title: PETER001_HEPG2_24H_X1_B46:B10

value: Cobicistat|Emtricitabine 0.1|0.1 uM


title: Single-cell RNA-seq of E14.5 mouse ventricular tissue, ETS1 endothelial knockout replicate 1

status: Public on Feb 11 2026

type: SRA

city: San Diego

first: Zeyu

last: Chen

state: CA

address: 9500 Gilman Drive, BFRII 1217

department: School of Medicine

country: USA

institute: UCSD

description:
Library name: ETS1eKO_1
Ventricle from  E14.5 mouse ventricular tissue, ETS1 endothelial knockout replicate 1

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the mouse mm10 reference transcriptome and quantified using Cell Ranger (v7.1.0) (10X Genomics).
Cells with 200–7000 detected genes were retained. Cells were further filtered based on mitochondrial gene percentage (≤ 20%), ribosomal gene percentage (≤ 35%), and hemoglobin gene percentage (≤ 2%).
CellBender was applied to remove ambient RNA contamination.
DoubletFinder (v2.0.3) was used to identify and remove potential doublets with a score > 0.4.
Cells were filtered based on exon ratio (0.18 < exon ratio ≤ 0.5) and total read count thresholds to remove dead or damaged cells.
Data were normalized using SCTransform (Seurat v4.3.0), and batch effects were corrected using Harmony.
Principal component analysis (PCA) followed by UMAP was performed. Clusters were identified using graph-based clustering methods.
Clusters were annotated based on canonical markers and reference datasets of embryonic mouse heart cells.
Differential expression between control and knockout samples was conducted within each major cell type using Seurat’s FindMarkers function, with adjusted p-value < 0.001.
GO and KEGG pathway enrichment analyses were performed using clusterProfiler, with Benjamini-Hochberg correction (adjusted p-value < 0.05).
Assembly: mm10(Mus musculus)
Supplementary files format and content: Tab-separated values files and matrix files for each sample
Supplementary files format and content: An RDS file (Ets1.eKO.scRNA.All_CellType.2024_12.19.rds) containing a processed Seurat object(v4.3.0) with cell type annotations and quality-controlled single-cell RNA-seq data.

molecule: polyA RNA

organism: Mus musculus

source_name: heart (ventricle)

growth_protocol: Mice were maintained under specific pathogen-free (SPF) conditions with a 12-hour light/dark cycle and free access to food and water. ETS1 flox/flox, Tie2Cre mice were maintained on a C57BL/6 background. Embryonic mice of both sexes at E14.5 were used without prior genotyping for gender.

extract_protocol:
Ventricular tissues were enzymatically dissociated using 0.25% trypsin (Gibco) at 37 °C for 20–30 minutes with gentle pipetting to obtain a single-cell suspension. The digestion was stopped by adding DMEM supplemented with 10% fetal bovine serum (FBS). Cells were filtered through a 40-μm cell strainer, centrifuged at 400 g, and resuspended in DMEM with 2% FBS. Viability was assessed by Trypan Blue staining.
Single-cell suspensions were processed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer’s instructions. Single cells were partitioned into Gel Beads-in-Emulsion (GEMs), followed by reverse transcription, cDNA amplification, fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR. Final libraries included sample indices, UMIs, barcodes, and Illumina sequencing adapters, and were sequenced on the Illumina NextSeq S4 platform.

treatment_protocol: No treatment was applied prior to tissue collection. Embryonic day 14.5 ventricles were directly harvested for single-cell dissociation and RNA extraction.

tag: tissue

value: heart (ventricle)

tag: cell type

value: ventricular cells

tag: genotype

value: Tie2Cre; Ets1^fl/fl

tag: treatment

value: No

tag: batch


title: HOW_rep2_L

city: Leeds

first: Michaela

last: Agapiou

address: Woodhouse Lane

country: United Kingdom

institute: University of Leeds

library_source: transcriptomic

data_processing:
The adaptor sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) was trimmed from reads using Cutadapt (version 1.1) via Galaxy.
Reads were filtered out (using ‘Filter by quality’ tool in Galaxy (version 1.0.2)) if the quality score was below 20 for 10% or more of the read.
rRNA and tRNA reads were removed using Subread (version 2.0.0). The tRNA fasta file was from release 6.22 of the D. melanogaster genome. The rRNA fasta file was from RiboGalaxy’s Shared Data library (UUID: 0f0983aa-3afb-4b5f-a417-23593a3df1ef).
Transcriptome indexing was carried out using Salmon (version 0.14.2). A decoy-aware transcriptome was indexed with a pre-computed decoy sequence file provided by the Salmon developers. The k-mer size selected for indexing the transcriptome was 31.
Quasi-mapping was carried out using Salmon (version 0.14.2). The reads remaining after filtering were used, and the library parameter (-l) was set to SR, and the k-mer parameter (-k) was set to 31.
Assembly: dmel_r6.22
Supplementary files format and content: Quantification output file from Salmon with: transcript name, length, effective length, TPM, and estimated number of reads.

molecule: total RNA

organism: Drosophila melanogaster

source_name: testes

growth_protocol: Flies were kept in a 25°C humidified room with a 12:12 hour light:dark cycle and raised on 10 ml standard sugar-yeast-agar medium (Bass et al., 2007)

extract_protocol:
The RIP protocol was adapted from Keene, J.D. et al (2006) using anti-HA beads (Pierce, #88837). RNA was extracted from total lysate samples and from the elutions (i.e. the anti-HA magnetic beads at the end of the pull-down experiment). Both types of samples were treated with proteinase K prior to TRIzol extraction. This was then followed by isopropanol precipitation. RNA was stored at -80 ºC in nuclease free water.
RNA samples were prepared using Illumina’s Ribo-Zero rRNA Removal Kit followed by Illumina’s TruSeq Stranded Total RNA Library Prep. 100 ng from each sample was pooled and sequenced on the same lane on a NextSeq 500 Illumina sequencer using the High Output Kit v2.5 (75 Cycles), i.e. 75 bp single-end sequencing.

value: testes

tag: rip antibody beads

tag: molecule subtype

value: total RNA


title: Single-cell RNA-seq of E14.5 mouse ventricular tissue, control replicate 2

description:
Library name: Control_2
Ventricle from E14.5 mouse ventricular tissue, control replicate 2

value: Tie2Cre; Ets1^fl/+


title: Skin, iridophore-enriched, rerioXalbolineatus, rep3

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

description: Library name: Dal3I

data_processing:
We mapped each of the 48 libraries against combined references containing both parental genomes  (BBMap v38.57 with parameters: k=13, maxindel=100000, minid=0.76, ambiguous=best) to distinguish parental alleles in hybrid samples. Only a single best mapping location was retained for each read.
The 48 sequencing libraries  were split into two species-specific sublibraries. One sublibrary (denoted "Drerio") contained all reads that aligned best to the maternal D. rerio genome. The other sublibrary ("Dother" to denote the other Danio species) contained all reads that aligned best to the genome of the paternal species used to generate the hybrid.
We remapped each sublibrary to the D. rerio genome (BBMap v38.57 with parameters: k=13, maxindel=100000, minid=0.76, ambiguous=best) to utilize the available high quality GRCz11 gene annotations.
Gene expression was quantified using featureCounts (Rsubread v2.18). To mitigate the possibility of mapping bias toward the D. rerio reference in regions with poor sequence conservation, we excluded reads mapping to 3’ and 5’ untranslated regions. These feature counts are included in the processed data files DrerioAlleleCounts.csv and PaternalAllelelCounts.csv.
Statistical analysis was performed using DESeq2 (v1.44.0), filtering genes with less than 1 normalized count per sample (retaining 24,672 of 29,005 genes).
Assembly: GRCz11
Supplementary files format and content: DrerioAlleleCounts.csv quantifies the expression of the maternal D. rerio alleles for each gene.
Supplementary files format and content: PaternalAlleleCounts.csv quantifies the expression of the alleles from the paternal species used to generate each hybrid.

organism: Danio rerio x Danio albolineatus

source_name: Whole skin

extract_protocol:
Takara Bio SMART-seq2 RNA-seq kit
Nextera paired-end library preps

value: Whole skin

value: Iridophore-enriched


title: HOW_rep1_E

value: anti-HA beads (Pierce, #88837)

value: pull down elution RNA


title: PETER001_HEPG2_24H_X1_B46:A20

type: RNA

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: Ritonavir

scan_protocol: Following treatment and lysis, gene expression was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

label: biotin

organism: Homo sapiens

source_name: HEPG2 treated with Ritonavir 0.5 uM for 24.0 h

label_protocol: biotin labeling. Processing was done by th Broad Institute as previously described (10.1016/j.cell.2017.10.049)

growth_protocol:
HepG2 cells (5000 cells/well; ATCC, HB-8065) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC, cat. no.  30-2003), supplemented with 10% FBS and 1% P/S  at 37°C, 5% CO2.
HK-2 cells (5000 cells/well; ATCC, cat. no. CRL-2190) were cultured in Keratinocyte Serum Free Medium (K-SFM), Kit (Gibco, cat. no. 17005-042)  at 37°C, 5% CO2.
THP-1 cells (10,000 cells/well; ATCC, cat. no. TIB-202) were cultured in RPMI-40 medium (Gibco, cat. no. 11875-093) supplemented with 10% fetal bovine serum (FBS, Gibco, cat. no. 10438026) and 1% penicillin/streptomycin (P/S, Corning, cat. no. 30-002) at 37°C, 5% CO2. Macrophage differentiation was induced in vitro with phorbol-12-myristate-13-acetate (PMA, 50 ng/mL; Sigma) for 72 hours at 37°C in 5% CO2

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

treatment_protocol: After 24 hours of culture for HepG2 and HK-2 cells, and 72 hours for THP-1 macrophages, the cells were placed in their respected culture media supplemented with 2% FBS for 16 hours. Subsequently, they were treated for 6 or 24 hours with either vehicle (DMSO) or with ART medications at a concentration of 0.1, or 0.5 µM.

tag: cell line

value: Ritonavir 0.5 uM

tag: duration

tag: plate

tag: well


title: PETER001_HEPG2_24H_X1_B46:A19


title: PETER001_HEPG2_24H_X1_B46:A18

description: L1000 inferred profile; pert_id: Abacavir

source_name: HEPG2 treated with Abacavir 0.5 uM for 24.0 h

value: Abacavir 0.5 uM


title: Single-cell RNA-seq of E14.5 mouse ventricular tissue, control replicate 1

description:
Library name: Control_1
Ventricle from E14.5 mouse ventricular tissue, control replicate 1


title: mouse embryonic stem cell, Ino80 iKO, replicate2

city: Seoul

first: Kwonho

last: Hong

address: 120 Neungdong

country: South Korea

institute: Konkuk university

description: Library name: KO rep2

library_source: other

data_processing:
Reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.5.4)
Raw BAM files were processed using SAMtools
Reads mapping to ENCODE mm10 blacklist regions were removed using bedtools intersect (v2.31.1)
Coverage tracks were generated using deepTools (v3.5.5) bamCoverage
Peak calling was performed using MACS3 (v3.0.2) callpeak
Assembly: mm10
Supplementary files format and content: bigwig. Normalized read count per genomic coverage
Library strategy: CUT&Tag

molecule: other

source_name: embryonic stem cell

growth_protocol: ESCs were maintained under serum-free 2i/LIF culture conditions.

extract_protocol:
cells were harvested according to the manufacturer’s instructions provided with the CUT&Tag-IT R-loop Assay Kit (Active motif).
libraries were prepared using the CUT&Tag-IT R-loop Assay Kit (Active motif).

