title: Ventricle_Trpc6-/-_rep1

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Ventricle muscle, TRPC6 knockout

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

value: male

value: TRPC6 KO


title: Ventricle_Wild type_rep2

status: Public on Feb 04 2026

molecule: total RNA

organism: Mus musculus

source_name: Ventricle muscle, wild type

tag: strain

tag: Sex

tag: genotype

value: WT


title: INTS11 depletion 24hrs, INTS11-degron mESCs rep2

type: SRA

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library name: Rep2_24h

library_source: transcriptomic

data_processing:
Data were processed using the snakePipes ncRNAseq (version 3.2.0) with parameters   ncRNAseq -i fastq -o snakepipe_noncoding mm10_gencodeM19 --trim --trimmer cutadapt
Assembly: mm10
Supplementary files format and content: Rep1_0h.cntTable, Rep1_24h.cntTable, Rep2_0h.cntTable, Rep2_24h.cntTable

growth_protocol: INTS11-degron mESCs (E14) were cultured on gelatin-coated dishes in High Glucose DMEM (Sigma) supplemented with 15% FBS (Gibco), 2 mM L-glutamine (Sigma), 1x non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 100 U/mL penicillin-streptomycin, 0.1 mM 2-mercaptoethanol (Gibco), 1000 U/ml mouse recombinant LIF (Stemcell, 78056) and 10 µM Trimethoprim (Cayman Chemical, 16473).

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 µg of total RNA was further processed to remove the remaining DNA with 4 U of TURBO DNase for 30 min and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.

treatment_protocol: For INTS11-degron depletion, cells were washed twice with PBS to remove Trimethoprim and then cultivated in fresh ESC medium that contained DMSO (1 µL/ml).

tag: tissue

tag: cell line

value: mouse embryonic stem cells

tag: cell type

value: INTS11-degron depletion for 24 hrs

value: INTS11-degron depletion


title: TGF37, Biopsy Day15

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

country: USA

institute: Earle A. Chiles Research Institute

description: Library name: TGF37_Day15

data_processing:
Expression counts were quantified using salmon-v.0.12.0
Normalization and differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: comma separated file includes normalized counts for all samples and timepoint

organism: Homo sapiens

source_name: RNA Exome

extract_protocol:
Total RNA were purified from 5 µm FFPE tumor sections on an automated QiaCube instrument using DNA/RNA AllPrep reagents (Qiagen) according to the manufacturer’s instructions.
The RNA is fragmented using divalent cations under elevated temperature. cDNA is generated from the cleaved RNA fragments using random priming during first and second strand synthesis. Then, sequencing adapters are ligated to the resulting double-stranded cDNA fragments. The coding regions of the transcriptome are captured from this library using sequence-specific probes to create the final library. Captured library pools were normalized and loaded onto a Illumina Novaseq 6000 for sequencing.

value: Tumor

tag: treatment

value: galunisertib+chemoradiation

tag: time

value: Day 15


title: TGF36, Biopsy Day15

description: Library name: TGF36_Day15


title: anti_tRF_8cell_5

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

description:
Library name: anti_tRF_8cell_5
single embryo RNA-seq 8-cell embryo

data_processing:
Bioinformatic pipelines were assembled using Via Foundry, formerly DolphinNext, pipeline generator for all RNA-sequencing data analyzed in this study.
mRNA libraries were first aligned to the C. elegans genome (WS245) using STAR and quantified and normalized to transcripts per million (TPM) using the RSEM package. Significance calls were made based on t-tests (unpaired, two-tailed), where we identified up- and down-regulated genes using the following cutoff:  log2(fold change) >1 or less than –1 and an adjusted P-value ≤0.01. For differentially expressed genes WormBase enrichment analysis was used to determine tissue, pathway, and gene ontology enrichment.
Small RNA libraries were trimmed of adapter sequences using trimmomatic and aligned (in order) sequentially to C. elegans rRNAs, miRNAs, tRNAs, and piRNAs using Bowtie 2. STAR was used to align small RNAs to the C. elegans genome (WS245), featureCounts was then used to quantify reads mapping to genomic features (mRNA fragments, and endo siRNA). Mapped reads were normalized to reads per million using custom python scripts, to total genome mapping reads or to a specific RNA class, for subsequent analysis.
Assembly: WS245
Supplementary files format and content: csv files for small RNA data include raw count values for each Sample
Supplementary files format and content: csv files for mRNA data include TPM values for each Sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: 8 cell embryo

extract_protocol:
Unless otherwise stated all RNA-seq experiments, beyond single embryo experiments (below) were conducted on adult animals. To generate rnst-2 mutant males, heterozygous rnst-2/tmc16 males and females were mated to generate progeny that’s parents had equivalent genotypes. Individual ~50 F1 L4 from these crosses, propagated at 20°C, were then picked as males and females separately to NGM OP50 plates.  These animals were then developed at 20°C for 24 hours to generate adult animals. These animals were then picked into 1X M9 media with 0.5% polyethylene glycol (mPEG) in a 1.5 mL low adhesion microcentrifuge tube. Worms were washed three times with M9/mPEG and once with cold nuclease free water before resuspending in 1 volume 2X worm lysis buffer (1% SDS, 80mM Tris HCl, 400 mM NaCl, 20 mM EDTA, 0.8 mg/mL Proteinase K). The samples were then incubated at 55°C for 15 minutes while shaking and visually inspected to ensure complete lysis. Following worm lysis, 2X volume of TRI reagent (Invitrogen, AM9738) was added followed by 1/5th volume of BCP (catalog #). This solution was mixed thoroughly and transferred a Phase Lock Gel Heavy tube (QuantaBio, 2302830; pre-spun at 14,000 RPM for 1 minute) and spun at 14,000 RPM for 4 minutes at 4°C. The aqueous layer was then transferred to a new low-adhesion microcentrifuge tube, and 15 μg of GlycoBlue coprecipitant (Invitrogen AM9515) was added prior to the addition of 1.1 volume isopropanol. Samples were then precipitated at -20°C for at least 1 hours, and up to a month in isopropanol (longer storage times at -80°C) to purify total RNA. To generate small RNA and mRNA-seq libraries RNA samples in isopropanol were centrifuged at 14,000 RPM for 15 minutes at 4°C, then washed with cold 70% ethanol, spun again at 14,000 RPM for 5 minutes at 4°C, and finally reconstituted in nuclease-free water. RNA isolation from 50 adult male and females, yields ~500ng and ~1µg, respectively.
For small RNA 200 ng of total RNA was used as input for all small RNA sequencing experiments with library construction carried out using a modified Illumina Tru-Seq small RNA library prep protocol (Illumina RS-200). Small RNAs (18 – 40 nt) were first purified by was size selection from denaturing 15% polyacrylamide 7M urea TBE gel electrophoresis. Small RNAs from eluted in 10mM Tris-HCl pH 7.5, 300mM NaCl, and 1mM EDTA shaking overnight at room temperature. Small RNAs were then precipitated by separating the gel debris using 0.45µM cellulose-acetate filters, adding 1ul GlycoBlue and 1.1 volume of isopropanol, mixing well, and placing the samples at -20°C for at least 1 hour. The samples then were centrifuged at 14,000 RPM for 15 minutes at 4°C and the supernatant was discarded before washing with 1X volume of cold 70% ethanol. Following a 14,000 RPM spin at 4°C for five minutes and after complete ethanol removal, the pellet was reconstituted in RNA 5´ Pyrophosphohydrolase (RppH - NEB M0356S) per manufacturers guidelines and incubated at 37°C for one hour. Following RppH treatment, small RNAs were precipitated and ligated to the 3´ adapter using Truncated T4 RNA ligase (Lucigen LR2D11310K). Small RNAs were then ligated to the 5´ adapter using T4 ligase, and subsequently reverse transcribed using Superscript II (Invitrogen 18064014) following the Tru-Seq small RNA protocol. Following PCR optimization, to determine the proper number of cycles for amplification, the libraries were amplified, gel purified on a 8% TBE polyacrylamide gel (to remove cloned products with no insert) and combined at equimolar concentration. Libraries were then sequenced using an Illumina NextSeq1000 (75-bp single read).
For standard  mRNA-seq library construction was carried out using the Illumina stranded mRNA kit as per manufacturer’s instructions (Illumina 20040534). In brief, poly-adenylated RNAs were captured using oligo(dT) magnetic beads from 200-800ng total RNA. The RNA was then fragmented, primed for cDNA synthesis and subsequently cleaned up using AMPure XP beads (Beckman Coulter, Cat# A63881). Following PCR optimization, to determine the proper number of cycles from amplification, the libraries were amplified and combined at equimolar concentrations before being purified using non-denaturing PAGE. Paired-end sequencing (50 bp per read) was performed using an Illumina NextSeq1000.
For single embryo RNA-seq cross plates were prepared by placing 50 WT (fog-2(q71) L4-stage females and 50 rnst-2 Δ/Δ (pen1); fog-2(q71) L4-stage males on 60 mM NGM plates seeded with OP50. The next day mated females full of eggs were picked and washed several times with M9 mPEG and then subjected to a 5-minute hypochlorite treatment. Early-stage embryos, identified under the microscope, were then transferred to 10ug/ul chitanase in M9 mPEG treatment and incubated at room temperature for 8-10 minutes. Following chitinase treatment 2-cell and 8-cell embryos, identified visually under a dissecting microscope were placed in RNA worm lysis buffer in PCR tubes and incubated at 55°C for 10 minutes. Embryo lysates were then stored at -80°C before proceeding to library preparation. Single-embryo mRNA-seq libraries were constructed using the SMART-Seq protocol, used previously for single mouse preimplantation embryos. RNA was isolated with RNAClean-XP beads (Beckman Coulter, Cat# A63987) and full-length polyadenylated RNA was reverse transcribed using Superscript II (Invitrogen, Cat# 18064014). The cDNA was then amplified using 10 cycles and subsequently 0.33 ng of cDNA was used to construct a pool of uniquely indexed samples using the Nextera XT kit (Illumina, Cat# FC-131-1096). Finally, pooled libraries were sequenced on a NextSeq1000 with paired-end sequencing (50 bp per read).

