title: A_J16_CYTO

description:
Library name: AJ16_CYTO_S6_R1_001
transcriptome - replicate A - time D16

value: cytoplasmic RNA at D16

value: A


title: B_J7_CYTO

status: Public on Dec 07 2025

type: SRA

city: Montpellier

first: Eric

last: Rivals

address: 161 Rue Ada

department: Montpellier University and CNRS

country: France

institute: Laboratoire d'informatique, de robotique et de microélectronique de Montpellier

description:
Library name: BJ7_CYTO_S22_R1_001
transcriptome - replicate B - time D7

library_source: transcriptomic

data_processing:
Transcriptome (cytosomal fraction) and translatome (polysomal fraction) libraries read quality were assessed using FastQC v0.11.9 (Babraham Institute, Cambridge, UK). Reads were filtered according to quality threshold Q35, and were trimmed of 10 bases at their start, using Cutadapt v3.2. With Cutadapt, we set the minimal length of trimmed reads at 50 nucleotides; all trimmed reads shorter than 50 were removed from the analysis. High quality reads were then aligned using STAR v2.7.9a, on the release 104 of the Homo sapiens reference genome GRCh38 primary_assembly, and annotated with the GRCh38.104 Ensembl annotation file. Quantification of mapped reads was performed using featureCounts from subread v2.0.1. Statistical differential analyses were performed between the different times of the kinetic. Day 0 (D0) was used as control and compared to others times of the kinetic (D1, D2, D7, D14 and D16) for each fraction, whether cytoplasmic and polysomal (> at 3 ribosomes on the RNA). Statistics used Wald test from DESeq2 R package v1.30.1 (Supplemental Tables 1, 2 and 3).
For each dataset, the read counts were filtered with a minimum of 1 count per million per biological sample after size factors estimation (Relative Log Expression normalization), and then dispersion was estimated (using DESeq2). P-value adjustment that corrects for multiple tests to lower the risk of false discovery was performed with the method of Benjamini and Hochberg. Genes with BH corrected p-values below 0.05 were kept. Then, results from these simple comparisons are used in a double comparison between fractions to categorize genes involved in transcription or translation or in both mechanisms, using Pandas v1.1.5. Gene identifications were performed with biodbnet dbtodb API. Functional annotations were performed with gProfileR v0.2.1 using a g:SCS threshold < at 0.05. GO terms were then classified according to their depths and levels using goatools v1.3.1. Differential transcripts were annotated from the databases with msigdb R package v1.2.0. Fisher p-value corrected by FDR were performed on results from the enrichment according to the probability of their presence in the human genome. The heatmap was performed using matplotlib v3.3.0, seaborn v0.11.2, pandas v1.1.5 and clustergrammer v2. PCA in 3 dimensions was performed with rgl R package.
Assembly: GRCh38 v104
Supplementary files format and content: tab-delimited text files include count values for each Sample.

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: The CRC cell line HCT-116 (ATCC CCL-247) was obtained from ATCC. This cell line was authenticated by PCR single-locus-technology (Eurofins, Ebersberg, Germany). CRC cells were maintained in Dulbecco Minimum Essential Medium— GlutaMax (Invitrogen) supplemented with 10% fetal bovine serum (FBS), penicillin (100U/mL) and streptomycin (100μg/mL) at 37 °C with 5% CO2. Cells were routinely tested against mycoplasma infection.

extract_protocol:
At each time point of the experiment (namely D0 (before adding 5-FU to medium), D1, D2, D7, D14 and D16), cells were treated for 10 min with emetin (Sigma) 25µg/ml, washed twice with PBS, and harvested by trypsination. Cytoplasmic lysates were prepared by incubation of cells for 10 min in hypotonic buffer (10 mM Tris-HCl pH 7.4, 0.5 mM MgCl2, 10 mM KCl, 1X CompleteTM EDTA free protease inhibitor (Roche) and 10 U/mL RNAseOutTM (Invitrogen)) followed by addition of 0.7 % NP-40. Swelling cells are lysed by shaking in Precellys Evolution tissue homogenizer (10s, 4500rpm). Nuclei were pelleted by centrifugation at 750 g for 5 min at 4°C, and mitochondria were pelleted by centrifugation at 12,000 g for 10 min at 4°C. The protein content of the cytosolic extract was measured by Bradford assay and samples containing 2mg protein were loaded over 15–50% sucrose gradients (poured using the Gradient Master (Serlabo Technologies)). After ultracentrifugation at 38,000rpm for 105 min at 4°C on a SW41 Beckman rotor, 18 fractions of 700µl each were collected from each gradient while 254nm absorbance profiles were generated using an ISCO UA-6 detector. RNA sampless were extracted from 150 µL of each polysomal fraction using TRIzolTM LS reagent (Invitrogen) following manufacturer’s instructions and suspended in RNAse-free water. A fraction of each sample was loaded on an agarose gel, to identify their RNA content, and polysomal fractions containing mRNA with more than three ribosomes were pooled.
RNA-seq libraries were prepared using the Universal Plus mRNA-seq kit (Tecan Trading AG, Switzerland) according to the manufacturer’s instructions. Briefly, polyadenylated RNAs were selected using oligo-dT magnetic beads. We fragmented the polyA+ RNAs using divalent cations at elevated temperature and reverse-transcribed them using random hexamers, reverse transcriptase and actinomycin D. Deoxy-TTP was replaced by dUTP during the second strand synthesis to prevent its amplification by PCR. We repaired the double-stranded cDNAs and we adenylated them at their 3' ends followed by a ligation to Tecan adaptors including UDIs. We submitted ligated cDNAs to a strand selection prior to a PCR amplification for 15 cycles and purified the PCR products using AMPure XP Beads (Beckman Coulter Genomics, Brea, CA, USA). The size distribution of the resulting libraries was monitored using a Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were quantified using the KAPA Library quantification kit (Roche, Basel, Switzerland). Libraries were denatured with NaOH, neutralized with Tris-HCl, and diluted to 300 pM. We performed the clustering and sequencing on a NovaSeq 6000 (Illumina, San Diego, CA, USA) using the single-read 100nt protocol on an S2 flow cell, to generate 50 to 84 million sequences.

treatment_protocol: Cells were plated 48 h before 5-FU treatment. 5-FU was kindly provided by the Centre Léon Bérard (Lyon, FRANCE). The stock solution (ACCORD 50mg/ml) was diluted immediately before use in DMEM and added to cell culture medium. CRC cells were seeded at 10^6 cells/10cm dish. Forty-eight hours after seeding, HCT-116 were treated with 10μM 5-FU over 48h.

tag: cell line

value: HCT-116 (ATCC CCL-247)

tag: cell type

value: CRC cancerous colorectal cell

tag: treatment

value: cytoplasmic RNA at D7

tag: batch

value: B


title: B_J2_CYTO

description:
Library name: BJ2_CYTO_S21_R1_001
transcriptome - replicate B - time D2

value: cytoplasmic RNA at D2


title: B_J2_H

description:
Library name: B_J2_H_S33_R1_001
polysome profiling - replicate B - time D2

value: heavy fraction RNA at D2


title: CT11 thalamus snRNA-seq

city: Tokyo

first: Masaki

last: Nishioka

address: Bunkyo-ku Hongo 2-1-1

country: Japan

institute: Juntendo University

description:
Library name: CT11-Tha
10x Genomics 3' GEM dual index v3.1

library_source: transcriptomic single cell

data_processing:
Sequencing output files were processed with Cell Ranger (v7.0.0, 10x Genomics) using default parameters and the GRCh38-A reference genome to generate count data. All samples achieved a read depth exceeding 50,000 reads per nucleus, with a median depth of 74,000.
Assembly: GRCh38 (10x Genomics GRCh38-2020-A)
Supplementary files format and content: Tab-separated barcode and matrix files were generated in the 10x Genomics Cell Ranger format. The features.tsv.gz file was shared across all samples.

molecule: total RNA

source_name: Medial thalamus

extract_protocol:
Thalamic sections were prepared from the medial portion of the thalamic slab encompassing the mammillary body, and frontal cortex sections were prepared from the BA10 cortical slab. Section thickness ranged from 100–200 μm. Cell nuclei were isolated from ~50 mg of thalamic or frontal cortex tissue, with myelin removed by four-layer density-gradient centrifugation using OptiPrep (35%, 29%, 25%, and 0%) supplemented with RNase inhibitor. To minimize systematic bias due to experimental batches, two specimens (one from a bipolar disorder patient and one from a control subject) were processed in parallel from nuclei isolation through snRNA-seq library preparation. All procedures were performed by the same experimenter, who was blinded to disease status, to avoid inter-experimenter variability.
Nuclei isolated from the medial thalamus and frontal cortex were subjected to library preparation using the 10x Genomics Chromium Single Cell 3’ RNA v3.1 dual index protocol, following the manufacturer’s instructions (10x Genomics). The target recovery was 5,000 nuclei per sample, and libraries were amplified with 14 PCR cycles. Sequencing was performed on the Illumina NextSeq 2000 platform according to the protocols provided by Illumina and 10x Genomics. To minimize experimental bias, all library preparations were carried out by the same experimenter, with case–control pairs processed in parallel.

tag: tissue

value: Medial thalamus


title: CT10 thalamus snRNA-seq

description:
Library name: CT10-Tha
10x Genomics 3' GEM dual index v3.1


title: CT09 thalamus snRNA-seq

description:
Library name: CT09-Tha
10x Genomics 3' GEM dual index v3.1


title: B_J1_H

description:
Library name: B_J1_H_S32_R1_001
polysome profiling - replicate B - time D1

value: heavy fraction RNA at D1


title: B_J1_CYTO

description:
Library name: BJ1_CYTO_S20_R1_001
transcriptome - replicate B - time D1

value: cytoplasmic RNA at D1


title: CT08 thalamus snRNA-seq

description:
Library name: CT08-Tha
10x Genomics 3' GEM dual index v3.1


title: BD03 cortex snRNA-seq

description:
Library name: BD03-FrC
10x Genomics 3' GEM dual index v3.1

source_name: Frontal cortex (BA10)

value: Frontal cortex (BA10)


title: CT06 thalamus snRNA-seq

description:
Library name: CT06-Tha
10x Genomics 3' GEM dual index v3.1


title: CT05 thalamus snRNA-seq

description:
Library name: CT05-Tha
10x Genomics 3' GEM dual index v3.1


title: Maxillary M1 of P1 mouse,Ascl5WT/WT,2

city: Bangkok

first: Thanakorn

last: Theerapanon

address: 34 Henri-Dunant Road, Wangmai, Patumwan

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn university

description: Library name: RNA_P122_M1_maxillar

data_processing:
RNA libraries were map to Mus_musculus (UCSC mm10) reference genome using Illumina RNA-Seq Alignment | Version: 2.0.2.
The alignment data was annotated and gene count of each sample was calculated using DESeq2 Global Analysis 3.18.20.11.
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: The files are tab-delimited text files containing normalized gene counts for each sample within the comparison group.

organism: Mus musculus

source_name: maxillary first molars

extract_protocol:
Total RNA was extracted using Rneasy plus mini kit (QIAGEN)
RNA lbraries for RNA-seq were prepared using SMARTer Stranded RNA-Seq Kit.

