title: RNA-Seq of CDO1-overexpressing human gastric cancer AGS cells, biological replicate 3

first: Fazhi

last: Wang

address: No. 213, Hongkou Road

institute: Shanghai Jiao Tong University

description:
Library name: TREAT3
Biological replicate 3 of CDO1-overexpressing human gastric cancer AGS cells used for paired-end RNA sequencing.

data_processing:
Raw paired-end sequencing reads were subjected to quality control and filtering to remove adapter sequences and low-quality reads.
Filtered reads were aligned to the Homo sapiens reference genome; the exact genome build and software versions must be added before final GEO submission.
Assembly: REPLACE_WITH_GENOME_BUILD
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all six RNA-seq samples.

source_name: stomach

extract_protocol:
Total RNA was extracted using TRIzol Reagent. RNA purity was assessed using NanoDrop, RNA concentration was measured using the Qubit RNA BR (Broad-Range) Assay Kit, and RNA integrity was evaluated by agarose gel electrophoresis.
For each sample, 0.1-1 microgram of total RNA was used. Poly(A)+ mRNA was isolated using the Hieff NGS mRNA Isolation Master Kit V2, and sequencing libraries were constructed using the Hieff NGS EvoMax RNA Library Prep Kit (dNTP). Library concentration was measured using the Equalbit 1x dsDNA HS Assay Kit and fragment-size distribution was assessed using an Agilent 4200 TapeStation. Libraries were circularized using the Hieff NGS Dual Barcode Fast-Pace DNA Cyclization Kit for MGI, quantified using the Equalbit ssDNA Assay Kit, and sequenced on a DNBSEQ-T7RS instrument with FCL PE150 V3.0 reagents to generate paired-end 150-bp reads.

treatment_protocol: CDO1-overexpressing AGS gastric cancer cells and corresponding control AGS cells were prepared in parallel. Three independent biological replicates were collected for each group.

value: stomach

value: AGS

value: epithelial-like cell

value: CDO1 overexpression


title: Arabidopsis ckx3ckx5 mutant rosette region at bolt, rep4

status: Public on Jul 25 2026

type: SRA

city: Auckland

first: Zhiwei

last: Luo

state: Auckland

address: 120 Mt Albert Road

country: New Zealand

institute: PLANT AND FOOD RESEARCH

description: Library name: ckx_R5

library_source: transcriptomic

data_processing:
RNA-seq reads were processed using nf-core/rnaseq v3.10 (https://doi: 10.5281/zenodo.1400710) of the nf-core pipeline (Ewels et al., 2020), and the filtered raw reads were mapped to Arabidopsis genome TAIR10 (https://www.arabidopsis.org/index.jsp). Raw read counts were processed using DESeq2 R package (Love et al., 2014).
Assembly: Arabidopsis genome TAIR10
Supplementary files format and content: txt

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: tissue at the rosette region, leaves, stem and roots are removed.

growth_protocol: Arabidopsis seeds of scl28, ckx3 ckx5, Atd14 and WT were stratified in the dark at 4°C for two days then sowed and grown in a growth room under long-day conditions (16/8-hour light/dark cycle) using Heliospectra LX601C's LED units (each unit has lights of three wavelengths: 450 nm, 660 nm, and 735 nm) and the photon flux densities on the pot surface are between 120 and 172 µmol m-2 s-1, with an average density of 150 µmol m-2 s-1. The temperature of the growth room was maintained at 20 – 22°C

extract_protocol:
Total RNA was extracted from the powder using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA) according to the instruction manual and treated with DNase using On-Column DNase I Digestion Set (Sigma-Aldrich, St. Louis, MO, USA). The quantities and purity of the extracted RNA samples were measured using a NanoDrop™ 1000 Spectrophotometer (Thermofisher, Waltham, MA, USA) and RNA integrity was checked using the RNA 6000 Nano kit and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
NEBNext® Ultra™ RNA Library Prep Kit

tag: tissue

tag: genotype

value: ckx3 ckx5 knock out


title: RNA-Seq of CDO1-overexpressing human gastric cancer AGS cells, biological replicate 2

city: Shanghai

country: China

description:
Library name: TREAT2
Biological replicate 2 of CDO1-overexpressing human gastric cancer AGS cells used for paired-end RNA sequencing.

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: Split dCas9-KRAB sgSTC ABA ctrl Day4 Rep3

city: Berlin

first: Edda

middle: G.

last: Schulz

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Library name: sgSTC_ABA_ctrl_D4_Rep3

library_source: genomic

data_processing:
Sequencing reads were trimmed with Trim Galore, with [--clip_R1 10 --three_prime_clip_R1 5 --clip_R2 15 --three_prime_clip_R2 5 --paired].
They were mapped using bsmapz with settings -m 0 -g 3 -n 1 -v 0.1 -w 10 to the reference fasta file that contains the amplicon sequences.
bam files were sorted and indexed with samtools, and merged if the sample was sequenced multiple times.
bam files were used for methylation calling by mcall command of MOABS package (Sun et al, 2014) [--trimWGBSEndRepairPE2Seq 0 --trimWGBSEndRepairPE1Seq 0 --reportCHX 0].
Assembly: mm10
Supplementary files format and content: bed files with MOABS methylation calls.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: TX1072 mouse ES cells and all derived cell lines were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich D6429), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). For CasTuner lines, 500nM dTAG-13 was added to the medium. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 flasks (Corning). The medium was changed daily, and the cells were split every two days.  WT F121.9 mouse ESCs and the derived deletion cell lines Rnf12-/- and Rnf12 -/- Rex1 -/- (DKO) were adapted to feeder-free 2i/LIF conditions (DMEM (GIBCO 11995065), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 100 U/mL penicillin/streptomycin (Thermo Fisher Scientifc), 1x NEAA (Gibco 11140035), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)) for 5 passages. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 plates (Corning). The medium was changed daily, and the cells were split every two days.

extract_protocol:
Genomic DNA was extracted from harvested cells using the DNeasy Blood & Tissue kit (Qiagen). 1μg of DNA were bisulfite-converted with EZ DNA Methylation-Gold kit (Zymo). One fifth of the eluted DNA was used per amplicon PCR. Primers for bisulfite-converted DNA targeting the Xist-promoter proximal CpG island (chrX:103,482,090-103,482,350 mm10 from UCSC Genome Browser) were designed with MethPrimer2.0 (Li & Dahiya, 2002). PCR was performed with EpiTaq polymerase (Takara), using 25mM MgCl2. DNA was amplified for 27 cycles, at an annealing temperature of 53oC. PCR reactions of each sample were pooled (total volume for Xist amplicons) and cleaned with MinElute Reaction Cleanup kit (Qiagen) (2 columns per sample).
Libraries were prepared with NEBNext Ultra II DNA Library Prep kit (New England Biolabs), indexed with NEBNext Multiplex Oligos for Illumina Dual Index Set 1 (New England Biolabs) and cleaned with AMPure XP beads (Beckman Coulter). Concentration and size distribution of libraries were analyzed with Qubit 1x dsDNA HS (Thermo Fisher Scientific) and HS DNA D1000 Tapestation (Agilent), respectively. Libraries were sequenced 2x150bp paired-end with MiSeq, DNBSEQ G400 or Aviti sequencers.

treatment_protocol: Differentiation of all cell lines was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded for differentiation, the medium was changed every day and the cells were not split until harvesting.  For the knock-down of Zfp36l1 and Zfp280c, the CasTuner system was induced with dTAG-13 removal for 6 days in total, the last 4 of which differentiation was also induced. The control condition was cultured with dTAG-13 and differentiated for 4 days. To knock-down the transcription of Rex1 and Zfp281, the dCas9-KRAB system was induced with ABA for 5 days in total, the last 4 of which differentiation was also induced. The safe-targeting control line with “STC” guides was cultured in the same conditions as the knock-down cell lines. To knock-down the transcription of Rnf12 and Zic3, the CasTuner system was induced by dTAG-13 removal for 7 days in total, and during the last 3 days differentiation was induced. The control condition was cultured with dTAG-13 and differentiated for 3 days.

value: Embryonic stem cells

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD

tag: timepoint

value: Differentiation Day 4


title: N008 cells,siATF3 1

first: Luju

last: Jiang

state: State...

address: Dongchuan Road 800, Minhang, Shanghai, China

institute: Shanghai Jiaotong University

description: Library name: Sample7

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: GRCh38 (hg38) from the Genome Reference Consortium
Supplementary files format and content: txt files include fpkm values for each sample

growth_protocol: N008 cell was maintained in primary Schwann cell media (iCell bioscience, Shanghai, China) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin according to ATCC protocols.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: human primary Schwann cell

value: ATF3 knockdown


title: LX2_DBP_4

city: Jeju

first: Eun Bok

last: Baek

address: 102 Jeju Daehak-ro

country: South Korea

institute: Jeju National University

description:
Library name: LX2_DBP_4
DBP

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform to generate 151 bp paired-end reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38(NCBI) whole genome using STAR
Calculation mapped reads using salmon
TMM + CPM calculation using conorm
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files contain Read count values for each sample.