treatment_protocol: 4-hydroxytamoxifen (4-OHT) was administrated for three days.

value: embryonic stem cell

value: Ino80 knockout


title: PETER001_HEPG2_24H_X1_B46:A21


title: HOW_rep1_L


title: Human_vpMN_rep2

first: Sumin

last: Jang

institute: Columbia University

description: Library name: vpMN_rep2

data_processing:
Aligned to reference genome via STAR
Assembly: mm10, hg38
Supplementary files format and content: read count (tab-delimited text)

source_name: spinal motor neuron organoid

extract_protocol:
Qiagen FFPE Rneasy for human, Qiagen Rneasy for mouse
Illumina Truseq PolyA library prep

value: spinal motor neuron organoid

value: vpMN


title: MMTV-PyMT Prrx1 f/f Tumors Homo Rep4

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

description: Library name: T10

data_processing:
Reads were processed with CellRanger v6.1.0 pipeline (10x Genomics) to generate gene expression matrices using CRGm38 (mm10) mouse reference genome. Downstream analysis, including QC, normalization, and clustering, was performed using Seurat v.5.1.0.
Assembly: GRCm38
Supplementary files format and content: Tab seperated values file and matrix files

source_name: Breast tumor

extract_protocol:
Mammary gland carcinomas were collected from 14- to 15-week-old female PyMT mice. Tissues were minced and dissociated in digestion buffer (PBS, TH Liberase, DNase I) at 37°C for 45 minutes. Cell suspensions were filtered (70 µm, 40 µm), centrifuged, treated with ACK buffer, and resuspended in FACS buffer with EDTA. Viability was assessed using Trypan Blue, and cells were adjusted to 1,000 cells/µL for GEM preparation.
Single-cell suspensions from ten mice (3 Prrx1 +/+, 3 Prrx1 +/f, 4 Prrx1 f/f) were processed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (10x Genomics) and sequenced on an Illumina NextSeq 2000 (100 bp read length).

value: Breast tumor

value: homozygous


title: Human_vpMN_rep1

description: Library name: vpMN_rep1


title: PETER001_HEPG2_24H_X1_B46:A17


title: MMTV-PyMT Prrx1 f/f Tumors Homo Rep3

description: Library name: T9


title: Human_pMN_rep1

description: Library name: pMN_rep1

value: pMN


title: MMTV-PyMT Prrx1 f/f Tumors Homo Rep1

description: Library name: T7

value: heterozygous


title: mouse embryonic stem cell, Ino80 iKO, replicate1

description: Library name: KO rep1


title: PETER001_HEPG2_24H_X1_B46:A14

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: mouse embryonic stem cell, control, replicate1

description: Library name: CON rep1

value: control


title: mouse embryonic stem cell, control, replicate2

description: Library name: CON rep2


title: PETER001_HEPG2_24H_X1_B46:A12

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HEPG2 treated with Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM for 24.0 h


title: PETER001_HEPG2_24H_X1_B46:A16


title: Human_pMN_rep2

description: Library name: pMN_rep2


title: BT_Mouse4

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

description: Library name: Sample4

data_processing:
The resulting FASTQ files were preprocessed with Trimmomatic (v0.39) for adapter trimming and low-quality filtering of the reads. Filtered sequence reads were aligned to reference GRCm38 mouse transcriptome with HISAT2 aligner (v2.2.1) and raw counts were obtained with FeatureCounts (subread v2.0.1).
Assembly: GRCm38
Supplementary files format and content: Tab-limited .csv files containing raw counts per sample

source_name: Distal Colon

extract_protocol:
Mice were sacrificed and transcardially perfused with PBS. The spleen and the distal colon were collected to perform the total RNA extraction. Cells from the spleen were obtained by smashing on a 70 μm cell (Corning) as long as the sample was completely dissected. The suspension was centrifuged (1000g, 10min, RT) and the pellet lysed in Trizol reagent (Sigma-Aldrich). The distal colon samples (1 cm) were dissected mechanically in Trizol reagent (Sigma-Aldrich) by a cell homogenizer. Isolated total RNA from colon tissue was processed with RNAse-free DNaseI (Invitrogen). Next, total RNA was processed to Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Nextflex Ribonaut rRNA depletion kit and UDIs (PerkinElmer) .
Libraries were prepared with the kit Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Nextflex Ribonaut rRNA depletion kit and UDIs (PerkinElmer). The libraries were sequenced on Illumina NovaSeq X with 2x150 bp paired-end run; Seq throughput: 50 M PE read per sample; Q30 ≥ 85% .

treatment_protocol: A total cell suspension of 5x10 4 GL261 into 4 ml of sterile PBS was injected with a Hamilton syringe at a rate of 1 μl/min at 3 mm depth. After three days, mice were treated by oral gavage with 2x10 9 bacteria in 0.2 ml of anaerobic broth  once a week for three weeks.

value: Distal Colon

tag: strain

value: C57BL6/N mice

value: Murine GL261 cell line

value: wt

value: BT


title: CTR_Mouse1

description: Library name: Sample5

treatment_protocol: A total cell suspension of 5x10 4 GL261 into 4 ml of sterile PBS was injected with a Hamilton syringe at a rate of 1 μl/min at 3 mm depth. After three days, mice were treated by oral gavage with  0.2 ml of anaerobic broth  once a week for three weeks.

value: CTR


title: MMTV-PyMT Prrx1 +/+ Tumors WT Rep2

description: Library name: T2

value: Wildtype


title: CTR_Mouse4

description: Library name: Sample8


title: MMTV-PyMT Prrx1 +/f Tumors Het  Rep2

description: Library name: T5


title: MMTV-PyMT Prrx1 f/f Tumors Homo Rep2

description: Library name: T8


title: MMTV-PyMT Prrx1 +/f Tumors Het Rep3

description: Library name: T6


title: Treated 4hr HCT116 Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Treated 4hr HCT116

hyb_protocol: Five and one-half micrograms (5.5 ìg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software

source_name: Treated 4hr HCT116

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

extract_protocol: RNA was extracted after 4h or 24h treatment and RNA was purified


title: CTR_Mouse3

description: Library name: Sample7


title: MMTV-PyMT Prrx1 +/+ Tumors WT Rep1

description: Library name: T1


title: BT_Mouse3

description: Library name: Sample3


title: Treated 24hr HCT116 Replicate 3

description: Gene expression from Treated 24hr HCT116

source_name: Treated 24hr HCT116


title: PETER001_HEPG2_24H_X1_B46:A09

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HEPG2 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 24.0 h


title: PETER001_HEPG2_24H_X1_B46:A15

value: Dolutegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: MMTV-PyMT Prrx1 +/+ Tumors WT Rep3

description: Library name: T3


title: MMTV-PyMT Prrx1 +/f Tumors Het  Rep1

description: Library name: T4


title: PETER001_HEPG2_24H_X1_B46:A10

value: Bictegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.5|0.1|0.5 uM


title: wounded_cortical_biol_rep_2

city: Durham

first: Terry

last: Lechler

address: 307 Research Dr

institute: Duke University

data_processing:
Base calling with CASAVA performed by Novogene
Alignment  with HISAT2 performed by Novogene
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: translating fraction fromcortex of wounded cells

growth_protocol: Cells were grown in E no Ca2+ media until confluent. At that point, 1.2 micromolar calcium and 2 microgram/mL doxycycline were added to induce differentiation and expression of the DP(1-584)-BirA protein. Cells were then wounded or left unwounded, then pulsed with biotin for 16 hrs to label the cortical translatome.

extract_protocol:
Lysate from the cells was centrifuged over sucrose gradients, then the translating fraction was incubated with neutravidin resin to isolate the cortical translatome. RNA from the depleted (referred to as total translatome) fraction and the cortical fraction was then isolated using the Qiagen RNeasy MinElute kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. Performed by Novogene.

value: keratinocyte

value: WT DP-BirA(1-584)

value: scratch wounded


title: PETER001_HEPG2_24H_X1_B46:A11


title: Treated 24hr HCT116 Replicate 2


title: MMTV-PyMT Prrx1 +/+ Tumors Rep3

description: Library name: T3

library_source: genomic single cell

data_processing:
Sequenced samples were processed using the CellRanger-atac v2.1.0 pipeline (10x Genomics) and aligned to the GRCm38 (mm10) mouse reference genome (Ensembl annotation v99). MACS2 v2.2.9 was used for peak calling with default parameters. Downstream analysis, including QC, normalization, and clustering, was performed using Seurat v5.0.1 and Signac v1.12.0.
Assembly: GRCm38
Supplementary files format and content: Tab seperated values file and matrix files

molecule: genomic DNA

extract_protocol:
Mammary gland carcinomas from 14- to 15-week-old MMTV-PyMT mice were manually minced and homogenized in Solution D (20 mM Tris-HCl pH 7.5, 0.1% Tween 20, 0.25 M Sucrose, 25 mM KCl, 5 mM MgCl2). The lysate was filtered (70 μm, 40 μm), centrifuged, and resuspended in Wash Buffer. Nuclei were isolated using Optiprep gradient centrifugation and lysed in 0.1X lysis buffer. After filtration (20 μm) and final centrifugation, nuclei were resuspended in Nuclei Dilution Buffer for downstream processing. Viability and count were assessed using Trypan Blue and an automated cell counter.
Single-nuclei suspensions from four mice were processed using the Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics). Nuclei were transposed, encapsulated with the 10x Chromium Controller, and multiplexed using the Chromium Single Index Kit N. Libraries were sequenced on an Illumina NextSeq 2000 (50 bp read length).

value: Breast tumor


title: PETER001_HEPG2_24H_X1_B46:A13


title: Treated 24hr HCT116 Replicate 1


title: BT_Mouse2

description: Library name: Sample2


title: wounded_cortical_biol_rep_3


title: PETER001_HEPG2_24H_X1_B46:A08

value: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM


title: Treated 4hr HCT116 Replicate 1

description: Gene expression from Treated 4hr HCT116


title: PETER001_HEPG2_24H_X1_B46:A07


title: wounded_cortical_biol_rep_1


title: MMTV-PyMT Prrx1 +/+ Tumors Rep4

description: Library name: T4


title: Treated 4hr HCT116 Replicate 2

description: Gene expression from Treated 4hr HCT116


title: wounded_total_biol_rep_1

source_name: translating fraction from wounded cells


title: PETER001_HEPG2_24H_X1_B46:A06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir|Emtricitabine

source_name: HEPG2 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 24.0 h


title: MMTV-PyMT Prrx1 +/+ Tumors Rep2

description: Library name: T2


title: wounded_total_biol_rep_2


title: Untreated HCT116 Controls Replicate 2

description: Gene expression from Untreated HCT116 Controls

source_name: Untreated HCT116 Controls


title: PETER001_HEPG2_24H_X1_B46:A05


title: MMTV-PyMT Prrx1 +/+ Tumors Rep1

description: Library name: T1


title: P6364_FLKO_Rep4

city: Chicago

first: Ellen

last: Fruzyna

address: 1349 E Washington St

institute: Northwestern University

description: Library name: sample16

data_processing:
Sequences were aligned to mm10 using STAR version 2.5.2 with ‘--outFilterMultimapNmax 1’ and  ‘--outFilterMismatchNmax 4’.
Tag directories were generated in HOMER v4.10 using 'makeTagDirectory' with '-flip' and 'format sam' parameters. Bedgraphs were generated using 'makeUCSCfile'
Raw counts were generated using Homer's 'analyzeRepeats.pl' with '-noadj' parameter.
Assembly: mm10
Supplementary files format and content: Ileum_RNA_RawCounts.txt' contains raw counts for each sample
Supplementary files format and content: UCSC_*.gz ' files contain Bedgraph files for visualization on the UCSC Genome Browser for each sample

source_name: Ileum

extract_protocol:
1cm of ileum just proximal to the cecum was excised, rinsed, and stored in RNA-later (Ambion). Samples were bead-homogenized in Trizol (Ambion). 20% chloroform by volume was added, and the aqueous phase was isolated following centrifugation. RNA was further purified using the RNAeasy kit (Qiagen).
Sequencing libraries were made using the Truseq Stranded mRNA Kit (Illumina) and sequencing was performed on the Illumina NextSeq 2000 using 100 bp single-end reads.