value: maxillary first molars

tag: genotype


title: Maxillary M1 of P1 mouse,Ascl5WT/WT,1

description: Library name: RNA_P117_M1_maxillar


title: CT03 thalamus snRNA-seq

description:
Library name: CT03-Tha
10x Genomics 3' GEM dual index v3.1


title: CT04 thalamus snRNA-seq

description:
Library name: CT04-Tha
10x Genomics 3' GEM dual index v3.1


title: A_J7_H

description:
Library name: AJ7_H_S16_R1_001
polysome profiling - replicate A - time D7

value: heavy fraction RNA at D7


title: CT02 thalamus snRNA-seq

description:
Library name: CT02-Tha
10x Genomics 3' GEM dual index v3.1


title: B_J0_H

description:
Library name: B_J0_H_S31_R1_001
polysome profiling - replicate B - time D0

value: heavy fraction RNA at D0


title: Maxillary M1 of P1 mouse,Ascl5Mut/WT,2

description: Library name: RNA_P105_M1_maxillar


title: A_J7_CYTO

description:
Library name: AJ7_CYTO_S4_R1_001
transcriptome - replicate A - time D7


title: CT12 thalamus snRNA-seq

description:
Library name: CT12-Tha
10x Genomics 3' GEM dual index v3.1


title: BD21 thalamus snRNA-seq

description:
Library name: BD21-Tha
10x Genomics 3' GEM dual index v3.1


title: BD19 thalamus snRNA-seq

description:
Library name: BD19-Tha
10x Genomics 3' GEM dual index v3.1


title: A_J2_H

description:
Library name: AJ2_H_S15_R1_001
polysome profiling - replicate A - time D2


title: CT01 thalamus snRNA-seq

description:
Library name: CT01-Tha
10x Genomics 3' GEM dual index v3.1


title: Maxillary M1 of P1 mouse,Ascl5Mut/WT,1

description: Library name: RNA_P104_M1_maxillar


title: Maxillary M1 of P1 mouse,Ascl5Mut/Mut,2

description: Library name: RNA_P102_M1_maxillar


title: BD17 thalamus snRNA-seq

description:
Library name: BD17-Tha
10x Genomics 3' GEM dual index v3.1


title: A_J2_CYTO

description:
Library name: AJ2_CYTO_S3_R1_001
transcriptome - replicate A - time D2


title: A_J1_H

description:
Library name: AJ1_H_S14_R1_001
polysome profiling - replicate A - time D1


title: Maxillary M1 of P1 mouse,Ascl5Mut/Mut,1

description: Library name: RNA_P101_M1_maxillar


title: BD15 thalamus snRNA-seq

description:
Library name: BD15-Tha
10x Genomics 3' GEM dual index v3.1


title: Mandubular dental arch E17.5 Ascl5MutMut E14

data_processing:
RNA libraries were map to Mus_musculus (UCSC mm10) reference genome using Illumina RNA-Seq Alignment | Version: 2.0.2.
The alignment data was annotated and gene count of each sample was calculated using DESeq2 Global Analysis 3.18.20.11.
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: tab-delimited text file containing raw gene count of each sample

source_name: Mandubular dental arch

extract_protocol:
Total RNA was extracted using Rneasy plus mini kit (QIAGEN)
RNA lbraries for RNA-seq were prepared using TruSeq stranded mRNA library prep kit.

value: Mandubular dental arch

value: MutMut


title: BD18 thalamus snRNA-seq

description:
Library name: BD18-Tha
10x Genomics 3' GEM dual index v3.1


title: A_J1_CYTO

description:
Library name: AJ1_CYTO_S2_R1_001
transcriptome - replicate A - time D1


title: B_J0_CYTO

description:
Library name: BJ0_CYTO_S19_R1_001
transcriptome - replicate B - time D0

value: cytoplasmic RNA at D0


title: BD16 thalamus snRNA-seq

description:
Library name: BD16-Tha
10x Genomics 3' GEM dual index v3.1


title: Mandubular dental arch E17.5 Ascl5MutMut E18


title: A_J0_H

description:
Library name: AJ0_H_S13_R1_001
polysome profiling - replicate A - time D0

value: A


title: BD20 thalamus snRNA-seq

description:
Library name: BD20-Tha
10x Genomics 3' GEM dual index v3.1


title: Mandubular dental arch E17.5 Ascl5WTWT E15


title: BD13 thalamus snRNA-seq

description:
Library name: BD13-Tha
10x Genomics 3' GEM dual index v3.1


title: A_J0_CYTO

description:
Library name: AJ0_CYTO_S1_R1_001
transcriptome - replicate A - time D0

value: HCT-116 (ATCC CCL-247)


title: Mandubular dental arch E17.5 Ascl5WTWT E20


title: BD12 thalamus snRNA-seq

description:
Library name: BD12-Tha
10x Genomics 3' GEM dual index v3.1


title: BP04_hom_ta

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

country: Germany

institute: BIOTEChnology Center TU Dresden

data_processing:
bcl2fastq2: bcl2fastq2 2.20.0
alignment: Fragments were aligned to the mouse reference genome mm10 with support of the Ensembl 98 splice sites using the aligner gsnap (v2020-12-16) (gsnap -d mm10 --gunzip -A sam -t 16 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0)
genecounts: Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1) (featureCounts -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o genecount/bfx1606.mm10.e98.txt -Q 1 -T 8)
Assembly: mm10
Supplementary files format and content: tab separated file from featureCounts. Each row is a gene. Each column is either gene information (Start, End, Strand, …) or a sample. The file list per gene per sample the number of counted fragments

source_name: Small intestine

extract_protocol:
At 4 days  after the induction of mutagenesis, intestinal crypts  were dissociated into single cells with TrypLE Express (Thermo Fisher  Scientific) for 30min at 37°C. Dissociated cells were passed through  70µm cell strainer and washed wit 5% FBS/PBS. Cells were stained with  PE-conjugated anti-CD24,  APC-conjugated anti-CD326 (EpCAM) antibody and  Alexa-Fluor 700 CD45 antibodies for 45min on ice. Stained cells were  collected by centrifugation and resuspended in SYTOX blue dead cell  stain. FACS sorting was performed on a FACS AriaTM III cell sorter (BD).
Cells are FACsorted into a PCR tube containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at ‑80°C. After thawing the samples, RNA is denatured for 3 minutes at 72 °C in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer* and 4 U RNase Inhibitor (NEB). The reverse transcription and addition of the template switch oligo is performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase is inactivated at 70 °C for 15 min. The single stranded cDNA is subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 250 nM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 17 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration is determined with the Fragment Analyzer (Agilent).  For library preparation in 5ul volume 3 ng cDNA was tagmented using 0.5 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 10 min. Next, Illumina indices are added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 700 nM dual indexing primers. After PCR, libraries are purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer

treatment_protocol: Mutagenesis was induced in mice by intraperitoneal injections of 1mg   tamoxifen on 3 consecutive days.

value: Small intestine

value: Epithelial cells

value: Setd1aFC/FC; Lgr5-eGFP-CreERT2

value: Tamoxifen


title: GSC11_shNANP-1_rep2

city: New York

first: Erik

last: Sulman

state: NY

address: 522 First Avenue

department: Radiation Oncology

country: USA

institute: NYU Langone

data_processing:
Reads were trimmed for adapters and quality using Trimmomatic version 0.36
Trimmed reads were aligned to the human reference genome (hg19) using STAR version 2.5 with standard settings
The featureCounts program was employed to generate a genes-to-samples counts matrix
Assembly: hg19
Supplementary files format and content: A comma separated value (csv) file includes raw read counts for each sample.

source_name: brain

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, 74134)
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit following the manual.

value: brain

value: glioblstoma stem cells

value: NANP knockdown


title: NCI-H2452_BFA_1

type: RNA

city: Nagoya

first: Tatsuhiro

last: Sato

state: Aichi

address: 1-1 Kanokoden

department: Division of Cancer Biology

institute: Aichi Cancer Center Research Institute

description: Mesothelioma cells treated with brefeldin A

hyb_protocol: Hybridization was performed by Aproscience Inc. using Agilent Human GE 8x60K v3 arrays and standard protocols.

scan_protocol: Arrays were scanned by Aproscience Inc. using Agilent microarray scanners. Detailed scan parameters are not available.

data_processing: Raw data were extracted by Aproscience Inc. using Agilent Feature Extraction Software. Signal intensities were log₂-transformed and quantile-normalized.

label_protocol: cRNA labeling was performed by Aproscience Inc. using standard Agilent protocols. Specific labeling details are not available.

growth_protocol: Cells were cultured using RPMI-1640 or equivalent medium supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol: Total RNA was extracted usingTotal RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 10 ng/mL brefeldin A for 48 hours. Control samples were treated with an equivalent volume of DMSO.

value: mesothelium

tag: gender

value: male

value: brefeldin A


title: BD11 thalamus snRNA-seq

description:
Library name: BD11-Tha
10x Genomics 3' GEM dual index v3.1

value: Medial thalamus


title: NCI-H2452_Control_1

description: Mesothelioma cells treated with DMSO

value: DMSO


title: GSC11_shNANP-1_rep1


title: BD10 thalamus snRNA-seq

description:
Library name: BD10-Tha
10x Genomics 3' GEM dual index v3.1


title: GSC11_shCTL_rep2

value: control


title: BP04_hom_sc


title: BP04_hom_pc


title: BD14 thalamus snRNA-seq

description:
Library name: BD14-Tha
10x Genomics 3' GEM dual index v3.1


title: NCI-H2052_Control_1

description: Mesothelioma cells treated with DMSO


title: CT07 thalamus snRNA-seq

description:
Library name: CT07-Tha
10x Genomics 3' GEM dual index v3.1


title: BP03_het_ta

value: Setd1aFC/+;  Lgr5-eGFP-CreERT2


title: NCI-H2052_BFA_1


title: BD08 thalamus snRNA-seq

description:
Library name: BD08-Tha
10x Genomics 3' GEM dual index v3.1


title: GSC20_shNANP-3_rep2


title: BP03_het_pc


title: Y-MESO-27_BFA_1


title: Y-MESO-27_Control_1

description: Mesothelioma cells treated with DMSO


title: GSC20_shNANP-3_rep1


title: w Mac, H3N2, bascal, 3

city: Boston

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

description:
AlveolusChip_Basal_wViruswMac_3
Processed data_Basal_AlvMacPaper.xls

data_processing:
The paired reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b, and unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: raw counts

source_name: Lung

extract_protocol:
Total RNA was extracted using Qiagen Micro Plus kit and sent to Genewiz
Genewiz prepared the libraries for standard bulk RNA-seq

value: Lung

value: Human lung microvascular endothelial cells

value: Influenza H3N2


title: BD06 thalamus snRNA-seq

description:
Library name: BD06-Tha
10x Genomics 3' GEM dual index v3.1


title: w Mac, H3N2, bascal, 4

description:
AlveolusChip_Basal_wViruswMac_4
Processed data_Basal_AlvMacPaper.xls


title: BD07 thalamus snRNA-seq

description:
Library name: BD07-Tha
10x Genomics 3' GEM dual index v3.1


title: BP03_het_sc

value: Small intestine


title: MeT-5A_Control_1

description: Mesothelial cells treated with DMSO


title: BD04 thalamus snRNA-seq

description:
Library name: BD04-Tha
10x Genomics 3' GEM dual index v3.1


title: BD05 thalamus snRNA-seq

description:
Library name: BD05-Tha
10x Genomics 3' GEM dual index v3.1


title: BO58_het_ta

value: Epithelial cells


title: GSC11_shCTL_rep1


title: w Mac, H3N2, bascal, 2

description:
AlveolusChip_Basal_wViruswMac_2
Processed data_Basal_AlvMacPaper.xls