source_name: liver

growth_protocol: DMEM supplemented with 10% FBS

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

treatment_protocol: DMEM supplemented with 1% FBS

value: liver

value: Human fetal hepatocyte

value: WT

value: DBP


title: RNA-Seq of CDO1-overexpressing human gastric cancer AGS cells, biological replicate 1

description:
Library name: TREAT1
Biological replicate 1 of CDO1-overexpressing human gastric cancer AGS cells used for paired-end RNA sequencing.


title: Arabidopsis ckx3ckx5 mutant rosette region at bolt, rep3

description: Library name: ckx_R3

value: tissue at the rosette region, leaves, stem and roots are removed.


title: N008 cells,siARRDC4 3

description: Library name: Sample6

value: ARRDC4 knockdown


title: LX2_DBP_3

description:
Library name: LX2_DBP_3
DBP


title: N008 cells,siARRDC4 2

description: Library name: Sample5


title: Arabidopsis ckx3ckx5 mutant rosette region at bolt, rep2

description: Library name: ckx_R2


title: RNA-Seq of control human gastric cancer AGS cells, biological replicate 3

description:
Library name: CONTROL3
Biological replicate 3 of control human gastric cancer AGS cells used for paired-end RNA sequencing.

value: stomach

value: control


title: LX2_DBP_2

description:
Library name: LX2_DBP_2
DBP


title: RNA-Seq of control human gastric cancer AGS cells, biological replicate 2

description:
Library name: CONTROL2
Biological replicate 2 of control human gastric cancer AGS cells used for paired-end RNA sequencing.

value: AGS

value: epithelial-like cell


title: Arabidopsis ckx3ckx5 mutant rosette region at bolt, rep1

description: Library name: ckx_R1

value: ckx3 ckx5 knock out


title: N008 cells,siARRDC4 1

description: Library name: Sample4


title: RNA-Seq of control human gastric cancer AGS cells, biological replicate 1

description:
Library name: CONTROL1
Biological replicate 1 of control human gastric cancer AGS cells used for paired-end RNA sequencing.


title: LX2_DBP_1

description:
Library name: LX2_DBP_1
DBP


title: Arabidopsis Col-0 rosette region at bolt, rep3

description: Library name: Col_R4


title: Well-watered, polymer control, biological replicate 3

city: christchurch

first: Jesus

middle: Francisco

last: Echaide Aquino

address: 85084 Ellesmere Junction Road, Lincoln

department: agls

institute: lincoln university

description: Library name: W_P_3_1

data_processing:
Raw paired-end sequencing reads were imported into CLC Genomics Workbench version 21.0.4. Initial quality control included assessment of read length, base quality, nucleotide composition, and potential sequence contamination.
Raw sequencing reads were trimmed in CLC Genomics Workbench version 21.0.4 to remove low-quality sequence and other undesirable read regions before alignment.
High-quality paired-end reads were aligned to the Phaseolus vulgaris cv. BAT93 reference genome using CLC Genomics Workbench version 21.0.4. Alignment parameters were mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, and maximum number of hits per read = 10.
Gene-level expression values were calculated in CLC Genomics Workbench and normalized as transcripts per million mapped reads, TPM.
Differential expression analysis was performed using the CLC RNA-Seq Analysis Toolkit. Genes were classified as differentially expressed when they met the following thresholds: absolute log2 fold change ≥ 0.6, false discovery rate ≤ 0.01, and Bonferroni-adjusted P value ≤ 0.05. Principal component analysis, volcano plots, and Venn diagrams were generated within CLC Genomics Workbench.
Assembly: Phaseolus vulgaris cv. BAT93 reference genome, CoGe Genome ID 20365
Supplementary files format and content: TPM, RPKM

organism: Phaseolus vulgaris

source_name: Leaf

growth_protocol: Drought stressed plant, 6PP treated, rep 1

extract_protocol:
Total RNA was extracted from 100 mg of ground tissue using 1 mL TRIzol reagent. Samples were vortexed, mixed with 200 µL chloroform, incubated at room temperature for 3 min, and centrifuged at 12,000 rpm and 4°C for 15 min. The aqueous phase was transferred to a new tube, mixed with 500 µL isopropanol, incubated on ice for 10 min, and centrifuged at 12,000 rpm and 4°C for 10 min. RNA pellets were washed with 75% ethanol, centrifuged at 12,000 rpm and 4°C for 5 min, air-dried, resuspended in 35 µL DEPC-treated water, and incubated at 55°C for 10 min. RNA was further purified using a modified Plant Total RNA Extraction Miniprep System protocol. The RNA solution was mixed with 450 µL RX buffer and 230 µL 98% ethanol and loaded onto a spin column. Columns were centrifuged at 10,000 rpm for 1 min, washed with 500 µL WF buffer at 14,000 rpm for 1 min, and washed twice with 700 µL WS buffer. After a final centrifugation at 14,000 rpm for 3 min, RNA was eluted with 50 µL RNase-free water and stored at −80°C. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer. Only samples with an RNA integrity number greater than 6.8 were used for sequencing.
cDNA libraries were prepared by Novogene (HK) Co., Ltd. and sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

treatment_protocol: Seedworx Bio Friendly 1 polymer was used as the carrier for 6-pentyl-α-pyrone (6PP). The polymer was mixed with sterile water at a 1:1 ratio. For the 6PP treatment, 114 mM 6PP was incorporated into the polymer mixture, with the water volume adjusted to maintain the specified polymer-to-remaining-components ratio. The mixture was homogenized using a FastPrep-24 homogenizer at 5.5 m/s for 60 s. One milliliter of coating mixture was combined with 50 g of surface-sterilized seeds and mixed manually for 5 min using circular and rotational movements. Control seeds were coated with polymer and water without 6PP. Plants from each seed treatment were maintained under either well-watered or drought-stress conditions. Drought stress was imposed at the second-trifoliate-leaf stage by withholding irrigation for approximately 16 days. Leaf tissue was collected when drought-stressed plants reached wilting stage 3, while well-watered plants continued to receive irrigation. The experiment therefore comprised four conditions: polymer control under well-watered conditions, 6PP treatment under well-watered conditions, polymer control under drought stress, and 6PP treatment under drought stress.

value: Leaf

value: mixed leaf cells

value: Dwarf messi

value: Polymer-coated seed; well-watered


title: Arabidopsis Col-0 rosette region at bolt, rep4

description: Library name: Col_R5


title: N008 cells,siNC 3

description: Library name: Sample3

value: human primary Schwann cell


title: LX2_control_4

description:
Library name: LX2_control_4
vehicle


title: N008 cells,siNC 2

description: Library name: Sample2


title: LX2_control_3

description:
Library name: LX2_control_3
vehicle


title: N008 cells,siNC 1

description: Library name: Sample1


title: Arabidopsis Col-0 rosette region at bolt, rep2

description: Library name: Col_R2


title: LX2_control_2

description:
Library name: LX2_control_2
vehicle


title: Well-watered, polymer control, biological replicate 1

description: Library name: W_P_1_1


title: Arabidopsis Col-0 rosette region at bolt, rep1

description: Library name: Col_R1


title: LX2_control_1

description:
Library name: LX2_control_1
vehicle


title: SAMPLE4, HCAEC cells, medin 5 uM for 20 hours

city: Phoenix

first: Ming

last: Li

state: AZ

address: 650 E Indian School Road

country: USA

institute: Phoenix VA Health Care System

description:
Library name: HCAEC2B
replicate 4 - medin 5 uM

data_processing:
Libraries were sequenced on the DNBSEQ platform (BGI, Shenzhen, China) using a paired-end 150-bp (PE150) strategy.
Raw sequencing reads were processed using SOAPnuke (v2.3) to remove adapter-contaminated, low-quality, and ambiguous reads. Clean reads were aligned to the human reference genome (GRCh38.p14) using HISAT2 (v2.0.4)
Assembly: GRCh38.p14
Supplementary files format and content: .txt; count matrix, fpkm, tpm

source_name: coronary artery

growth_protocol: HCAEC cells were maintained in Cell Systems Normal Glcuose Media in humidified air with 5% CO2 at 37 degree.