value: 8 cell embryo


title: anti_tRF_8cell_6

description:
Library name: anti_tRF_8cell_6
single embryo RNA-seq 8-cell embryo


title: anti_tRF_8cell_10

description:
Library name: anti_tRF_8cell_10
single embryo RNA-seq 8-cell embryo


title: no depletion, control INTS11-degron mESCs rep2

description: Library name: Rep2_0h

value: INTS11-degron without depletion

value: untreated


title: TGF35, Biopsy Day15

description: Library name: TGF35_Day15


title: anti_tRF_8cell_1

description:
Library name: anti_tRF_8cell_1
single embryo RNA-seq 8-cell embryo


title: Ventricle_Trpc6-/-_rep2


title: anti_tRF_8cell_8

description:
Library name: anti_tRF_8cell_8
single embryo RNA-seq 8-cell embryo


title: no depletion, control INTS11-degron mESCs rep1

description: Library name: Rep1_0h


title: anti_tRF_8cell_7

description:
Library name: anti_tRF_8cell_7
single embryo RNA-seq 8-cell embryo


title: TGF38, Biopsy Day0

description: Library name: TGF38_Day0


title: TGF34, Biopsy Day15

description: Library name: TGF34_Day15


title: anti_tRF_8cell_4

description:
Library name: anti_tRF_8cell_4
single embryo RNA-seq 8-cell embryo


title: anti_tRF_8cell_3

description:
Library name: anti_tRF_8cell_3
single embryo RNA-seq 8-cell embryo


title: anti_tRF_2cell_21

description:
Library name: anti_tRF_2cell_21
single embryo RNA-seq 2-cell embryo

source_name: 2 cell embryo

value: 2 cell embryo


title: anti_tRF_8cell_9

description:
Library name: anti_tRF_8cell_9
single embryo RNA-seq 8-cell embryo


title: TGF33, Biopsy Day15

description: Library name: TGF33_Day15


title: anti_tRF_8cell_2

description:
Library name: anti_tRF_8cell_2
single embryo RNA-seq 8-cell embryo


title: TGF36, Biopsy Day0

description: Library name: TGF36_Day0


title: TGF32, Biopsy Day0

description: Library name: TGF32_Day0


title: TGF35, Biopsy Day0

description: Library name: TGF35_Day0


title: anti_tRF_2cell_17

description:
Library name: anti_tRF_2cell_17
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_23

description:
Library name: anti_tRF_2cell_23
single embryo RNA-seq 2-cell embryo


title: Ventricle_Wild type_rep1


title: anti_tRF_2cell_15

description:
Library name: anti_tRF_2cell_15
single embryo RNA-seq 2-cell embryo


title: TGF32, Biopsy Day15

description: Library name: TGF32_Day15


title: anti_tRF_2cell_22

description:
Library name: anti_tRF_2cell_22
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_16

description:
Library name: anti_tRF_2cell_16
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_19

description:
Library name: anti_tRF_2cell_19
single embryo RNA-seq 2-cell embryo


title: TGF30, Biopsy Day15

description: Library name: TGF30_Day15


title: TGF34, Biopsy Day0

description: Library name: TGF34_Day0


title: TGF31, Biopsy Day0

description: Library name: TGF31_Day0


title: anti_tRF_2cell_14

description:
Library name: anti_tRF_2cell_14
single embryo RNA-seq 2-cell embryo


title: TGF30, Biopsy Day0

description: Library name: TGF30_Day0


title: TGF29, Biopsy Day15

description: Library name: TGF29_Day15


title: anti_tRF_2cell_13

description:
Library name: anti_tRF_2cell_13
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_18

description:
Library name: anti_tRF_2cell_18
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_20

description:
Library name: anti_tRF_2cell_20
single embryo RNA-seq 2-cell embryo


title: TGF33, Biopsy Day0

description: Library name: TGF33_Day0


title: anti_tRF_2cell_11

description:
Library name: anti_tRF_2cell_11
single embryo RNA-seq 2-cell embryo


title: TGF29, Biopsy Day0

description: Library name: TGF29_Day0


title: TGF31, Biopsy Day15

description: Library name: TGF31_Day15


title: anti_tRF_2cell_12

description:
Library name: anti_tRF_2cell_12
single embryo RNA-seq 2-cell embryo


title: TGF28, Biopsy Day15

description: Library name: TGF28_Day15


title: anti_tRF_2cell_9

description:
Library name: anti_tRF_2cell_9
single embryo RNA-seq 2-cell embryo


title: TGF27, Biopsy Day0

description: Library name: TGF27_Day0


title: TGF26, Biopsy Day15

description: Library name: TGF26_Day15


title: TGF28, Biopsy Day0

description: Library name: TGF28_Day0


title: TGF27, Biopsy Day15

description: Library name: TGF27_Day15


title: anti_tRF_2cell_8

description:
Library name: anti_tRF_2cell_8
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_5