title: BO58_het_pc


title: MeT-5A_BFA_1

description: Mesothelial cells treated with brefeldin A


title: BD09 thalamus snRNA-seq

description:
Library name: BD09-Tha
10x Genomics 3' GEM dual index v3.1


title: GSC20_shCTL_rep2


title: GSC20_shNANP-1_rep1


title: w Mac, H3N2, bascal, 1

description:
AlveolusChip_Basal_wViruswMac_1
Processed data_Basal_AlvMacPaper.xls


title: wo Mac, H3N2, basal, 4

description:
AlveolusChip_Basal_wViruswoMac_4
Processed data_Basal_AlvMacPaper.xls


title: BO58_het_sc


title: wo Mac, H3N2, basal, 3

description:
AlveolusChip_Basal_wViruswoMac_3
Processed data_Basal_AlvMacPaper.xls


title: BO57_hom_ta

value: Setd1aFC/FC; Lgr5-eGFP-CreERT2


title: BD02 thalamus snRNA-seq

description:
Library name: BD02-Tha
10x Genomics 3' GEM dual index v3.1


title: BD01 thalamus snRNA-seq

description:
Library name: BD01-Tha
10x Genomics 3' GEM dual index v3.1


title: GSC20_shNANP-1_rep2


title: wo Mac, H3N2, basal, 2

description:
AlveolusChip_Basal_wViruswoMac_2
Processed data_Basal_AlvMacPaper.xls


title: BO57_hom_pc

value: Tamoxifen


title: WZR12 cells, MCB-613, biol rep 2

city: Durham

first: Kris

last: Wood

state: NC

address: 450 Research Drive, LSRC C259, PO Box 3813

department: Department of Pharmacology and Cancer Biology

institute: Duke University

data_processing:
Paired-end sequencing reads from raw fastq files were trimmed using TrimGalore followed by quality control analysis with FastQC.
Processed reads were subsequently aligned to reference human genome GRCh38 (hg38) using the HISAT2 aligner.
Read counts were processed using featureCounts prior to differential expression analyses with DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: PC9, GR4, and WZR12 cells were maintained in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were maintained in a humidified incubator at 37 °C  with 5% CO2.

extract_protocol:
RNA was extracted using the RNEasy Mini Kit (Qiagen) according to the manufacturer's instructions.
The library was prepared using the KAPA Stranded mRNA-Seq Kit (Kapa) according to the manufacturer's instructions.

treatment_protocol: PC9, GR4, and WZR12 cells were seeded on D0 and allowed to adhere overnight at 37 °C. After 24 hours, cells were treated with either DMSO or 2 µM MCB-613 in triplicate and returned to the incubator. After 24 hours of drug treatment, cells were collected, pelleted, and snap frozen.


title: WZR12 cells, MCB-613, biol rep 3


title: BO57_hom_sc


title: DNA Input control for Vancomycin treated mouse bone marrow progenitor cells supplemented with BAP

city: Vancouver

first: Misha

last: Bilenky

state: BC

address: 500 W Broadway

country: Canada

institute: BCGSC

description: Library name: LSK VANC + BAP, DNA Input

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq-2.20 of HiSeq output
pair-end sequence reads were aligned using bwa 0.7.6a
duplicated reads were marked using sambamba 0.5.5
Fragment coverage files were generated using in-house BAM2WIG java tool in a wig format after collapsing duplicated reads and apply mapping quality threshold of 5
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
Cells were sorted on a FACSAria II sorter (Becton Dickinson Biosciences, San Jose, CA). Approximately 10,000 viable HSPCs (live-gatedCD45+Lin-Sca1(Ly6A/E)+cKit+) were sorted from the BM of two pooled naïve C57BL/6 mice.
Native ChIP-seq of the HSPCs was performed using standard operating procedures for ChIP-seq library construction for Illumina platform sequencing

value: Bone marrow

value: hematopoietic stem and progenitor cells

value: Vancomycin + BAP


title: wo Mac, H3N2, basal, 1

description:
AlveolusChip_Basal_wViruswoMac_1
Processed data_Basal_AlvMacPaper.xls


title: BO27_het_ta


title: H3K27me3 ChIP-Seq for Vancomycin treated mouse bone marrow progenitor cells supplemented with BAP

description: Library name: LSK VANC + BAP, H3K27me3 ChIP

tag: chip antibody


title: w Mac, mock, basal, 4

description:
AlveolusChip_Basal_woViruswMac_4
Processed data_Basal_AlvMacPaper.xls

value: Mock


title: WZR12 cells, DMSO, biol rep 3

value: vehicle


title: H3K27ac ChIP-Seq for Vancomycin treated mouse bone marrow progenitor cells supplemented with BAP

description: Library name: LSK VANC + BAP, H3K27ac ChIP

value: H3K27ac (Hiroshi Lab, CMA309-IgG1)


title: w Mac, mock, basal, 3

description:
AlveolusChip_Basal_woViruswMac_3
Processed data_Basal_AlvMacPaper.xls


title: BO27_het_sc


title: BO27_het_pc


title: w Mac, mock, basal, 2

description:
AlveolusChip_Basal_woViruswMac_2
Processed data_Basal_AlvMacPaper.xls


title: WZR12 cells, DMSO, biol rep 1


title: DNA Input control for Vancomycin treated mouse bone marrow progenitor cells

description: Library name: LSK VANC, DNA Input

value: Vancomycin


title: WZR12 cells, DMSO, biol rep 2


title: BD03 thalamus snRNA-seq

description:
Library name: BD03-Tha
10x Genomics 3' GEM dual index v3.1

value: Medial thalamus


title: H3K27me3 ChIP-Seq for Vancomycin treated mouse bone marrow progenitor cells

description: Library name: LSK VANC, H3K27me3 ChIP


title: BO25_hom_ta


title: w Mac, mock, basal, 1

description:
AlveolusChip_Basal_woViruswMac_1
Processed data_Basal_AlvMacPaper.xls


title: GSC20_shCTL_rep1

value: brain

value: glioblstoma stem cells

value: control


title: H3K27ac ChIP-Seq for Vancomycin treated mouse bone marrow progenitor cells

description: Library name: LSK VANC, H3K27ac ChIP


title: BO25_hom_pc


title: GR4 cells, MCB-613, biol rep 3


title: w Mac, H3N2, apical, 4

description:
AlveolusChip_Apical_wViruswMac_4
Processed data_Apical_AlvMacPaper.xls

value: Lung

value: Human alveolar epithelial cells and macrophages


title: WZR12 cells, TF, biol rep 3

data_processing:
Demultiplexed fastq.gz files were concatened across lanes for each sample.
Raw sequencing reads were then aligned against a database of sgRNA sequences (containing the sgRNA name, trimmed sgRNA sequence, and target gene name) and a normalized counts table was generated utilizing the MAGeCK (v0.5.9.2) count sub-command with default settings.
Gene level enrichment or depletion was then evaluated across samples using the MAGeCK (v0.5.9.2) MLE sub-command with the normalized counts table as input, default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes statistical analysis (beta score, z-score, p-value, fdr, wald-p-value, wald-fdr) of resistant cell lines (GR4 and WZR12) compared to parental (PC9) at TF compared to plasmid pool as a representation of T0.
Library strategy: CRISPR

extract_protocol:
Genomic DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen) according to the manufacturer's instructions.
Extracted DNA was amplified with a two-step protocol. First, sgRNA libraries were PCR-amplified from genomic DNA using NEBNext Ultra II Q5 Master Mix according to the manufacturer’s protocol using the PCR 1 Forward and Reverse primers (F: GAGGGCCTATTTCCCATGATTC, R: GTTGCGAAAAAGAACGTTCACGG). Following the initial amplification, a second PCR step was undertaken to append the PCR 1 product for each condition with a unique combination of staggered forward and barcoded reverse primers to facilitate pooled sequencing (F: AATGATACGGCGACCACCGAGATCTACAC(8-bp index)ACACTCTTTCCCTACACGACGCTCTTCCGATCT(0-5 bp stagger)TTGTGGAAAGGACGAAACACCG, R: CAAGCAGAAGACGGCATACGAGAT(8-bp index)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACTTGCTATTTCTAGCTCTAAAAC). In all cases, the amplified libraries were purified with SPRIselect beads (Beckman Coulter) using right-sided selection. Samples were quantified with the Quant-iT dsDNA Broad Range Assay Kit (Thermo Fisher), pooled, and sequenced on an Illumina NextSeq 500 with 75 bp single-end sequencing.

treatment_protocol: On Day 0, PC9, GR4, and WZR12 cells were seeded into 6-well plates at a density of 150,000 cells per well and allowed to adhere overnight. On Day 1, the cells were exposed to media containing library virus and the polybrene transduction reagent (8 µg/ml) before spinfection via centrifugation at 900 x g for 1 hour at room temperature. On Day 2, the media containing library virus and polybrene was removed and replaced with fresh media. On Day 3, the cells were subjected to selection with puromycin (2 µg/ml) for 48 hours. Then, on Day 5, the cells were resuspended, counted, divided into triplicates, and carried forward with passage every five days for an estimated 14 population doublings. Throughout the entirety of the screen, each replicate was represented at any given point in time by at least 4 x 106 cells to guarantee at least 1000x coverage of the custom library. Pellets of at least 4 x 106 cells were taken at T0, Tf, and at each passage as well. Upon completion of the screen, pellets were lysed and genomic DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen).


title: w Mac, H3N2, apical, 3

description:
AlveolusChip_Apical_wViruswMac_3
Processed data_Apical_AlvMacPaper.xls

value: Influenza H3N2


title: WZR12 cells, MCB-613, biol rep 1


title: WZR12 cells, TF, biol rep 2


title: GR4 cells, MCB-613, biol rep 2


title: GR4 cells, MCB-613, biol rep 1


title: BN45_hom_ta

value: Small intestine

value: Epithelial cells


title: WZR12 cells, TF, biol rep 1


title: GR4 cells, DMSO, biol rep 3


title: BN45_hom_pc

value: Setd1aFC/FC; Lgr5-eGFP-CreERT2

value: Tamoxifen


title: w Mac, H3N2, apical, 2

description:
AlveolusChip_Apical_wViruswMac_2
Processed data_Apical_AlvMacPaper.xls


title: w Mac, H3N2, apical, 1

description:
AlveolusChip_Apical_wViruswMac_1
Processed data_Apical_AlvMacPaper.xls


title: BN45_hom_sc


title: BN44_het_ta

value: Setd1aFC/+;  Lgr5-eGFP-CreERT2


title: wo Mac, H3N2, apical, 4

description:
AlveolusChip_Apical_wViruswoMac_4
Processed data_Apical_AlvMacPaper.xls

value: Human alveolar epithelial cells


title: GR4 cells, TF, biol rep 3


title: wo Mac, H3N2, apical, 3

description:
AlveolusChip_Apical_wViruswoMac_3
Processed data_Apical_AlvMacPaper.xls


title: GR4 cells, TF, biol rep 1


title: PC9 cells, MCB-613, biol rep 3


title: GR4 cells, DMSO, biol rep 2


title: wo Mac, H3N2, apical, 2

description:
AlveolusChip_Apical_wViruswoMac_2
Processed data_Apical_AlvMacPaper.xls


title: BO25_hom_sc


title: GR4 cells, DMSO, biol rep 1


title: BN44_het_pc


title: PC9 cells, MCB-613, biol rep 1


title: PC9 cells, TF, biol rep 2


title: wo Mac, H3N2, apical, 1

description:
AlveolusChip_Apical_wViruswoMac_1
Processed data_Apical_AlvMacPaper.xls


title: PC9 cells, MCB-613, biol rep 2


title: BN44_het_sc


title: dorsal shaved skin, 9wk

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

description: F4/80+MHCII-hi sorted, young

data_processing:
Fastq files were aligned to Mus musculus mm10 reference with Cell Ranger (v4.0.0) using function cellranger count.
Files from different samples were then aggregated by Cell Ranger (v4.0.0) to construct count tables (genes as rows and cells as columns) with function cellranger aggr.
Assembly: mm10
Supplementary files format and content: Processed data files are zipped aggregated output directory of Cell Ranger.