extract_protocol:
Aurum Total RNA kit according to instructions
Strand-specific mRNA libraries were constructed using a dUTP-based protocol. Briefly, poly(A)+ mRNA was enriched using oligo(dT)-conjugated magnetic beads, fragmented, and reverse-transcribed to generate first-strand cDNA. Second-strand cDNA synthesis was performed with dUTP incorporation to preserve strand information. Following end repair, adapter ligation, and PCR amplification, libraries were converted into DNA nanoballs (DNBs)

treatment_protocol: vehicle or medin 5 uM for 20 hours

value: coronary artery

value: HCAEC

value: endothelial cells

value: medin


title: Lewis rat thymocytes

city: Shimotuga

first: Yasushi

last: Sawanobori

state: Tochigi

address: Kitakobayashi 880, Mibu

country: Japan

institute: Dokkyo medical university

description:
Library name: 60-1216959069
10x Genomics

library_source: transcriptomic single cell

data_processing:
For scRNA-seq, FASTQ files were processed using the Cell Ranger pipeline (ver. 8.0.0), with the mRatBN7.2 genome assembly as the reference. The resulting expression matrices were converted into Seurat (ver. 5.3.0) objects. Rat thymocyte and thymic stromal scRNA-seq datasets were integrated with published mouse thymocyte and thymic stromal datasets, respectively. The mouse thymocyte dataset was obtained from GEO accession GSE186078, and the mouse thymic stromal dataset was obtained from Zenodo accession 12516405. Mouse gene symbols were converted to rat orthologs, and mouse cluster annotations were projected onto rat cells. The resulting rat reference datasets were used as references for robust cell-type decomposition (RCTD).
For spatial transcriptomics, FASTQ files and the ssDNA-stained tissue image were processed using the Stereo-seq Analysis Workflow pipeline (ver. 8.1.3), with the mRatBN7.2 genome assembly as the reference. StereoMap (ver. 4.1.2) was used for initial visualization of spatial gene expression. The output files, cellbin_1.0.adjusted.h5ad and bin20_1.0.h5ad, were converted into Seurat objects. Cell-type composition in the spatial transcriptomics datasets was inferred using RCTD with the rat scRNA-seq reference object. Spatial distributions of inferred cell types and region-associated gene expression patterns were then analyzed in Seurat.
Assembly: mRatBN7.2
Supplementary files format and content: 60-919422446: st_barcodes.tsv.gz, st_features.tsv.gz, st_matrix.mtx.gz: Matrix files
Supplementary files format and content: 60-919422446: RatThymicStromaMetadata.csv: Metadata file of the Seurat object
Supplementary files format and content: 60-919422446: 2024_03_31_rat_thymic_stroma.loom: velocyto-generated loom file
Supplementary files format and content: 60-1216959069: thy_barcodes.tsv.gz, thy_features.tsv.gz, thy_matrix.mtx.gz: Matrix files
Supplementary files format and content: 60-1216959069: RatThymocyteMetadata.csv: Metadata file of the Seurat object
Supplementary files format and content: 60-1169740824: visualization.tar.gz: tar.gz file containing h5ad and stereo files
Supplementary files format and content: 60-1169740824: CellBin_objMetadata.csv: Matadata file of the cellbin Seurat object
Supplementary files format and content: 60-1169740824: bin20_objMetadata.csv: Matadata file of the bin20 Seurat object
Supplementary files format and content: 60-1169740824: Y01052GC.barcodeToPos.h5: Spatial coordinate. Required for the initial processing
Supplementary files format and content: 60-1169740824: Y01052GC_ssDNA.tif: Picture of the section. Required for the initial processing

organism: Rattus norvegicus

source_name: Thymus

extract_protocol:
For scRNA-seq analysis, thymi were minced and enzymatically digested. For thymocyte preparation, tissues were digested with collagenase D (Roche) and DNase I (Roche). For thymic stromal cell preparation, tissues were digested with Liberase TH (Roche) and DNase I in HBSS supplemented with 1.25 mM Ca²⁺, 1.45% bovine serum albumin (BSA), and 2% fetal calf serum (FCS) at 37°C for 25 min. During incubation, tissues were mechanically dissociated every 5 min by sequential pipetting. After enzymatic digestion, EDTA was added to a final concentration of 2.5 mM, and samples were incubated for an additional 5 min. The digested tissue was filtered through 50-μm nylon mesh, and red blood cells were lysed with ACK buffer. For stromal cell preparation, CD45⁻ cells were further enriched using an autoMACS instrument (Miltenyi Biotec) and sorted using a FACSAria III cell sorter (Becton, Dickinson and Company). For spatial transcriptomics, a thymus was cut horizontally into three pieces, and the middle portion was embedded in O.C.T. compound in a 1 × 1 cm plastic tray. To maximize the tissue area within the tray, the right and left lobes were positioned back to back. A 10-μm-thick section was mounted onto a Chip T (STOmics). The slide was incubated at 37°C for 5 min and then stored in an airtight container at −80°C until further processing.
Single-cell RNA-seq library construction, spatial transcriptomics library construction, and sequencing were outsourced to GENEWIZ (Tokyo, Japan). Briefly, for scRNA-seq, libraries were prepared using the 10x Genomics Chromium system and sequenced on an Illumina NovaSeq sequencer. For spatial transcriptomics, a frozen section mounted on a Chip T was processed using the Stereo-seq Transcriptomics Set for ssDNA staining, reverse transcription, and cDNA amplification. The resulting library was sequenced on an MGI DNBSEQ sequencer.

value: Thymus

value: Thymocytes


title: Drought stress, polymer control, biological replicate 3

description: Library name: D_P_3_1

value: Polymer-coated seed; drought stress


title: Drought stress, polymer control, biological replicate 2

description: Library name: D_P_2_1


title: Lewis rat thymic stromal cells

description:
Library name: 60-919422446
10x Genomics

value: CD45 negative stromal cells


title: LO2_DBP_2

description:
Library name: LO2_DBP_2
DBP

value: liver

value: Human fetal hepatocyte

value: WT

value: DBP


title: Amniotic fluid cells, preeclampsia 3

city: Chengdu

first: Jiashuo

last: Zhang

state: Sichuan

address: No. 28, Dianxin South Road

institute: West China Hospital

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt  https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). Then sequence quality was verified using FastQC including the Q20, Q30 and GC-content of the clean data.
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters.
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM value.
Assembly: Hisat2
Supplementary files format and content: Tab-delimited text file includes FPKM values and raw counts for each sample.

source_name: amniotic fluid

growth_protocol: Amniotic fluid cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under conventional conditions (37 °C, 5% CO2).

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
After passing the quality inspection of the total RNA, magnetic beads connected to Oligo (dT) were used to enrich eukaryotic mRNA (for prokaryotes, rRNA was removed using a reagent kit to enrich mRNA), and then Fragmentation Buffer was added to randomly break the mRNA into short fragments. Using fragmented mRNA as a template, synthesize a single strand of cDNA using six base random primers, and then connect an adapter with Unique Molecular Identifiers (UMI); Finally, PCR amplification was performed to obtain the final sequencing library.

value: amniotic fluid

value: mesenchymal stem cells

tag: condition

value: preeclampsia


title: CTRL4, HCAEC cell, vehicle for 20 hours

description:
Library name: HCAEC1B
replicate 4 - vehicle

value: vehicle


title: Drought stress, polymer control, biological replicate 1

description: Library name: D_P_1_1

value: Leaf

value: mixed leaf cells

value: Dwarf messi


title: Amniotic fluid cells, preeclampsia 2


title: LO2_DBP_4

description:
Library name: LO2_DBP_4
DBP


title: Well-watered, 114 mM 6PP, biological replicate 3

description: Library name: W_6PP3_1

value: 114 mM 6PP seed coating; well-watered


title: CTRL3, HCAEC cell, vehicle for 20 hours

description:
Library name: HCAEC04221B
replicate 3 - vehicle

value: coronary artery

value: HCAEC

value: endothelial cells


title: Well-watered, 114 mM 6PP, biological replicate 2

description: Library name: W_6PP2_1


title: Amniotic fluid cells, preeclampsia 1


title: LO2_DBP_1

description:
Library name: LO2_DBP_1
DBP


title: SAMPLE2, HCAEC cells, medin 5 uM for 20 hours

description:
Library name: HCAEC2A
replicate 2 - medin 5 uM

value: medin


title: LO2_control_4

description:
Library name: LO2_control_4
vehicle

value: control


title: Amniotic fluid cells, control pregnancy 3


title: Well-watered, 114 mM 6PP, biological replicate 1

description: Library name: W_6PP1_1


title: CTRL2, HCAEC cell, vehicle for 20 hours

description:
Library name: HCAEC1A
replicate 2 - vehicle


title: LO2_control_3

description:
Library name: LO2_control_3
vehicle

value: liver


title: Drought stress, 114 mM 6PP, biological replicate 3

description: Library name: D_6PP3_1

value: 114 mM 6PP seed coating; drought stress


title: Amniotic fluid cells, control pregnancy 2


title: SAMPLE1, HCAEC cells, medin 5 uM for 20 hours

description:
Library name: HCAEC2
replicate 1 - medin 5 uM

value: WT


title: LO2_control_2

description:
Library name: LO2_control_2
vehicle

value: Human fetal hepatocyte


title: CTRL1, HCAEC cell, vehicle for 20 hours

description:
Library name: HCAEC1
replicate 1 - vehicle


title: Drought stress, 114 mM 6PP, biological replicate 2

description: Library name: D_6PP2_1


title: Drought stress, 114 mM 6PP, biological replicate 1

description: Library name: D_6PP1_1


title: LO2_control_1

description:
Library name: LO2_control_1
vehicle


title: long read RNA-seq from large intestine (ENCLB069GNQ)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR992UMK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992UMK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB069GNQ