description:
Library name: anti_tRF_2cell_5
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_7

description:
Library name: anti_tRF_2cell_7
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_10

description:
Library name: anti_tRF_2cell_10
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_6

description:
Library name: anti_tRF_2cell_6
single embryo RNA-seq 2-cell embryo


title: TGF25, Biopsy Day0

description: Library name: TGF25_Day0


title: anti_tRF_2cell_3

description:
Library name: anti_tRF_2cell_3
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_2

description:
Library name: anti_tRF_2cell_2
single embryo RNA-seq 2-cell embryo


title: anti_tRF_2cell_1

description:
Library name: anti_tRF_2cell_1
single embryo RNA-seq 2-cell embryo


title: TGF25, Biopsy Day15

description: Library name: TGF25_Day15


title: wt_8cell_20

description:
Library name: wt_8cell_20
single embryo RNA-seq 8-cell embryo


title: TGF24, Biopsy Day15

description: Library name: TGF24_Day15


title: wt_8cell_19

description:
Library name: wt_8cell_19
single embryo RNA-seq 8-cell embryo


title: TGF22, Biopsy Day15

description: Library name: TGF22_Day15


title: anti_tRF_2cell_4

description:
Library name: anti_tRF_2cell_4
single embryo RNA-seq 2-cell embryo


title: TGF26, Biopsy Day0

description: Library name: TGF26_Day0


title: TGF24, Biopsy Day0

description: Library name: TGF24_Day0


title: TGF22, Biopsy Day0

description: Library name: TGF22_Day0


title: TGF23, Biopsy Day0

description: Library name: TGF23_Day0


title: TGF23, Biopsy Day15

description: Library name: TGF23_Day15


title: wt_8cell_18

description:
Library name: wt_8cell_18
single embryo RNA-seq 8-cell embryo


title: wt_8cell_16

description:
Library name: wt_8cell_16
single embryo RNA-seq 8-cell embryo


title: TGF21, Biopsy Day15

description: Library name: TGF21_Day15


title: wt_8cell_14

description:
Library name: wt_8cell_14
single embryo RNA-seq 8-cell embryo


title: wt_8cell_15

description:
Library name: wt_8cell_15
single embryo RNA-seq 8-cell embryo


title: wt_8cell_13

description:
Library name: wt_8cell_13
single embryo RNA-seq 8-cell embryo


title: TGF20, Biopsy Day15

description: Library name: TGF20_Day15


title: TGF21, Biopsy Day0

description: Library name: TGF21_Day0


title: TGF19, Biopsy Day0

description: Library name: TGF19_Day0


title: TGF20, Biopsy Day0

description: Library name: TGF20_Day0


title: wt_8cell_12

description:
Library name: wt_8cell_12
single embryo RNA-seq 8-cell embryo


title: wt_8cell_17

description:
Library name: wt_8cell_17
single embryo RNA-seq 8-cell embryo


title: TGF19, Biopsy Day15

description: Library name: TGF19_Day15


title: wt_8cell_11

description:
Library name: wt_8cell_11
single embryo RNA-seq 8-cell embryo


title: wt_8cell_7

description:
Library name: wt_8cell_7
single embryo RNA-seq 8-cell embryo


title: TGF18, Biopsy Day0

description: Library name: TGF18_Day0


title: wt_8cell_6

description:
Library name: wt_8cell_6
single embryo RNA-seq 8-cell embryo


title: wt_8cell_8

description:
Library name: wt_8cell_8
single embryo RNA-seq 8-cell embryo


title: TGF17, Biopsy Day15

description: Library name: TGF17_Day15


title: TGF18, Biopsy Day15

description: Library name: TGF18_Day15


title: wt_8cell_9

description:
Library name: wt_8cell_9
single embryo RNA-seq 8-cell embryo


title: TGF17, Biopsy Day0

description: Library name: TGF17_Day0


title: TGF15, Biopsy Day15

description: Library name: TGF15_Day15


title: wt_8cell_4

description:
Library name: wt_8cell_4
single embryo RNA-seq 8-cell embryo


title: wt_8cell_3

description:
Library name: wt_8cell_3
single embryo RNA-seq 8-cell embryo


title: wt_8cell_10

description:
Library name: wt_8cell_10
single embryo RNA-seq 8-cell embryo


title: wt_8cell_2

description:
Library name: wt_8cell_2
single embryo RNA-seq 8-cell embryo


title: TGF14, Biopsy Day15

description: Library name: TGF14_Day15


title: TGF16, Biopsy Day15

description: Library name: TGF16_Day15


title: TGF16, Biopsy Day0

description: Library name: TGF16_Day0


title: TGF13, Biopsy Day0

description: Library name: TGF13_Day0


title: wt_8cell_1

description:
Library name: wt_8cell_1
single embryo RNA-seq 8-cell embryo


title: wt_2cell_28

description:
Library name: wt_2cell_28
single embryo RNA-seq 2-cell embryo


title: TGF14, Biopsy Day0

description: Library name: TGF14_Day0


title: TGF15, Biopsy Day0

description: Library name: TGF15_Day0


title: TGF12, Biopsy Day0

description: Library name: TGF12_Day0


title: wt_8cell_5

description:
Library name: wt_8cell_5
single embryo RNA-seq 8-cell embryo


title: TGF11, Biopsy Day15

description: Library name: TGF11_Day15


title: TGF13, Biopsy Day15

description: Library name: TGF13_Day15


title: wt_2cell_30

description:
Library name: wt_2cell_30
single embryo RNA-seq 2-cell embryo


title: wt_2cell_29

description:
Library name: wt_2cell_29
single embryo RNA-seq 2-cell embryo


title: wt_2cell_27

description:
Library name: wt_2cell_27
single embryo RNA-seq 2-cell embryo


title: wt_2cell_26

description:
Library name: wt_2cell_26
single embryo RNA-seq 2-cell embryo


title: TGF09, Biopsy Day15

description: Library name: TGF09_Day15


title: wt_2cell_25

description:
Library name: wt_2cell_25
single embryo RNA-seq 2-cell embryo


title: TGF12, Biopsy Day15

description: Library name: TGF12_Day15


title: TGF07, Biopsy Day15

description: Library name: TGF07_Day15


title: TGF11, Biopsy Day0

description: Library name: TGF11_Day0


title: wt_2cell_21

description:
Library name: wt_2cell_21
single embryo RNA-seq 2-cell embryo


title: wt_2cell_20

description:
Library name: wt_2cell_20
single embryo RNA-seq 2-cell embryo


title: wt_2cell_23

description:
Library name: wt_2cell_23
single embryo RNA-seq 2-cell embryo


title: wt_2cell_24

description:
Library name: wt_2cell_24
single embryo RNA-seq 2-cell embryo


title: wt_2cell_18

description:
Library name: wt_2cell_18
single embryo RNA-seq 2-cell embryo


title: TGF09, Biopsy Day0

description: Library name: TGF09_Day0


title: TGF08, Biopsy Day15

description: Library name: TGF08_Day15


title: wt_2cell_22

description:
Library name: wt_2cell_22
single embryo RNA-seq 2-cell embryo


title: wt_2cell_17

description:
Library name: wt_2cell_17
single embryo RNA-seq 2-cell embryo


title: TGF07, Biopsy Day0

description: Library name: TGF07_Day0


title: wt_2cell_19

description:
Library name: wt_2cell_19
single embryo RNA-seq 2-cell embryo


title: TGF06, Biopsy Day15

description: Library name: TGF06_Day15


title: TGF06, Biopsy Day0

description: Library name: TGF06_Day0


title: wt_2cell_12

description:
Library name: wt_2cell_12
single embryo RNA-seq 2-cell embryo


title: wt_2cell_11