source_name: male, 9wk, pooled from 2 mice

growth_protocol: (cells were isolated directly from mouse tissues of indicated ages, no cell culture was involved)

extract_protocol:
Dorsal skin samples (2 mice pooled per sample) were excised and digested in 0.3% collagenase-A, 0.25mg/ml Dispase-II, 10U/ml DNaseI and 2%FBS in RPMI for one hour to obtain single cell suspension. FcR was blocked with 2.4G2 before incubating with staining antibodies (). F4/80+MHCII-hi macrophages were sorted and subjected to sequencing profiling.
Library was prepared with Chromium Single Cell 3’ Reagent Kits (v3.1 Chemistry; 10x Genomics). The 3’ gene expression libraries with paired-end Read 1 (containing 16-bp barcode and 12-bp UMI), Read 2 (91-bp insert) and i7 index (8-bp) were analysed by Illumina HiSeq X.

treatment_protocol: (not applicable)

value: Skin

tag: Sex

value: male

tag: age

value: 9 week

value: macrophage

value: WT


title: PC9 cells, DMSO, biol rep 3

value: vehicle


title: dorsal shaved skin, 108wk

description: F4/80+MHCII-hi sorted, old

source_name: male, 108wk, pooled from 2 mice

value: 108 week


title: w Mac, mock, apical, 4

description:
AlveolusChip_Apical_woViruswMac_4
Processed data_Apical_AlvMacPaper.xls

value: Mock


title: PC9 cells, DMSO, biol rep 2


title: GR4 cells, TF, biol rep 2


title: w Mac, mock, apical, 3

description:
AlveolusChip_Apical_woViruswMac_3
Processed data_Apical_AlvMacPaper.xls

value: Lung


title: PC9 cells, TF, biol rep 1


title: w Mac, mock, apical, 2

description:
AlveolusChip_Apical_woViruswMac_2
Processed data_Apical_AlvMacPaper.xls

value: Human alveolar epithelial cells and macrophages


title: w Mac, mock, apical, 1

description:
AlveolusChip_Apical_woViruswMac_1
Processed data_Apical_AlvMacPaper.xls


title: D21SPNpi NKs

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur

data_processing:
Using the R package Seurat3 (https://doi.org/10.1016/j.cell.2019.05.031), cells with more than 20% of mitochondrial genes expressed or with less than 1e3 or more than 3.5e3 UMIs were filtered out. Counts were then log normalized.
Marker genes of Control and Memory conditions were determined using the Wilcoxon rank sum test.
Assembly: mm10
Supplementary files format and content: tab-delimited table with ENSEMBL ids and gene names
Supplementary files format and content: tab-delimited table with barcodes information
Supplementary files format and content: tab-delimited MarketMatrix with nonzero counts
Supplementary files format and content: tab-delimited table with ENSEMBL ids and gene names
Supplementary files format and content: tab-delimited table with barcodes information
Supplementary files format and content: tab-delimited MarketMatrix with nonzero counts

source_name: sorted NK cells

extract_protocol:
RNA extraction: cells were lysed in a water-based hypotonic buffer, containing 0.2% Triton X-100 and RNAse inhibitors.
1. polyadenylated RNAs were Reverse Transcribed, with a polyT oligonucleotide, containing a Unique Moleculer Identifier and a cell barcode. 2. cDNA was subject to In Vitro Transcription amplification, prior to adaptor ligation (that included a batch barcode) and library preparation (through 16 cycles of PCR amplification). 3. Libraries were sequenced in a NextSeq 500 machine, using a v2 mid-ouput 75 cycles kit (Illumina).

treatment_protocol: Mice were treated with PBS or infected with S. pneumoniae. 21 days later, NK cells from naive mice or pre-infected mice were collected from spleen, higlhy purified and transferred into naive congenic mice by retro-orbital injection. 24 hours later, all recipient mice were infected with S. pneumoniae. 40 hours post-infection, transferred naive (D21PBSpi NKs) and pre-infected NK cells (D21SPNpi NKs) from lungs were sorted and used for scRNAseq

value: Lung tissue

tag: strain

value: 7-12 weeks old

value: D21SPNpi NKs


title: D21PBSpi NKs

value: D21PBSpi NKs


title: Covid infection, Symptomatic, V2, Batch1, 1046-2-A, 16S

status: Public on Dec 06 2025

city: PITTSBURGH

first: Xiangyu

last: Ye

state: Pennsylvania

address: 4401 Penn Ave

institute: UPMC

description:
Library name: zr8768_52
16S validation

library_source: other

data_processing:
DADA2 pipeline (v.2023.7.0, python v.3.8.15) in QIMME2 was employed for QC, denoise, and amplicon sequence variants (ASVs) identification on 16S sequencing data. Specifically, raw fastq files were first imported in Phred33 V2 formation, and cutadapt (v.2023.7.0) was used to remove adapters and merge PE reads with a minimum 10bp overlap length and a maximum 0.2 mismatch ratio allowed in the overlap area. Then FASTQC (v.0.12.1) and MultiQC (v.1.15) were used to assess the quality of merged reads and determine the truncation position and pruning length for DADA2 denoise. Finally, scikit-learn (v.2023.7.0), together with a pre-trained classifier based on SILVA (https://data.qiime2.org/2023.7/common/silva-138-99-nb-classifier.qza), was used for taxonomic annotation on DADA2 denoised ASVs.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: 16S rRNA-seq

molecule: other

source_name: Nasopharynx swab

extract_protocol:
Collected swab samples were in Zymo DNA/RNA shield. Nucleic acid was extracted using Quick DNA/RNA Microprep Plus kit (Zymo Reserch, Cat No D7005). The extracted RNA was then utilized for RNA sequencing, while the extracted DNA was used for 16S microbiome test.
Library was prepared using Quick-16S Plus NGS Library Prep kit (Zymo Research, Cat No D6430) targeting V4 by running 1-step PCR and sequenced on Illumina MiSeq with v3 reagent kit, 600cycles. Bisulfite converted amplified DNA was hybridized to an Illumina chip.

value: Nasopharynx swab

tag: sampleID

tag: isolate

tag: visit

value: Male

tag: age (year)

tag: race

value: White

value: omicron

tag: covid vaccine

value: Yes

tag: group

value: Symptomatic


title: PC9 cells, DMSO, biol rep 1

tag: cell line


title: Covid infection, Symptomatic, V2, Batch1, 1041-2-A, 16S

description:
Library name: zr8768_49
16S validation

value: Non-White


title: Covid infection, Asymptomatic, V2, Batch1, 1046-3-C, 16S

description:
Library name: zr8768_53
16S validation

value: Asymptomatic


title: PC9 cells, TF, biol rep 3


title: Plasmid pool, replicate 1 (T0)


title: Covid infection, Symptomatic, V2, Batch1, 1046-1-C, 16S

description:
Library name: zr8768_51
16S validation

value: Female

value: No


title: Covid infection, Asymptomatic, V2, Batch1, 1042-1-A, 16S

description:
Library name: zr8768_50
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1041-1-A, 16S

description:
Library name: zr8768_48
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1040-1-C, 16S

description:
Library name: zr8768_47
16S validation


title: Covid infection, Asymptomatic, V2, Batch1, 1039-2-C, 16S

description:
Library name: zr8768_46
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1038-2-A, 16S

description:
Library name: zr8768_44
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1039-1-A, 16S

description:
Library name: zr8768_45
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1037-1-A, 16S

description:
Library name: zr8768_42
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1036-3-A, 16S

description:
Library name: zr8768_41
16S validation


title: Plasmid pool, replicate 2 (T0)


title: Covid infection, Symptomatic, V2, Batch1, 1030-3-A, 16S

description:
Library name: zr8768_40
16S validation

value: delta


title: Covid infection, Symptomatic, V2, Batch1, 1032-1-C, 16S

description:
Library name: zr8768_39
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1016-1-C, 16S

description:
Library name: zr8768_37
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1022-1-A, 16S

description:
Library name: zr8768_36
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1034-1-C, 16S

description:
Library name: zr8768_35
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1016-2-C, 16S

description:
Library name: zr8768_34
16S validation


title: Covid infection, Asymptomatic, V2, Batch1, 1028-1-C, 16S

description:
Library name: zr8768_32
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1029-2-C, 16S

description:
Library name: zr8768_30
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1008-1-C, 16S

description:
Library name: zr8768_33
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1017-1-C, 16S

description:
Library name: zr8768_29
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1028-2-A, 16S

description:
Library name: zr8768_28
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1015-1-C, 16S

description:
Library name: zr8768_31
16S validation


title: Covid infection, Asymptomatic, V2, Batch1, 1001-2-C, 16S

description:
Library name: zr8768_24
16S validation

value: pre-delta


title: Covid infection, Symptomatic, V2, Batch1, 1005-1-C, 16S

description:
Library name: zr8768_23
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1025-1-A, 16S

description:
Library name: zr8768_27
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1038-2-A, 16S

description:
Library name: zr8768_19
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1005-2-C, 16S

description:
Library name: zr8768_25
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1046-1-C, 16S

description:
Library name: zr8768_21
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1037-1-A, 16S

description:
Library name: zr8768_17
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1037-2-C, 16S

description:
Library name: zr8768_43
16S validation


title: Covid infection, Asymptomatic, V1, Batch1, 1039-2-C, 16S

description:
Library name: zr8768_20
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1037-2-C, 16S

description:
Library name: zr8768_18
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1017-3-A, 16S

description:
Library name: zr8768_38
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1046-2-A, 16S

description:
Library name: zr8768_22
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1014-3-C, 16S

description:
Library name: zr8768_14
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1030-3-A, 16S

description:
Library name: zr8768_15
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1036-1-C, 16S

description:
Library name: zr8768_16
16S validation


title: Covid infection, Asymptomatic, V1, Batch1, 1030-1-C, 16S

description:
Library name: zr8768_13
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1017-3-A, 16S

description:
Library name: zr8768_12
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1008-1-C, 16S

description:
Library name: zr8768_10
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1022-1-A, 16S

description:
Library name: zr8768_11
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1017-1-C, 16S

description:
Library name: zr8768_8
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1029-2-C, 16S

description:
Library name: zr8768_9
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1022-2-A, 16S

description:
Library name: zr8768_6
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1005-2-C, 16S

description:
Library name: zr8768_5
16S validation


title: Covid infection, Symptomatic, V2, Batch1, 1022-2-A, 16S

description:
Library name: zr8768_26
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1002-5-A, 16S

description:
Library name: zr8768_4
16S validation


title: Covid infection, Symptomatic, V1, Batch1, 1005-1-C, 16S

description:
Library name: zr8768_3
16S validation


title: T47D_CK1

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

country: China

institute: 川北医学院

description: Library name: sample1

data_processing:
Sequencing data quality control、Reference genome alignment、Quantification、Differential analysis、Enrichment analysis、Alternative splicing analysis、Variant calling
Assembly: GRCh38
Supplementary files format and content: File 'gene_count.xls': Tab-delimited text file constituting the raw gene expression count matrix. Rows represent genes (with gene identifiers in the first column), and columns represent individual libraries/samples (e.g., T47D_CK1, T47D_CQ2). The values are the raw read counts aligned to each gene, serving as the primary data for differential expression analysis.