value: Ileum

value: Alb-cre,  Bcl6 fl/fl


title: P6361_FLKO_Rep2

description: Library name: sample14


title: Treated 24hr HT29 Replicate 3

description: Gene expression from Treated 24hr HT29

source_name: Treated 24hr HT29


title: wounded_total_biol_rep_3


title: Skin, unenriched, rerioXaesculapii, rep5

description: Library name: Dae5S

organism: Danio rerio x Danio aesculapii

source_name: Whole skin

value: Whole skin

value: Unenriched


title: control_cortical_biol_rep_3

source_name: translating fraction from cortex of unwoudned cells

value: unwoudned


title: Skin, unenriched, rerioXaesculapii, rep4

description: Library name: Dae4S


title: control_cortical_biol_rep_1


title: P6310_FLKO_Rep1

description: Library name: sample13


title: Untreated HCT116 Controls Replicate 3


title: Treated 24hr HT29 Replicate 1

description: Gene expression from Treated 24hr HT29


title: Treated 4hr HT29 Replicate 3

description: Gene expression from Treated 4hr HT29

source_name: Treated 4hr HT29


title: PETER001_HEPG2_24H_X1_B46:A04


title: P6363_FLKO_Rep3

description: Library name: sample15


title: control_cortical_biol_rep_2


title: control_total_biol_rep_3

source_name: translating fraction from unwounded cells


title: Skin, unenriched, rerioXaesculapii, rep3

description: Library name: Dae3S


title: P6362_FWT_Rep4

description: Library name: sample12

value: Bcl6 fl/fl


title: Treated 4hr HT29 Replicate 2

description: Gene expression from Treated 4hr HT29


title: Untreated HCT116 Controls Replicate 1


title: Skin, xanthophore-enriched, rerioXaesculapii, rep5

description: Library name: Dae5X

value: Xanthophore-enriched


title: P6342_FWT_Rep3

description: Library name: sample11


title: Skin, xanthophore-enriched, rerioXaesculapii, rep4

description: Library name: Dae4X


title: P6309_FWT_Rep2

description: Library name: sample10


title: Treated 4hr HT29 Replicate 1

description: Gene expression from Treated 4hr HT29


title: Skin, xanthophore-enriched, rerioXaesculapii, rep3

description: Library name: Dae3X


title: Treated 24hr HT29 Replicate 2

description: Gene expression from Treated 24hr HT29


title: P6308_FWT_Rep1

description: Library name: sample9


title: P6444_MLKO_Rep4

description: Library name: sample8


title: Skin, melanophore-enriched, rerioXaesculapii, rep4

description: Library name: Dae4M

value: Melanophore-enriched


title: control_total_biol_rep_1


title: control_total_biol_rep_2


title: Skin, melanophore-enriched, rerioXaesculapii, rep5

description: Library name: Dae5M


title: 15_WT_fin_amputation_plane_21_dpa

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

description: Library name: dpa21_REP3

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7, with cutadapt v 3.5) and counted by salmon (v 1.4.0) by supplying the UCSC danRer11 annotation
The counts were normalized to transcripts per million (TPM)
Assembly: danRer11
Supplementary files format and content: csv file with TPM counts

organism: Danio rerio

source_name: Fin

extract_protocol:
Tissue was homogenized with a stainless-steel bead (5mm, Cat. No. 69989) in Tri-Reagent. RNA was extracted by cholorform followed by an isopropanol precipitation. Remaining DNA was digested by DNase. RNA was purified with a Zymo RNA Clean & Concentrator Kit.
For amputation plane tissue samples, cDNA was prepared by Maxima H-minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adapter primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel-cutting and extraction, and 300 - 800 bp DNA fragments were collected for sequencing.

value: Fin

value: WT

tag: time point


title: Untreated HT29 Controls Replicate 2

description: Gene expression from Untreated HT29 Controls

source_name: Untreated HT29 Controls


title: Untreated HT29 Controls Replicate 3


title: P6392_MLKO_Rep2

description: Library name: sample6


title: Untreated HT29 Controls Replicate 1


title: SNU638 sh-SKA2-3 rep2

city: Shenzhen

first: Hong

middle: Lei

state: Guangdong

address: Room 3025, Shen Nan Middle Road, Futian District

department: Gastrointestinal Endoscopy Center

country: China

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

description: Library name: SKAsh32

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke, a BGI developed filtering software.  reads containing >5 % ambiguous bases (N), and low-quality reads (>20 % of bases with Q ≤15), yielding “clean” reads.
Clean reads are aligned to the reference genome with HISAT and Bowtie2. Mapping rate and read distribution across genes are examined to confirm data quality.
Gene expression levels (FPKM/TPM) are calculated with RSEM.
Differential expression analysis is carried out using DESeq2 (|log2FC| ≥ 1 and FDR < 0.05).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: PROCESSED DATA.txt

extract_protocol:
Total RNA was extracted using the Trizol® reagent kit (Invitrogen, CA, USA), and the integrity (quantity and quality) and concentration were measured using NanoDropTM OneC spectrophotometer (ThermoScientific, MA, USA).
Total RNA was harvested from SNU638 shCTRL and SNU638 shSKA2 stable cells. The mRNA with polyA tail was enriched by magnetic beads with OligodT. The RNA obtained was segmented by interrupting buffer, the random N6 primers were used for reverse transcription, and then the cDNA two-strand was synthesized to form double-stranded DNA. The end of the synthesized double-stranded DNA is blunted, and the 5’ end is phosphorylated, while the 3’ end forms a sticky end with an “A” protruding, and then a bubbling linker with a protruding “T” at the 3’ end is connected. The constructed cDNA library was inspected and sequenced after being qualified. The ligated products are amplified by PCR with specific primers. The PCR product was heat-denatured into single-stranded DNA, and then a single-stranded circular DNA library was obtained by circularizing the single-stranded DNA with a bridge primer. The constructed library is qualified by a standard cDNA library and sequenced after it is qualified.

value: gastric cancer cell

value: SKA2 knockdown


title: RNA_JMURTK2_Mock_NT

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

country: Japan

institute: National Cancer Center Research Institute

description: Library name: RNA_JMURTK2_Mock_NT

data_processing:
Raw sequencing reads were first trimmed using fastp (version 0.12.4) (RRID: SCR_016962).
Trimmed reads were then mapped to the human reference genome (hg38) using HISAT2 (version 2.2.1) (RRID: SCR_015530) .
The bamCoverage command was used (parameters: --normalizeUsing CPM --binSize 10 --smoothLength 30).
BigWig files were visualized using the Integrative Genomics Viewer (IGV) (version 2.13.2) (RRID: SCR_011793)
Assembly: hg38
Supplementary files format and content: fq (Raw sequencing reads)
Supplementary files format and content: bw (Mapping data for visualizeation by IGV)

source_name: Rabdoid Sarcoma

extract_protocol:
After washing with PBS, total RNA was isolated using the RNeasy Mini Kit (Qiagen).
Library preparation was performed by BGI using the Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: JMU-RTK-2 -SMARCB1 and +SMARCB1 cells (n=1 sample per condition) were seeded in 6-well plates at 5 × 10⁵ cells per well and cultured for 24 h.

value: Rabdoid Sarcoma

value: Non-Treatment

value: single


title: RNA_JMURTK2_SMARCB1_NT

description: Library name: RNA_JMURTK2_SMARCB1_NT


title: P6360_MLKO_Rep1

description: Library name: sample5


title: P6395_MLKO_Rep3

description: Library name: sample7


title: P6359_MWT_Rep4

description: Library name: sample4


title: Skin, iridophore-enriched, rerioXaesculapii, rep4

description: Library name: Dae4I

value: Iridophore-enriched


title: SNU638 sh-SKA2-3 rep1

description: Library name: SKAsh31


title: 10_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP1


title: SNU638 sh-SKA2-3 rep3

description: Library name: SKAsh33


title: 12_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP3


title: P6340_MWT_Rep2

description: Library name: sample2


title: Skin, melanophore-enriched, rerioXaesculapii, rep3

description: Library name: Dae3M


title: SNU638 sh-SKA2-2 rep3

description: Library name: SKAsh23


title: Skin, iridophore-enriched, rerioXaesculapii, rep5

description: Library name: Dae5I


title: Skin, iridophore-enriched, rerioXaesculapii, rep3

description: Library name: Dae3I


title: P6341_MWT_Rep3

description: Library name: sample3


title: 9_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP3


title: Brain_APP_NLGF_IDs_22_and_23

city: London

first: Samuel

middle: J

last: Barnes

address: Hammersmith Hospital Campus, Du Cane Road

institute: Imperial College London

description:
Coronal sections (visual, retroslplenial and adjacent regions) of two individual mice
seurat object data includes: @assays[["Nanostring"]] with counts per cell; @assays[["SCT"]] with SCTransform-normalised data; @images contains cells and molecules spatial information; @reductions contains pca and umap cell embeddings; @meta.data contains per cell full metada annotation

hyb_protocol: The sample processing, staining, and imaging, were performed as previously described   [Platform: GPL36279 NanoString CosMx SMI (Mus musculus)]. Published protocols were followed for tissue staining   and probe acquisition (https://university.nanostring.com/page/document-library).

scan_protocol: RNA target readout on the CosMx SMI instrument was performed [Platform: GPL36279 NanoString CosMx SMI (Mus musculus)].   Previously published protocols were followed for tissue staining and probe acquisition (https://university.nanostring.com/page/document-library).   Briefly, the assembled flow cell was loaded onto the instrument and flushed with Reporter Wash Buffer to remove air bubbles.   A preview scan was performed, and 6–10 fields of view were selected per section to capture regions of interest, including visual and retrosplenial cortex,   and some adjacent regions. RNA detection was initiated by introducing Reporter Pool 1 followed by incubation, washing, and imaging buffer addition.   For each FoV, nine Z-stack images (0.8 μm steps) were acquired, after which fluorophores were cleaved by UV illumination and removed with   Strip Wash buffer. This hybridization and imaging workflow was repeated across 16 reporter pools and multiple cycles to increase RNA detection sensitivity.  Morphology and segmentation markers included Histone H3 and DAPI for nuclei, 18S rRNA for cytoplasm, and GFAP for astrocytes. After washing,  imaging buffer was reintroduced and Z-stack images were acquired for all channels.

data_processing: Image processing, including cell segmentation and read counting, were performed with AtoMx (Nanostring (Bruker).   Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806.   The cell quality check parameters involved filtering out any cells that contained fewer than 20 transcripts and any cells that had an area greater   than 5*geometric mean of all cells in the dataset. The transcript matrices, cell expression matrices, cell metadata, FOV position, and cell polygon files were read   into a Seurat object, where data were integrated and normalised (Seurat v5, SCTransform v2). Transcripts from negative probes were excluded from   the count matrices. To identify main cell types, clustering analysis was performed following integration, using the Seurat pipeline. Main cell types were   identified using automated cell-typing with the Expression Weighted Celltype Enrichment (EWCE) algorithm against a cell-type generated dataset reference   (visual and retrosplenial cortex) from the Allen Mouse Whole Brain Atlas. Detailed description in manuscript [link TBC when published];   the Seurat processed object is included with this dataset;  code used is shared on Zenodo [link TBC when published].