description:
Library name: wt_2cell_11
single embryo RNA-seq 2-cell embryo


title: TGF05, Biopsy Day15

description: Library name: TGF05_Day15


title: TGF08, Biopsy Day0

description: Library name: TGF08_Day0


title: wt_2cell_16

description:
Library name: wt_2cell_16
single embryo RNA-seq 2-cell embryo


title: wt_2cell_13

description:
Library name: wt_2cell_13
single embryo RNA-seq 2-cell embryo


title: wt_2cell_15

description:
Library name: wt_2cell_15
single embryo RNA-seq 2-cell embryo


title: TGF02, Biopsy Day0

description: Library name: TGF02_Day0


title: wt_2cell_9

description:
Library name: wt_2cell_9
single embryo RNA-seq 2-cell embryo


title: TGF05, Biopsy Day0

description: Library name: TGF05_Day0


title: TGF01, Biopsy Day15

description: Library name: TGF01_Day15


title: wt_2cell_8

description:
Library name: wt_2cell_8
single embryo RNA-seq 2-cell embryo


title: TGF03, Biopsy Day0

description: Library name: TGF03_Day0


title: wt_2cell_10

description:
Library name: wt_2cell_10
single embryo RNA-seq 2-cell embryo


title: Smooth muscle cell, AngII, 24h, sST2, 24h, rep3

city: Shanghai

first: Chenfeng

last: Wang

address: West Huaihai Road

country: China

institute: Shanghai Chest Hospital

description: Library name: S6

data_processing:
The clustered, index-coded samples were sequenced on an Illumina Novaseq platform with 150 bp paired-end reads. Data processing and differential expression visualization was carried out using the R Studio (https://www.r-project.org/).
Assembly: hg38
Supplementary files format and content: gene counts file

source_name: human aortic smooth muscle cell

extract_protocol:
Total RNA was extracted from cells and tissues using the TRI Reagent (Molecular Research Center, TR118), following the manufacturer's protocol.
Total RNA was used for library preparation, where mRNA was purified using poly-T oligo-attached magnetic beads and fragmented for cDNA synthesis. First-strand cDNA synthesis was carried out using random hexamer primers and M-MuLV Reverse Transcriptase. Second-strand cDNA synthesis was then performed using DNA Polymerase I and RNase H, followed by conversion of remaining overhangs to blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, adaptors with hairpin loop structures were ligated for hybridization. cDNA fragments between 370-420 bp in length were selected and purified using the AMPure XP system (Beckman Coulter). PCR amplification was performed using Phusion High-Fidelity DNA Polymerase, universal PCR primers, and an index primer. The PCR products were purified (AMPure XP system) and assessed for library quality on the Agilent Bioanalyzer 2100 system.

value: human aortic smooth muscle cell


title: TGF02, Biopsy Day15

description: Library name: TGF02_Day15


title: TGF03, Biopsy Day15

description: Library name: TGF03_Day15


title: wt_2cell_14

description:
Library name: wt_2cell_14
single embryo RNA-seq 2-cell embryo


title: TGF04, Biopsy Day0

description: Library name: TGF04_Day0


title: wt_2cell_4

description:
Library name: wt_2cell_4
single embryo RNA-seq 2-cell embryo


title: wt_2cell_1

description:
Library name: wt_2cell_1
single embryo RNA-seq 2-cell embryo


title: wt_2cell_7

description:
Library name: wt_2cell_7
single embryo RNA-seq 2-cell embryo


title: hBMSC_H2O2_2

city: guiyang

first: dong

last: wentao

state: guizhou

address: No. 28, Guiyi Street

institute: The Affliated Hospital of Guizhou Medical University

description: Library name: OS2

data_processing:
Raw sequencing data quality control: Sequencing error rate and GC content distribution were checked.
Data filtering: Reads containing adapter sequences, reads with N bases, and low‑quality reads (Qphred ≤5 over 50% of read length) were removed.
Alignment: Clean reads were aligned to the reference genome using HISAT2.
Quantification: Read counts per gene were calculated using featureCounts.
Normalization: FPKM values were calculated to normalize for sequencing depth and gene length.
Assembly: hg38
Supplementary files format and content: Gene expression matrix in tab‑delimited text format: rows are genes, columns are samples, values are raw read counts.
Supplementary files format and content: Gene expression matrix in tab‑delimited text format: rows are genes, columns are samples, values are FPKM.

source_name: Bone marrow

growth_protocol: Cells were cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from tissues or cells using standard methods.
Libraries were constructed using either the standard NEB protocol or the strand‑specific protocol. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, reverse‑transcribed into cDNA, end‑repaired, A‑tailed, ligated with adapters, size‑selected, and PCR‑amplified.

treatment_protocol: reated with H2O2 concentrations (400μM) for 6 days

value: Bone marrow

value: Primary culture

value: human bone marrow-derived mesenchymal stem cell

value: wild type

value: hydrogen peroxide for 7 days

tag: batch


title: wt_2cell_3

description:
Library name: wt_2cell_3
single embryo RNA-seq 2-cell embryo


title: TGF04, Biopsy Day15

description: Library name: TGF04_Day15


title: hBMSC_Control_3

description: Library name: CONTROL3


title: rnstmale_8cell_25

description:
Library name: rnstmale_8cell_25
single embryo RNA-seq 8-cell embryo


title: Smooth muscle cell, AngII, 24h, rep3

description: Library name: S3


title: wt_2cell_5

description:
Library name: wt_2cell_5
single embryo RNA-seq 2-cell embryo


title: Smooth muscle cell, AngII, 24h, rep1

description: Library name: S1


title: Smooth muscle cell, AngII, 24h, sST2, 24h, rep2

description: Library name: S5


title: wt_2cell_2

description:
Library name: wt_2cell_2
single embryo RNA-seq 2-cell embryo


title: hBMSC_H2O2_1

description: Library name: OS1

value: hydrogen peroxide for 6 days


title: hBMSC_H2O2_3

description: Library name: OS3

value: hydrogen peroxide for 8 days


title: wt_2cell_6

description:
Library name: wt_2cell_6
single embryo RNA-seq 2-cell embryo


title: hBMSC_Control_1

description: Library name: CONTROL1


title: Smooth muscle cell, AngII, 24h, rep2

description: Library name: S2


title: rnstmale_8cell_23

description:
Library name: rnstmale_8cell_23
single embryo RNA-seq 8-cell embryo


title: hBMSC_Control_2

description: Library name: CONTROL2


title: rnstmale_8cell_21

description:
Library name: rnstmale_8cell_21
single embryo RNA-seq 8-cell embryo


title: Smooth muscle cell, AngII, 24h, sST2, 24h, rep1

description: Library name: S4


title: U251 cells, KD, rep2

city: Wuxi, Jiangsu 214023, China

first: Maorong

last: Cai

address: Wuxi, Jiangsu, China

institute: Department of Neurosurgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University

