with single end reads.
The sequence reads were aligned to the mm38 reference genome and differential gene expression was determined by EclipseBio.
Assembly: mm38
Supplementary files format and content: ALL WTFvsKOF Raw Data Merged.xlsx
Library strategy: Ribo-Seq

source_name: Heart

extract_protocol:
Female wt, and female Ddx3x KO embryonic hearts E=10.5 (n=3 replicates per genotype, 20 hearts/replicate) for each, were dissected in cold PBS and immediately snap frozen. Samples were kept in -80C until pooling in EcliplseBio lysis buffer.
RNA libraries were prepared for sequencing using EclipseBio's proprietary eRibo Pro methods

value: Heart

value: Ddx3x CM-KO


title: APOE4_veh_Cortex_DSP-1001660022855-A-G03

description:
Library name: DSP-1001660022855-A-G03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, Control, 12 weeks, biol rep 4

description: Library name: Sample_20

value: granulosa cells

value: Control


title: HGrC1 cells, 0.01 µM PFOS, 12 weeks, biol rep 2

description: Library name: Sample_22

value: 12 weeks


title: Ddx3x CM-KO E10.5 Female RPF-Seq Rep 2

description:
Library name: KO Female RPF-Seq Rep 2
RPF-seq


title: APOE4_DC_Cortex_DSP-1001660022855-A-F06

description:
Library name: DSP-1001660022855-A-F06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, 0.01 µM PFOS, 12 weeks, biol rep 1

description: Library name: Sample_21


title: HGrC1 cells, Control, 12 weeks, biol rep 3

description: Library name: Sample_19


title: WT E10.5 Female RPF-Seq Rep 3

description:
Library name: WT Female RPF-Seq Rep 3
RPF-seq

value: Ddx3x fl/fl


title: Ddx3x CM-KO E10.5 Female RPF-Seq Rep 1

description:
Library name: KO Female RPF-Seq Rep 1
RPF-seq


title: Rice whole roots 3 wpi, pARK1, total mRNA, Myc(+Ri), repB

description:
Library name: TC069_CR_B
Column name in gene_counts_matrix.csv: pARK1_TRAP_CR_Myc_B

value: Whole roots

value: Myc (+Ri)


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-F05

description:
Library name: DSP-1001660022855-A-F05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DD


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-F04

description:
Library name: DSP-1001660022855-A-F04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, pARK1, total mRNA, Myc(+Ri), repA

description:
Library name: TC067_CR_A
Column name in gene_counts_matrix.csv: pARK1_TRAP_CR_Myc_A


title: WT E10.5 Female RPF-Seq Rep 2

description:
Library name: WT Female RPF-Seq Rep 2
RPF-seq


title: HGrC1 cells, Control, 12 weeks, biol rep 1

description: Library name: Sample_17


title: WT E10.5 Female RPF-Seq Rep 1

description:
Library name: WT Female RPF-Seq Rep 1
RPF-seq


title: HGrC1 cells, 1 µM PFOS, 6 weeks, biol rep 4

description: Library name: Sample_16

value: 1 µM PFOS

value: 6 weeks


title: Rice whole roots 3 wpi, pPT11, total mRNA, Myc(+Ri), repC

description:
Library name: TC065_CR_C
Column name in gene_counts_matrix.csv: pPT11_TRAP_CR_Myc_C


title: Ddx3x CM-KO E10.5 Female RNA-Seq Rep 3

description:
Library name: KO Female RNA-Seq Rep 3
Input RNA-seq

data_processing:
Libraries were run on a NextSeq 200 with single end reads.
The sequence reads were aligned to the mm38 reference genome and differential gene expression was determined by EclipseBio.
Assembly: mm38
Supplementary files format and content: ALL WTFvsKOF Raw Data Merged.xlsx


title: HGrC1 cells, Control, 12 weeks, biol rep 2

description: Library name: Sample_18


title: APOE4_DD_Cortex_DSP-1001660022855-A-E11

description:
Library name: DSP-1001660022855-A-E11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repC

description:
Library name: TC066_TR_C
Column name in gene_counts_matrix.csv: pPT11_TRAP_TR_Myc_C


title: Rice whole roots 3 wpi, pARK1, TRAP mRNA, Myc(+Ri), repA

description:
Library name: TC068_TR_A
Column name in gene_counts_matrix.csv: pARK1_TRAP_TR_Myc_A


