title: SUBJECT27 [Block_2_FOV_7]

city: Denver

first: Rachel

last: Blumhagen

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment and Health

institute: National Jewish Health

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were rinsed of excess probes in 2X SSCT for 1 min and were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing: Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. After removing low quality cells and unexpressed features, 104,504 cells and 984 features remained. The rescaled log2-transformed counts per million (logCPM) of the data is provided as inputs for cell type annotation. InSituType was used to identify cell types from a reference dataset (Habermann, A. C. et al. Science Advances 2020) while incorporating additional data types through building “cohorts” based on spatial information.  Following anchor identification, “cohorts” were established using cell area, cell aspect ratio, and mean intensity of morphology markers.  Semi-supervised clustering allowing for 2-6 novel clusters yielded cell annotations.  Novel clusters were evaluated manually and grouped into identified cell populations based on their gene expression profile.

source_name: lung tissue FFPE

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 1:2,000 fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for CosMxTM SMI and tissue staining (IHC IF, ISH).

tag: disease

value: Control

value: GT


title: Cohouse old 10

status: Public on Nov 22 2025

type: SRA

city: Palo Alto

first: Christoph

last: Thaiss

state: CA

address: 3181 Porter Dr.

department: Immunology and Pathology

country: USA

institute: Arc Institute

description: Library name: T37

library_source: genomic

data_processing:
QIIME2: reads were demultiplexed, quality-filtered, and denoised using deblur with `trim-length 200`
Assembly: Silva 138 database
Supplementary files format and content: feature-table with counts for each OUT
Supplementary files format and content: Taxonomy for OUT mapping
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Fecal

extract_protocol:
tool DNA was purified using DNeasy PowerSoil Pro Kit (Qiagen, Cat. No. 47014) according to manufacturer’s instructions.
DNA was amplified using the KAPA Hifi HotStart ReadyMix (Roche, KK2602) and the F27/R338 primer-pair targeting the V1V2 region of the 16S gene (F27: 5’- AGAGTTTGATCCTGGCTCAG-3’, R338: 5’- TGCTGCCTCCCGTAGGAGT-3’). After PCR amplification, the pooled library underwent bead- based size selection using AMPure XP beads (Beckman Coulter, A63881) and was sequenced using 500 bp paired-end sequencing (Illumina MiSeq).

tag: tissue

value: Fecal

tag: genotype

value: WT

tag: treatment

value: CO


title: 2Gyx2, biological replicate 2

city: San Francisco

first: Iowis

last: Zhu

address: 1450 3rd Street, HD449

institute: University of California, San Francisco

description: Library name: JH022_2Gyx2-2

data_processing:
Enrichment or depletion of sgRNA abundances were determined by down sampling trimmed sequencing reads to equivalent amounts across all samples, and then calculating the log2 ratio of sgRNA abundance in experimental conditions to sgRNA abundance in control conditions at T10 (rho), or between sequencing reads from T10 and T0 timepoints within experimental (tau) or control (gamma) conditions. Specifically, we computed normalized log2 ratios for radiation-treated sgRNA abundance at T10 compared to T0 in order to identify mediators of radiation responses and computed normalized log2 ratios for sgRNA abundance in the control group at T10 compared to T0 to identify regulators of cell fitness independent of treatment. Any sgRNA’s not represented with an average of at least 50 normalized sequencing reads across all replicates were excluded from analysis. Statistical significance was calculated using Wald test comparing replicates across conditions without a log2 fold change threshold. Hits were prioritized by normalizing log2 ratios to the total number of population doublings in the screen and the standard deviations of the non-targeting control sgRNAs. Genes were filtered at an adjusted p-value<0.05 for statistical significance.
Assembly: hg38
Supplementary files format and content: counts_JH022.txt contains the raw counts for each sgRNA prior to normalization. counts_JH022_DESeq2_normalized.txt contains the normalized counts for each sgRNA. rhoR2Gyx2_vs_Control.txt contains the ratios of normalized sgRNA abundances between the experimental and control groups. tauR2Gyx2_vs_T0.txt contains the ratios of normalized sgRNA abundances between the experimental and T0 groups. gammaRControl_vs_T0.txt contains the ratios of normalized sgRNA abundances between the control and T0 groups.
Library strategy: sgRNA library

organism: Homo sapiens

source_name: tumor

growth_protocol: Human HEK 293T and JH-2-002 MPNST cells (gift from Christine Pratilas from Johns Hopkins University) were cultured in Dulbecco’s modified Eagle’s medium (#11960069, Life Technologies) with 10% FBS and 1X Pen-Strep (#15140122, Life Technologies) in a cell culture incubator at 37oC and 5% CO2.