extract_protocol:
After 48 hours of PM2.5 exposure, total RNA was extracted using TRIzol reagent (Invitrogen, USA).
Libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions, and sequencing was ultimately performed on an Illumina NovaSeq 6000 platform.


title: T47D_CQ3

description: Library name: sample6


title: T47D_CQ1

description: Library name: sample4


title: T47D_CQ2

description: Library name: sample5


title: T47D_CK3

description: Library name: sample3


title: T47D_CK2

description: Library name: sample2


title: Covid infection, Symptomatic, V2, Batch3, 1068-1-A, RNA_seq

description:
Library name: 1068_1_a_2_S17
Dual-transcriptomic analysis

data_processing:
A dual-transcriptome workflow was employed to split the sequencing reads into two parts and align them to human and microbiota genome to get host transcriptomic expression and taxonomic classification abundance matrix, respectively. In specific, for host transcriptomic quantification, fastp (v.0.24.0) was first used to assess the quality of raw reads, and adapter sequences and low-quality bases were trimmed off or filtered out. The cleaned reads were then aligned to human hg38 reference genome by STAR (v.2.7.9a). Mapped reads from STAR were quantified using HTSeq (v.0.13.5) according to the GTF file from GENCODE hg38 annotations, while unmapped reads were retained for meta-transcriptomics analysis. To quantify microbiota abundance, unmapped reads from STAR were first imported into KneadData (v.0.12.0) for additional quality control (QC) to further filter residual reads related to the human genome (hg37dec_v0.1) and human transcriptome (human_hg38_refMrna) references. Of note, we set accuracy threshold of adapter match to 0 in order to avoid a second adapter removal procedure. Retained reads were subjected to taxonomic classification using Kraken2 (v.2.1.3). The relative abundance of species within a sample was then estimated using Bracken (Bayesian Re-estimation of Abundance after Classification with Kraken).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Collected swab samples were in Zymo DNA/RNA shield. Nucleic acid was extracted using Quick DNA/RNA Microprep Plus kit (Zymo Reserch, Cat No D7005).
Library was prepared using Quick-16S Plus NGS Library Prep kit (Zymo Research, Cat No D6430) targeting V4 by running 1-step PCR and sequenced on Illumina MiSeq with v3 reagent kit, 600cycles. Bisulfite converted amplified DNA was hybridized to an Illumina chip.


title: Covid infection, Symptomatic, V2, Batch3, 1070-1-C, RNA_seq

description:
Library name: 1070_1_c_2_S21
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch4, 1023-2-C, RNA_seq

description:
Library name: Nader_Inspire_2_S2
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch4, 1023-1-C, RNA_seq

description:
Library name: Nader_Inspire_1_S1
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1064-3-A, RNA_seq

description:
Library name: NS_71_SHA5104A34_S16
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch3, 1068-1-A, RNA_seq

description:
Library name: 1068_1_a_1_S16
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1064-1-C, RNA_seq

description:
Library name: NS_70_SHA5104A61_S46
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1067-1-C, RNA_seq

description:
Library name: NS_73_SHA5104A35_S25
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1028-2-A, 16S

description:
Library name: zr8768_7
16S validation


title: Covid infection, Symptomatic, V1, Batch3, 1070-1-C, RNA_seq

description:
Library name: 1070_1_c_1_S20
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1066-1-C, RNA_seq

description:
Library name: NS_72_SHA5104A15_S58
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1055-1-A, RNA_seq

description:
Library name: NS_67_SHA5104A14_S49
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1056-2-A, RNA_seq

description:
Library name: NS_69_SHA5104A60_S37
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1053-1-C, RNA_seq

description:
Library name: NS_63_SHA5104A12_S31
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1054-2-A, RNA_seq

description:
Library name: NS_66_SHA5104A33_S6
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1052-1-C, RNA_seq

description:
Library name: NS_62_SHA5104A31_S60
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1007-1-C, 16S

description:
Library name: zr8768_2
16S validation


title: Covid infection, Asymptomatic, V2, Batch2, 1053-2-C, RNA_seq

description:
Library name: NS_64_SHA5104A32_S69
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1003-1-C, 16S

description:
Library name: zr8768_1
16S validation


title: Covid infection, Symptomatic, V2, Batch2, 1051-3-C, RNA_seq

description:
Library name: NS_61_SHA5104A58_S19
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1045-2-A, RNA_seq

description:
Library name: NS_60_SHA5104A57_S9
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch4, 1023-4-A, RNA_seq

description:
Library name: Nader_Inspire_3_S6
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1043-3-A, RNA_seq

description:
Library name: NS_59_SHA5104A11_S22
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1040-3-A, RNA_seq

description:
Library name: NS_58_SHA5104A73_S11
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1038-1-A, RNA_seq

description:
Library name: NS_57_SHA5104A56_S72
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1030-2-C, RNA_seq

description:
Library name: NS_55_SHA5104A10_S13
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1017-2-A, RNA_seq

description:
Library name: NS_53_SHA5104A70_S56
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1036-2-A, RNA_seq

description:
Library name: NS_56_SHA5104A72_S74
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1055-2-C, RNA_seq

description:
Library name: NS_68_SHA5104A59_S28
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1067-1-C, RNA_seq

description:
Library name: NS_49_SHA5104A53_S45
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1006-1-C, RNA_seq

description:
Library name: NS_52_SHA5104A30_S51
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1066-1-C, RNA_seq

description:
Library name: NS_48_SHA5104A9_S3
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1004-1-C, RNA_seq

description:
Library name: NS_51_SHA5104A55_S63
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1064-3-A, RNA_seq

description:
Library name: NS_47_SHA5104A52_S36
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch2, 1002-4-A, RNA_seq

description:
Library name: NS_50_SHA5104A54_S54
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1056-2-A, RNA_seq

description:
Library name: NS_45_SHA5104A51_S27
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1064-1-C, RNA_seq

description:
Library name: NS_46_SHA5104A29_S42
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1055-1-A, RNA_seq

description:
Library name: NS_43_SHA5104A68_S38
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1053-2-C, RNA_seq

description:
Library name: NS_40_SHA5104A50_S18
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1053-1-C, RNA_seq

description:
Library name: NS_39_SHA5104A27_S24
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1054-2-A, RNA_seq

description:
Library name: NS_42_SHA5104A28_S33
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1045-2-A, RNA_seq

description:
Library name: NS_36_SHA5104A25_S5
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1043-3-A, RNA_seq

description:
Library name: NS_35_SHA5104A24_S68
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1036-2-A, RNA_seq

description:
Library name: NS_32_SHA5104A46_S53
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1038-1-A, RNA_seq

description:
Library name: NS_33_SHA5104A47_S62
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1052-1-C, RNA_seq

description:
Library name: NS_38_SHA5104A26_S15
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1030-2-C, RNA_seq

description:
Library name: NS_31_SHA5104A45_S44
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1051-3-C, RNA_seq

description:
Library name: NS_37_SHA5104A49_S8
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch2, 1029-3-C, RNA_seq

description:
Library name: NS_54_SHA5104A71_S65
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1029-3-C, RNA_seq

description:
Library name: NS_30_SHA5104A23_S59
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1002-4-A, RNA_seq

description:
Library name: NS_26_SHA5104A44_S35
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1046-2-A, RNA_seq

description:
Library name: 95_SHA3001A95_S84
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1004-1-C, RNA_seq

description:
Library name: NS_27_SHA5104A8_S66
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1046-3-C, RNA_seq

description:
Library name: 96_SHA3001A96_S96
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1006-1-C, RNA_seq

description:
Library name: NS_28_SHA5104A65_S10
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1046-1-C, RNA_seq

description:
Library name: 94_SHA3001A94_S72
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1042-3-C, RNA_seq

description:
Library name: 93_SHA3001A93_S60
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1041-2-A, RNA_seq

description:
Library name: 90_SHA3001A90_S24
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1039-2-C, RNA_seq

description:
Library name: 87_SHA3001A87_S83
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1005-2-C, RNA_seq

description:
Library name: 9_SHA3001A9_S2
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1042-2-C, RNA_seq

description:
Library name: 92_SHA3001A92_S48
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1042-1-A, RNA_seq

description:
Library name: 91_SHA3001A91_S36
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1038-3-A, RNA_seq

description:
Library name: 85_SHA3001A85_S59
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1040-3-A, RNA_seq

description:
Library name: NS_34_SHA5104A48_S71
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1039-1-A, RNA_seq

description:
Library name: 86_SHA3001A86_S71
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1038-2-A, RNA_seq

description:
Library name: 84_SHA3001A84_S47
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1036-1-C, RNA_seq

description:
Library name: 80_SHA3001A80_S94
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1001-1-C, RNA_seq

description:
Library name: 8_SHA3001A8_S85
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1037-1-A, RNA_seq

description:
Library name: 82_SHA3001A82_S23
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1037-2-C, RNA_seq

description:
Library name: 83_SHA3001A83_S35
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1036-3-A, RNA_seq

description:
Library name: 81_SHA3001A81_S11
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1030-3-A, RNA_seq

description:
Library name: 79_SHA3001A79_S82
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1030-1-C, RNA_seq

description:
Library name: 76_SHA3001A76_S46
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch2, 1017-2-A, RNA_seq

description:
Library name: NS_29_SHA5104A66_S20
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1032-1-C, RNA_seq

description:
Library name: 78_SHA3001A78_S70
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1017-3-A, RNA_seq

description:
Library name: 75_SHA3001A75_S34
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1022-1-A, RNA_seq

description:
Library name: 73_SHA3001A73_S10
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1014-3-C, RNA_seq

description:
Library name: 77_SHA3001A77_S58
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1016-2-C, RNA_seq

description:
Library name: 71_SHA3001A71_S81
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch2, 1055-2-C, RNA_seq

description:
Library name: NS_44_SHA5104A69_S47
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1040-1-C, RNA_seq

description:
Library name: 88_SHA3001A88_S95
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1028-1-C, RNA_seq

description:
Library name: 69_SHA3001A69_S57
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1041-1-A, RNA_seq

description:
Library name: 89_SHA3001A89_S12
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1002-5-A, RNA_seq

description:
Library name: 7_SHA3001A7_S73
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1015-1-C, RNA_seq

description:
Library name: 66_SHA3001A66_S21
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1029-2-C, RNA_seq

description:
Library name: 65_SHA3001A65_S9
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1008-3-A, RNA_seq

description:
Library name: 67_SHA3001A67_S33
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1031-1-C, RNA_seq

description:
Library name: 68_SHA3001A68_S45
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1028-2-A, RNA_seq