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repB

description:
Library name: TC064_TR_B
Column name in gene_counts_matrix.csv: pPT11_TRAP_TR_Myc_B


title: APOE4_DD_Cortex_DSP-1001660022855-A-E10

description:
Library name: DSP-1001660022855-A-E10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Ddx3x CM-KO E10.5 Female RNA-Seq Rep 1

description:
Library name: KO Female RNA-Seq Rep 1
Input RNA-seq


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-E09

description:
Library name: DSP-1001660022855-A-E09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Hippocampus


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-E08

description:
Library name: DSP-1001660022855-A-E08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, 1 µM PFOS, 6 weeks, biol rep 2

description: Library name: Sample_14


title: APOE4_veh_Cortex_DSP-1001660022855-A-E03

description:
Library name: DSP-1001660022855-A-E03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Ddx3x CM-KO E10.5 Female RNA-Seq Rep 2

description:
Library name: KO Female RNA-Seq Rep 2
Input RNA-seq


title: HGrC1 cells, 1 µM PFOS, 6 weeks, biol rep 1

description: Library name: Sample_13


title: Rice whole roots 3 wpi, pPT11, total mRNA, Myc(+Ri), repB

description:
Library name: TC063_CR_B
Column name in gene_counts_matrix.csv: pPT11_TRAP_CR_Myc_B


title: HGrC1 cells, 1 µM PFOS, 6 weeks, biol rep 3

description: Library name: Sample_15


title: WT E10.5 Female RNA-Seq Rep 3

description:
Library name: WT Female RNA-Seq Rep 3
Input RNA-seq


title: HGrC1 cells, 0.1 µM PFOS, 6 weeks, biol rep 4

description: Library name: Sample_12

value: 0.1 µM PFOS


title: APOE4_veh_Cortex_DSP-1001660022855-A-E02

description:
Library name: DSP-1001660022855-A-E02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: WT E10.5 Female RNA-Seq Rep 2

description:
Library name: WT Female RNA-Seq Rep 2
Input RNA-seq


title: Rice whole roots 3 wpi, pPT11, TRAP mRNA, Myc(+Ri), repA

description:
Library name: TC062_TR_A
Column name in gene_counts_matrix.csv: pPT11_TRAP_TR_Myc_A


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-E01

description:
Library name: DSP-1001660022855-A-E01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, pAM1, total mRNA, Myc(+Ri), repC

description:
Library name: TC077_CR_C
Column name in gene_counts_matrix.csv: pAM1_TRAP_CR_Myc_C


title: WT E10.5 Female RNA-Seq Rep 1

description:
Library name: WT Female RNA-Seq Rep 1
Input RNA-seq


title: Rice whole roots 3 wpi, pAM1, TRAP mRNA, Myc(+Ri), repC

description:
Library name: TC078_TR_C
Column name in gene_counts_matrix.csv: pAM1_TRAP_TR_Myc_C


title: Rice whole roots 3 wpi, pPT11, total mRNA, Myc(+Ri), repA

description:
Library name: TC061_CR_A
Column name in gene_counts_matrix.csv: pPT11_TRAP_CR_Myc_A


title: HGrC1 cells, 0.1 µM PFOS, 6 weeks, biol rep 2

description: Library name: Sample_10


title: P0 Ddx3x-3HA Female Heart IgG Input Rep 1

description:
Library name: IgG Input  Rep1
Input RNA-seq

data_processing:
Data was analyzed using a modified single-end seCLIP protocol with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next, 3' adapters were trimmed from reads using Cutadapt (v3.2), and reads <18 bp were discarded. Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome mm38 using STAR (v2.7.7a); during the alignment multimapping, reads were not retained. PCR duplicates were removed using UMI-tools (v1.1.1). Peak calling was conducted with CLIPper 87. For each peak, IP versus input fold enrichment values were calculated as a ratio of counts of reads overlapping the peak region in the IP and the input samples, removing peaks from IgG control (IDR).
Assembly: mm39
Supplementary files format and content: eCLIP Analyzed Peak Data.xlsx