extract_protocol:
gDNA from all cells was harvested and sgRNA barcodes were amplified and processed for sgRNA abundance library preparation using Q5 High-Fidelity DNA Polymerase (NEB) and sequenced on an Illumina NovaSeq 6000
We used a previously optimized and validated, compact, highly active sgRNA library containing the top 2 on-target sgRNAs for 23,483 genes cloned into the library expression vector pU6-sgRNA EF1alpha Puro-T2A-GFP derived from pJR85(#140095, Addgene) and modified to express a second sgRNA using the human U6 promoter as previously described. Knockdown efficiency of all guide sequences is publicly available at https://gwps.wi.mit.edu. 1137 non-targeting sgRNA pairs were also included as negative controls in the screen.

treatment_protocol: Cells transduced with the sgRNA library were then flow sorted to obtain a pure population prior, and a portion of the cell pellet were subsequently frozen down at a “T0” (Day 0) timepoint. The screen was then carried out in biologic triplicate, with cells receiving 2 daily doses of 2 Gy or no radiation. Cells were harvested at Day 10.

value: tumor

tag: cell line

tag: cell type

value: MPNST


title: SUBJECT28 [Block_2_FOV_9]

type: RNA

molecule: total RNA

value: GG


title: S_933_24, Nbl1xCol4a5, HET, Batch 2

city: Bar Harbor

first: Courtney

last: Willey

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
Library name: S_933_24
Counts_S93324_GT24; TPM_S93324_GT24; FPKM_S93324_GT24

library_source: transcriptomic

data_processing:
JAX RNA-seq Nextflow Pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts, tpm, and fpkm for each sample.

source_name: Kidney

extract_protocol:
RNA was harvested using NucleoMag RNA Kit (Macherey-Nagel). Samples with RIN >8  was used for the construction of sequencing libraries.
RNA libraries for for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (Roche) following manufacturer's protocols.

value: Kidney

value: HET

tag: batch


title: Postnatal day 5 Nkx2.1-CreER;Ai47 mouse sample-2

city: Columbus

first: Hiroki

last: Taniguchi

state: OH

address: 333 W 10th Ave

department: Department of Neuroscience

institute: Ohio State University

description: Library name: Nkx2.1-Ai47_P5-2

data_processing:
Samples were sequenced in the NextSeq500 with paired-end 75bp reads. Demultiplexed and quality filtered raw reads (fastq) generated from the NextSeq 500 were trimmed using Flexbar 2.4 and aligned to the reference genome (Mus musculus, mm10) using TopHat version 2.0.9. HT seq-count version 0.6.1 was used to generate gene counts and differential gene expression analysis was performed using DESeq2.
Assembly: Mus musculus, mm10
Supplementary files format and content: CSV

source_name: GFP+ dissociated cortical cells

extract_protocol:
Fresh brains were taken from P5 ChC-GFP, SST-GFP, and VIP-GFP pups, and 300- to 400-μm-thick slices were prepared using a tissue chopper. Cortical strips containing L2/3 cells were dissected from the mPFC and the ACC and dissociated into individual cells in Hibernate E medium containing Pronase E (1 mg/ml) and DNaseI (5 U/mL) at 37°C for 10 min. After washing with Hibernate E medium once, one hundred fifty GFP+ cells were picked up using a glass micropipette under a fluorescence dissecting stereomicroscope. Total RNA was extracted by RNAeasy kit
After RNA extraction, the samples were then kept on ice and processed for library preparation using Illumina Seq according to the manufacturer’s protocol.