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female embryo (107 days) large intestine tissue

value: large intestine

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

tag: age

value: 107 day

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Ian Glass

tag: link

value: ENCBS849ZYL at ENCODE; https://www.encodeproject.org/ENCBS849ZYL/


title: long read RNA-seq from stomach (ENCLB654RMY)

description:
https://www.encodeproject.org/experiments/ENCSR993RKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR993RKQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB654RMY

source_name: Homo sapiens female embryo (147 days) stomach tissue

value: stomach

value: 147 day

value: ENCBS663BTK at ENCODE; https://www.encodeproject.org/ENCBS663BTK/


title: long read RNA-seq from muscle of arm (ENCLB903WMX)

description:
https://www.encodeproject.org/experiments/ENCSR989PGQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR989PGQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB903WMX

source_name: Homo sapiens male embryo (91 days) muscle of arm tissue

value: muscle of arm

value: male

value: 91 day

value: ENCBS859GFP at ENCODE; https://www.encodeproject.org/ENCBS859GFP/


title: long read RNA-seq from testis (ENCLB314AJG)

description:
https://www.encodeproject.org/experiments/ENCSR966PBL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR966PBL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB314AJG

source_name: Homo sapiens male embryo testis tissue

value: testis

value: ENCBS228NHI at ENCODE; https://www.encodeproject.org/ENCBS228NHI/


title: long read RNA-seq from muscle of leg (ENCLB405KHS)

description:
https://www.encodeproject.org/experiments/ENCSR979UPD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979UPD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB405KHS

source_name: Homo sapiens female embryo (115 days) muscle of leg tissue

value: muscle of leg

value: 115 day

value: ENCBS252AST at ENCODE; https://www.encodeproject.org/ENCBS252AST/


title: long read RNA-seq from muscle of back (ENCLB245SDW)

description:
https://www.encodeproject.org/experiments/ENCSR952SBK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR952SBK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB245SDW

source_name: Homo sapiens female embryo (85 days) muscle of back tissue

value: muscle of back

value: tissue

value: female

value: embryonic

value: 85 day

value: ENCBS975ZZI at ENCODE; https://www.encodeproject.org/ENCBS975ZZI/


title: long read RNA-seq from spinal cord (ENCLB323OIS)

description:
https://www.encodeproject.org/experiments/ENCSR959XNI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR959XNI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB323OIS

source_name: Homo sapiens male embryo (105 days) spinal cord tissue

value: spinal cord

value: 105 day

value: John Stamatoyannopoulos, UW

value: Ian Glass

value: ENCBS206GZL at ENCODE; https://www.encodeproject.org/ENCBS206GZL/


title: long read RNA-seq from kidney (ENCLB845NIH)

description:
https://www.encodeproject.org/experiments/ENCSR941IFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR941IFA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB845NIH

source_name: Homo sapiens female embryo (105 days) kidney tissue

value: kidney

value: ENCBS578ZPC at ENCODE; https://www.encodeproject.org/ENCBS578ZPC/


title: long read RNA-seq from heart (ENCLB958GMG)

description:
https://www.encodeproject.org/experiments/ENCSR934VNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR934VNZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB958GMG

source_name: Homo sapiens female embryo (147 days) heart tissue

value: heart

value: 147 day

value: ENCBS692EIN at ENCODE; https://www.encodeproject.org/ENCBS692EIN/


title: long read RNA-seq from muscle of arm (ENCLB741SSV)

description:
https://www.encodeproject.org/experiments/ENCSR910OEU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR910OEU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB741SSV

source_name: Homo sapiens male embryo (96 days) muscle of arm tissue

value: muscle of arm

value: male

value: 96 day

value: ENCBS603CIP at ENCODE; https://www.encodeproject.org/ENCBS603CIP/


title: long read RNA-seq from muscle of arm (ENCLB108CKV)

description:
https://www.encodeproject.org/experiments/ENCSR908EKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908EKJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB108CKV

source_name: Homo sapiens female embryo (120 days) muscle of arm tissue

value: tissue

value: female

value: embryonic

value: 120 day

value: ENCBS076WQR at ENCODE; https://www.encodeproject.org/ENCBS076WQR/


title: long read RNA-seq from left lung (ENCLB208TGF)

description:
https://www.encodeproject.org/experiments/ENCSR906DLM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906DLM
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB208TGF

source_name: Homo sapiens female embryo (110 days) left lung tissue

value: left lung

value: 110 day

value: John Stamatoyannopoulos, UW

value: ENCBS505RWO at ENCODE; https://www.encodeproject.org/ENCBS505RWO/


title: long read RNA-seq from right kidney (ENCLB572ZDR)

description:
https://www.encodeproject.org/experiments/ENCSR907BCF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR907BCF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB572ZDR

source_name: Homo sapiens female embryo (98 days) right kidney tissue

value: right kidney

value: 98 day

value: Ian Glass

value: ENCBS252LKK at ENCODE; https://www.encodeproject.org/ENCBS252LKK/


title: long read RNA-seq from brain (ENCLB265MJU)

description:
https://www.encodeproject.org/experiments/ENCSR887OJA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR887OJA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265MJU

source_name: Homo sapiens male embryo (101 days) brain tissue

value: brain

value: 101 day

value: ENCBS263QHM at ENCODE; https://www.encodeproject.org/ENCBS263QHM/


title: long read RNA-seq from muscle of leg (ENCLB282BKM)

description:
https://www.encodeproject.org/experiments/ENCSR899FUU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR899FUU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB282BKM

source_name: Homo sapiens female embryo (105 days) muscle of leg tissue

value: muscle of leg

value: 105 day

value: ENCBS586VBD at ENCODE; https://www.encodeproject.org/ENCBS586VBD/


title: long read RNA-seq from renal pelvis (ENCLB587ODV)

description:
https://www.encodeproject.org/experiments/ENCSR885ASQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885ASQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB587ODV

source_name: Homo sapiens female embryo (89 days) renal pelvis tissue

value: renal pelvis

value: tissue

value: female

value: embryonic

value: 89 day

value: ENCBS965EVC at ENCODE; https://www.encodeproject.org/ENCBS965EVC/


title: long read RNA-seq from renal pelvis (ENCLB595WBF)

description:
https://www.encodeproject.org/experiments/ENCSR870FIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR870FIJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB595WBF

source_name: Homo sapiens male embryo (105 days) renal pelvis tissue

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS926WTU at ENCODE; https://www.encodeproject.org/ENCBS926WTU/


title: long read RNA-seq from placenta (ENCLB512NTA)

description:
https://www.encodeproject.org/experiments/ENCSR868WMK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR868WMK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB512NTA

source_name: Homo sapiens male embryo (85 days) placenta tissue

value: placenta

value: 85 day

value: Ian Glass

value: ENCBS770VOR at ENCODE; https://www.encodeproject.org/ENCBS770VOR/


title: long read RNA-seq from large intestine (ENCLB088JTC)

description:
https://www.encodeproject.org/experiments/ENCSR863ZSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863ZSG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB088JTC

source_name: Homo sapiens female embryo (120 days) large intestine tissue

value: large intestine

value: 120 day

value: ENCBS150RKS at ENCODE; https://www.encodeproject.org/ENCBS150RKS/


title: long read RNA-seq from thymus (ENCLB314DZE)

description:
https://www.encodeproject.org/experiments/ENCSR861YGQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR861YGQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB314DZE

source_name: Homo sapiens female embryo (98 days) thymus tissue

value: thymus

value: 98 day

value: ENCBS442ILA at ENCODE; https://www.encodeproject.org/ENCBS442ILA/


title: long read RNA-seq from right kidney (ENCLB096QNO)

description:
https://www.encodeproject.org/experiments/ENCSR861CLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR861CLZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB096QNO

source_name: Homo sapiens male embryo (87 days) right kidney tissue

value: right kidney

value: tissue

value: 87 day

value: ENCBS061HNT at ENCODE; https://www.encodeproject.org/ENCBS061HNT/


title: long read RNA-seq from brain (ENCLB061LSO)

description:
https://www.encodeproject.org/experiments/ENCSR859DYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859DYW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB061LSO

source_name: Homo sapiens female embryo (109 days) brain tissue

value: brain

value: female

value: embryonic

value: 109 day

value: ENCBS162MIW at ENCODE; https://www.encodeproject.org/ENCBS162MIW/


title: Well-watered, polymer control, biological replicate 2

description: Library name: W_P_2_1

source_name: Leaf

value: Leaf

value: mixed leaf cells

value: Dwarf messi

value: Polymer-coated seed; well-watered


title: long read RNA-seq from brain (ENCLB094ZHV)

description:
https://www.encodeproject.org/experiments/ENCSR852YUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR852YUV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB094ZHV

source_name: Homo sapiens embryo (112 days) brain tissue

value: not collected

value: 112 day

value: John Stamatoyannopoulos, UW

value: Ian Glass

value: ENCBS370ZVO at ENCODE; https://www.encodeproject.org/ENCBS370ZVO/


title: long read RNA-seq from renal cortex interstitium (ENCLB263YFZ)

description:
https://www.encodeproject.org/experiments/ENCSR856JRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR856JRV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB263YFZ

source_name: Homo sapiens female embryo (120 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: tissue

value: 120 day

value: ENCBS686CHQ at ENCODE; https://www.encodeproject.org/ENCBS686CHQ/


title: long read RNA-seq from renal cortex interstitium (ENCLB217ZLC)

description:
https://www.encodeproject.org/experiments/ENCSR847IOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR847IOQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB217ZLC