extract_protocol:
P0 Ddx3x-3XHA/+ female hearts (n=3 replicates, 8 hearts/rep HA eCLIP, n=1 replicate, 4 hearts/rep IgG eCLIP) were dissected and snap frozen. Tissue was cryogenically ground and UV crosslinked. HA and IgG immunoprecipitation were performed. RNAse treatment and subsequent seqeuncing of bound RNA and total RNA input were perfformed.
RNA libraries were prepared for sequencing according to published eCLIP protocols and performed by Eclipse Bioinnovations.


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-D12

description:
Library name: DSP-1001660022855-A-D12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE4_DC_Cortex_DSP-1001660022855-A-D07

description:
Library name: DSP-1001660022855-A-D07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, 0.01 µM PFOS, 6 weeks, biol rep 4

description: Library name: Sample_8

value: 0.01 µM PFOS


title: Rice whole roots 3 wpi, pAM1, total mRNA, Myc(+Ri), repB

description:
Library name: TC075_CR_B
Column name in gene_counts_matrix.csv: pAM1_TRAP_CR_Myc_B


title: HGrC1 cells, 0.1 µM PFOS, 6 weeks, biol rep 3

description: Library name: Sample_11


title: P0 Ddx3x-3HA Female Heart DDX3X Input Rep 3

description:
Library name: DDX3X Input  Rep 3
Input RNA-seq


title: Rice whole roots 3 wpi, pAM1, TRAP mRNA, Myc(+Ri), repB

description:
Library name: TC076_TR_B
Column name in gene_counts_matrix.csv: pAM1_TRAP_TR_Myc_B


title: P0 Ddx3x-3HA Female Heart DDX3X Input Rep 2

description:
Library name: DDX3X Input Rep 2
Input RNA-seq


title: APOE4_DC_Cortex_DSP-1001660022855-A-D06

description:
Library name: DSP-1001660022855-A-D06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DC


title: Rice whole roots 3 wpi, pAM1, TRAP mRNA, Myc(+Ri), repA

description:
Library name: TC074_TR_A
Column name in gene_counts_matrix.csv: pAM1_TRAP_TR_Myc_A


title: P0 Ddx3x-3HA Female Heart DDX3X Input Rep 1

description:
Library name: DDX3X Input Rep 1
Input RNA-seq


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-D05

description:
Library name: DSP-1001660022855-A-D05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, 0.01 µM PFOS, 6 weeks, biol rep 2

description: Library name: Sample_6


title: P0 Ddx3x-3HA Female Heart IgG eCLIP Rep 1

description:
Library name: IgG eCLIP Rep1
eCLIP-seq


title: HGrC1 cells, 0.1 µM PFOS, 6 weeks, biol rep 1

description: Library name: Sample_9


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Myc(+Ri), repC

description:
Library name: TC084_TR_C
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Myc_C


title: APOE4_DD_Cortex_DSP-1001660022855-A-C11

description:
Library name: DSP-1001660022855-A-C11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Cortex


title: HGrC1 cells, 0.01 µM PFOS, 6 weeks, biol rep 3

description: Library name: Sample_7


title: HGrC1 cells, 0.01 µM PFOS, 6 weeks, biol rep 1

description: Library name: Sample_5


title: P0 Ddx3x-3HA Female Heart DDX3X eCLIP Rep 3

description:
Library name: DDX3X eCLIP Rep 3
eCLIP-seq


title: Rice whole roots 3 wpi, pAM1, total mRNA, Myc(+Ri), repA

description:
Library name: TC073_CR_A
Column name in gene_counts_matrix.csv: pAM1_TRAP_CR_Myc_A


title: HGrC1 cells, Control, 6 weeks, biol rep 4

description: Library name: Sample_4


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-D04

description:
Library name: DSP-1001660022855-A-D04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-C09

description:
Library name: DSP-1001660022855-A-C09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: veh