description:
Library name: 62_SHA3001A62_S68
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1017-1-C, RNA_seq

description:
Library name: 63_SHA3001A63_S80
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1015-2-C, RNA_seq

description:
Library name: 64_SHA3001A64_S92
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1025-1-A, RNA_seq

description:
Library name: 60_SHA3001A60_S44
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1025-2-A, RNA_seq

description:
Library name: 61_SHA3001A61_S56
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1022-2-A, RNA_seq

description:
Library name: 59_SHA3001A59_S32
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1001-2-C, RNA_seq

description:
Library name: 6_SHA3001A6_S61
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1002-5-A, RNA_seq

description:
Library name: 55_SHA3001A55_S79
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1001-1-C, RNA_seq

description:
Library name: 56_SHA3001A56_S91
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1016-1-C, RNA_seq

description:
Library name: 74_SHA3001A74_S22
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1005-2-C, RNA_seq

description:
Library name: 57_SHA3001A57_S8
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1034-1-C, RNA_seq

description:
Library name: 72_SHA3001A72_S93
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1001-2-C, RNA_seq

description:
Library name: 54_SHA3001A54_S67
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1001-3-A, RNA_seq

description:
Library name: 58_SHA3001A58_S20
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1008-1-C, RNA_seq

description:
Library name: 70_SHA3001A70_S69
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1002-1-C, RNA_seq

description:
Library name: 5_SHA3001A5_S49
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1003-1-C, RNA_seq

description:
Library name: 49_SHA3001A49_S7
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1002-2-C, RNA_seq

description:
Library name: 52_SHA3001A52_S43
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V2, Batch1, 1002-1-C, RNA_seq

description:
Library name: 53_SHA3001A53_S55
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1005-1-C, RNA_seq

description:
Library name: 51_SHA3001A51_S31
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V2, Batch1, 1007-1-C, RNA_seq

description:
Library name: 50_SHA3001A50_S19
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1046-3-C, RNA_seq

description:
Library name: 48_SHA3001A48_S90
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1046-2-A, RNA_seq

description:
Library name: 47_SHA3001A47_S78
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1042-1-A, RNA_seq

description:
Library name: 43_SHA3001A43_S30
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1041-1-A, RNA_seq

description:
Library name: 41_SHA3001A41_S6
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1042-3-C, RNA_seq

description:
Library name: 45_SHA3001A45_S54
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1042-2-C, RNA_seq

description:
Library name: 44_SHA3001A44_S42
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1041-2-A, RNA_seq

description:
Library name: 42_SHA3001A42_S18
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1046-1-C, RNA_seq

description:
Library name: 46_SHA3001A46_S66
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1040-1-C, RNA_seq

description:
Library name: 40_SHA3001A40_S89
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1038-2-A, RNA_seq

description:
Library name: 36_SHA3001A36_S41
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1002-2-C, RNA_seq

description:
Library name: 4_SHA3001A4_S37
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1037-2-C, RNA_seq

description:
Library name: 35_SHA3001A35_S29
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1037-1-A, RNA_seq

description:
Library name: 34_SHA3001A34_S17
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1036-1-C, RNA_seq

description:
Library name: 32_SHA3001A32_S88
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1005-1-C, RNA_seq

description:
Library name: 3_SHA3001A3_S25
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1030-1-C, RNA_seq

description:
Library name: 28_SHA3001A28_S40
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1038-3-A, RNA_seq

description:
Library name: 37_SHA3001A37_S53
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1017-3-A, RNA_seq

description:
Library name: 27_SHA3001A27_S28
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1016-1-C, RNA_seq

description:
Library name: 26_SHA3001A26_S16
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1030-3-A, RNA_seq

description:
Library name: 31_SHA3001A31_S76
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1014-3-C, RNA_seq

description:
Library name: 29_SHA3001A29_S52
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1034-1-C, RNA_seq

description:
Library name: 24_SHA3001A24_S87
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1016-2-C, RNA_seq

description:
Library name: 23_SHA3001A23_S75
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1036-3-A, RNA_seq

description:
Library name: 33_SHA3001A33_S5
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1031-1-C, RNA_seq

description:
Library name: 20_SHA3001A20_S39
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1028-1-C, RNA_seq

description:
Library name: 21_SHA3001A21_S51
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1007-1-C, RNA_seq

description:
Library name: 2_SHA3001A2_S13
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1008-1-C, RNA_seq

description:
Library name: 22_SHA3001A22_S63
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1008-3-A, RNA_seq

description:
Library name: 19_SHA3001A19_S27
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1029-2-C, RNA_seq

description:
Library name: 17_SHA3001A17_S3
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1015-1-C, RNA_seq

description:
Library name: 18_SHA3001A18_S15
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1039-2-C, RNA_seq

description:
Library name: 39_SHA3001A39_S77
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1039-1-A, RNA_seq

description:
Library name: 38_SHA3001A38_S65
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1015-2-C, RNA_seq

description:
Library name: 16_SHA3001A16_S86
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1028-2-A, RNA_seq

description:
Library name: 14_SHA3001A14_S62
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1025-1-A, RNA_seq

description:
Library name: 12_SHA3001A12_S38
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1017-1-C, RNA_seq

description:
Library name: 15_SHA3001A15_S74
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1025-2-A, RNA_seq

description:
Library name: 13_SHA3001A13_S50
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1001-3-A, RNA_seq

description:
Library name: 10_SHA3001A10_S14
Dual-transcriptomic analysis


title: Covid infection, Asymptomatic, V1, Batch1, 1003-1-C, RNA_seq

description:
Library name: 1_SHA3001A1_S1
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1022-2-A, RNA_seq

description:
Library name: 11_SHA3001A11_S26
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1032-1-C, RNA_seq

description:
Library name: 30_SHA3001A30_S64
Dual-transcriptomic analysis


title: Covid infection, Symptomatic, V1, Batch1, 1022-1-A, RNA_seq

description:
Library name: 25_SHA3001A25_S4
Dual-transcriptomic analysis


title: SPCN332 Functionalis stroma

city: Liverpool

first: Alison

last: Maclean

state: Merseyside

address: Crown Street

department: Department of Women's and Children's Health

country: United Kingdom

institute: University of Liverpool, Institute of Life Course and Medical Sciences

description:
Library name: DSP-1001660011750-B-G08
FFPE spatial transcriptome sequencing

data_processing:
Raw sequenicng data were processed using the NanoSring GeoMx digital spatial profiling pipeline
Photocleaved oligonucleotides from ROI aspirates, containing target-specific readout tags and unique molecular identifiers (UMIs), were used for library preparation
Libraries were quality-checked using a Bioanalyzer system (Agilent) and quantified with a Qubit high-sensitivity DNA kit
Sequencing was conducted on an Illumina NovaSeq system using NovaSeq S1 flow cells with paired-end 2 x 50 bp reads, generating approximately 1300 million clusters per cell.
Digital count conversion (DCC) files were produced for each target probe.
Assembly: Human
Supplementary files format and content: .dcc files
Library strategy: Spatial Transcriptomics

source_name: Uterus

extract_protocol:
Formalin-fixed, paraffin embedded tissue samples were sectioned at 5uM with a microtome onto RNAse free superfrost plus slides.
Spatial transcriptome sequencing libraries were prepared with NanoString GeoMx digital spatial profiling reagent kit according to manufacturers guidelines.

value: Uterus


title: SPCN332 Functionalis panCK

description:
Library name: DSP-1001660011750-B-G07
FFPE spatial transcriptome sequencing


title: SPCN332 Functionalis CD45

description:
Library name: DSP-1001660011750-B-G05
FFPE spatial transcriptome sequencing


title: SPCN332 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-G03
FFPE spatial transcriptome sequencing


title: SPCN332 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-G04
FFPE spatial transcriptome sequencing


title: SPCN332 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-G02
FFPE spatial transcriptome sequencing


title: SPCN332 Functionalis CD31

description:
Library name: DSP-1001660011750-B-G06
FFPE spatial transcriptome sequencing


title: SPCN332 Adenomyosis CD45

description:
Library name: DSP-1001660011750-B-G01
FFPE spatial transcriptome sequencing


title: SPCN332 Basalis stroma

description:
Library name: DSP-1001660011750-B-F11
FFPE spatial transcriptome sequencing


title: SPCN332 LE panCK

description:
Library name: DSP-1001660011750-B-F08
FFPE spatial transcriptome sequencing


title: SPCN332 Basalis panCK

description:
Library name: DSP-1001660011750-B-F10
FFPE spatial transcriptome sequencing


title: SPCE078 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-F07
FFPE spatial transcriptome sequencing


title: SPCE078 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-F06
FFPE spatial transcriptome sequencing


title: SPCE078 Functionalis CD45 01

description:
Library name: DSP-1001660011750-B-F02
FFPE spatial transcriptome sequencing


title: SPCE078 Functionalis CD45 02

description:
Library name: DSP-1001660011750-B-F03
FFPE spatial transcriptome sequencing


title: SPCE078 Basalis stroma

description:
Library name: DSP-1001660011750-B-F01
FFPE spatial transcriptome sequencing


title: SPCE078 Basalis panCK

description:
Library name: DSP-1001660011750-B-E12
FFPE spatial transcriptome sequencing


title: SPCE078 Basalis CD45-02

description:
Library name: DSP-1001660011750-B-E11
FFPE spatial transcriptome sequencing


title: SPCE078 Functionalis panCK

description:
Library name: DSP-1001660011750-B-F04
FFPE spatial transcriptome sequencing


title: SPCE078 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-E10
FFPE spatial transcriptome sequencing


title: SPCE078 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-E09
FFPE spatial transcriptome sequencing


title: SPCN365 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-E07
FFPE spatial transcriptome sequencing


title: SPCE078 LE panCK

description:
Library name: DSP-1001660011750-B-E08
FFPE spatial transcriptome sequencing


title: SPCN365 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-E06
FFPE spatial transcriptome sequencing


title: SPCN365 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-E05
FFPE spatial transcriptome sequencing


title: SPCN365 Adenomyosis CD45

description:
Library name: DSP-1001660011750-B-E04
FFPE spatial transcriptome sequencing


title: SPCN332 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-F12
FFPE spatial transcriptome sequencing


title: SPCN365 Basalis CD31

description:
Library name: DSP-1001660011750-B-E01
FFPE spatial transcriptome sequencing


title: SPCN365 Basalis stroma

description:
Library name: DSP-1001660011750-B-E03
FFPE spatial transcriptome sequencing


title: SPCN365 Basalis cd45

description:
Library name: DSP-1001660011750-B-D12
FFPE spatial transcriptome sequencing


title: SPCN365 Functionalis CD31

description:
Library name: DSP-1001660011750-B-D09
FFPE spatial transcriptome sequencing


title: SPCN365 LE panCK

description:
Library name: DSP-1001660011750-B-D07
FFPE spatial transcriptome sequencing


title: SPCN365 Basalis panCK

description:
Library name: DSP-1001660011750-B-E02
FFPE spatial transcriptome sequencing


title: SPCN365 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-D06
FFPE spatial transcriptome sequencing


title: SPCN365 Functionalis stroma

description:
Library name: DSP-1001660011750-B-D11
FFPE spatial transcriptome sequencing


title: SPCN365 Functionalis panCK

description:
Library name: DSP-1001660011750-B-D10
FFPE spatial transcriptome sequencing