source_name: Homo sapiens female embryo (96 days) renal cortex interstitium tissue

value: female

value: 96 day

value: ENCBS702MUH at ENCODE; https://www.encodeproject.org/ENCBS702MUH/


title: long read RNA-seq from testis (ENCLB479RDL)

description:
https://www.encodeproject.org/experiments/ENCSR819LQD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR819LQD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB479RDL

source_name: Homo sapiens male embryo testis tissue

value: testis

value: male

value: embryonic

value: ENCBS718UBE at ENCODE; https://www.encodeproject.org/ENCBS718UBE/


title: long read RNA-seq from muscle of leg (ENCLB491DPH)

description:
https://www.encodeproject.org/experiments/ENCSR813KVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813KVN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491DPH

source_name: Homo sapiens male embryo (104 days) muscle of leg tissue

value: muscle of leg

value: 104 day

value: ENCBS810RAL at ENCODE; https://www.encodeproject.org/ENCBS810RAL/


title: long read RNA-seq from heart (ENCLB482KXO)

description:
https://www.encodeproject.org/experiments/ENCSR809SJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR809SJR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB482KXO

source_name: Homo sapiens male embryo (110 days) heart tissue

value: heart

value: 110 day

value: John Stamatoyannopoulos, UW

value: ENCBS649NOQ at ENCODE; https://www.encodeproject.org/ENCBS649NOQ/


title: long read RNA-seq from left kidney (ENCLB112QFK)

description:
https://www.encodeproject.org/experiments/ENCSR822NSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR822NSX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB112QFK

source_name: Homo sapiens female embryo (98 days) left kidney tissue

value: left kidney

value: tissue

value: 98 day

value: Ian Glass

value: ENCBS245QVS at ENCODE; https://www.encodeproject.org/ENCBS245QVS/


title: long read RNA-seq from large intestine (ENCLB637DUN)

description:
https://www.encodeproject.org/experiments/ENCSR805BHF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805BHF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB637DUN

source_name: Homo sapiens male embryo (113 days) large intestine tissue

value: large intestine

value: 113 day

value: ENCBS359EQT at ENCODE; https://www.encodeproject.org/ENCBS359EQT/


title: long read RNA-seq from muscle of arm (ENCLB411PMK)

description:
https://www.encodeproject.org/experiments/ENCSR796ZII/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR796ZII
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB411PMK

source_name: Homo sapiens female embryo (115 days) muscle of arm tissue

value: muscle of arm

value: female

value: embryonic

value: 115 day

value: ENCBS849AYJ at ENCODE; https://www.encodeproject.org/ENCBS849AYJ/


title: long read RNA-seq from kidney (ENCLB361HTG)

description:
https://www.encodeproject.org/experiments/ENCSR799GBH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR799GBH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB361HTG

source_name: Homo sapiens female embryo (121 days) kidney tissue

value: kidney

value: 121 day

value: ENCBS817ZLE at ENCODE; https://www.encodeproject.org/ENCBS817ZLE/


title: long read RNA-seq from renal pelvis (ENCLB900FLS)

description:
https://www.encodeproject.org/experiments/ENCSR793ODF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793ODF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB900FLS

source_name: Homo sapiens female embryo (96 days) renal pelvis tissue

value: renal pelvis

value: 96 day

value: John Stamatoyannopoulos, UW

value: ENCBS605FSD at ENCODE; https://www.encodeproject.org/ENCBS605FSD/


title: long read RNA-seq from small intestine (ENCLB559CFQ)

description:
https://www.encodeproject.org/experiments/ENCSR793FMU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793FMU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB559CFQ

source_name: Homo sapiens female embryo (107 days) small intestine tissue

value: small intestine

value: tissue

value: 107 day

value: Ian Glass

value: ENCBS821BQE at ENCODE; https://www.encodeproject.org/ENCBS821BQE/


title: long read RNA-seq from lung (ENCLB291YON)

description:
https://www.encodeproject.org/experiments/ENCSR768LJU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR768LJU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB291YON

source_name: Homo sapiens female embryo (96 days) lung tissue

value: lung

tag: description

value: Primary lung tissue from a healthy day 96 female fetus from Ian Glass of University of Washington, Congenital Defects Lab.

value: ENCBS611ZZU at ENCODE; https://www.encodeproject.org/ENCBS611ZZU/

value: Derived from ENCODE donor ENCDO370HUJ; https://www.encodeproject.org/ENCDO370HUJ/


title: long read RNA-seq from muscle of arm (ENCLB086QLB)

description:
https://www.encodeproject.org/experiments/ENCSR759MRC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR759MRC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB086QLB

source_name: Homo sapiens male embryo (96 days) muscle of arm tissue

value: muscle of arm

value: male

value: embryonic

value: ENCBS182IQI at ENCODE; https://www.encodeproject.org/ENCBS182IQI/


title: long read RNA-seq from renal cortex interstitium (ENCLB399TJA)

description:
https://www.encodeproject.org/experiments/ENCSR760VAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR760VAB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB399TJA

source_name: Homo sapiens male embryo (91 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: 91 day

value: ENCBS519LQI at ENCODE; https://www.encodeproject.org/ENCBS519LQI/


title: long read RNA-seq from heart (ENCLB443INF)

description:
https://www.encodeproject.org/experiments/ENCSR746FEO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR746FEO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB443INF

source_name: Homo sapiens embryo (101 days) heart tissue

value: heart

tag: note

value: Heart tissue from a healthy day 101 fetus from Ian Glass of University of Washington, Congenital Defects Lab.

value: not collected

value: 101 day

value: John Stamatoyannopoulos, UW

tag: url

value: ENCBS289LTS at ENCODE; https://www.encodeproject.org/ENCBS289LTS/


title: long read RNA-seq from thymus (ENCLB593FQI)

description:
https://www.encodeproject.org/experiments/ENCSR736GCG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736GCG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB593FQI

source_name: Homo sapiens male embryo (113 days) thymus tissue

value: thymus

value: tissue

value: 113 day

value: Ian Glass

value: ENCBS998SRS at ENCODE; https://www.encodeproject.org/ENCBS998SRS/


title: long read RNA-seq from stomach (ENCLB274BZO)

description:
https://www.encodeproject.org/experiments/ENCSR735XFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR735XFJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB274BZO

source_name: Homo sapiens female embryo (108 days) stomach tissue

value: stomach

value: female

value: 108 day

value: ENCBS246DND at ENCODE; https://www.encodeproject.org/ENCBS246DND/


title: long read RNA-seq from left lung (ENCLB923JMF)

description:
https://www.encodeproject.org/experiments/ENCSR730RYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR730RYS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB923JMF

source_name: Homo sapiens female embryo (91 days) left lung tissue

value: left lung

value: embryonic

value: 91 day

value: ENCBS837XWY at ENCODE; https://www.encodeproject.org/ENCBS837XWY/


title: long read RNA-seq from muscle of arm (ENCLB873FIP)

description:
https://www.encodeproject.org/experiments/ENCSR735BJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR735BJF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB873FIP

source_name: Homo sapiens female embryo (98 days) muscle of arm tissue

value: muscle of arm

value: 98 day

value: ENCBS250SNK at ENCODE; https://www.encodeproject.org/ENCBS250SNK/


title: long read RNA-seq from right kidney (ENCLB548TDF)

description:
https://www.encodeproject.org/experiments/ENCSR729EEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR729EEX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB548TDF

source_name: Homo sapiens female embryo (107 days) right kidney tissue

value: right kidney

value: 107 day

value: John Stamatoyannopoulos, UW

value: ENCBS078FAV at ENCODE; https://www.encodeproject.org/ENCBS078FAV/


title: long read RNA-seq from renal pelvis (ENCLB236IZD)

description:
https://www.encodeproject.org/experiments/ENCSR720KOH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR720KOH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB236IZD

source_name: Homo sapiens female embryo (103 days) renal pelvis tissue

value: renal pelvis

value: tissue

value: 103 day

value: Ian Glass

value: ENCBS694MLX at ENCODE; https://www.encodeproject.org/ENCBS694MLX/


title: long read RNA-seq from thymus (ENCLB275HJJ)

description:
https://www.encodeproject.org/experiments/ENCSR728RUN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR728RUN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB275HJJ

source_name: Homo sapiens female embryo (147 days) thymus tissue

value: thymus

value: female

value: 147 day

value: ENCBS925KXO at ENCODE; https://www.encodeproject.org/ENCBS925KXO/


title: long read RNA-seq from muscle of leg (ENCLB710DHF)

description:
https://www.encodeproject.org/experiments/ENCSR710TAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR710TAV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB710DHF

source_name: Homo sapiens male embryo (120 days) muscle of leg tissue

value: muscle of leg

value: male

value: embryonic

value: 120 day

value: ENCBS126JEC at ENCODE; https://www.encodeproject.org/ENCBS126JEC/


title: long read RNA-seq from renal cortex interstitium (ENCLB295XIA)

description:
https://www.encodeproject.org/experiments/ENCSR728OMS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR728OMS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295XIA

source_name: Homo sapiens male embryo (120 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: ENCBS346NVY at ENCODE; https://www.encodeproject.org/ENCBS346NVY/