title: HGrC1 cells, Control, 6 weeks, biol rep 3

description: Library name: Sample_3


title: Rice whole roots 3 wpi, p35S, total mRNA, Myc(+Ri), repC

description:
Library name: TC083_CR_C
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Myc_C


title: P0 Ddx3x-3HA Female Heart DDX3X eCLIP Rep 2

description:
Library name: DDX3X eCLIP Rep 2
eCLIP-seq

value: Heart


title: APOE4_DD_Cortex_DSP-1001660022855-A-C10

description:
Library name: DSP-1001660022855-A-C10
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, p35S, total mRNA, Myc(+Ri), repB

description:
Library name: TC081_CR_B
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Myc_B


title: P0 Ddx3x-3HA Female Heart DDX3X eCLIP Rep 1

description:
Library name: DDX3X eCLIP Rep 1
eCLIP-seq


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Myc(+Ri), repB

description:
Library name: TC082_TR_B
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Myc_B


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-C08

description:
Library name: DSP-1001660022855-A-C08
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: APOE4_veh_Cortex_DSP-1001660022855-A-C03

description:
Library name: DSP-1001660022855-A-C03
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: HGrC1 cells, Control, 6 weeks, biol rep 1

description: Library name: Sample_1


title: Liver_MD_MP_3

city: Oklahoma City

first: Tae

middle: Gyu

last: Oh

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Oncology Science

institute: University of Oklahoma Health Science Center

description:
Library name: S55
column name in MP_raw_counts_gene_level.csv: MD_MP_3_S55

data_processing:
Samples were normalized and pooled onto a 150 paired end run on Illumina's NextSeq 2000 Platform to obtain 15M reads per sample at the OUHSC's Genomics Core. Raw RNA-seq reads were preprocessed for quality control using fastp (v0.23.4) with adapter trimming, poly-G, and poly-X removal. Following QC, filtered paired-end RNA-seq reads were quantified using Salmon (v1.10.3) with selective alignment mode enabled (--validateMapping), allowing more accurate mapping of reads to the GRCm39 transcriptome from the GENCODE. Library type was automatically detected (-l A), and sequence bias correction (--seqBias) and variational Bayesian optimization (--useVBOpt) were applied. Resulting quantification files (quant.sf) were collected for downstream analysis. Gene-level abundance estimates were imported into R using the tximport package, using a transcript-to-gene mapping file. Differential expression analysis was performed using DESeq2.
Assembly: GRCm39 M35
Supplementary files format and content: Raw counts

source_name: Liver

extract_protocol:
RNA was extracted from four randomly selected (using Randomice tool) snap-frozen mouse liver tissues (~ 50 mg) using Trizol. Overall quality of RNA was verified using Agilent’s 2100 Bioanalyzer (Agilent)
Standard RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit (New England Biolabs, Ipswich, MA) followed directly by IDT’s XGen Broad Range RNA Library Prep Kit (Integrated DNA technologies, Coralville, IA) and the established protocols. The library construction was done using 500 ng of RNA. Each of the libraries was indexed during library construction to multiplex the sequencing. Libraries were quantified using Invitrogen’s Qubit 4 fluorometer (Thermofisher Scientific) and checked for size and quality using Agilent’s 2100 Bioanalyzer (Agilent).

value: Liver

value: WT

value: MASH Diet + Microplastics


title: Liver_MD_MP_5

description:
Library name: S57
column name in MP_raw_counts_gene_level.csv: MD_MP_5_S57


title: Liver_MD_MP_4

description:
Library name: S56
column name in MP_raw_counts_gene_level.csv: MD_MP_4_S56


title: DU145_ONC212_N3

city: Beirut

first: AUB

last: Submission

address: Bliss street

country: Lebanon

institute: American University of Beirut

description: Library name: DU145_ONC212_replicate_1

data_processing:
Quality check was done using Fastqc
Alignment step was performed using HISAT2
FeatureCounts was used to generate the count matrix
DESeq2 was used to perform differential expression
Assembly: Hg38
Supplementary files format and content: Count matrix in tab-separated format

growth_protocol: PC3 and DU145 human prostate cancer cell lines were cultured in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin, and Plasmocin® prophylactic. Cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2 and were routinely confirmed to be mycoplasma-free.