description:
Library name: sample5
B1-2

data_processing:
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA‑seq Library Prep Kit strictly following the manufacturer's protocol. The procedure included RNA fragmentation, cDNA synthesis, end repair, A‑tailing, adapter ligation, and library PCR amplification. The final libraries were quality‑checked and then subjected to sequencing.
Clean reads were aligned to the specified reference genome using HISAT2. Read counts mapped to each gene were obtained with HTSeq‑count, and FPKM values were calculated based on gene length and mapped read counts to quantify gene expression levels.
Principal component analysis (PCA) was performed on gene expression counts using R (v3.2.0), and plots were generated to evaluate the consistency of biological replicates. Differential expression analysis was then conducted with DESeq2, where genes with an adjusted q‑value < 0.05 and fold change > 2 or < 0.5 were defined as differentially expressed genes (DEGs).
Hierarchical clustering analysis was performed on the identified DEGs using R packages, and heatmaps were plotted to display their expression patterns. A radar chart for the top 30 genes was generated with the ggradar package. Subsequently, GO, KEGG, Reactome, and WikiPathways enrichment analyses were carried out based on the hypergeometric test, and significant enriched terms were visualized using bar plots, chord diagrams, or enrichment circle plots in R.
Gene Set Enrichment Analysis (GSEA) was performed using predefined gene sets to examine whether a priori defined sets of genes were significantly enriched at the top or bottom of a ranked list of genes ordered by expression difference, thereby systematically interpreting phenotypic differences at the pathway level.
Assembly: This study employed a reference‑based transcriptome analysis strategy. The reference genome and corresponding gene annotation files used were obtained from public genome databases, with specific version information indicated in the analysis pipeline and applied for sequence alignment and all subsequent quantification and differential analyses.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity (A260/A280) were measured with a NanoDrop 2000 spectrophotometer, and RNA integrity (RIN) was assessed using an Agilent 2100 Bioanalyzer to ensure sample quality met the requirements for subsequent library construction.
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA‑seq Library Prep Kit strictly following the manufacturer's protocol. The procedure included RNA fragmentation, cDNA synthesis, end repair, A‑tailing, adapter ligation, and library PCR amplification. The final libraries were quality‑checked and then subjected to sequencing.


title: U251 cells, KD, rep3

description:
Library name: sample6
B1-3


title: rnstmale_8cell_20

description:
Library name: rnstmale_8cell_20
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_26

description:
Library name: rnstmale_8cell_26
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_19

description:
Library name: rnstmale_8cell_19
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_18

description:
Library name: rnstmale_8cell_18
single embryo RNA-seq 8-cell embryo


title: U251 cells, KD, rep1

description:
Library name: sample4
B1-1


title: rnstmale_8cell_24

description:
Library name: rnstmale_8cell_24
single embryo RNA-seq 8-cell embryo


title: U251 cells,TNF_Alpha_,rep3

description:
Library name: sample6
TNF_Alpha_3

data_processing:
Raw sequencing data (fastq format) were subjected to quality control using in-house Perl scripts. Reads containing adapters, poly‑N sequences, or low‑quality bases were removed to obtain high‑quality clean reads. Q20, Q30, and GC content of the clean data were calculated simultaneously. All downstream analyses were based on these high‑quality clean reads.
The reference genome and corresponding gene model annotation files were downloaded directly from the official genome website. A genome index was built using Hisat2 v2.0.5, and the paired‑end clean reads were aligned to the reference genome using the same software.
Mapped reads from each sample were assembled into transcripts using StringTie (v1.3.3b) in a reference‑guided approach. Gene‑level read counts were obtained with featureCounts v1.5.0‑p3, and FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) values were calculated for each gene based on its length and the mapped read count.
Differential expression analysis between groups was performed using the DESeq2 or edgeR R package, with a significance threshold of adjusted P‑value < 0.05 and absolute fold‑change ≥ 2. Subsequently, GO and KEGG enrichment analyses of the differentially expressed genes were conducted with the clusterProfiler R package, considering terms with a corrected P‑value < 0.05 as significantly enriched.
SNP calling was performed with GATK2 (v3.7), and the resulting variants were annotated using SnpEff. Alternative splicing events were analyzed with rMATS (v3.2.5). Protein‑protein interaction (PPI) analysis of differentially expressed genes was based on the STRING database, and weighted gene co‑expression network analysis (WGCNA) was carried out using the WGCNA R package.
Assembly: The reference genome and gene model annotation files used in this study were downloaded directly from the official genome website. The genome index was constructed with Hisat2 v2.0.5 and was employed for all subsequent read alignment steps.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: The human glioblastoma cell line U251 was cultured in high-glucose Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. Cells were maintained in a humidified incubator at 37 °C with 5% CO₂. Cells were passaged upon reaching 80–90% confluence and were used for experiments within 20 passages.

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy Mini Plus Kit. Specifically, cells were lysed with TRIzol, and the lysate was transferred to an RNase-free tube. Ethanol was added according to the kit instructions, and the mixture was loaded onto a purification column. After washing sequentially with wash buffers, total RNA was eluted with RNase-free water. RNA degradation and contamination were then monitored by 1% agarose gel electrophoresis. RNA purity was checked using a NanoPhotometer® spectrophotometer, and RNA integrity was assessed with the RNA Nano 6000 Assay Kit on an Agilent Bioanalyzer 2100 system.
Libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina®. Briefly, 1 µg of total RNA was used for mRNA purification with oligo(dT)-attached magnetic beads. Purified mRNA was fragmented using divalent cations at elevated temperature. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand synthesis with DNA Polymerase I. After end repair, A-tailing, and adapter ligation (NEBNext Adaptor), library fragments of ~250–300 bp were selected with AMPure XP beads. The adapter-ligated DNA was treated with USER enzyme, amplified by PCR (Phusion High-Fidelity DNA polymerase), and purified again with AMPure XP beads. Final library quality was evaluated on an Agilent Bioanalyzer 2100 system.

treatment_protocol: U251 cells were seeded and grown to approximately 80% confluence before treatment. The experiment consisted of two groups: (1) negative control group, treated with an equal volume of sterile deionized water; and (2) experimental group, treated with recombinant human TNF‑α at a final concentration of 10 ng/mL. Both groups were incubated for 24 hours under standard culture conditions. Each treatment condition was performed with three independent biological replicates. After treatment, cells were harvested for RNA extraction and subsequent transcriptome sequencing.


title: U251 cells, NC, rep1

description:
Library name: sample1
A1-1


title: rnstmale_8cell_15

description:
Library name: rnstmale_8cell_15
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_10

description:
Library name: rnstmale_8cell_10
single embryo RNA-seq 8-cell embryo


title: U251 cells,NC,rep1

description:
Library name: sample1
NC1_1


title: rnstmale_8cell_16

description:
Library name: rnstmale_8cell_16
single embryo RNA-seq 8-cell embryo


title: U251 cells, NC, rep3

description:
Library name: sample3
A1-3


title: rnstmale_8cell_17

description:
Library name: rnstmale_8cell_17
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_14

description:
Library name: rnstmale_8cell_14
single embryo RNA-seq 8-cell embryo


title: U251 cells,TNF_Alpha_,rep2

description:
Library name: sample5
TNF_Alpha_2


title: rnstmale_8cell_22

description:
Library name: rnstmale_8cell_22
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_13

description:
Library name: rnstmale_8cell_13
single embryo RNA-seq 8-cell embryo


title: U251 cells,NC,rep3

description:
Library name: sample3
NC1_3


title: U251 cells,NC,rep2

description:
Library name: sample2
NC1_2


title: U251 cells,TNF_Alpha_,rep1

description:
Library name: sample4
TNF_Alpha_1


title: rnstmale_8cell_9

description:
Library name: rnstmale_8cell_9
single embryo RNA-seq 8-cell embryo


title: U251 cells, NC, rep2

description:
Library name: sample2
A1-2


title: rnstmale_8cell_11

description:
Library name: rnstmale_8cell_11
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_12