title: SPCE078 Functionalis stroma

description:
Library name: DSP-1001660011750-B-F05
FFPE spatial transcriptome sequencing


title: SPCN035 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-D05
FFPE spatial transcriptome sequencing


title: SPCN035 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-D03
FFPE spatial transcriptome sequencing


title: SPCN035 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-D04
FFPE spatial transcriptome sequencing


title: SPCN035 Adenomyosis CD31

description:
Library name: DSP-1001660011750-B-D02
FFPE spatial transcriptome sequencing


title: SPCN035 Adenomyosis CD45

description:
Library name: DSP-1001660011750-B-D01
FFPE spatial transcriptome sequencing


title: SPCN035 Functionalis panCK

description:
Library name: DSP-1001660011750-B-C10
FFPE spatial transcriptome sequencing


title: SPCN035 Functionalis CD31

description:
Library name: DSP-1001660011750-B-C09
FFPE spatial transcriptome sequencing


title: SPCN035 Basalis stroma

description:
Library name: DSP-1001660011750-B-C08
FFPE spatial transcriptome sequencing


title: SPCN035 Basalis panCK

description:
Library name: DSP-1001660011750-B-C07
FFPE spatial transcriptome sequencing


title: SPCN332 Basalis CD45

description:
Library name: DSP-1001660011750-B-F09
FFPE spatial transcriptome sequencing


title: SPCN035 Basalis CD31

description:
Library name: DSP-1001660011750-B-C06
FFPE spatial transcriptome sequencing


title: SPCN035 Basalis cd45

description:
Library name: DSP-1001660011750-B-C05
FFPE spatial transcriptome sequencing


title: SPCN307 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-C03
FFPE spatial transcriptome sequencing


title: SPCN307 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-C02
FFPE spatial transcriptome sequencing


title: SPCN307 Basalis panCK

description:
Library name: DSP-1001660011750-B-B09
FFPE spatial transcriptome sequencing


title: SPCN365 Functionalis CD45

description:
Library name: DSP-1001660011750-B-D08
FFPE spatial transcriptome sequencing


title: SPCN307 Adenomyosis CD45

description:
Library name: DSP-1001660011750-B-B12
FFPE spatial transcriptome sequencing


title: SPCN307 Basalis stroma

description:
Library name: DSP-1001660011750-B-B11
FFPE spatial transcriptome sequencing


title: SPCN307 Basalis CD45

description:
Library name: DSP-1001660011750-B-B10
FFPE spatial transcriptome sequencing


title: SPCN307 Adenomyosis CD31

description:
Library name: DSP-1001660011750-B-C01
FFPE spatial transcriptome sequencing


title: LWB210144 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-B03
FFPE spatial transcriptome sequencing


title: SPCN307 Functionalis stroma

description:
Library name: DSP-1001660011750-B-B07
FFPE spatial transcriptome sequencing


title: SPCN307 Functionalis panCK

description:
Library name: DSP-1001660011750-B-B05
FFPE spatial transcriptome sequencing


title: LWB210144 Adenomyosis stroma

description:
Library name: DSP-1001660011750-B-B01
FFPE spatial transcriptome sequencing


title: SPCN307 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-B08
FFPE spatial transcriptome sequencing


title: SPCN307 Functionalis CD45

description:
Library name: DSP-1001660011750-B-B06
FFPE spatial transcriptome sequencing


title: LWB210144 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-B02
FFPE spatial transcriptome sequencing


title: SPCN035 Myometrium_near_endo

description:
Library name: DSP-1001660011750-B-C12
FFPE spatial transcriptome sequencing


title: LWB210144 Functionalis CD45

description:
Library name: DSP-1001660011750-B-A07
FFPE spatial transcriptome sequencing


title: LWB210144 Adenomyosis CD45

description:
Library name: DSP-1001660011750-B-A11
FFPE spatial transcriptome sequencing


title: SPCN035 Functionalis stroma

description:
Library name: DSP-1001660011750-B-C11
FFPE spatial transcriptome sequencing


title: LWB210144 Adenomyosis CD31

description:
Library name: DSP-1001660011750-B-A12
FFPE spatial transcriptome sequencing


title: LWB210144 Adenomyosis panCK

description:
Library name: DSP-1001660011750-B-A10
FFPE spatial transcriptome sequencing


title: LWB210144 Functionalis stroma

description:
Library name: DSP-1001660011750-B-A09
FFPE spatial transcriptome sequencing


title: LWB210144 Functionalis panCK

description:
Library name: DSP-1001660011750-B-A06
FFPE spatial transcriptome sequencing


title: LWB210144 Basalis CD31

description:
Library name: DSP-1001660011750-B-A04
FFPE spatial transcriptome sequencing


title: SPCN307 Myometrium_near_adeno

description:
Library name: DSP-1001660011750-B-C04
FFPE spatial transcriptome sequencing


title: LWB210144 Functionalis CD31

description:
Library name: DSP-1001660011750-B-A08
FFPE spatial transcriptome sequencing


title: SPCE078 Basalis CD45-01

description:
Library name: DSP-1001660011751-A-F07
FFPE spatial transcriptome sequencing


title: SPCN307 LE panCK

description:
Library name: DSP-1001660011750-B-B04
FFPE spatial transcriptome sequencing


title: LWB210144 Basalis panCK

description:
Library name: DSP-1001660011750-B-A02
FFPE spatial transcriptome sequencing


title: SPCN277 Adenomyosis CD45-02

description:
Library name: DSP-1001660011751-A-F01
FFPE spatial transcriptome sequencing


title: LWB210144 Basalis CD45

description:
Library name: DSP-1001660011750-B-A03
FFPE spatial transcriptome sequencing


title: No template control 02

description:
Library name: DSP-1001660011750-B-A01
FFPE spatial transcriptome sequencing


title: SPCN277 Basalis CD31

description:
Library name: DSP-1001660011751-A-E09
FFPE spatial transcriptome sequencing


title: SPCN277 Myometrium_near_adeno

description:
Library name: DSP-1001660011751-A-E12
FFPE spatial transcriptome sequencing


title: SPCN277 Myometrium_near_endo

description:
Library name: DSP-1001660011751-A-E11
FFPE spatial transcriptome sequencing


title: SPCN277 Basalis CD45

description:
Library name: DSP-1001660011751-A-E08
FFPE spatial transcriptome sequencing


title: SPCN277 Basalis stroma

description:
Library name: DSP-1001660011751-A-E10
FFPE spatial transcriptome sequencing


title: SPCN277 Adenomyosis CD31

description:
Library name: DSP-1001660011751-A-E05
FFPE spatial transcriptome sequencing


title: SPCN277 Adenomyosis stroma

description:
Library name: DSP-1001660011751-A-E06
FFPE spatial transcriptome sequencing


title: SPCN277 Basalis panCK

description:
Library name: DSP-1001660011751-A-E07
FFPE spatial transcriptome sequencing


title: SPCN277 Functionalis stroma

description:
Library name: DSP-1001660011751-A-E02
FFPE spatial transcriptome sequencing


title: LWB210144 Basalis stroma

description:
Library name: DSP-1001660011750-B-A05
FFPE spatial transcriptome sequencing


title: SPCN277 Adenomyosis panCK

description:
Library name: DSP-1001660011751-A-E03
FFPE spatial transcriptome sequencing


title: SPCN277 Functionalis CD31

description:
Library name: DSP-1001660011751-A-E01
FFPE spatial transcriptome sequencing


title: SPCN277 Functionalis panCK

description:
Library name: DSP-1001660011751-A-D11
FFPE spatial transcriptome sequencing


title: SPCN277 Functionalis CD45

description:
Library name: DSP-1001660011751-A-D12
FFPE spatial transcriptome sequencing


title: SPCN044 Adenomyosis stroma

description:
Library name: DSP-1001660011751-A-D09
FFPE spatial transcriptome sequencing


title: SPCN044 Adenomyosis panCK

description:
Library name: DSP-1001660011751-A-D06
FFPE spatial transcriptome sequencing


title: SPCN044 Adenomyosis CD31

description:
Library name: DSP-1001660011751-A-D08
FFPE spatial transcriptome sequencing


title: SPCN044 Adenomyosis CD45

description:
Library name: DSP-1001660011751-A-D07
FFPE spatial transcriptome sequencing


title: SPCN044 Myometrium_near_adeno

description:
Library name: DSP-1001660011751-A-D05
FFPE spatial transcriptome sequencing


title: SPCN044 Functionalis stroma

description:
Library name: DSP-1001660011751-A-D04
FFPE spatial transcriptome sequencing


title: SPCN044 Functionalis CD45

description:
Library name: DSP-1001660011751-A-D02
FFPE spatial transcriptome sequencing


title: SPCN044 Functionalis CD31

description:
Library name: DSP-1001660011751-A-D03
FFPE spatial transcriptome sequencing


title: SPCN044 Basalis stroma

description:
Library name: DSP-1001660011751-A-C12
FFPE spatial transcriptome sequencing


title: SPCN044 Functionalis panCK

description:
Library name: DSP-1001660011751-A-D01
FFPE spatial transcriptome sequencing


title: SPCN044 Basalis CD31

description:
Library name: DSP-1001660011751-A-C11
FFPE spatial transcriptome sequencing


title: SPCN044 Basalis panCK

description:
Library name: DSP-1001660011751-A-C09
FFPE spatial transcriptome sequencing


title: SPCN044 LE panCK

description:
Library name: DSP-1001660011751-A-C08
FFPE spatial transcriptome sequencing


title: LWB220063 Adenomyosis stroma

description:
Library name: DSP-1001660011751-A-C05
FFPE spatial transcriptome sequencing


title: LWB220063 Adenomyosis panCK

description:
Library name: DSP-1001660011751-A-C06
FFPE spatial transcriptome sequencing


title: SPCN277 LE panCK

description:
Library name: DSP-1001660011751-A-C07
FFPE spatial transcriptome sequencing


title: LWB220063 Adenomyosis CD31

description:
Library name: DSP-1001660011751-A-C04
FFPE spatial transcriptome sequencing


title: SPCN277 Adenomyosis CD45-01

description:
Library name: DSP-1001660011751-A-E04
FFPE spatial transcriptome sequencing


title: LWB220063 Basalis CD31

description:
Library name: DSP-1001660011751-A-B11
FFPE spatial transcriptome sequencing


title: LWB220063 Basalis panCK

description:
Library name: DSP-1001660011751-A-C01
FFPE spatial transcriptome sequencing


title: SPCN044 Myometrium_near_endo

description:
Library name: DSP-1001660011751-A-D10
FFPE spatial transcriptome sequencing


title: LWB220063 LE panCK 02

description:
Library name: DSP-1001660011751-A-B09
FFPE spatial transcriptome sequencing


title: LWB220063 Myometrium_near_adeno

description:
Library name: DSP-1001660011751-A-C03
FFPE spatial transcriptome sequencing


title: LWB220063 Myometrium_near_endo

description:
Library name: DSP-1001660011751-A-C02
FFPE spatial transcriptome sequencing


title: LWB220063 Basalis CD45

description:
Library name: DSP-1001660011751-A-B10
FFPE spatial transcriptome sequencing


title: LWB220063 LE panCK 01

description:
Library name: DSP-1001660011751-A-B08
FFPE spatial transcriptome sequencing


title: SPCN351 Adenomyosis stroma

description:
Library name: DSP-1001660011751-A-B06
FFPE spatial transcriptome sequencing