extract_protocol:
Total RNA was extracted from PC3 and DU145 cells using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA library.

treatment_protocol: Approximately 50% confluent PC3 and DU145 cells were treated with either ONC206 at 0.5 µM or ONC212 at 0.1 µM for 48 hours. Vehicle control samples were treated with DMSO matched to the corresponding treatment conditions.

value: Prostate cancer cells


title: HGrC1 cells, Control, 6 weeks, biol rep 2

description: Library name: Sample_2

value: granulosa cells

value: Control


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Myc(+Ri), repA

description:
Library name: TC080_TR_A
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Myc_A

value: Whole roots

value: Myc (+Ri)


title: Rice whole roots 3 wpi, p35S, total mRNA, Myc(+Ri), repA

description:
Library name: TC079_CR_A
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Myc_A


title: Liver_MD_MP_2

description:
Library name: S54
column name in MP_raw_counts_gene_level.csv: MD_MP_2_S54


title: Liver_MD_MP_1

description:
Library name: S53
column name in MP_raw_counts_gene_level.csv: MD_MP_1_S53


title: DU145_ONC212_N4

description: Library name: DU145_ONC212_replicate_2


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-C01

description:
Library name: DSP-1001660022855-A-C01
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Mock(-Ri), repC

description:
Library name: TC108_TR_C
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Mock_C

value: Mock (-Ri)


title: Liver_CD_MP_5

description:
Library name: S52
column name in MP_raw_counts_gene_level.csv: CD_MP_5_S52

value: Chow Diet + Microplastics


title: APOE4_DC_Cortex_DSP-1001660022855-A-B06

description:
Library name: DSP-1001660022855-A-B06
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: DU145_ONC206_N4

description: Library name: DU145_ONC206_replicate_3


title: DU145_CN_Ve_N4

description: Library name: DU145_control_replicate_3

value: Untreated


title: DU145_ONC206_N1

description: Library name: DU145_ONC206_replicate_1


title: APOE4_DC_Hippocampus_DSP-1001660022855-A-B12

description:
Library name: DSP-1001660022855-A-B12
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Hippocampus


title: APOE4_veh_Cortex_DSP-1001660022855-A-C02

description:
Library name: DSP-1001660022855-A-C02
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Rice whole roots 3 wpi, p35S, total mRNA, Mock(-Ri), repC

description:
Library name: TC101_CR_C
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Mock_C


title: DU145_CN_Ve_N3

description: Library name: DU145_control_replicate_2


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Mock(-Ri), repB

description:
Library name: TC106_TR_B
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Mock_B


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-B04

description:
Library name: DSP-1001660022855-A-B04
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DD


title: APOE4_DC_Cortex_DSP-1001660022855-A-B07

description:
Library name: DSP-1001660022855-A-B07
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: DC


title: Rice whole roots 3 wpi, p35S, total mRNA, Mock(-Ri), repB

description:
Library name: TC105_CR_B
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Mock_B


title: DU145_ONC206_N3

description: Library name: DU145_ONC206_replicate_2


title: Liver_CD_MP_4

description:
Library name: S51
column name in MP_raw_counts_gene_level.csv: CD_MP_4_S51


title: Liver_CD_MP_3

description:
Library name: S50
column name in MP_raw_counts_gene_level.csv: CD_MP_3_S50


title: PC3_ONC212_N4

description: Library name: PC3_ONC212_replicate_3


title: Liver_CD_MP_2

description:
Library name: S49
column name in MP_raw_counts_gene_level.csv: CD_MP_2_S49


title: Rice whole roots 3 wpi, p35S, TRAP mRNA, Mock(-Ri), repA

description:
Library name: TC104_TR_A
Column name in gene_counts_matrix.csv: p35S_TRAP_TR_Mock_A


title: Rice whole roots 3 wpi, p35S, total mRNA, Mock(-Ri), repA

description:
Library name: TC103_CR_A
Column name in gene_counts_matrix.csv: p35S_TRAP_CR_Mock_A


title: DU145_CN_Ve_N1

description: Library name: DU145_control_replicate_1


title: APOE4_DD_Hippocampus_DSP-1001660022855-A-B05

description:
Library name: DSP-1001660022855-A-B05
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)