source_name: brain

treatment_protocol: Following perfusion of App NL-G-F and wild-type mice,brains were collected, snap-frozen, and stored at -80°C.   Fresh frozen 10 μm-thick coronal sections were collected using a cryostat and four sections were mounted per slide.

value: App NL-G-F

tag: age

value: 6-8 months


title: 13_WT_fin_amputation_plane_21_dpa

description: Library name: dpa21_REP1


title: Brain_APP_NLGF_IDs_21_and_24

label_protocol: The sample processing, staining, and imaging, were performed as previously described   [Platform: GPL36279 NanoString CosMx SMI (Mus musculus)]. Published protocols were followed for tissue staining   and probe acquisition (https://university.nanostring.com/page/document-library).


title: SNU638 sh-SKA2-2 rep2

description: Library name: SKAsh22


title: 14_WT_fin_amputation_plane_21_dpa

description: Library name: dpa21_REP2


title: 8_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP2


title: 11_WT_fin_amputation_plane_14_dpa

description: Library name: dpa14_REP2


title: 7_WT_fin_amputation_plane_7_dpa

description: Library name: dpa7_REP1


title: SNU638 sh-SKA2-2 rep1

description: Library name: SKAsh21


title: SNU638 sh-SKA2-1 rep3

description: Library name: SKAsh13


title: 5_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP2


title: Input_WT_FXRChIP

description: Library name: sample5

library_source: genomic

data_processing:
FASTQ files were aligned to the mm10 genome using Bowtie 1.2 with '--best' and '-m 1'  parameters.
Tag directories were generated in HOMER v4.10 using 'makeTagDirectory' with '-tbp1' to remove clonal reads.
Homer's 'getDifferentialPeaksReplicates.pl' command was used with '-style factor' and default parameters to call peaks in comparison to input controls for each condition.
Assembly: mm10
Supplementary files format and content: WT_FXRChIP_peaks.txt' and 'LKO_FXRChIP_peaks.txt' contain annotated lists of peaks for each condition
Supplementary files format and content: UCSC_*.gz ' files contain Bedgraph files for visualization on the UCSC Genome Browser for each sample

source_name: Liver

extract_protocol:
Liver was dounce homogenized and dual-crosslinked in 2mM DSG for 30 minutes and 1% formaldehyde for 10 minutes and subsequently quenched with glycine. Nuclei were sonicated/lysed in 1% SDS buffer and then subjected to immunoprecipitation with 5ug of FXR (E4B8P, Cell Signaling) overnight. Complexes were isolated with anti-rabbit IgG paramagnetic beads, followed by washing and DNA purification by column (Qiagen Min-Elute).
Samples were made into libraries using the KAPA Hyperprep Kit (Kapa Biosystems) and sequenced using the Illumina NextSeq 2000 with 100 bp single-end reads.

value: Liver


title: SNU638 sh-SKA2-1 rep2

description: Library name: SKAsh12


title: 6_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP3


title: P6339_MWT_Rep1

description: Library name: sample1

value: Ileum


title: Input_LKO_FXRChIP

description: Library name: sample6

value: Alb-cre,  Bcl6 fl/fl


title: Brain_APP_NLGF_IDs_13_and_16

extract_protocol: The sample processing, staining, and imaging, were performed as previously described   [Platform: GPL36279 NanoString CosMx SMI (Mus musculus)]. Published protocols were followed for tissue staining   and probe acquisition (https://university.nanostring.com/page/document-library).

value: 3-4 months


title: SNU638 sh-SKA2-1 rep1

description: Library name: SKAsh11


title: Brain_WT_IDs_10_and_11


title: P5599_LKO_Rep2_FXRChIP

description:
Library name: sample4
column name in LKO_FXRChIP_peaks.txt:LKO_Rep2.tag


title: 4_WT_fin_amputation_plane_4_dpa

description: Library name: dpa4_REP1


title: P5601_WT_Rep2_FXRChIP

description:
Library name: sample2
column name in WT_FXRChIP_peaks.txt:WT_Rep2.tag

value: Bcl6 fl/fl


title: 3_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP3


title: Brain_WT_IDs_18_and_19


title: P5597 _LKO_Rep1_FXRChIP

description:
Library name: sample3
column name in LKO_FXRChIP_peaks.txt:LKO_Rep1.tag


title: SNU638 sh-control rep2

description: Library name: SKACON2

value: wt


title: Brain_WT_IDs_9_and_12


title: 1_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP1


title: Brain_APP_NLGF_IDs_14_and_15


title: SNU638 sh-control rep3

description: Library name: SKACON3


title: Brain_WT_IDs_17_and_20


title: SNU638 sh-control rep1

description: Library name: SKACON1


title: X28dpl.rep2

status: Public on Feb 10 2026

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were pre-processed and quality-trimmed usingTrim Galore!https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Reads were aligned to the rat reference genome rn7 usingTophat(version 2.1.1,https://ccb.jhu.edu/software/tophat/index.shtml) allowing for one mismatch and selecting uniquely mapping reads only. Normalization was performed and differential expression of genes was statistically evaluated by using the R Bioconductor DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: mRatBN7.2/rn7
Supplementary files format and content: Raw counts extracted by 'featureCounts' from the python/bioconda subread package on ENSEMBL (101) transcripts.

organism: Rattus norvegicus

source_name: demyelinated neurons

growth_protocol: The caudal cerebellar peduncle (CCP) of 9-12-week-old Sprague Dawley rats was bilaterally injected with 4 μl of ethidium bromide to induce focal white matter demyelination. Briefly, isoflurane anaesthesia was induced (4%) and rats administered with 1.5ml of saline (i.p.) and 0.05 mg/Kg buprenorphine (i.p.) (Buprecare, Animalcare Ltda). Isoflurane was maintained at 1.5-2% and the animal placed in a stereotaxic frame. After incision of the skin and levelling of the head, a craniotomy was performed and a 10 μ Hamilton syringe lowered in place for injection at 1 μl min-1. The skin was sutured and post-op analgesia provided (0.5 mg/Kg buprenorphine in chocolate spread). Rats were monitored twice a day, for a minimum of five days for potential side effects. In ageing experiments, CCP demyelinating lesions were induced in 18 month-old rats

extract_protocol:
RNA was extracted using RNeasy Micro Kit (QIAGEN) according to manufacturer’s instructions.
The library was prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Clontech) according to manufacturer’s instructions.

value: demyelinated neurons

value: Sprague Dawley

tag: time

value: Day 28


title: P5598_WT_Rep1_FXRChIP

description:
Library name: sample1
column name in WT_FXRChIP_peaks.txt:WT_Rep1.tag


title: X28dpl.rep1


title: X28dpl.rep3


title: 2_WT_fin_amputation_plane_0_dpa

description: Library name: dpa0_REP2

value: Fin

value: WT


title: X14dpl.rep1

value: Day 14


title: X14dpl.rep3


title: X3dpl.rep3

value: Day 3


title: X7dpl.rep3

value: Day 7


title: X7dpl.rep2


title: X14dpl.rep2


title: X3dpl.rep2


title: X3dpl.rep1


title: X7dpl.rep1


title: Saline.rep3

value: Day 0


title: genomic_DNAmethylation_207183170164_R02C01

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to beadchips (Infinium MethylationEPIC v1.0) using standard Illumina protocol.

scan_protocol: Arrays were imaged using a iSCAN using standard Illumina settings.

data_processing: Raw .idat files were read into R (v4.3.1). minfi preprocessNoob() and wateRmelon dasen() normalization.

label: Cy3 and Cy5

source_name: placental chorionic villi

label_protocol: Standard Illumina protocol.

extract_protocol: Three ~0.4 cm3 samples of chorionic villi were taken from three distinct cotyledons (sites) from below the surface of the fetal-facing side of the placenta. Genomic DNA was extracted with the PerkinElmer Chemagic 360 System (PerkinElmer, USA) using a process based on the PerkinElmer chemagen M-PVA Magnetic Bead technology. Purified DNA from the three cotyledons was pooled in equal amounts then 500ng was bisulfite converted using the standard Illumina Protocol.

value: placental chorionic villi

tag: resourcescomposite

tag: socialpositioncomposite

tag: disadvantagecomposite

tag: Sex

value: XY

tag: ga

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc

value: Plate 2


title: genomic_DNAmethylation_207183170164_R04C01

tag: tissue


title: Saline.rep1


title: Ies6, clone 2

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

country: France

institute: Institute Pasteur

description: Library name: S2_Ies6_C2

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016). Paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options. Bam files were generated using samtools (Li et al., 2009). Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Assembly: Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: Signal intensity in bigWig file format

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were grown to OD600 0.8 in 500 ml YPAD media. Spheroplasts were prepared by treating cells with 2 mg zymolyase at 30 °C for 20 min, followed by washing with ice-cold 1 M sorbitol. Nuclei were resuspended in MNase digestion buffer (15 mM Tris–Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA pH 8.0, 0.2 mM EDTA pH 8.0, 5 mM β-mercaptoethanol) and digested with increasing amounts of MNase for 20 min at 37 °C. DNA was purified via Proteinase K treatment, followed by Phenol: Chloroform: Isoamyl alcohol extraction and RNase digestion.
Samples with ~70% mononucleosome content were selected for library preparation. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina and sequenced in 50 bp paired-end mode, yielding five to ten million reads per sample.