value: GFP+ dissociated cortical cells

value: Tamoxifen at E17


title: Cohouse old 7

description: Library name: T27


title: S_292_24, Nbl1xCol4a5, HET, Batch 2

description:
Library name: S_929_24
Counts_S92924_GT24; TPM_S92924_GT24; FPKM_S92924_GT24


title: Old 9

description: Library name: T34

value: O


title: Postnatal day 5 Nkx2.1-CreER;Ai47 mouse sample-3

description: Library name: Nkx2.1-Ai47_P5-3


title: 2Gyx2, biological replicate 1

description: Library name: JH022_2Gyx2-1


title: Young 7

description: Library name: T21

value: Y


title: SUBJECT23 [Block_2_FOV_23]


title: Cohouse young 6

description: Library name: T24

value: CY


title: Old 5

description: Library name: T19


title: Postnatal day 5 Nkx2.1-CreER;Ai47 mouse sample-1

description: Library name: Nkx2.1-Ai47_P5-1


title: S_930_24, Nbl1xCol4a5, HET, Batch 2

description:
Library name: S_930_24
Counts_S93024_GT24; TPM_S93024_GT24; FPKM_S93024_GT24


title: SUBJECT27 [Block_2_FOV_8]


title: Young 8

description: Library name: T22


title: SUBJECT23 [Block_2_FOV_22]


title: Cohouse old 4

description: Library name: T20


title: Cohouse old 3

description: Library name: T18


title: S_23_23, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_23_23
Counts_2206_S; TPM_2206_S; FPKM_2206_S


title: SUBJECT21 [Block_2_FOV_18]


title: Cohouse young 5

description: Library name: T17


title: Cohouse old 2

description: Library name: T16


title: Postnatal day 5 SOM-Cre;Ai47 mouse sample-2

description: Library name: SOM-Ai47_P5-2


title: Postnatal day 5 SOM-Cre;Ai47 mouse sample-1

description: Library name: SOM-Ai47_P5-1


title: S_6001_22, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_6001_22
Counts_2206_6001; TPM_2206_6001; FPKM_2206_6001


title: SUBJECT21 [Block_2_FOV_17]


title: S_5999_22, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_5999_22
Counts_2206_5999; TPM_2206_5999; FPKM_2206_5999


title: Young 6

description: Library name: T15


title: SUBJECT19 [Block_2_FOV_14]

value: IPF


title: S_5330_22, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_5330_22
Counts_2206_5330; TPM_2206_5330; FPKM_2206_5330


title: SUBJECT12 [Block_1_FOV_5]


title: Old 4

description: Library name: T14


title: Postnatal day 5 VIP-Cre;Ai47 mouse sample-3

description: Library name: VIP-Ai47_P5-3


title: SUBJECT17 [Block_2_FOV_10]


title: Postnatal day 5 VIP-Cre;Ai47 mouse sample-2

description: Library name: VIP-Ai47_P5-2


title: S_928_24, Nbl1xCol4a5, HET, Batch 2

description:
Library name: S_928_24
Counts_S92824_GT24; TPM_S92824_GT24; FPKM_S92824_GT24


title: Postnatal day 5 SOM-Cre;Ai47 mouse sample-3

description: Library name: SOM-Ai47_P5-3


title: S_5329_22, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_5329_22
Counts_2206_5329; TPM_2206_5329; FPKM_2206_5329


title: S_5324_22, Nbl1xCol4a5, HET, Batch 1

description:
Library name: S_5324_22
Counts_2206_5324; TPM_2206_5324; FPKM_2206_5324


title: Postnatal day 5 VIP-Cre;Ai47 mouse sample-1

description: Library name: VIP-Ai47_P5-1


title: Young 5

description: Library name: T12


title: Old 3

description: Library name: T13


title: SUBJECT10 [Block_1_FOV_25]


title: BMDM, Slc7a7+/+, OxLDL, rep3

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

description:
BMDM_WT_oxLDL_ID969_S8
salmon.merged.gene_counts.tsv

data_processing:
Fastq files were processed using the nf-core RNA-Seq pipeline (version 3.2; https://nf-co.re/rnaseq/) using the STAR-salmon workflow (default).
Assembly: mm10
Supplementary files format and content: gene count matrix from salmon quantification (tab-delimited)

source_name: bone marrow-derived macrophage

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro Plus kit.
Bulk RNA-Seq libraries were prepared using the SMARTer v2 Stranded Total RNA-Seq Pico Kit (Takara Bio).