title: long read RNA-seq from muscle of back (ENCLB512UFU)

description:
https://www.encodeproject.org/experiments/ENCSR707LOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR707LOP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB512UFU

source_name: Homo sapiens female embryo (105 days) muscle of back tissue

value: muscle of back

value: 105 day

value: John Stamatoyannopoulos, UW

value: ENCBS912CLZ at ENCODE; https://www.encodeproject.org/ENCBS912CLZ/


title: long read RNA-seq from renal pelvis (ENCLB410PLP)

description:
https://www.encodeproject.org/experiments/ENCSR709ZJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR709ZJR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB410PLP

source_name: Homo sapiens male embryo (105 days) renal pelvis tissue

value: renal pelvis

value: tissue

value: Ian Glass

value: ENCBS501TEA at ENCODE; https://www.encodeproject.org/ENCBS501TEA/


title: long read RNA-seq from small intestine (ENCLB074QAD)

description:
https://www.encodeproject.org/experiments/ENCSR683JMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR683JMZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB074QAD

source_name: Homo sapiens female embryo (91 days) small intestine tissue

value: small intestine

value: female

value: 91 day

value: ENCBS395MDO at ENCODE; https://www.encodeproject.org/ENCBS395MDO/


title: long read RNA-seq from muscle of back (ENCLB567PEE)

description:
https://www.encodeproject.org/experiments/ENCSR663LFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR663LFJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB567PEE

source_name: Homo sapiens male embryo (91 days) muscle of back tissue

value: male

value: embryonic

value: ENCBS372OIM at ENCODE; https://www.encodeproject.org/ENCBS372OIM/


title: long read RNA-seq from left kidney (ENCLB641EXM)

description:
https://www.encodeproject.org/experiments/ENCSR660EZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660EZD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB641EXM

source_name: Homo sapiens female embryo (87 days) left kidney tissue

value: left kidney

value: 87 day

value: ENCBS187WLN at ENCODE; https://www.encodeproject.org/ENCBS187WLN/


title: long read RNA-seq from right kidney (ENCLB227GZL)

description:
https://www.encodeproject.org/experiments/ENCSR655VWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR655VWF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB227GZL

source_name: Homo sapiens male embryo (115 days) right kidney tissue

value: right kidney

value: 115 day

value: ENCBS406KYT at ENCODE; https://www.encodeproject.org/ENCBS406KYT/


title: long read RNA-seq from muscle of arm (ENCLB851HAJ)

description:
https://www.encodeproject.org/experiments/ENCSR649UAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR649UAP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB851HAJ

source_name: Homo sapiens male embryo (105 days) muscle of arm tissue

value: muscle of arm

value: 105 day

value: John Stamatoyannopoulos, UW

value: ENCBS653XSR at ENCODE; https://www.encodeproject.org/ENCBS653XSR/


title: long read RNA-seq from muscle of leg (ENCLB934LDJ)

description:
https://www.encodeproject.org/experiments/ENCSR646BMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR646BMO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB934LDJ

source_name: Homo sapiens male embryo (96 days) muscle of leg tissue

value: muscle of leg

value: tissue

value: 96 day

value: Ian Glass

value: ENCBS224LQJ at ENCODE; https://www.encodeproject.org/ENCBS224LQJ/


title: long read RNA-seq from renal cortex interstitium (ENCLB749KAD)

description:
https://www.encodeproject.org/experiments/ENCSR645EEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR645EEX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB749KAD

source_name: Homo sapiens male embryo (105 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: male

value: embryonic

value: ENCBS720TLL at ENCODE; https://www.encodeproject.org/ENCBS720TLL/


title: long read RNA-seq from thymus (ENCLB279EMX)

description:
https://www.encodeproject.org/experiments/ENCSR641JDY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR641JDY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB279EMX

source_name: Homo sapiens male embryo (97 days) thymus tissue

value: thymus

value: 97 day

value: ENCBS302LML at ENCODE; https://www.encodeproject.org/ENCBS302LML/


title: long read RNA-seq from renal pelvis (ENCLB801KQT)

description:
https://www.encodeproject.org/experiments/ENCSR639PHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639PHC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB801KQT

source_name: Homo sapiens male embryo (97 days) renal pelvis tissue

value: renal pelvis

value: ENCBS548LLM at ENCODE; https://www.encodeproject.org/ENCBS548LLM/


title: long read RNA-seq from heart (ENCLB857CMN)

description:
https://www.encodeproject.org/experiments/ENCSR636RRH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR636RRH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB857CMN

source_name: Homo sapiens female embryo (103 days) heart tissue

value: heart

value: female

value: 103 day

value: ENCBS609WOE at ENCODE; https://www.encodeproject.org/ENCBS609WOE/


title: long read RNA-seq from lung (ENCLB797OIC)

description:
https://www.encodeproject.org/experiments/ENCSR616YXE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616YXE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB797OIC

source_name: Homo sapiens male embryo (82 days) lung tissue

value: lung

value: tissue

value: 82 day

value: John Stamatoyannopoulos, UW

value: ENCBS931PHM at ENCODE; https://www.encodeproject.org/ENCBS931PHM/


title: long read RNA-seq from right lung (ENCLB966JHL)

description:
https://www.encodeproject.org/experiments/ENCSR602XVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR602XVJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB966JHL

source_name: Homo sapiens male embryo (87 days) right lung tissue

value: right lung

value: male

value: 87 day

value: Ian Glass

value: ENCBS854EOM at ENCODE; https://www.encodeproject.org/ENCBS854EOM/


title: long read RNA-seq from right lung (ENCLB700WZD)

description:
https://www.encodeproject.org/experiments/ENCSR598BKD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR598BKD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB700WZD

source_name: Homo sapiens female embryo (105 days) right lung tissue

value: embryonic

value: 105 day

value: ENCBS358EAY at ENCODE; https://www.encodeproject.org/ENCBS358EAY/


title: long read RNA-seq from brain (ENCLB998KYW)

description:
https://www.encodeproject.org/experiments/ENCSR598UIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR598UIY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB998KYW

source_name: Homo sapiens male embryo (104 days) brain tissue

value: brain

value: 104 day

value: ENCBS251VVQ at ENCODE; https://www.encodeproject.org/ENCBS251VVQ/


title: long read RNA-seq from right kidney (ENCLB530PSB)

description:
https://www.encodeproject.org/experiments/ENCSR592OXC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR592OXC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530PSB

source_name: Homo sapiens female embryo (117 days) right kidney tissue

value: right kidney

value: female

value: 117 day

value: ENCBS669GZU at ENCODE; https://www.encodeproject.org/ENCBS669GZU/


title: long read RNA-seq from thymus (ENCLB851YLE)

description:
https://www.encodeproject.org/experiments/ENCSR697CGA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR697CGA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB851YLE

source_name: Homo sapiens male embryo (104 days) thymus tissue

value: thymus

value: tissue

value: John Stamatoyannopoulos, UW

value: ENCBS290BRD at ENCODE; https://www.encodeproject.org/ENCBS290BRD/


title: long read RNA-seq from right lung (ENCLB232ETX)

description:
https://www.encodeproject.org/experiments/ENCSR588HDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR588HDZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB232ETX

source_name: Homo sapiens female embryo (108 days) right lung tissue

value: right lung

value: 108 day

value: ENCBS860RVH at ENCODE; https://www.encodeproject.org/ENCBS860RVH/


title: long read RNA-seq from left lung (ENCLB979RZS)

description:
https://www.encodeproject.org/experiments/ENCSR681DGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR681DGI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB979RZS

source_name: Homo sapiens male embryo (96 days) left lung tissue

value: left lung

value: male

value: embryonic

value: 96 day

value: Ian Glass

value: ENCBS666IYH at ENCODE; https://www.encodeproject.org/ENCBS666IYH/


title: long read RNA-seq from spleen (ENCLB735UKL)

description:
https://www.encodeproject.org/experiments/ENCSR602MDH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR602MDH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB735UKL

source_name: Homo sapiens male embryo (120 days) spleen tissue

value: spleen

value: 120 day

value: ENCBS904VGJ at ENCODE; https://www.encodeproject.org/ENCBS904VGJ/


title: long read RNA-seq from left lung (ENCLB446BZG)

description:
https://www.encodeproject.org/experiments/ENCSR585QNX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR585QNX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB446BZG

source_name: Homo sapiens female embryo (98 days) left lung tissue

value: female

value: 98 day

value: ENCBS910BDD at ENCODE; https://www.encodeproject.org/ENCBS910BDD/


title: long read RNA-seq from brain (ENCLB799IYQ)

description:
https://www.encodeproject.org/experiments/ENCSR582TMC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582TMC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799IYQ

source_name: Homo sapiens female embryo (105 days) brain tissue

value: brain

value: tissue

value: 105 day

value: John Stamatoyannopoulos, UW

value: ENCBS657WVW at ENCODE; https://www.encodeproject.org/ENCBS657WVW/


title: long read RNA-seq from placenta (ENCLB437DKJ)

description:
https://www.encodeproject.org/experiments/ENCSR567LHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR567LHH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB437DKJ