tag: genotype


title: Ies6, clone 1

description: Library name: S1_Ies6_C1

tag: strain


title: genomic_DNAmethylation_207183170164_R08C01


title: genomic_DNAmethylation_207183170164_R03C01


title: genomic_DNAmethylation_207183170164_R06C01


title: genomic_DNAmethylation_207179240186_R04C01

value: XX

value: Plate 6


title: genomic_DNAmethylation_207179240186_R03C01


title: genomic_DNAmethylation_207179240186_R05C01


title: genomic_DNAmethylation_207183170164_R05C01


title: genomic_DNAmethylation_207179240186_R02C01


title: genomic_DNAmethylation_207183170164_R01C01


title: Saline.rep2


title: genomic_DNAmethylation_207183170164_R07C01


title: genomic_DNAmethylation_207179240186_R01C01


title: genomic_DNAmethylation_207179240185_R08C01


title: genomic_DNAmethylation_207179240185_R07C01


title: genomic_DNAmethylation_207179240185_R06C01


title: genomic_DNAmethylation_207179240185_R04C01


title: genomic_DNAmethylation_207179240185_R05C01


title: genomic_DNAmethylation_207179240185_R02C01


title: genomic_DNAmethylation_207179240185_R01C01


title: genomic_DNAmethylation_207179240177_R08C01


title: genomic_DNAmethylation_207179240177_R07C01


title: genomic_DNAmethylation_207179240177_R05C01


title: genomic_DNAmethylation_207179240177_R06C01


title: genomic_DNAmethylation_207179240177_R04C01


title: genomic_DNAmethylation_207179240167_R08C01


title: genomic_DNAmethylation_207179240177_R02C01


title: genomic_DNAmethylation_207179240177_R03C01


title: genomic_DNAmethylation_207179240157_R07C01


title: genomic_DNAmethylation_207179240157_R08C01


title: genomic_DNAmethylation_207179240177_R01C01


title: genomic_DNAmethylation_207179240167_R04C01


title: genomic_DNAmethylation_207179240167_R07C01


title: genomic_DNAmethylation_207179240167_R03C01


title: genomic_DNAmethylation_207179240167_R05C01


title: genomic_DNAmethylation_207179240157_R03C01


title: genomic_DNAmethylation_207179240185_R03C01


title: genomic_DNAmethylation_207179240167_R01C01


title: genomic_DNAmethylation_207179240167_R02C01


title: genomic_DNAmethylation_207179240167_R06C01


title: genomic_DNAmethylation_207179240154_R08C01

value: Plate 4


title: genomic_DNAmethylation_207179240157_R04C01


title: genomic_DNAmethylation_207179240157_R05C01


title: genomic_DNAmethylation_207179240157_R01C01


title: genomic_DNAmethylation_207179240157_R06C01


title: genomic_DNAmethylation_207179240154_R05C01


title: genomic_DNAmethylation_207179240154_R04C01


title: genomic_DNAmethylation_207179240150_R07C01


title: genomic_DNAmethylation_207179240150_R08C01


title: genomic_DNAmethylation_207179240154_R03C01


title: genomic_DNAmethylation_207179240157_R02C01


title: genomic_DNAmethylation_207179240154_R01C01


title: genomic_DNAmethylation_207179240150_R02C01


title: genomic_DNAmethylation_207179240154_R06C01


title: genomic_DNAmethylation_207179240154_R07C01


title: genomic_DNAmethylation_207179240150_R06C01


title: genomic_DNAmethylation_207179240150_R04C01


title: genomic_DNAmethylation_207179240149_R07C01


title: genomic_DNAmethylation_207179240150_R03C01


title: genomic_DNAmethylation_207179240150_R01C01


title: genomic_DNAmethylation_207179240149_R08C01


title: genomic_DNAmethylation_207179240149_R05C01


title: genomic_DNAmethylation_207179240149_R03C01


title: genomic_DNAmethylation_207179240147_R07C01


title: genomic_DNAmethylation_207179240149_R01C01


title: genomic_DNAmethylation_207179240147_R06C01


title: genomic_DNAmethylation_207179240147_R08C01


title: genomic_DNAmethylation_207179240147_R03C01


title: genomic_DNAmethylation_207179240147_R05C01


title: genomic_DNAmethylation_207179240154_R02C01


title: genomic_DNAmethylation_207179240149_R06C01


title: genomic_DNAmethylation_207179240147_R02C01


title: genomic_DNAmethylation_207179240149_R02C01


title: genomic_DNAmethylation_207179240147_R01C01


title: genomic_DNAmethylation_207179240147_R04C01


title: genomic_DNAmethylation_207179240145_R08C01


title: genomic_DNAmethylation_207179240145_R06C01


title: genomic_DNAmethylation_207179240145_R05C01


title: genomic_DNAmethylation_207179240145_R07C01


title: genomic_DNAmethylation_207179240145_R04C01


title: genomic_DNAmethylation_207179240145_R02C01


title: genomic_DNAmethylation_207179240134_R06C01


title: genomic_DNAmethylation_207179240134_R08C01


title: genomic_DNAmethylation_207179240145_R01C01


title: genomic_DNAmethylation_207179240134_R03C01


title: genomic_DNAmethylation_207179240134_R04C01


title: genomic_DNAmethylation_207179240134_R02C01


title: genomic_DNAmethylation_207179240134_R01C01


title: genomic_DNAmethylation_207179240132_R08C01


title: genomic_DNAmethylation_207179240132_R07C01


title: genomic_DNAmethylation_207179240145_R03C01


title: genomic_DNAmethylation_207179240132_R05C01


title: genomic_DNAmethylation_207179240132_R04C01


title: genomic_DNAmethylation_207179240131_R08C01


title: genomic_DNAmethylation_207179240132_R03C01


title: genomic_DNAmethylation_207179240131_R07C01


title: genomic_DNAmethylation_207179240134_R05C01


title: genomic_DNAmethylation_207179240132_R02C01


title: genomic_DNAmethylation_207179240131_R06C01


title: genomic_DNAmethylation_207179240132_R01C01


title: genomic_DNAmethylation_207179240131_R02C01


title: genomic_DNAmethylation_207179240131_R01C01


title: genomic_DNAmethylation_207179240129_R08C01


title: genomic_DNAmethylation_207179240131_R05C01


title: genomic_DNAmethylation_207179240132_R06C01


title: genomic_DNAmethylation_207179240129_R06C01


title: genomic_DNAmethylation_207179240129_R07C01


title: genomic_DNAmethylation_207179240129_R03C01


title: genomic_DNAmethylation_207179240129_R02C01


title: genomic_DNAmethylation_207179240131_R03C01


title: genomic_DNAmethylation_207179240131_R04C01


title: genomic_DNAmethylation_207179240127_R08C01


title: genomic_DNAmethylation_207179240127_R06C01


title: genomic_DNAmethylation_207179240127_R04C01


title: genomic_DNAmethylation_207179240127_R05C01


title: genomic_DNAmethylation_207179240127_R02C01


title: genomic_DNAmethylation_207179240129_R01C01


title: genomic_DNAmethylation_207179240104_R08C01


title: genomic_DNAmethylation_207179240127_R01C01


title: genomic_DNAmethylation_207179240104_R03C01


title: genomic_DNAmethylation_207179240129_R05C01


title: genomic_DNAmethylation_207179240104_R06C01


title: genomic_DNAmethylation_207179240127_R07C01


title: genomic_DNAmethylation_207179240103_R07C01


title: genomic_DNAmethylation_207179240103_R05C01


title: genomic_DNAmethylation_207179240103_R08C01


title: genomic_DNAmethylation_207179240104_R04C01


title: genomic_DNAmethylation_207179240104_R01C01


title: genomic_DNAmethylation_207179240104_R02C01


title: genomic_DNAmethylation_207179240103_R06C01


title: genomic_DNAmethylation_207179240103_R02C01


title: genomic_DNAmethylation_207179240103_R01C01


title: genomic_DNAmethylation_207179240104_R07C01


title: genomic_DNAmethylation_207179240103_R03C01


title: genomic_DNAmethylation_207179240094_R07C01


title: genomic_DNAmethylation_207179240094_R06C01


title: genomic_DNAmethylation_207179240094_R05C01


title: genomic_DNAmethylation_207179240094_R03C01


title: genomic_DNAmethylation_207179240094_R01C01


title: genomic_DNAmethylation_207179240094_R08C01


title: genomic_DNAmethylation_207179240089_R08C01


title: genomic_DNAmethylation_207179240089_R07C01


title: genomic_DNAmethylation_207179240089_R05C01


title: genomic_DNAmethylation_207179240094_R02C01


title: genomic_DNAmethylation_207179240089_R04C01


title: genomic_DNAmethylation_207179240089_R02C01


title: genomic_DNAmethylation_207179240089_R03C01


title: genomic_DNAmethylation_207179240081_R08C01


title: genomic_DNAmethylation_207179240081_R05C01


title: genomic_DNAmethylation_207179240081_R03C01


title: genomic_DNAmethylation_207179240081_R06C01


title: genomic_DNAmethylation_207179240081_R02C01


title: genomic_DNAmethylation_207179240081_R04C01


title: genomic_DNAmethylation_207179240089_R01C01


title: genomic_DNAmethylation_207179240089_R06C01


title: genomic_DNAmethylation_207179240080_R05C01

value: Plate 5


title: genomic_DNAmethylation_207179240081_R07C01


title: genomic_DNAmethylation_207179240080_R07C01


title: genomic_DNAmethylation_207179240080_R08C01


title: genomic_DNAmethylation_207179240080_R04C01


title: genomic_DNAmethylation_207179240080_R02C01


title: genomic_DNAmethylation_207179240080_R06C01


title: genomic_DNAmethylation_207179240080_R03C01


title: genomic_DNAmethylation_207179240081_R01C01


title: genomic_DNAmethylation_207179240065_R08C01


title: genomic_DNAmethylation_207179240065_R04C01


title: genomic_DNAmethylation_207179240065_R03C01


title: genomic_DNAmethylation_207179240080_R01C01


title: genomic_DNAmethylation_207179240065_R05C01


title: genomic_DNAmethylation_207179240050_R06C01

value: Plate 3


title: genomic_DNAmethylation_207179240050_R04C01


title: genomic_DNAmethylation_207179240065_R01C01


title: genomic_DNAmethylation_207179240065_R02C01


title: genomic_DNAmethylation_207179240050_R01C01


title: genomic_DNAmethylation_207179240065_R06C01


title: genomic_DNAmethylation_207179240050_R03C01


title: genomic_DNAmethylation_207179240065_R07C01


title: genomic_DNAmethylation_207179240044_R06C01


title: genomic_DNAmethylation_207179240044_R07C01


title: genomic_DNAmethylation_207179240044_R04C01


title: genomic_DNAmethylation_207179240044_R03C01


title: genomic_DNAmethylation_207179240044_R08C01


title: genomic_DNAmethylation_207179240044_R02C01


title: genomic_DNAmethylation_207179240044_R05C01


title: genomic_DNAmethylation_207179240050_R08C01