title: Liver_MD_4

description:
Library name: S46
column name in MP_raw_counts_gene_level.csv: MD_4_S46

value: MASH Diet


title: APOE4_veh_Hippocampus_DSP-1001660022855-A-A09

description:
Library name: DSP-1001660022855-A-A09
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: veh


title: MDA-MB-231 cells, p-CTD-S5, rep2, batch2

city: Zhengzhou City

first: Leixi

last: Cao

address: Zhengzhou University People's Hospital, Fengchan Road Subdistrict, Jinshui District, Zhengzhou City, Henan Province

institute: Zhengzhou University People's Hospital, Translational Medicine Research Center

description: Library name: pCTD_S5_2

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

source_name: Breast; Mammary gland

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: Breast; Mammary gland

value: Breast cancer cell, epithelial cell


title: MDA-MB-231 cells, TRIM27-KO, siPARP1, CTD, rep1, batch3

description:
Library name: WRJ-H27_S28_L003
Normalized BigWig files for CUT&Tag (CTD) in MDA-MB-231 cells

data_processing:
Raw sequencing reads were generated by Frasergen on the MGISEQ-2000 platform. 1. Quality control: Raw reads were filtered to remove low-quality sequences, adapter sequences, and short reads using fastp. 2. Alignment: Clean reads were aligned to the human reference genome GRCh38/hg38 using Bowtie2 with default parameters. 3. Filtering: Mapped reads were filtered to remove duplicates, low-quality alignments (MAPQ < 30), and mitochondrial reads using SAMtools. 4. Signal track generation: Filtered bam files were used to generate normalized BigWig (.bw) signal tracks using bamCoverage (deepTools), with reads per kilobase per million mapped reads (RPKM) normalization for visualization. 5. IgG control tracks were generated using the same pipeline for all experimental groups. 6. Peak calling was performed using MACS2 with default parameters, and peak files are provided as supplementary processed data.
Assembly: GRCh38
Supplementary files format and content: Normalized BigWig (.bw) files for CUT&Tag signal visualization. Tracks show genome-wide read coverage for target proteins and IgG controls aligned to GRCh38.
Library strategy: CUT&Tag

growth_protocol: MDA-MB-231 wild-type and TRIM27 knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained in a humidified atmosphere of 5% CO2 at 37℃

extract_protocol:
Genomic chromatin was extracted from intact MDA-MB-231 human breast cancer cells using native nuclear isolation conditions suitable for CUT&Tag. No cross-linking (fixation) was performed. Crude nuclei were isolated gently and used directly for the CUT&Tag reaction without further fragmentation, in accordance with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) protocol.
Libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following the manufacturer’s instructions. Briefly, intact nuclei were isolated and incubated with primary antibodies targeting TRIM27, CTD, p-CTD-S2, or IgG control. Protein A/G-tn5 transposase was then added to bind the antibodies and fragment chromatin. Library fragments were enriched by PCR amplification and purified using magnetic beads. Final libraries were quantified and subjected to high-throughput sequencing on the MGISEQ-2000 platform.

treatment_protocol: For Olaparib treatment, cells were seeded at a density of 2×10⁵ cells per well in 6-well plates and allowed to adhere overnight. The next day, medium was replaced with fresh medium containing 2 μM Olaparib (or an equivalent volume of vehicle control, DMSO), and cells were incubated for 24 hours prior to RNA extraction. For PARP1 knockdown, cells were transfected with 100 pM PARP1-specific siRNA (or non-targeting control siRNA) using Lipofectamine RNAiMAX reagent, following the manufacturer's instructions. After 48 hours of incubation, cells were harvested for RNA isolation.

value: epithelial cell

value: TRIM27 Knockout (TRIM27-KO)

value: siPARP1, 48h

tag: cut&tag antibody

value: CTD (Cell Signaling Technology, 2629)


title: APOE4_DD_Cortex_DSP-1001660022855-A-A11

description:
Library name: DSP-1001660022855-A-A11
NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) sequencing of mouse brain regions of interest (ROIs)

value: Cortex