source_name: Homo sapiens female embryo (85 days) placenta tissue

value: placenta

value: 85 day

value: ENCBS168RJJ at ENCODE; https://www.encodeproject.org/ENCBS168RJJ/


title: long read RNA-seq from thymus (ENCLB064DZF)

description:
https://www.encodeproject.org/experiments/ENCSR562KIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR562KIZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB064DZF

source_name: Homo sapiens male embryo (127 days) thymus tissue

value: thymus

value: male

value: embryonic

value: 127 day

value: ENCBS469IWQ at ENCODE; https://www.encodeproject.org/ENCBS469IWQ/


title: long read RNA-seq from muscle of back (ENCLB534ADS)

description:
https://www.encodeproject.org/experiments/ENCSR559DWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR559DWD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB534ADS

source_name: Homo sapiens male embryo (96 days) muscle of back tissue

value: muscle of back

value: 96 day

value: Ian Glass

value: ENCBS526KAM at ENCODE; https://www.encodeproject.org/ENCBS526KAM/


title: long read RNA-seq from renal pelvis (ENCLB882RYZ)

description:
https://www.encodeproject.org/experiments/ENCSR558FSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR558FSR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB882RYZ

source_name: Homo sapiens male embryo (105 days) renal pelvis tissue

value: renal pelvis

value: ENCBS677PZN at ENCODE; https://www.encodeproject.org/ENCBS677PZN/


title: long read RNA-seq from left kidney (ENCLB571KGZ)

description:
https://www.encodeproject.org/experiments/ENCSR555RBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR555RBI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB571KGZ

source_name: Homo sapiens female embryo (147 days) left kidney tissue

value: left kidney

value: tissue

value: female

value: 147 day

value: ENCBS276UDX at ENCODE; https://www.encodeproject.org/ENCBS276UDX/


title: long read RNA-seq from placenta (ENCLB115TYS)

description:
https://www.encodeproject.org/experiments/ENCSR638WIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR638WIV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB115TYS

source_name: Homo sapiens male embryo (91 days) placenta tissue

value: placenta

value: 91 day

value: John Stamatoyannopoulos, UW

value: ENCBS444TAO at ENCODE; https://www.encodeproject.org/ENCBS444TAO/


title: long read RNA-seq from muscle of back (ENCLB085TQZ)

description:
https://www.encodeproject.org/experiments/ENCSR557ZVE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR557ZVE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB085TQZ

source_name: Homo sapiens male embryo (101 days) muscle of back tissue

value: male

value: embryonic

value: 101 day

value: ENCBS716WPZ at ENCODE; https://www.encodeproject.org/ENCBS716WPZ/


title: long read RNA-seq from large intestine (ENCLB781PYK)

description:
https://www.encodeproject.org/experiments/ENCSR555FAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR555FAZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB781PYK

source_name: Homo sapiens male embryo (105 days) large intestine tissue

value: large intestine

value: 105 day

value: Ian Glass

value: ENCBS540OFM at ENCODE; https://www.encodeproject.org/ENCBS540OFM/


title: long read RNA-seq from small intestine (ENCLB491APN)

description:
https://www.encodeproject.org/experiments/ENCSR541NRY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541NRY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491APN

source_name: Homo sapiens male embryo (115 days) small intestine tissue

value: small intestine

value: 115 day

value: ENCBS526NVK at ENCODE; https://www.encodeproject.org/ENCBS526NVK/


title: long read RNA-seq from muscle of arm (ENCLB924FRF)

description:
https://www.encodeproject.org/experiments/ENCSR617WTI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR617WTI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB924FRF

source_name: Homo sapiens embryo (101 days) muscle of arm tissue

value: muscle of arm

value: tissue

value: not collected

value: ENCBS148RFP at ENCODE; https://www.encodeproject.org/ENCBS148RFP/


title: long read RNA-seq from muscle of back (ENCLB544QRJ)

description:
https://www.encodeproject.org/experiments/ENCSR540GZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR540GZD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB544QRJ

source_name: Homo sapiens male embryo (105 days) muscle of back tissue

value: muscle of back

value: John Stamatoyannopoulos, UW

value: ENCBS620CHX at ENCODE; https://www.encodeproject.org/ENCBS620CHX/


title: long read RNA-seq from adrenal gland (ENCLB763LZL)

description:
https://www.encodeproject.org/experiments/ENCSR539XOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR539XOD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB763LZL

source_name: Homo sapiens male embryo (101 days) adrenal gland tissue

value: adrenal gland

value: male

value: embryonic

value: ENCBS422GGI at ENCODE; https://www.encodeproject.org/ENCBS422GGI/


title: Lewis rat thymus Stereo-seq

description:
Library name: 60-1169740824
STOmics

data_processing:
For scRNA-seq, FASTQ files were processed using the Cell Ranger pipeline (ver. 8.0.0), with the mRatBN7.2 genome assembly as the reference. The resulting expression matrices were converted into Seurat (ver. 5.3.0) objects. Rat thymocyte and thymic stromal scRNA-seq datasets were integrated with published mouse thymocyte and thymic stromal datasets, respectively. The mouse thymocyte dataset was obtained from GEO accession GSE186078, and the mouse thymic stromal dataset was obtained from Zenodo accession 12516405. Mouse gene symbols were converted to rat orthologs, and mouse cluster annotations were projected onto rat cells. The resulting rat reference datasets were used as references for robust cell-type decomposition (RCTD).
For spatial transcriptomics, FASTQ files and the ssDNA-stained tissue image were processed using the Stereo-seq Analysis Workflow pipeline (ver. 8.1.3), with the mRatBN7.2 genome assembly as the reference. StereoMap (ver. 4.1.2) was used for initial visualization of spatial gene expression. The output files, cellbin_1.0.adjusted.h5ad and bin20_1.0.h5ad, were converted into Seurat objects. Cell-type composition in the spatial transcriptomics datasets was inferred using RCTD with the rat scRNA-seq reference object. Spatial distributions of inferred cell types and region-associated gene expression patterns were then analyzed in Seurat.
Assembly: mRatBN7.2
Supplementary files format and content: 60-919422446: st_barcodes.tsv.gz, st_features.tsv.gz, st_matrix.mtx.gz: Matrix files
Supplementary files format and content: 60-919422446: RatThymicStromaMetadata.csv: Metadata file of the Seurat object
Supplementary files format and content: 60-919422446: 2024_03_31_rat_thymic_stroma.loom: velocyto-generated loom file
Supplementary files format and content: 60-1216959069: thy_barcodes.tsv.gz, thy_features.tsv.gz, thy_matrix.mtx.gz: Matrix files
Supplementary files format and content: 60-1216959069: RatThymocyteMetadata.csv: Metadata file of the Seurat object
Supplementary files format and content: 60-1169740824: visualization.tar.gz: tar.gz file containing h5ad and stereo files
Supplementary files format and content: 60-1169740824: CellBin_objMetadata.csv: Matadata file of the cellbin Seurat object
Supplementary files format and content: 60-1169740824: bin20_objMetadata.csv: Matadata file of the bin20 Seurat object
Supplementary files format and content: 60-1169740824: Y01052GC.barcodeToPos.h5: Spatial coordinate. Required for the initial processing
Supplementary files format and content: 60-1169740824: Y01052GC_ssDNA.tif: Picture of the section. Required for the initial processing
Library strategy: Spatial Transcriptomics

source_name: Thymus

tag: tissue

value: Thymus


title: LO2_DBP_3

description:
Library name: LO2_DBP_3
DBP

source_name: liver

value: liver

tag: cell line

value: Human fetal hepatocyte

tag: genotype

value: WT

value: DBP


title: long read RNA-seq from small intestine (ENCLB060XBW)

description:
https://www.encodeproject.org/experiments/ENCSR527XXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR527XXI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB060XBW

source_name: Homo sapiens male embryo (108 days) small intestine tissue

value: small intestine

value: 108 day

value: Ian Glass

value: ENCBS162DUO at ENCODE; https://www.encodeproject.org/ENCBS162DUO/


title: long read RNA-seq from heart (ENCLB809REL)

description:
https://www.encodeproject.org/experiments/ENCSR508BRD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR508BRD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB809REL

source_name: Homo sapiens female embryo (110 days) heart tissue

value: heart

value: tissue

value: female

value: 110 day

value: ENCBS132XGS at ENCODE; https://www.encodeproject.org/ENCBS132XGS/


title: long read RNA-seq from thymus (ENCLB299LQW)

description:
https://www.encodeproject.org/experiments/ENCSR526NUC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR526NUC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB299LQW

source_name: Homo sapiens female embryo (105 days) thymus tissue

value: thymus

value: 105 day

value: John Stamatoyannopoulos, UW

value: ENCBS185CYM at ENCODE; https://www.encodeproject.org/ENCBS185CYM/


title: long read RNA-seq from muscle of trunk (ENCLB348SMJ)

description:
https://www.encodeproject.org/experiments/ENCSR504PXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR504PXZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB348SMJ