title: genomic_DNAmethylation_207179240043_R08C01


title: genomic_DNAmethylation_207179240043_R07C01


title: genomic_DNAmethylation_207179240050_R05C01


title: genomic_DNAmethylation_207179240044_R01C01


title: genomic_DNAmethylation_207179240050_R07C01


title: genomic_DNAmethylation_207179240043_R05C01


title: genomic_DNAmethylation_207179240043_R04C01


title: genomic_DNAmethylation_207179240043_R02C01


title: genomic_DNAmethylation_207179240042_R07C01


title: genomic_DNAmethylation_207179240050_R02C01


title: genomic_DNAmethylation_207179240042_R06C01


title: genomic_DNAmethylation_207179240042_R03C01


title: genomic_DNAmethylation_207179240042_R05C01


title: genomic_DNAmethylation_207179240042_R04C01


title: genomic_DNAmethylation_207179240042_R08C01


title: genomic_DNAmethylation_207179240043_R03C01


title: genomic_DNAmethylation_207179240041_R04C01


title: genomic_DNAmethylation_207179240041_R03C01


title: genomic_DNAmethylation_207179240040_R08C01


title: genomic_DNAmethylation_207179240041_R06C01


title: genomic_DNAmethylation_207179240041_R07C01


title: genomic_DNAmethylation_207179240041_R01C01


title: genomic_DNAmethylation_207179240041_R05C01


title: genomic_DNAmethylation_207179240043_R06C01


title: genomic_DNAmethylation_207179240043_R01C01


title: genomic_DNAmethylation_207179240041_R08C01


title: genomic_DNAmethylation_207179240040_R06C01


title: genomic_DNAmethylation_207179240042_R02C01


title: genomic_DNAmethylation_207179240040_R07C01


title: genomic_DNAmethylation_207179240041_R02C01


title: genomic_DNAmethylation_207179240040_R01C01


title: genomic_DNAmethylation_207179240035_R08C01


title: genomic_DNAmethylation_207179240040_R03C01


title: genomic_DNAmethylation_207179240006_R08C01


title: genomic_DNAmethylation_207179240035_R04C01


title: genomic_DNAmethylation_207179240040_R02C01


title: genomic_DNAmethylation_207179240035_R05C01


title: genomic_DNAmethylation_207179240035_R07C01


title: genomic_DNAmethylation_207179240006_R05C01


title: genomic_DNAmethylation_207179240035_R01C01


title: genomic_DNAmethylation_207179240040_R04C01


title: genomic_DNAmethylation_207179240035_R02C01


title: genomic_DNAmethylation_207179240006_R02C01


title: genomic_DNAmethylation_207179240006_R01C01


title: genomic_DNAmethylation_207179240006_R04C01


title: genomic_DNAmethylation_207179240035_R06C01


title: genomic_DNAmethylation_207179240035_R03C01


title: genomic_DNAmethylation_207179230173_R08C01


title: genomic_DNAmethylation_207179240006_R07C01


title: genomic_DNAmethylation_207179240006_R06C01


title: genomic_DNAmethylation_207179240006_R03C01


title: genomic_DNAmethylation_207179230173_R07C01


title: genomic_DNAmethylation_207179240042_R01C01


title: genomic_DNAmethylation_207179230173_R06C01


title: genomic_DNAmethylation_207179230173_R05C01


title: genomic_DNAmethylation_207179230173_R04C01


title: genomic_DNAmethylation_207179230173_R03C01


title: genomic_DNAmethylation_207179230169_R07C01


title: genomic_DNAmethylation_207179230173_R02C01


title: genomic_DNAmethylation_207179230169_R05C01


title: genomic_DNAmethylation_207179230169_R03C01


title: genomic_DNAmethylation_207179230169_R02C01


title: genomic_DNAmethylation_207179230169_R06C01


title: genomic_DNAmethylation_207179230173_R01C01


title: genomic_DNAmethylation_207179230169_R04C01


title: genomic_DNAmethylation_207179230163_R07C01


title: genomic_DNAmethylation_207179230163_R02C01


title: genomic_DNAmethylation_207179230163_R04C01


title: genomic_DNAmethylation_207179230163_R01C01


title: genomic_DNAmethylation_207179230169_R01C01


title: genomic_DNAmethylation_207179230163_R05C01


title: genomic_DNAmethylation_207179230163_R03C01


title: genomic_DNAmethylation_207179230161_R06C01


title: genomic_DNAmethylation_207179230169_R08C01


title: genomic_DNAmethylation_207179230161_R07C01


title: genomic_DNAmethylation_207179230161_R05C01


title: genomic_DNAmethylation_207179230161_R08C01


title: genomic_DNAmethylation_207179230163_R08C01


title: genomic_DNAmethylation_207179230161_R02C01


title: genomic_DNAmethylation_207179230161_R01C01


title: genomic_DNAmethylation_207179230161_R04C01


title: genomic_DNAmethylation_207179230156_R08C01


title: genomic_DNAmethylation_207179230156_R07C01


title: genomic_DNAmethylation_207179230156_R05C01


title: genomic_DNAmethylation_207179230156_R06C01


title: genomic_DNAmethylation_207179230156_R03C01


title: genomic_DNAmethylation_207179230161_R03C01


title: genomic_DNAmethylation_207179230156_R04C01


title: genomic_DNAmethylation_207179230146_R07C01


title: genomic_DNAmethylation_207179230146_R05C01


title: genomic_DNAmethylation_207179240040_R05C01


title: genomic_DNAmethylation_207179230156_R01C01


title: genomic_DNAmethylation_207179230146_R04C01


title: genomic_DNAmethylation_207179230146_R06C01


title: genomic_DNAmethylation_207179230156_R02C01


title: genomic_DNAmethylation_207179230146_R08C01


title: genomic_DNAmethylation_207179230146_R03C01


title: genomic_DNAmethylation_207179230146_R02C01


title: genomic_DNAmethylation_207179230130_R07C01

value: Plate 1


title: genomic_DNAmethylation_207179230130_R08C01


title: genomic_DNAmethylation_207179230130_R06C01


title: genomic_DNAmethylation_207179230146_R01C01


title: genomic_DNAmethylation_207179230130_R05C01


title: genomic_DNAmethylation_207179230130_R04C01


title: genomic_DNAmethylation_207179230125_R08C01


title: genomic_DNAmethylation_207179230125_R04C01


title: genomic_DNAmethylation_207179230125_R02C01


title: genomic_DNAmethylation_207179230130_R02C01


title: genomic_DNAmethylation_207179230130_R03C01


title: genomic_DNAmethylation_207179230125_R05C01


title: genomic_DNAmethylation_207179230125_R07C01


title: genomic_DNAmethylation_207179230125_R01C01


title: genomic_DNAmethylation_207179230125_R06C01


title: genomic_DNAmethylation_207179230125_R03C01


title: genomic_DNAmethylation_207179230122_R08C01


title: genomic_DNAmethylation_207179230122_R06C01


title: genomic_DNAmethylation_207179230122_R04C01


title: genomic_DNAmethylation_207179230122_R02C01


title: genomic_DNAmethylation_207179230122_R07C01


title: genomic_DNAmethylation_207179230122_R05C01


title: genomic_DNAmethylation_207179230122_R01C01


title: genomic_DNAmethylation_207179230122_R03C01


title: genomic_DNAmethylation_207179230116_R07C01


title: genomic_DNAmethylation_207179230116_R06C01


title: genomic_DNAmethylation_207179230116_R08C01


title: ACLF15

status: Public on Feb 13 2026

city: Shanghai

first: Yun

last: Song

address: 1111 Xianxia Road, Shanghai 200336, China

institute: shanghai jiao tong university

description: Library name: Sample43

data_processing:
RNA-seq
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text fles include raw count values for each Sample

source_name: liver

extract_protocol:
RNA was hanested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing librares.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit folowing manufacturer's protocols.

value: liver


title: genomic_DNAmethylation_207179230116_R03C01


title: genomic_DNAmethylation_207179230116_R05C01


title: genomic_DNAmethylation_207179230115_R07C01


title: genomic_DNAmethylation_207179230115_R03C01


title: genomic_DNAmethylation_207179230115_R01C01


title: genomic_DNAmethylation_207179230116_R04C01


title: genomic_DNAmethylation_207179230107_R06C01


title: genomic_DNAmethylation_207179230115_R08C01


title: genomic_DNAmethylation_207179230115_R06C01


title: genomic_DNAmethylation_207179230115_R05C01


title: genomic_DNAmethylation_207179230115_R04C01


title: genomic_DNAmethylation_207179230106_R05C01


title: genomic_DNAmethylation_207179230116_R02C01


title: genomic_DNAmethylation_207179230106_R07C01


title: genomic_DNAmethylation_207179230106_R06C01


title: genomic_DNAmethylation_207179230106_R03C01


title: genomic_DNAmethylation_207179230106_R02C01


title: genomic_DNAmethylation_207179230115_R02C01


title: genomic_DNAmethylation_207179230106_R08C01


title: genomic_DNAmethylation_207179230106_R01C01


title: genomic_DNAmethylation_207179230107_R07C01


title: genomic_DNAmethylation_207179230107_R08C01


title: genomic_DNAmethylation_207179230106_R04C01


title: genomic_DNAmethylation_207179230116_R01C01


title: genomic_DNAmethylation_207179230107_R02C01


title: genomic_DNAmethylation_207179230107_R04C01


title: genomic_DNAmethylation_207179230107_R03C01


title: genomic_DNAmethylation_207179230102_R03C01


title: genomic_DNAmethylation_207179230107_R01C01


title: genomic_DNAmethylation_207179230102_R02C01


title: genomic_DNAmethylation_207179230107_R05C01


title: genomic_DNAmethylation_207179230102_R08C01


title: genomic_DNAmethylation_207179230100_R08C01


title: genomic_DNAmethylation_207179230102_R05C01


title: genomic_DNAmethylation_207179230100_R02C01


title: genomic_DNAmethylation_207179230102_R06C01


title: genomic_DNAmethylation_207179230102_R07C01


title: P24

city: Valencia

first: Patricia

last: Diaz-Gimeno

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

institute: IIS La Fe / IVIRMA Global Research Alliance

description: Library name: P24_run5

data_processing:
Raw data were evaluated using FastQC. STAR was employed to align high-quality data using GRCh37/hg19 as a reference. Gene counts obtained using featureCounts.
Assembly: GRCh37/hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Endometrium

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were sequenced using the AmpliSeq for Illumina® Transcriptome Human Gene Expression Panel23 in a NextSeq 500/550 system.