description:
Library name: rnstmale_8cell_12
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_7

description:
Library name: rnstmale_8cell_7
single embryo RNA-seq 8-cell embryo


title: 6971-EC-S1_ROI_106

city: Ann Arbor

first: Eileen

last: Carpenter

state: MI

address: 1137 E Catherine St Med Sci II R 7712

department: Internal Medicine

institute: University of Michigan

description:
Library name: DSP-1001660013357-F-A12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

library_source: other

data_processing:
We used the GeoMxWorkflows package [https://bioconductor.org/packages/release/workflows/html/GeoMxWorkflows.html] for quality control and processing of Nanostring GeoMx data. Briefly, Quality control was performed to exclude the ROIs with less than 10% genes detection rate (less than 10% of the original WTA panel genes were detected) and exclude genes detected in less than 10% of the ROIs. Q3-normalization was performed for each ROI in the gene expression matrix followed by log normalization. For visualization purposes, we performed PCA analysis which clearly showed a batch effect. We used limma package batch correction function to regress out the batch effect which showed clustering of ROIs from the same cell type together. To define cell-type-specific markers, we used a linear mixed model to perform DGE between each cell type and the rest of the ROIs, similar to how we define markers in single cells data.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts of genes for each ROI
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Pancreas

growth_protocol: FFPE Blocks

extract_protocol:
Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 310 regions of interest (ROIs), segmented into panCK positive areas of interest (AOIs) for spatial transcriptomics. During collection, each capture area was exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics. The released barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol.
The resulted libraries were sequenced by the Illumina NextSeq 6000 platform using reversed, 2 x 27 base paired reads. The resulting GeoMx DSP data was then coupled to next generation sequencing (NGS) readout. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Slides were deparaffinized and subjected to antigen retrieval (Tris-EDTA, pH 9.0; 15 minutes; >99°C), and enzymatic exposure of RNA targets (1.0µg/ml Proteinase K; 15 minutes; 37°C). Slides were then hybridized with human whole transcriptome overnight (nanoString) at 37°C.  The next morning slides underwent stringent washes and were prepared for morphology marker staining. Slides were co-incubated with fluorescently labeled visualization antibodies to detect tumor cells (pan-cytokeratin [CK]), all immune cells (CD45), and with SYTO 13 for nuclei detection. The samples were imaged, and regions of interest (ROIs) were selected.

value: Pancreas

value: Stroma


title: 1556_IPMN

description: Library name: 1556

library_source: transcriptomic single cell

data_processing:
Samples were run using 50-cycle paired-end reads on the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.  Cell Ranger count version 6.1.2 was used with default settings, with an initial expected cell count of 10,000.  The GCH38 refererence genome was used for aligment.Ambient RNA correction was done for each sample independently using SoupX. Briefly, SoupX estimates the ambient RNA profile from the cell-free RNA, then it estimates the cell-specific contamination fraction using a set of user-specified negative markers. Then, we used Seurat’s recommended workflow for scRNASeq data processing and integration. Briefly, we removed low-quality cells with more than a 15% fraction of mitochondrial genes expression or less than 200 features (genes) detected.
Assembly: GRCH38
Supplementary files format and content: RawCountsMatrix.csv contains comma-separated value files of the raw counts and cell annotation of each barcode after processing and filtration.
Supplementary files format and content: CorrectedCountsMatrix.csv contains comma-separated value files of the ambient-RNA corrected counts and cell annotation of each barcode after processing and filtration.

source_name: Pancreatic Cyst

extract_protocol:
For single cell processing, tissue was minced into 1mm3 pieces, then digested with 1 mg/mL collagenase P for 20-30 min at 37°C with gentle agitation.  Digested tissue was rinsed three times with DMEM/1%BSA/10μM Y27632, then filtered through a 40μm mesh.  Resulting live cells were submitted to the University of Michigan Advanced Genomics Core for 3’ single cell sequencing using the 10x Genomics Platform.
Single-cell complementary DNA libraries were prepared and sequenced at the University of Michigan Sequencing Core using the 10× Genomics Platform.

value: Pancreatic Cyst


title: 6971-EC-S1_ROI_107

description:
Library name: DSP-1001660013357-F-B01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 1593_IPMN

description: Library name: 1593


title: rnstmale_8cell_5

description:
Library name: rnstmale_8cell_5
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_8

description:
Library name: rnstmale_8cell_8
single embryo RNA-seq 8-cell embryo


title: rnstmale_8cell_6

description:
Library name: rnstmale_8cell_6
single embryo RNA-seq 8-cell embryo


title: 6971-EC-S1_ROI_104

description:
Library name: DSP-1001660013357-F-A10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_8cell_4

description:
Library name: rnstmale_8cell_4
single embryo RNA-seq 8-cell embryo


title: 6971-EC-S1_ROI_105

description:
Library name: DSP-1001660013357-F-A11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_8cell_3

description:
Library name: rnstmale_8cell_3
single embryo RNA-seq 8-cell embryo


title: 6971-EC-S1_ROI_103

description:
Library name: DSP-1001660013357-F-A09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_8cell_2

description:
Library name: rnstmale_8cell_2
single embryo RNA-seq 8-cell embryo


title: 6971-EC-S1_ROI_100

description:
Library name: DSP-1001660013357-F-A06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_24

description:
Library name: rnstmale_2cell_24
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_101

description:
Library name: DSP-1001660013357-F-A07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_23

description:
Library name: rnstmale_2cell_23
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_97

description:
Library name: DSP-1001660013357-F-A03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_96

description:
Library name: DSP-1001660013357-F-A02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_8cell_1

description:
Library name: rnstmale_8cell_1
single embryo RNA-seq 8-cell embryo


title: rnstmale_2cell_22

description:
Library name: rnstmale_2cell_22
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_95

description:
Library name: DSP-1001660013356-E-H12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: IPMN


title: 6971-EC-S1_ROI_94

description:
Library name: DSP-1001660013356-E-H11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_21

description:
Library name: rnstmale_2cell_21
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_93

description:
Library name: DSP-1001660013356-E-H10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_25

description:
Library name: rnstmale_2cell_25
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_99

description:
Library name: DSP-1001660013357-F-A05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_17

description:
Library name: rnstmale_2cell_17
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_98

description:
Library name: DSP-1001660013357-F-A04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_19

description:
Library name: rnstmale_2cell_19
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_16

description:
Library name: rnstmale_2cell_16
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_18

description:
Library name: rnstmale_2cell_18
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_92

description:
Library name: DSP-1001660013356-E-H09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_15

description:
Library name: rnstmale_2cell_15
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_20

description:
Library name: rnstmale_2cell_20
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_91

description:
Library name: DSP-1001660013356-E-H08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_13

description:
Library name: rnstmale_2cell_13
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_89

description:
Library name: DSP-1001660013356-E-H06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_14

description:
Library name: rnstmale_2cell_14
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_102

description:
Library name: DSP-1001660013357-F-A08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_90

description:
Library name: DSP-1001660013356-E-H07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_87

description:
Library name: DSP-1001660013356-E-H04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: NormalDuct


title: 6971-EC-S1_ROI_88

description:
Library name: DSP-1001660013356-E-H05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_10