source_name: Homo sapiens female embryo (120 days) muscle of trunk tissue

value: muscle of trunk

value: embryonic

value: 120 day

value: ENCBS964RCC at ENCODE; https://www.encodeproject.org/ENCBS964RCC/


title: SAMPLE3, HCAEC cells, medin 5 uM for 20 hours

description:
Library name: HCAEC04222B
replicate 3 - medin 5 uM

source_name: coronary artery

value: coronary artery

value: HCAEC

tag: cell type

value: endothelial cells

value: WT

tag: treatment

value: medin


title: long read RNA-seq from ovary (ENCLB118AGU)

description:
https://www.encodeproject.org/experiments/ENCSR504FSC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR504FSC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB118AGU

source_name: Homo sapiens female embryo ovary tissue

value: ovary

value: tissue

value: Ian Glass

value: ENCBS102VVS at ENCODE; https://www.encodeproject.org/ENCBS102VVS/


title: long read RNA-seq from renal pelvis (ENCLB179DWY)

description:
https://www.encodeproject.org/experiments/ENCSR503DHX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503DHX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB179DWY

source_name: Homo sapiens male embryo (105 days) renal pelvis tissue

value: renal pelvis

value: male

value: ENCBS140CZM at ENCODE; https://www.encodeproject.org/ENCBS140CZM/


title: long read RNA-seq from kidney (ENCLB856PFR)

description:
https://www.encodeproject.org/experiments/ENCSR476STT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR476STT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB856PFR

source_name: Homo sapiens male embryo (105 days) kidney tissue

value: kidney

value: 105 day

value: John Stamatoyannopoulos, UW

value: ENCBS416UPP at ENCODE; https://www.encodeproject.org/ENCBS416UPP/


title: long read RNA-seq from left lung (ENCLB363PHR)

description:
https://www.encodeproject.org/experiments/ENCSR475XGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR475XGB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB363PHR

source_name: Homo sapiens female embryo (105 days) left lung tissue

value: left lung

value: female

value: embryonic

value: ENCBS894YFO at ENCODE; https://www.encodeproject.org/ENCBS894YFO/


title: long read RNA-seq from lung (ENCLB902JSN)

description:
https://www.encodeproject.org/experiments/ENCSR475SHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR475SHG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB902JSN

source_name: Homo sapiens male embryo (115 days) lung tissue

value: lung

value: 115 day

value: ENCBS519EXR at ENCODE; https://www.encodeproject.org/ENCBS519EXR/


title: long read RNA-seq from kidney (ENCLB563FPU)

description:
https://www.encodeproject.org/experiments/ENCSR469YWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR469YWQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB563FPU

source_name: Homo sapiens male embryo (85 days) kidney tissue

value: tissue

value: 85 day

value: ENCBS767UZF at ENCODE; https://www.encodeproject.org/ENCBS767UZF/


title: long read RNA-seq from renal pelvis (ENCLB933FER)

description:
https://www.encodeproject.org/experiments/ENCSR457PDH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR457PDH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB933FER

source_name: Homo sapiens female embryo (105 days) renal pelvis tissue

value: renal pelvis

value: Ian Glass

value: ENCBS049MTD at ENCODE; https://www.encodeproject.org/ENCBS049MTD/


title: long read RNA-seq from adrenal gland (ENCLB094QXM)

description:
https://www.encodeproject.org/experiments/ENCSR458UIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR458UIY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB094QXM

source_name: Homo sapiens male embryo (85 days) adrenal gland tissue

value: adrenal gland

value: male

value: ENCBS277YPY at ENCODE; https://www.encodeproject.org/ENCBS277YPY/


title: long read RNA-seq from muscle of arm (ENCLB126ZEE)

description:
https://www.encodeproject.org/experiments/ENCSR457CLX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR457CLX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB126ZEE

source_name: Homo sapiens female embryo (108 days) muscle of arm tissue

value: muscle of arm

value: 108 day

value: John Stamatoyannopoulos, UW

value: ENCBS652EAN at ENCODE; https://www.encodeproject.org/ENCBS652EAN/


title: Amniotic fluid cells, control pregnancy 1

source_name: amniotic fluid

value: amniotic fluid

value: mesenchymal stem cells

tag: condition

value: control


title: long read RNA-seq from right kidney (ENCLB045SWT)

description:
https://www.encodeproject.org/experiments/ENCSR448TJV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR448TJV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB045SWT

source_name: Homo sapiens female embryo (147 days) right kidney tissue

value: right kidney

tag: biosample encode accession

value: female

value: embryonic

value: 147 day

value: ENCBS548TCA at ENCODE; https://www.encodeproject.org/ENCBS548TCA/


title: long read RNA-seq from stomach (ENCLB013CLV)

description:
https://www.encodeproject.org/experiments/ENCSR431KBL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR431KBL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB013CLV

source_name: Homo sapiens female embryo (105 days) stomach tissue

value: stomach

value: tissue

tag: encode accession

value: 105 day

value: Ian Glass

value: ENCBS288AYP at ENCODE; https://www.encodeproject.org/ENCBS288AYP/


title: long read RNA-seq from thymus (ENCLB759HMA)

description:
https://www.encodeproject.org/experiments/ENCSR437ODI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR437ODI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB759HMA

source_name: Homo sapiens female embryo (117 days) thymus tissue

value: thymus

tag: Sex

value: 117 day

value: ENCBS061BBD at ENCODE; https://www.encodeproject.org/ENCBS061BBD/


title: long read RNA-seq from heart (ENCLB600YZX)

description:
https://www.encodeproject.org/experiments/ENCSR416HNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR416HNH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB600YZX

source_name: Homo sapiens female embryo (105 days) heart tissue

value: heart

tag: dev stage

value: John Stamatoyannopoulos, UW

value: ENCBS915TYO at ENCODE; https://www.encodeproject.org/ENCBS915TYO/


title: long read RNA-seq from renal cortex interstitium (ENCLB802COJ)

description:
https://www.encodeproject.org/experiments/ENCSR446EHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR446EHC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB802COJ

source_name: Homo sapiens male embryo (108 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: male

tag: age

value: 108 day

value: ENCBS328QXA at ENCODE; https://www.encodeproject.org/ENCBS328QXA/


title: long read RNA-seq from stomach (ENCLB959ZFU)

description:
https://www.encodeproject.org/experiments/ENCSR414YMK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR414YMK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB959ZFU

source_name: Homo sapiens female embryo (96 days) stomach tissue

value: female

value: embryonic

value: 96 day

tag: lab

value: ENCBS101TEB at ENCODE; https://www.encodeproject.org/ENCBS101TEB/


title: long read RNA-seq from right lung (ENCLB196JAJ)

description:
https://www.encodeproject.org/experiments/ENCSR997XFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR997XFO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB196JAJ

source_name: Homo sapiens female embryo (91 days) right lung tissue

value: right lung

value: tissue

value: 91 day

tag: source

value: ENCBS585YRE at ENCODE; https://www.encodeproject.org/ENCBS585YRE/


title: long read RNA-seq from stomach (ENCLB445XWI)

description:
https://www.encodeproject.org/experiments/ENCSR400AEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR400AEX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB445XWI

source_name: Homo sapiens male embryo (127 days) stomach tissue

value: stomach

value: 127 day

value: Ian Glass

tag: link

value: ENCBS152MQG at ENCODE; https://www.encodeproject.org/ENCBS152MQG/


title: long read RNA-seq from large intestine (ENCLB454RXY)

description:
https://www.encodeproject.org/experiments/ENCSR410YNQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410YNQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB454RXY

source_name: Homo sapiens female embryo (98 days) large intestine tissue

value: large intestine

value: 98 day

value: John Stamatoyannopoulos, UW

value: ENCBS472ZYM at ENCODE; https://www.encodeproject.org/ENCBS472ZYM/


title: long read RNA-seq from renal pelvis (ENCLB744IQX)

description:
https://www.encodeproject.org/experiments/ENCSR390AHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR390AHP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB744IQX

source_name: Homo sapiens male embryo (91 days) renal pelvis tissue

value: renal pelvis

value: male

value: ENCBS465DYX at ENCODE; https://www.encodeproject.org/ENCBS465DYX/


title: long read RNA-seq from spinal cord (ENCLB494UGA)

description:
https://www.encodeproject.org/experiments/ENCSR383POI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383POI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB494UGA

source_name: Homo sapiens female embryo (87 days) spinal cord tissue

value: spinal cord

value: female

value: embryonic

value: 87 day

value: ENCBS204TIE at ENCODE; https://www.encodeproject.org/ENCBS204TIE/


title: long read RNA-seq from kidney (ENCLB509QLM)

description:
https://www.encodeproject.org/experiments/ENCSR397AFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR397AFD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB509QLM

source_name: Homo sapiens female embryo (105 days) kidney tissue

value: kidney

value: tissue

value: 105 day

value: ENCBS659IQR at ENCODE; https://www.encodeproject.org/ENCBS659IQR/


title: long read RNA-seq from heart (ENCLB987QWN)

description:
https://www.encodeproject.org/experiments/ENCSR394MBR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR394MBR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB987QWN

source_name: Homo sapiens male embryo (105 days) heart tissue

value: heart

value: Ian Glass

value: ENCBS777TEG at ENCODE; https://www.encodeproject.org/ENCBS777TEG/