value: Endometrium

tag: batch


title: genomic_DNAmethylation_207179230098_R06C01


title: genomic_DNAmethylation_207179230102_R01C01


title: genomic_DNAmethylation_207179230100_R06C01


title: genomic_DNAmethylation_207179230098_R05C01


title: genomic_DNAmethylation_207179230100_R05C01


title: genomic_DNAmethylation_207179230100_R07C01


title: genomic_DNAmethylation_207179230098_R02C01


title: genomic_DNAmethylation_207179230098_R03C01


title: genomic_DNAmethylation_207179230100_R03C01


title: genomic_DNAmethylation_207179230100_R01C01


title: genomic_DNAmethylation_207179230098_R01C01


title: genomic_DNAmethylation_207179230089_R04C01


title: genomic_DNAmethylation_207179230089_R03C01


title: genomic_DNAmethylation_207179230100_R04C01


title: genomic_DNAmethylation_207179230098_R04C01


title: genomic_DNAmethylation_207179230098_R08C01


title: genomic_DNAmethylation_207179230089_R08C01


title: genomic_DNAmethylation_207179230089_R07C01


title: genomic_DNAmethylation_207179230089_R02C01


title: genomic_DNAmethylation_207179230088_R07C01


title: genomic_DNAmethylation_207179230088_R08C01


title: genomic_DNAmethylation_207179230098_R07C01


title: genomic_DNAmethylation_207179230102_R04C01


title: genomic_DNAmethylation_207179230088_R06C01


title: genomic_DNAmethylation_207179230088_R01C01


title: genomic_DNAmethylation_207179230088_R03C01


title: genomic_DNAmethylation_207179230088_R04C01


title: genomic_DNAmethylation_207179230088_R02C01


title: genomic_DNAmethylation_207179230074_R07C01


title: genomic_DNAmethylation_207179230074_R06C01


title: genomic_DNAmethylation_207179230089_R01C01


title: genomic_DNAmethylation_207179230074_R04C01


title: genomic_DNAmethylation_207179230074_R05C01


title: genomic_DNAmethylation_207179230074_R01C01


title: genomic_DNAmethylation_207179230071_R05C01


title: genomic_DNAmethylation_207179230071_R03C01


title: genomic_DNAmethylation_207179230071_R06C01


title: genomic_DNAmethylation_207179230071_R08C01


title: genomic_DNAmethylation_207179230071_R04C01


title: genomic_DNAmethylation_207179230071_R01C01


title: genomic_DNAmethylation_207179230074_R03C01


title: genomic_DNAmethylation_207179230074_R02C01


title: genomic_DNAmethylation_207179230065_R03C01


title: genomic_DNAmethylation_207179230065_R07C01


title: genomic_DNAmethylation_207179230065_R08C01


title: genomic_DNAmethylation_207179230065_R04C01


title: genomic_DNAmethylation_207179230065_R05C01


title: genomic_DNAmethylation_207179230071_R07C01


title: genomic_DNAmethylation_207179230052_R03C01


title: genomic_DNAmethylation_207179230052_R02C01


title: genomic_DNAmethylation_207179230065_R01C01


title: genomic_DNAmethylation_207179230052_R01C01


title: genomic_DNAmethylation_207179230065_R02C01


title: genomic_DNAmethylation_207179230052_R05C01


title: genomic_DNAmethylation_207179230052_R08C01


title: genomic_DNAmethylation_207179230043_R08C01


title: genomic_DNAmethylation_207179230052_R06C01


title: genomic_DNAmethylation_207179230043_R07C01


title: genomic_DNAmethylation_207179230043_R06C01


title: genomic_DNAmethylation_207179230043_R01C01


title: genomic_DNAmethylation_207179230043_R05C01


title: genomic_DNAmethylation_207179230043_R02C01


title: genomic_DNAmethylation_207179230052_R07C01


title: genomic_DNAmethylation_207179230043_R04C01


title: genomic_DNAmethylation_207179230039_R08C01


title: genomic_DNAmethylation_207179230039_R07C01


title: genomic_DNAmethylation_207179230039_R06C01


title: genomic_DNAmethylation_207179230039_R05C01


title: genomic_DNAmethylation_207179230031_R07C01


title: genomic_DNAmethylation_207179230031_R06C01


title: genomic_DNAmethylation_207179230043_R03C01


title: genomic_DNAmethylation_207179230039_R04C01


title: genomic_DNAmethylation_207179230039_R02C01


title: genomic_DNAmethylation_207179230031_R04C01


title: genomic_DNAmethylation_207179230031_R03C01


title: genomic_DNAmethylation_207179230027_R08C01


title: genomic_DNAmethylation_207179230031_R05C01


title: genomic_DNAmethylation_207179230027_R06C01


title: genomic_DNAmethylation_207179230031_R08C01


title: genomic_DNAmethylation_207179230027_R07C01


title: genomic_DNAmethylation_207179230039_R03C01


title: genomic_DNAmethylation_207179230027_R01C01


title: genomic_DNAmethylation_207179230026_R04C01


title: genomic_DNAmethylation_207179230026_R05C01


title: genomic_DNAmethylation_207179230027_R04C01


title: genomic_DNAmethylation_207179230027_R03C01


title: genomic_DNAmethylation_207179230027_R05C01


title: genomic_DNAmethylation_207179230027_R02C01


title: genomic_DNAmethylation_207179230026_R08C01


title: genomic_DNAmethylation_207179230026_R03C01


title: genomic_DNAmethylation_207179230026_R01C01


title: genomic_DNAmethylation_207179230025_R08C01


title: genomic_DNAmethylation_207179230026_R06C01


title: genomic_DNAmethylation_207179230026_R07C01


title: genomic_DNAmethylation_207179230031_R02C01


title: genomic_DNAmethylation_207179230025_R07C01


title: genomic_DNAmethylation_207179230031_R01C01


title: genomic_DNAmethylation_207179230026_R02C01


title: genomic_DNAmethylation_207179230025_R05C01


title: genomic_DNAmethylation_207179230025_R06C01


title: genomic_DNAmethylation_207179230039_R01C01


title: genomic_DNAmethylation_207179230025_R04C01


title: genomic_DNAmethylation_207179230025_R03C01


title: genomic_DNAmethylation_207179230020_R08C01


title: genomic_DNAmethylation_207179230020_R05C01


title: genomic_DNAmethylation_207179230020_R06C01


title: genomic_DNAmethylation_207179230020_R07C01


title: genomic_DNAmethylation_207179230020_R04C01


title: genomic_DNAmethylation_207179230020_R03C01


title: genomic_DNAmethylation_207179230020_R02C01


title: genomic_DNAmethylation_207179230019_R06C01


title: genomic_DNAmethylation_207179230019_R07C01


title: genomic_DNAmethylation_207179230025_R02C01


title: genomic_DNAmethylation_207179230019_R05C01


title: genomic_DNAmethylation_207179230009_R05C01


title: genomic_DNAmethylation_207179230019_R01C01


title: genomic_DNAmethylation_207179230019_R02C01


title: genomic_DNAmethylation_207179230009_R01C01


title: genomic_DNAmethylation_207179230009_R07C01


title: genomic_DNAmethylation_207179230009_R06C01


title: genomic_DNAmethylation_207179230019_R08C01


title: genomic_DNAmethylation_207179230020_R01C01


title: genomic_DNAmethylation_207179230007_R08C01


title: genomic_DNAmethylation_207179230019_R04C01


title: genomic_DNAmethylation_207179230009_R02C01


title: genomic_DNAmethylation_207179230009_R08C01


title: genomic_DNAmethylation_207179230009_R04C01


title: genomic_DNAmethylation_207179230007_R06C01


title: genomic_DNAmethylation_207179230007_R02C01


title: genomic_DNAmethylation_207179230009_R03C01


title: genomic_DNAmethylation_207179230007_R07C01


title: genomic_DNAmethylation_207179230007_R05C01


title: genomic_DNAmethylation_207179230007_R01C01


title: genomic_DNAmethylation_207179230025_R01C01


title: genomic_DNAmethylation_207179230007_R03C01


title: genomic_DNAmethylation_207179230007_R04C01


title: genomic_DNAmethylation_207179230002_R07C01


title: genomic_DNAmethylation_207179230002_R05C01


title: genomic_DNAmethylation_207179230002_R06C01


title: genomic_DNAmethylation_207179230002_R04C01


title: genomic_DNAmethylation_207179230002_R03C01


title: genomic_DNAmethylation_207179230002_R08C01


title: T68

city: Ann Arbor

first: Phillip

middle: John

last: McCown

state: MI

address: 1500 E. Medical Center Drive

department: Internal Medicine - Nephrology

institute: University of Michigan Medicine

description:
Library name: T68
10x Genomics

data_processing:
Demuliplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0.1. SoupX (v1.5) was conducted within Seurat (v.4.0.4) on all samples at default parameters to remove ambient RNA from all samples. Mitochondrial transcript threshold, which was to retain cells that had 50% or less, was a filtration step. Integration consisted of CCA-based integration. Default scaling and PCA analysis was then used on the integrated object. Clusters were cell typed manually by examining for cell type markers that are specific to a specific kidney cell type.
Assembly: hg38 and NC_001538 (BK polyomavirus)
Supplementary files format and content: MTX files for matrix, TSV for barcodes and features

source_name: Kidney

extract_protocol:
Cortical human kidney biopsies that were preserved in CryoStor were subjected to a cellular extraction protocol from the Kidney Precision Medicine Project.
Library construction was performed according to manufacturer's protocol or instructions from 10x Genomics, specifically the Chromium Next GEM Single Cell 3' v3.1 kit and protocol.

value: Kidney

tag: cell type

value: Kidney and immune cells

value: hg38 + BK Virus

tag: bk phase

value: Peaking

tag: viral load

tag: age range

value: M

tag: days post_transplant


title: T45SV-F2

description:
Library name: T45SV-F2
10x Genomics

tag: Sex

value: F


title: T5-SV-F2

description:
Library name: T5-SV-F2
10x Genomics

value: Resolving


title: T45-CA

description:
Library name: T45-CA
10x Genomics


title: T36

description:
Library name: T36
10x Genomics


title: T30-CA

description:
Library name: T30-CA
10x Genomics


title: genomic_DNAmethylation_207179230002_R01C01

value: placental chorionic villi

tag: resourcescomposite

tag: socialpositioncomposite

tag: disadvantagecomposite

value: XY

tag: ga


title: T12-2

description:
Library name: T12-2
10x Genomics


title: genomic_DNAmethylation_207179230002_R02C01

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial


title: T105-SV

description:
Library name: T105-SV
10x Genomics

tag: tissue

tag: genotype


title: T12_F2

description:
Library name: T12_F2
10x Genomics


title: T105-CA-2

description:
Library name: T105-CA-2
10x Genomics


title: T_98_F2

description:
Library name: T_98_F2
10x Genomics

value: Control


title: T_5_1

description:
Library name: T_5_1
10x Genomics


title: T_8_F2

description:
Library name: T_8_F2
10x Genomics


title: T_6_1

description:
Library name: T_6_1
10x Genomics


title: T_23

description:
Library name: T_23
10x Genomics


title: T30_F2

description:
Library name: T30_F2
10x Genomics


title: T_39

description:
Library name: T_39
10x Genomics


title: T_33_F2

description:
Library name: T_33_F2
10x Genomics


title: T_12_1

description:
Library name: T_12_1
10x Genomics


title: T_27_F2

description:
Library name: T_27_F2
10x Genomics


title: T_11_F2

description:
Library name: T_11_F2
10x Genomics


title: T_4_1

description:
Library name: T_4_1
10x Genomics


title: T_2_2

description:
Library name: T_2_2
10x Genomics


title: T_13_1

description:
Library name: T_13_1
10x Genomics


title: T_20

description:
Library name: T_20
10x Genomics


title: CRU00246183-015

city: Cambridge

first: Matthew

last: Eldridge

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

description: Library name: SITSG1

data_processing:
Sequencing data were processed using 10x Genomics Space Ranger 2.1 with GRCh38-2020-A transcriptomic reference and probe set
Assembly: GRCh38
Supplementary files format and content: cytassist_image.tiff: CytAssist slide image
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in JSON format
Supplementary files format and content: spatial_enrichment.csv: table of Morans's I values for each feature
Supplementary files format and content: tissue_hires_image.png: high resolution downsampled image of the tissue sample
Supplementary files format and content: tissue_lowres_image.png: low resolution downsampled image of the tissue sample
Supplementary files format and content: tissue_positions.csv: spot coordinates
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market exchange format
Supplementary files format and content: filtered_feature_bc_matrix.h5: feature barcode expression count matrices in HDF5 format
Library strategy: Spatial Transcriptomics

source_name: normal colon

extract_protocol:
Visium CytAssist Spatial Gene Expression for FFPE (human), 10X
Visium CytAssist Spatial Gene Expression for FFPE (human), 10X

value: normal colon


title: CRU00239667-028

description: Library name: SITSE1


title: CRU00239667-027

description: Library name: SITSF1


title: RGT00448535-040

description: Library name: SITSH3


title: CRU00253213-022

description: Library name: SITSH1


title: RGT00448227-041

description: Library name: SITSA3


title: RGT00524583-034

description: Library name: SITSG3


title: RGT00513035-052

description: Library name: SITSG6


title: RGT00452167-015

description: Library name: SITSC7


title: RGT00520045-037

description: Library name: SITSH6


title: RGT00513655-022

description: Library name: SITSD7


title: RGT00455251-034

description: Library name: SITSB3


title: RGT00456815-037

description: Library name: SITSF7


title: CRU00246200-015

description: Library name: SITSF6


title: RGT00445809-015

description: Library name: SITSE7


title: CHZ,bladder cancer patient

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

institute: Chongqing Daping Hospital

description:
Library name: Sample5
10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
10X Genomics: Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter. BD Rhapsody:The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38) using STARsolo with default parameter.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: bladder cancer

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I (Worthington) and DNase I (Worthington) for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
10X Genomics: Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Chromium platform. Related operations including Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all carried out following the manufacturer’s protocol. BD Rhapsody:BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries.

value: bladder cancer


title: ZKS,bladder cancer patient

description:
Library name: Sample4
10X Genomics


title: CRU00246174-015

description: Library name: SITSE6


title: RGT00452166-020

description: Library name: SITSE10


title: RGT00457306-030

description: Library name: SITSF10


title: CRU00055309-013

description: Library name: SITSC10


title: OCSCC38, Pre, Unsorted, TCR

city: Saint Louis

first: Sidharth

last: Puram

address: 660 Euclid Ave

institute: Washington University in St Louis

description: Library name: OCSCC38_Pre_Unsorted_TCR

data_processing:
FASTQ files were aligned to a pre-built human reference genome hg19 (10X Genomics, July 24, 2019) using CellRanger v3.1.0 (10X Genomics) 'count' command with default options.
VDJ librarires (prepared from the 5' Single Cell Librarires) were aligned to a pre-built human reference genome hg19 (10X Genomics, July 24, 2019) using CellRanger v3.1.0 (10X Genomics) 'vdj' command with default options.
Assembly: hg19
Supplementary files format and content: filtered_feature_bc_matrix.h5 files include raw cell x count matrix CellRanger ouptut for each Sample
Supplementary files format and content: all_contig_annotations.csv files include TCR clonotype information cell for each Sample
Supplementary_files_format_and_content: GSE301741_Seurat_Object_QCpass_137020cells_withMetaData.rds is a matrix and metadata object of all post-filtered high quality (QC passing) cells, created using Seurat (v5), with cell typing, TCR assignment, and subtypes as described in the accompanying citation.