description:
Library name: rnstmale_2cell_10
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_11

description:
Library name: rnstmale_2cell_11
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_12

description:
Library name: rnstmale_2cell_12
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_8

description:
Library name: rnstmale_2cell_8
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_85

description:
Library name: DSP-1001660013356-E-H02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_86

description:
Library name: DSP-1001660013356-E-H03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_84

description:
Library name: DSP-1001660013356-E-H01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_9

description:
Library name: rnstmale_2cell_9
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_5

description:
Library name: rnstmale_2cell_5
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_80

description:
Library name: DSP-1001660013356-E-G09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_6

description:
Library name: rnstmale_2cell_6
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_7

description:
Library name: rnstmale_2cell_7
single embryo RNA-seq 2-cell embryo


title: rnstmale_2cell_1

description:
Library name: rnstmale_2cell_1
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_81

description:
Library name: DSP-1001660013356-E-G10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_76

description:
Library name: DSP-1001660013356-E-G05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_77

description:
Library name: DSP-1001660013356-E-G06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_3

description:
Library name: rnstmale_2cell_3
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_82

description:
Library name: DSP-1001660013356-E-G11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_79

description:
Library name: DSP-1001660013356-E-G08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_83

description:
Library name: DSP-1001660013356-E-G12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_4

description:
Library name: rnstmale_2cell_4
single embryo RNA-seq 2-cell embryo


title: 6971-EC-S1_ROI_78

description:
Library name: DSP-1001660013356-E-G07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnstmale_2cell_2

description:
Library name: rnstmale_2cell_2
single embryo RNA-seq 2-cell embryo


title: wt_F1male_3

description:
Library name: wt_F1male_3
mRNA-seq on whole male

source_name: whole male

value: whole male


title: 6971-EC-S1_ROI_75

description:
Library name: DSP-1001660013356-E-G04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wt_F1male_2

description:
Library name: wt_F1male_2
mRNA-seq on whole male


title: 6971-EC-S1_ROI_73

description:
Library name: DSP-1001660013356-E-G02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_74

description:
Library name: DSP-1001660013356-E-G03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wt_F1female_1

description:
Library name: wt_F1female_1
mRNA-seq on whole female

source_name: whole female

value: whole female


title: wt_F1male_1

description:
Library name: wt_F1male_1
mRNA-seq on whole male


title: wt_F1female_3

description:
Library name: wt_F1female_3
mRNA-seq on whole female


title: 6971-EC-S1_ROI_69

description:
Library name: DSP-1001660013356-E-F10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_F1male_2

description:
Library name: rnst2_F1male_2
mRNA-seq on whole male


title: 6971-EC-S1_ROI_67

description:
Library name: DSP-1001660013356-E-F08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_71

description:
Library name: DSP-1001660013356-E-F12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: wt_F1female_2

description:
Library name: wt_F1female_2
mRNA-seq on whole female


title: 6971-EC-S1_ROI_68

description:
Library name: DSP-1001660013356-E-F09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_70

description:
Library name: DSP-1001660013356-E-F11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_72

description:
Library name: DSP-1001660013356-E-G01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_F1male_3

description:
Library name: rnst2_F1male_3
mRNA-seq on whole male


title: 6971-EC-S1_ROI_66

description:
Library name: DSP-1001660013356-E-F07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_64

description:
Library name: DSP-1001660013356-E-F05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_del_homo_female_4

description:
Library name: rnst2_del_homo_female_4
small RNA-seq on whole female


title: rnst2_F1female_3

description:
Library name: rnst2_F1female_3
mRNA-seq on whole female


title: rnst2F1female_1

description:
Library name: rnst2_F1female_1
mRNA-seq on whole female


title: 6971-EC-S1_ROI_62

description:
Library name: DSP-1001660013356-E-F03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_F1male_1

description:
Library name: rnst2_F1male_1
mRNA-seq on whole male


title: 6971-EC-S1_ROI_65

description:
Library name: DSP-1001660013356-E-F06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_63

description:
Library name: DSP-1001660013356-E-F04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_60

description:
Library name: DSP-1001660013356-E-F01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Tumor


title: rnst2_del_homo_female_3

description:
Library name: rnst2_del_homo_female_3
small RNA-seq on whole female


title: rnst2_del_homo_female_1

description:
Library name: rnst2_del_homo_female_1
small RNA-seq on whole female


title: rnst2_del_het_female_3

description:
Library name: rnst2_del_het_female_3
small RNA-seq on whole female


title: 6971-EC-S1_ROI_61

description:
Library name: DSP-1001660013356-E-F02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_57

description:
Library name: DSP-1001660013356-E-E10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_del_het_female_1

description:
Library name: rnst2_del_het_female_1
small RNA-seq on whole female


title: 6971-EC-S1_ROI_58

description:
Library name: DSP-1001660013356-E-E11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_del_homo_female_2

description:
Library name: rnst2_del_homo_female_2
small RNA-seq on whole female


title: 6971-EC-S1_ROI_59

description:
Library name: DSP-1001660013356-E-E12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_del_het_female_2

description:
Library name: rnst2_del_het_female_2
small RNA-seq on whole female


title: 6971-EC-S1_ROI_55

description:
Library name: DSP-1001660013356-E-E08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_56

description:
Library name: DSP-1001660013356-E-E09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_cat_homo_sperm_4

description:
Library name: rnst2_cat_homo_sperm_4
small RNA-seq on sperm

source_name: sperm

value: sperm


title: rnst2_cat_homo_sperm_3

description:
Library name: rnst2_cat_homo_sperm_3
small RNA-seq on sperm


title: rnst2_del_het_female_4

description:
Library name: rnst2_del_het_female_4
small RNA-seq on whole female


title: rnst2_cat_homo_sperm_2

description:
Library name: rnst2_cat_homo_sperm_2
small RNA-seq on sperm


title: 6971-EC-S1_ROI_53

description:
Library name: DSP-1001660013356-E-E06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_cat_homo_sperm_1

description:
Library name: rnst2_cat_homo_sperm_1
small RNA-seq on sperm


title: 6971-EC-S1_ROI_54

description:
Library name: DSP-1001660013356-E-E07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_cat_homo_male4

description:
Library name: rnst2_cat_homo_male4
small RNA-seq on whole male


title: 6971-EC-S1_ROI_51

description:
Library name: DSP-1001660013356-E-E04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_cat_homo_male3

description:
Library name: rnst2_cat_homo_male3
small RNA-seq on whole male


title: 6971-EC-S1_ROI_50

description:
Library name: DSP-1001660013356-E-E03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_48

description:
Library name: DSP-1001660013356-E-E01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_homo_male_4

description:
Library name: rnst_mut_homo_male_4
small RNA-seq on whole male


title: 6971-EC-S1_ROI_52

description:
Library name: DSP-1001660013356-E-E05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_47

description:
Library name: DSP-1001660013356-E-D12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_homo_male_6

description:
Library name: rnst_mut_homo_male_6
small RNA-seq on whole male


title: 6971-EC-S1_ROI_46

description:
Library name: DSP-1001660013356-E-D11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_homo_male_3

description:
Library name: rnst_mut_homo_male_3
small RNA-seq on whole male


title: rnst2_cat_homo_male1

description:
Library name: rnst2_cat_homo_male1
small RNA-seq on whole male


title: 6971-EC-S1_ROI_49

description:
Library name: DSP-1001660013356-E-E02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_homo_male_2