treatment_protocol: Bone marrow-derived macrophages (BMDM) from myeloid-specific (LysM-Cre) Slc7a7 knockout mice (Slc7a7-/-) and corresponding control mice (Slc7a7+/+) were treated with acetylated LDL (AcLDL), oxidized LDL (OxLDL) or mock treated (Control).

value: bone marrow-derived macrophage

value: OxLDL


title: BMDM, Slc7a7+/+, OxLDL, rep2

description:
BMDM_WT_oxLDL_ID958_S5
salmon.merged.gene_counts.tsv


title: SUBJECT16 [Block_2_FOV_1]


title: Cohouse young 4

description: Library name: T11


title: Young 4

description: Library name: T10


title: H3K27me3_3 million_WBM_2TX_Ezh2_KO_2_KSL_Cells

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Ezh2_KO_2
Cut_and_Tag_H3K27me3

data_processing:
Raw sequencing reads (FASTQ files) were first evaluated for quality using FastQC (v0.12.1) and summarized with MultiQC (v1.16) to assess per-base quality, adapter contamination, and GC content. Adapter trimming and low-quality read removal were performed using Trim Galore! (v0.6.10). Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.2) with parameters optimized for CUT&Tag’s short and low-background fragments. SAM files were converted to BAM, sorted, and indexed using SAMtools (v1.20). PCR duplicates were removed using Picard (v3.1.1). Only properly paired, uniquely mapped reads were retained for downstream analysis. Filtered BAM files were used to generate fragment files (BEDPEformat) using bedtools bamtobed. To visualize the CUT&Tag signal, normalized genome coverage tracks were generated using deepTools (v3.5.5). These BigWig files were used for global signal visualization, heatmaps, and representative genome browser tracks. Peak calling was performed using SEACR (v1.3) or MACS2 (v2.2.9.1) optimized for CUT&Tag data. Peak output files were converted to BED format for further comparative analysis. Peaks were annotated to the nearest genes and genomic features using ChIPseeker (v1.38.0) or HOMERannotatePeaks.pl. To assess shared and condition-specific binding sites across experimental groups (Control, Jarid2-KO, Ezh2-KO), Venn diagrams were generated using bedtools intersect and ChIPpeakAnno. The number of overlapping and unique peaks per condition was visualized with VennDiagram (R package) or Intervene (v0.6.5). Global enrichment or depletion of H3K27me3 across peaks was assessed using deepTools: Signal Matrix Generation, Heatmaps and Average Profiles. These “aggregate” or ornado plots visualize the mean H3K27me3 signal intensity across all peaks or gene bodies, revealing global depletion patterns between conditions. Representative loci were visualized using Integrative Genomics Viewer (IGV). BigWig tracks from each condition were loaded, and normalized signal intensities were displayed across selected gene regions of interest, highlighting the representative depletion of H3K27me3 peaks. Differential peak intensity analysis was performed using DiffBind (v3.10) or csaw, normalizing for library size and sequencing depth. Statistical significance of global H3K27me3 depletion between genotypes was determined using Wald tests with an FDR threshold of 0.05. Plots were generated using R (v4.3) and ggplot2 for consistency and reproducibility.
Assembly: mm39
Supplementary files format and content: reads are aligned to mm39
Supplementary files format and content: Trimmed and sorted bigwig files
Library strategy: CUT&Tag

source_name: Bone marrow

growth_protocol: To investigate mechanistic differences between genotypes, we performed competitive bone marrow transplantation by co-administering 500,000 CD45.2 donor cells (experimental genotypes) with 500,000 CD45.1 competitor cells into lethally irradiated recipients. 18 weeks post-transplantation, primary recipients were taken down and 3 million WBM was transplanted into secondary recipients. 18 weeks post-transplantation, secondary recipients were taken down and approximately 20,000  CD45.2 KSL (c‑Kit⁺ Sca1⁺ Lineage-)cells were sorted for downstream H3K27me3 analysis using Cut and Tag technique. Cut and Tag protocol is explained in details in the manuscript.