source_name: Oral Cavity

extract_protocol:
Fresh biopsies  from primary tumor sites  were dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec #130-095-929) followed by ACK red blood cell lysis. The single-cell suspension was sorted via magnetic column using either human CD45 magnetic MicroBeads (Miltenyi) or human CD3 magnetic MicroBeads (Miltenyi).  The positive and negative cell fractions were then mixed in a 1:2 ratio of positive:negative fractions to enrich for malignant/stromal cells.
Samples were processed using either the Chromium Single Cell 3’ (V2 Chemistry) or 5' (V2) platform with a target of ∼10,000 cells (10x Genomics) following the manufacturer’s instructions. T-cell receptor VDJ l and were sequenced on Illumina NovaSeq machines with a target minimum read count of 0.5 billion per sample

treatment_protocol: Clinical trial protocol under which patients is published and available at Pubmed ID: 37683037

value: Oral Cavity

tag: timepoint

value: Pre

tag: library type

value: TCR

value: Unsorted

tag: disease

value: HNSCC


title: RGT00445801-015

description: Library name: SITSD10


title: LBQ,bladder cancer patient

description:
Library name: Sample3
10X Genomics


title: LDS,bladder cancer patient

description:
Library name: Sample1
10X Genomics


title: OCSCC38, Pre, Unsorted, 5prime

description: Library name: OCSCC38_Pre_Unsorted_5prime

tag: cell type


title: OCSCC38, Post, CD3, TCR

description: Library name: OCSCC38_Post_CD3_TCR

value: Post


title: WYK,bladder cancer patient

description:
Library name: Sample2
10X Genomics


title: LSCC21, Pre, Unsorted, TCR

description: Library name: LSCC21_Pre_Unsorted_TCR

source_name: Larynx

value: Larynx


title: LSCC21, Post, CD3, TCR

description: Library name: LSCC21_Post_CD3_TCR


title: OCSCC38, Post, CD3, 5prime

description: Library name: OCSCC38_Post_CD3_5prime


title: SMG1i, Iso-seq, unlabeled

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

description:
Library name: Sample 10
Iso-seq from HEK-293 cells treated with 1µM SMG1i, no 4-thiouridine labeling

data_processing:
TL-seq: All processing was performed with fastq2EZbakR (https://github.com/isaacvock/fastq2EZbakR). In fastq2EZbakR, reads were trimmed with fastp and aligned to hg38 with STAR (default parameters and --outFilterType BySJout --twopassMode Basic --outSJfilterCountTotalMin 10 3 3 3 --alignEndsType EndToEnd --outSJfilterCountUniqueMin 10 3 3 3 --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4). Uniquely mapped reads were assigned to features with featureCounts, and mutations in those reads were counted with a custom script. Browser tracks were made using STAR. Tracks were converted to binary format using IGVtools (toTDF).
Iso-seq: Unaligned BAM files were converted into FASTQ format using the bam2fastq tool (https://github.com/jts/bam2fastq). FASTQ files were aligned to hg38 using minimap2 with the splice-aware option (Li, 2018), producing SAM files [minimap2 -ax splice -ub hg38.fa ccs.fastq.gz > ccs.sam]. The resulting SAM files were then converted to sorted BAM files using samtools [samtools view -bS ccs.sam | samtools sort -o .ccs_sorted.bam] (Li et al., 2009).
Assembly: hg38
Supplementary files format and content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).
Library strategy: Iso-seq

growth_protocol: DMEM, 5% FBS, 1% L-glutamine, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using Trizol Reagent and TimeLapse chemistry was performed as described (Schofield et al., 2018).
TL-seq: rRNA depletion was performed by oligo hybridization and digestion with thermostable RNase H (Baldwin et al, 2021). 100 ng of ribodepleted RNA was used as input for the NEBNext Ultra II Directional Library Prep Kit.
Iso-seq: 2 µg total RNA was used as input for the Clontech SMARTer PCR cDNA Synthesis kit, followed by PCR amplification. SMRTbell libraries were generated using the SMRTbell Template Prep Kit.

treatment_protocol: Treatment with 1 µM SMG1i or DMSO for 8 hours; TL-seq: labeling with 100 µM 4-thiouridine for 2 hours

tag: cell line

value: human embryonic kidney

tag: treatment

value: 1µM SMG1i, unlabeled


title: DMSO, Iso-seq, unlabeled

description:
Library name: Sample 9
Iso-seq from HEK-293 cells treated with DMSO, no 4-thiouridine labeling

value: DMSO, unlabeled


title: LSCC21, Post, CD3, 5prime

description: Library name: LSCC21_Post_CD3_5prime


title: OCSCC37, Post, CD3, 3prime

description: Library name: OCSCC37_Post_CD3_3prime


title: OCSCC37, Post, CD3, TCR

description: Library name: OCSCC37_Post_CD3_TCR


title: OCSCC37, Pre, CD3, 3prime

description: Library name: OCSCC37_Pre_CD3_3prime


title: LSCC21, Pre, Unsorted, 5prime

description: Library name: LSCC21_Pre_Unsorted_5prime


title: T36SV-F2

description:
Library name: T36SV-F2
10x Genomics

value: Kidney

value: Kidney and immune cells

value: hg38 + BK Virus

tag: bk phase

tag: viral load

tag: age range

tag: Sex

value: M

tag: days post_transplant


title: Control_St_T3_A

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

description:
Library name: Control_St_T3_A
Column name in AMsummary & TPsummary.csv:  Control_St_T3_A

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39, run in paired-end mode with the adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1, leading and trailing quality thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Paired-end reads were aligned with STAR v2.7.10b to the T. pseudonana genome (Thaps3, FilteredModels2) plus an additional “chromosome” containing an updated version of the ribosomal sequences or to a combined T. pseudonana -A. macleodii Te101.  Default parameters were used, with the maximum intron length limited to 500 nucleotides (‘–alignIntronMax 500’).
Reads per chromosome were calculated using the samtools idxstats command
Assigned to gene models using featureCounts
Assembly: T. pseudonana genome (Thaps3, FilteredModels2) & A. macleodii Te101 genome
Supplementary files format and content: AMsummary.csv and TPsummary.csv contain gene counts per gene model for each organism (A. macleodii and T. pseudonana).
Supplementary files format and content: ReadsPerChr.csv contains the number of reads aligned per chromosome for each treatment (Total RNA, PolyA selection, and Ribodepletion).

organism: Thalassiosira pseudonana

growth_protocol: T. pseudonana CCMP 1335 strain was maintained as a semicontinuous batch culture in 30ml L1+Si medium (NCMA) at 20°C with a 16:8h light cycle, under ~160µmol photons m−2 s−1. Before the experiments, diatom cells were acclimated to exponential growth after a minimum of three 1:10 dilutions and diluted in L1+Si medium to reach the designated growth phases before coculture. Growth was monitored by relative fluorescence units (RFU) using a fluorometer. In the exponential phase, cultures doubled in cell number approximately over 24 Hrs. Stationary phase cultures were defined as those sampled 7 days after the last doubling event when the culture reached ~800,000 cells/ml. Mid-exponential/Exponential cultures were defined as having undergone two doubling events before reaching stationary (~200,000 cells/ml). Early exponential phase cultures were defined as five doubling events before reaching stationary (~25,000 cells/ml).

extract_protocol:
Total RNA was extracted from 0.2 µm polycarbonate membrane filters using the Zymo Direct-zol RNA MiniPrep Plus kit for all samples.
For T. pseudonana transcriptome ribodepletion calibration, three samples obtained from exponentially growing cells were prepared: Total RNA, poly(A) selected with oligo dT-beads (Dynabeads mRNA DIRECT Kit, Life Technologies), and ribodepleted using a tailored Thalassiosira pseudonana riboPOOL following the manufacturer’s instructions. For Duo-RNA-seq, samples were prepared in triplicate for each time point and ribodepleted using the T.pseudonana riboPOOL combined with the Pan-Bacteria riboPOOL, with beads mixed in a 1:1 ratio. At this point, libraries were submitted for preparation, and sequencing to the Northwest Genomics Center (University of Washington) using a NextSeq (Illumina) platform.

treatment_protocol: For the coculture experiments, glycerol stocks of A. macleodii EP were streaked on marine agar plates (marine broth (MB) with 1.5% w/v agar) and grown at 25°C for 48 hours. Single colonies were grown overnight in Marine Broth with shaking at 25°C until an OD600 of ~0.5 was reached, measured using a NanoDrop One Microvolume UV-Vis Spectrophotometer. Cultures were then diluted 1:10 and allowed to double twice (~3:30 hours) before removing the media and washing twice with L1+Si. Finally, A. macleodii cells were added to the diatom culture to a ~40000 cells/ml concentration. All experiments were performed in L1+Si medium.

tag: time

value: Control


title: Control_St_T2_A

description:
Library name: Control_St_T2_A
Column name in AMsummary & TPsummary.csv:  Control_St_T2_A


title: OCSCC36, Post, Unsorted, 5prime

description: Library name: OCSCC36_Post_Unsorted_5prime


title: Control_St_T3_B

description:
Library name: Control_St_T3_B
Column name in AMsummary & TPsummary.csv:  Control_St_T3_B


title: OCSCC36, Pre, Unsorted, 3prime

description: Library name: OCSCC36_Pre_Unsorted_3prime


title: Control_St_T3_C

description:
Library name: Control_St_T3_C
Column name in AMsummary & TPsummary.csv:  Control_St_T3_C


title: Control_St_T1_C

description:
Library name: Control_St_T1_C
Column name in AMsummary & TPsummary.csv:  Control_St_T1_C


title: OCSCC36, Post, Unsorted, TCR

description: Library name: OCSCC36_Post_Unsorted_TCR


title: OCSCC36, Post, Unsorted, 3prime

description: Library name: OCSCC36_Post_Unsorted_3prime


title: Control_Exp_T3_B

description:
Library name: Control_Exp_T3_B
Column name in AMsummary & TPsummary.csv:  Control_Exp_T3_B


title: LSCC20, Pre, Unsorted, 3prime

description: Library name: LSCC20_Pre_Unsorted_3prime


title: OCSCC37, Post, CD3, 5prime

description: Library name: OCSCC37_Post_CD3_5prime


title: Control_St_T2_B

description:
Library name: Control_St_T2_B
Column name in AMsummary & TPsummary.csv:  Control_St_T2_B


title: Control_Exp_T2_C

description:
Library name: Control_Exp_T2_C
Column name in AMsummary & TPsummary.csv:  Control_Exp_T2_C


title: Control_St_T1_B

description:
Library name: Control_St_T1_B
Column name in AMsummary & TPsummary.csv:  Control_St_T1_B


title: OCSCC35, Pre, CD3, TCR

description: Library name: OCSCC35_Pre_CD3_TCR


title: Control_Exp_T1_A

description:
Library name: Control_Exp_T1_A
Column name in AMsummary & TPsummary.csv:  Control_Exp_T1_A