description:
Library name: rnst_mut_homo_male_2
small RNA-seq on whole male


title: rnst_mut_homo_male_1

description:
Library name: rnst_mut_homo_male_1
small RNA-seq on whole male


title: rnst_mut_homo_male_5

description:
Library name: rnst_mut_homo_male_5
small RNA-seq on whole male


title: 6971-EC-S1_ROI_45

description:
Library name: DSP-1001660013356-E-D10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_het_male_5

description:
Library name: rnst_mut_het_male_5
small RNA-seq on whole male


title: 6971-EC-S1_ROI_42

description:
Library name: DSP-1001660013356-E-D07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst2_F1female_2

description:
Library name: rnst2_F1female_2
mRNA-seq on whole female


title: 6971-EC-S1_ROI_44

description:
Library name: DSP-1001660013356-E-D09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_het_male_3

description:
Library name: rnst_mut_het_male_3
small RNA-seq on whole male


title: 6971-EC-S1_ROI_40

description:
Library name: DSP-1001660013356-E-D05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_41

description:
Library name: DSP-1001660013356-E-D06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_het_male_4

description:
Library name: rnst_mut_het_male_4
small RNA-seq on whole male


title: 6971-EC-S1_ROI_39

description:
Library name: DSP-1001660013356-E-D04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_38

description:
Library name: DSP-1001660013356-E-D03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_het_male_1

description:
Library name: rnst_mut_het_male_1
small RNA-seq on whole male


title: 6971-EC-S1_ROI_37

description:
Library name: DSP-1001660013356-E-D02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_mut_het_male_2

description:
Library name: rnst_mut_het_male_2
small RNA-seq on whole male


title: 6971-EC-S1_ROI_43

description:
Library name: DSP-1001660013356-E-D08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_homo_male_6

description:
Library name: rnst_cat_homo_male_6
small RNA-seq on whole male


title: rnst_cat_homo_male_3

description:
Library name: rnst_cat_homo_male_3
small RNA-seq on whole male


title: 6971-EC-S1_ROI_35

description:
Library name: DSP-1001660013356-E-C12
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_36

description:
Library name: DSP-1001660013356-E-D01
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_homo_male_4

description:
Library name: rnst_cat_homo_male_4
small RNA-seq on whole male


title: 6971-EC-S1_ROI_34

description:
Library name: DSP-1001660013356-E-C11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_homo_male_1

description:
Library name: rnst_cat_homo_male_1
small RNA-seq on whole male


title: 6971-EC-S1_ROI_32

description:
Library name: DSP-1001660013356-E-C09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_homo_male_2

description:
Library name: rnst_cat_homo_male_2
small RNA-seq on whole male


title: rnst_cat_het_male_5

description:
Library name: rnst_cat_het_male_5
small RNA-seq on whole male


title: 6971-EC-S1_ROI_33

description:
Library name: DSP-1001660013356-E-C10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_het_male_4

description:
Library name: rnst_cat_het_male_4
small RNA-seq on whole male


title: rnst_cat_homo_male_5

description:
Library name: rnst_cat_homo_male_5
small RNA-seq on whole male


title: 6971-EC-S1_ROI_31

description:
Library name: DSP-1001660013356-E-C08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_30

description:
Library name: DSP-1001660013356-E-C07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_het_male_1

description:
Library name: rnst_cat_het_male_1
small RNA-seq on whole male


title: 6971-EC-S1_ROI_29

description:
Library name: DSP-1001660013356-E-C06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: rnst_cat_het_male_2

description:
Library name: rnst_cat_het_male_2
small RNA-seq on whole male


title: rnst_cat_het_male_3

description:
Library name: rnst_cat_het_male_3
small RNA-seq on whole male


title: 6971-EC-S1_ROI_28

description:
Library name: DSP-1001660013356-E-C05
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: ce_sperm4

description:
Library name: ce_sperm4
small RNA-seq on sperm


title: 6971-EC-S1_ROI_26

description:
Library name: DSP-1001660013356-E-C03
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_27

description:
Library name: DSP-1001660013356-E-C04
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: ce_sperm3

description:
Library name: ce_sperm3
small RNA-seq on sperm


title: ce_sperm1

description:
Library name: ce_sperm1
small RNA-seq on sperm


title: 6971-EC-S1_ROI_25

description:
Library name: DSP-1001660013356-E-C02
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_21

description:
Library name: DSP-1001660013356-E-B10
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_22

description:
Library name: DSP-1001660013356-E-B11
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: ce_male4

description:
Library name: ce_male4
small RNA-seq on whole male


title: ce_male2

description:
Library name: ce_male2
small RNA-seq on whole male


title: 6971-EC-S1_ROI_17

description:
Library name: DSP-1001660013356-E-B06
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \

value: Acinar


title: ce_male1

description:
Library name: ce_male1
small RNA-seq on whole male


title: 6971-EC-S1_ROI_18

description:
Library name: DSP-1001660013356-E-B07
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: 6971-EC-S1_ROI_20

description:
Library name: DSP-1001660013356-E-B09
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: ce_male3

description:
Library name: ce_male3
small RNA-seq on whole male


title: F2FM_36

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

description: Library name: F2FM_36

data_processing:
Data cleaning involved the removal of adapters and reads with a Phred-Score < 30. Quality control (QC) and read statistics were assessed using FastQC v0.11.8 and MultiQC v1.9. The reads were mapped to the Bos taurus reference genome (ARS-UCD 1.2) available at http://www.ensembl.org/Bos_taurus/Info/Index/, using the STAR aligner v. 2.7.3a. Raw counts per gene were obtained using the –quantMode GeneCounts parameter from STAR and the gene annotation file from Ensembl (release 100). Post-mapping quality control was conducted using the tools MultiQC, NOISeq v.2.26.0, and edgeR v.3.24.3.
Assembly: Bos taurus reference genome (ARS-UCD 1.2, releas 100)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample. (BM - Samples at birth - F1, SM; Samples at slaugther - F1; FM, fetal samples day84 generation 2) TXT file

organism: Bos taurus

source_name: Longissimus dorsi (muscle)

extract_protocol:
Samples were first disrupted and homogenized in TRIzol Reagent (Invitrogen™, Thermo Fisher Scientific, Waltham, MA, USA), and the aqueous phase was then processed using the RNeasy Plus Universal Mini Kit (Qiagen®, Germantown, MD, USA) according to the manufacturer’s instructions. Sample integrity and purity were assessed using the Agilent 2100 Bioanalyzer and agarose gel electrophoresis.
Sixteen samples (8 per treatment) at birth, 15 at the harvest of F1 heifers (LG n = 7; MG n = 8), and 16 samples (8 per treatment) from F2 fetuses met the quantity and quality parameters for library preparation. This process was carried out using the NEBNext® Ultra™ II non-directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA). The libraries were sequenced on the Illumina® NovaSeq 6000 platform, generating 150 bp reads at 20 million per sample depth. Both library preparation and paired-end sequencing were conducted by Novogene Co. (Nanjing, China).

value: Longissimus dorsi (muscle)

tag: generation

value: LG

tag: timepoint

value: fetal(day 84)


title: F2FM_47

description: Library name: F2FM_47

value: MG


title: 6971-EC-S1_ROI_19

description:
Library name: DSP-1001660013356-E-B08
A total of 3 slides containing tissue sections from pancreatic cysts, associated malignancy, and/or adjacent normal tissue was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) together with DAPI for nuclei detection. 310 ROIs were captured for whole transcriptome profiling. \


title: F2FM_45

description: Library name: F2FM_45