title: LWB220063 Functionalis CD31

description:
Library name: DSP-1001660011751-A-B02
FFPE spatial transcriptome sequencing


title: SPCN351 Adenomyosis CD31

description:
Library name: DSP-1001660011751-A-B05
FFPE spatial transcriptome sequencing


title: LWB220063 Basalis stroma

description:
Library name: DSP-1001660011751-A-B12
FFPE spatial transcriptome sequencing


title: LWB220063 Functionalis stroma

description:
Library name: DSP-1001660011751-A-B03
FFPE spatial transcriptome sequencing


title: LWB220063 Functionalis CD45

description:
Library name: DSP-1001660011751-A-B01
FFPE spatial transcriptome sequencing


title: SPCN351 Basalis stroma

description:
Library name: DSP-1001660011751-A-A10
FFPE spatial transcriptome sequencing


title: SPCN044 Basalis CD45

description:
Library name: DSP-1001660011751-A-C10
FFPE spatial transcriptome sequencing


title: SPCN351 Basalis CD31

description:
Library name: DSP-1001660011751-A-A09
FFPE spatial transcriptome sequencing


title: SPCN351 Basalis CD45

description:
Library name: DSP-1001660011751-A-A08
FFPE spatial transcriptome sequencing


title: LWB220063 Functionalis panCK

description:
Library name: DSP-1001660011751-A-B04
FFPE spatial transcriptome sequencing


title: SPCN351 Myometrium_near_adeno

description:
Library name: DSP-1001660011751-A-A12
FFPE spatial transcriptome sequencing


title: SPCN351 Basalis panCK

description:
Library name: DSP-1001660011751-A-A11
FFPE spatial transcriptome sequencing


title: SPCN351 Functionalis panCK

description:
Library name: DSP-1001660011751-A-A07
FFPE spatial transcriptome sequencing


title: SPCN351 Functionalis CD45

description:
Library name: DSP-1001660011751-A-A04
FFPE spatial transcriptome sequencing


title: SPCN351 LE panCK

description:
Library name: DSP-1001660011751-A-A03
FFPE spatial transcriptome sequencing


title: SPCN351 Myometrium_near_endo

description:
Library name: DSP-1001660011751-A-A02
FFPE spatial transcriptome sequencing


title: SPCN351 Adenomyosis panCK

description:
Library name: DSP-1001660011751-A-B07
FFPE spatial transcriptome sequencing


title: No template control 01

description:
Library name: DSP-1001660011751-A-A01
FFPE spatial transcriptome sequencing


title: TMA8 | 003 | Full ROI

city: Baltimore

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans Street, room 305

department: Department of Gynecology and Obstetrics

institute: Johns Hopkins Medical Institutions

description: Library name: Sample 444

data_processing:
Raw sequencing data were processed using either NanoString GeoMx NGS Pipeline v2.3.4 or  v2.3.5.
Assembly: GRCh38
Supplementary files format and content: geo_count_data.xlsx: count data for each ROIs
Library strategy: Spatial Transcriptomics

source_name: fallopian tube

extract_protocol:
Following probe hybridization, UV‐cleavable indexing oligonucleotides were released from each ROI by targeted UV illumination on the GeoMx DSP instrument.
Spatial transcriptome sequencing library

value: fallopian tube

tag: tissue type

value: epithelium

tag: diagnosis

value: High grade serous carcinoma


title: TMA8 | 004 | Full ROI

description: Library name: Sample 445

tag: tissue

value: STIC

tag: batch


title: TMA7 | 015 | Full ROI

description: Library name: Sample 440

value: Normal fallopian tube epithelium


title: TMA8 | 005 | Full ROI

description: Library name: Sample 446


title: TMA8 | 002 | Full ROI

description: Library name: Sample 443


title: TMA7 | 014 | Full ROI

description: Library name: Sample 439


title: TMA8 | 001 | Full ROI

description: Library name: Sample 442


title: TMA7 | 013 | Full ROI

description: Library name: Sample 438


title: TMA7 | 012 | Full ROI

description: Library name: Sample 437


title: TMA7 | 016 | Full ROI

description: Library name: Sample 441


title: TMA7 | 011 | Full ROI

description: Library name: Sample 436


title: TMA7 | 010 | Full ROI

description: Library name: Sample 435

value: STIL


title: TMA7 | 007 | Full ROI

description: Library name: Sample 432


title: TMA7 | 006 | Full ROI

description: Library name: Sample 431


title: TMA7 | 009 | Full ROI

description: Library name: Sample 434


title: TMA6 | 041 | Full ROI

description: Library name: Sample 425

value: stroma

tag: corresponding epithelium

value: TMA6 | 032 | Full ROI


title: SPCN351 Functionalis stroma

description:
Library name: DSP-1001660011751-A-A06
FFPE spatial transcriptome sequencing


title: TMA7 | 004 | Full ROI

description: Library name: Sample 429


title: TMA7 | 001 | Full ROI

description: Library name: Sample 426


title: TMA6 | 039 | Full ROI

description: Library name: Sample 423

value: TMA6 | 036 | Full ROI


title: SPCN351 Functionalis CD31

description:
Library name: DSP-1001660011751-A-A05
FFPE spatial transcriptome sequencing


title: TMA7 | 008 | Full ROI

description: Library name: Sample 433


title: TMA7 | 003 | Full ROI

description: Library name: Sample 428


title: TMA7 | 002 | Full ROI

description: Library name: Sample 427


title: TMA6 | 038 | Full ROI

description: Library name: Sample 422

value: TMA6 | 037 | Full ROI


title: TMA6 | 035 | Full ROI

description: Library name: Sample 419


title: TMA6 | 030 | Full ROI

description: Library name: Sample 414

value: TMA6 | 029 | Full ROI


title: TMA6 | 031 | Full ROI

description: Library name: Sample 415


title: TMA6 | 034 | Full ROI

description: Library name: Sample 418


title: TMA6 | 027 | Full ROI

description: Library name: Sample 411


title: TMA6 | 037 | Full ROI

description: Library name: Sample 421


title: TMA6 | 029 | Full ROI

description: Library name: Sample 413


title: TMA6 | 032 | Full ROI

description: Library name: Sample 416


title: TMA6 | 028 | Full ROI

description: Library name: Sample 412

value: TMA6 | 027 | Full ROI


title: TMA6 | 026 | Full ROI

description: Library name: Sample 410

value: TMA6 | 025 | Full ROI


title: TMA6 | 025 | Full ROI

description: Library name: Sample 409


title: TMA6 | 036 | Full ROI

description: Library name: Sample 420


title: TMA6 | 022 | Full ROI

description: Library name: Sample 406

value: TMA6 | 021 | Full ROI


title: TMA6 | 021 | Full ROI

description: Library name: Sample 405


title: TMA6 | 023 | Full ROI

description: Library name: Sample 407

value: Endometrial endometrioid carcinoma


title: TMA6 | 020 | Full ROI

description: Library name: Sample 404

value: TMA6 | 019 | Full ROI


title: TMA6 | 040 | Full ROI

description: Library name: Sample 424

value: TMA6 | 033 | Full ROI


title: TMA6 | 018 | Full ROI

description: Library name: Sample 402

value: fallopian tube

value: TMA6 | 017 | Full ROI


title: TMA6 | 015 | Full ROI

description: Library name: Sample 399

value: epithelium


title: TMA6 | 017 | Full ROI

description: Library name: Sample 401

value: High grade serous carcinoma


title: TMA7 | 005 | Full ROI

description: Library name: Sample 430

value: Normal fallopian tube epithelium


title: TMA6 | 016 | Full ROI

description: Library name: Sample 400

value: TMA6 | 015 | Full ROI


title: TMA6 | 014 | Full ROI

description: Library name: Sample 398

value: stroma

value: STIL

value: TMA6 | 013 | Full ROI


title: TMA6 | 013 | Full ROI

description: Library name: Sample 397


title: TMA6 | 012 | Full ROI

description: Library name: Sample 396

value: TMA6 | 011 | Full ROI


title: TMA6 | 033 | Full ROI

description: Library name: Sample 417

value: STIC


title: TMA6 | 010 | Full ROI

description: Library name: Sample 394

value: TMA6 | 009 | Full ROI


title: TMA6 | 009 | Full ROI

description: Library name: Sample 393


title: TMA6 | 011 | Full ROI

description: Library name: Sample 395


title: TMA6 | 007 | Full ROI

description: Library name: Sample 391


title: TMA6 | 008 | Full ROI

description: Library name: Sample 392

value: TMA6 | 007 | Full ROI


title: TMA6 | 003 | Full ROI

description: Library name: Sample 387


title: TMA6 | 005 | Full ROI

description: Library name: Sample 389


title: TMA6 | 024 | Full ROI

description: Library name: Sample 408

value: TMA6 | 023 | Full ROI


title: TMA6 | 004 | Full ROI

description: Library name: Sample 388

value: TMA6 | 003 | Full ROI


title: TMA6 | 002 | Full ROI

description: Library name: Sample 386

value: TMA6 | 001 | Full ROI


title: TMA6 | 001 | Full ROI

description: Library name: Sample 385


title: TMA5 | 008 | Full ROI

description: Library name: Sample 383


title: TMA5 | 007 | Full ROI

description: Library name: Sample 382


title: TMA5 | 009 | Full ROI

description: Library name: Sample 384


title: TMA5 | 005 | Full ROI

description: Library name: Sample 380


title: TMA5 | 004 | Full ROI

description: Library name: Sample 379


title: TMA5 | 003 | Full ROI

description: Library name: Sample 378


title: TMA6 | 019 | Full ROI

description: Library name: Sample 403


title: TMA5 | 006 | Full ROI

description: Library name: Sample 381


title: TMA5 | 002 | Full ROI

description: Library name: Sample 377


title: TMA5 | 001 | Full ROI

description: Library name: Sample 376


title: TMA4 | 032 | Full ROI

description: Library name: Sample 373

value: TMA4 | 031 | Full ROI


title: TMA4 | 033 | Full ROI

description: Library name: Sample 374

value: fallopian tube


title: TMA4 | 031 | Full ROI

description: Library name: Sample 372


title: TMA4 | 030 | Full ROI

description: Library name: Sample 371

value: TMA4 | 029 | Full ROI


title: TMA4 | 029 | Full ROI

description: Library name: Sample 370

value: epithelium


title: TMA4 | 034 | Full ROI

description: Library name: Sample 375

value: TMA4 | 033 | Full ROI


title: TMA4 | 027 | Full ROI

description: Library name: Sample 368


title: TMA4 | 026 | Full ROI

description: Library name: Sample 367

value: High grade serous carcinoma

value: TMA4 | 025 | Full ROI


title: TMA4 | 025 | Full ROI

description: Library name: Sample 366


title: TMA4 | 024 | Full ROI

description: Library name: Sample 365

value: stroma

value: Normal fallopian tube epithelium

value: TMA4 | 023 | Full ROI


title: TMA4 | 023 | Full ROI

description: Library name: Sample 364


title: TMA6 | 006 | Full ROI

description: Library name: Sample 390

value: TMA6 | 005 | Full ROI


title: TMA4 | 022 | Full ROI

description: Library name: Sample 363

value: STIC

value: TMA4 | 021 | Full ROI


title: TMA4 | 021 | Full ROI

description: Library name: Sample 362


title: TMA4 | 020 | Full ROI

description: Library name: Sample 361

value: TMA4 | 019 | Full ROI