extract_protocol:
For Cut and Tag experiment, CD45.2+ c-Kit+ Sca1+ Lineage- cells were sorted from the CD45.2 c-Kit+ enriched bone marrow cells.
Libraries were constructed after adapters tagmentation, DNA fragmentation using protein A-Transposase 5, and PCR amplification of the fragmented Genomic DNA using specific i5 and i7 index primers for sequencing through NovaSeq X Plus (300 cycles)

treatment_protocol: No treatment

value: Bone marrow

value: C-Kit+ Sca1+ Lineage- Bone Marrow sorted Cells


title: H3K27me3_3 million_WBM_2TX_Ezh2_KO_1_KSL_Cells

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Ezh2_KO_1
Cut_and_Tag_H3K27me3


title: H3K27me3_3 million_WBM_2TX_Jarid2_KO_2_KSL_Cells

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Jarid2_KO_2
Cut_and_Tag_H3K27me3


title: SUBJECT10 [Block_1_FOV_24]


title: BMDM, Slc7a7+/+, OxLDL, rep1

description:
BMDM_WT_oxLDL_ID946_S2
salmon.merged.gene_counts.tsv


title: Young 3

description: Library name: T09

value: Fecal

value: WT


title: SUBJECT3 [Block_1_FOV_11]

value: GT


title: Cohouse young 3

description: Library name: T08


title: BMDM, Slc7a7+/+, Control, rep2

description:
BMDM_WT_Ctrl_ID958_S4
salmon.merged.gene_counts.tsv

value: Control


title: BMDM, Slc7a7+/+, Control, rep3

description:
BMDM_WT_Ctrl_ID969_S7
salmon.merged.gene_counts.tsv


title: Cohouse young 2

description: Library name: T07


title: H3K27me3_3 million_WBM_2TX_Jarid2_KO_1_KSL_Cells

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Jarid2_KO_1
Cut_and_Tag_H3K27me3


title: H3K27me3_3 million_WBM_2TX_Control_2_KSL_Cells

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Control_2
Cut_and_Tag_H3K27me3


title: H3K27me3_3 million_WBM_2TX_Control_1_KSL_Cells

description:
Library name: Cut_and_Tag_3 million_WBM_2TX_Control_1
Cut_and_Tag_H3K27me3


title: BMDM, Slc7a7+/+, Control, rep1

description:
BMDM_WT_Ctrl_ID946_S1
salmon.merged.gene_counts.tsv


title: SUBJECT7 [Block_1_FOV_18]


title: SUBJECT9 [Block_1_FOV_23]


title: Old 2

description: Library name: T05


title: Cohouse old 1

description: Library name: T06

value: CO


title: SUBJECT9 [Block_1_FOV_22]


title: BMDM, Slc7a7+/+, AcLDL, rep2

description:
BMDM_WT_acLDL_ID958_S6
salmon.merged.gene_counts.tsv

value: AcLDL


title: Young 2

description: Library name: T04


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 50 ng/mL aTc

city: Stanford

first: Xin

last: Gao

state: California

address: 327 Campus Drive

department: Department of Biology

institute: Stanford univerisity

description: Library name: Spike-in_PtetRpb_rnaseq_aTc50

data_processing:
For mRNA-seq, raw reads were trimmed with fastp v0.23.1 to remove adapter sequences and low-quality bases. A combined S. cerevisiae (sacCer3, R64) and C. glabrata (CGD assemblies) reference genome was built, and trimmed reads were aligned to this reference using STAR v2.5.2b. Then, in mixed S. cerevisiae and C. glabrata sequencing libraries, transcript-per-million (TPM) values for each gene were calculated by standard method.
Assembly: For spike-in RNA and DNA sequencing, a combined S. cerevisiae (sacCer3, R64) and C. glabrata (CGD assemblies) reference genome was built.
Supplementary files format and content: For RNA-seq, xlsx files include TPM for each sample.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was purified using the Direct-zol RNA Microprep Kit (Zymo Research) following the manufacturer’s instructions.
For mRNA-seq and WGS, library was constructed by Azenta standard protocols.


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 100 ng/mL aTc

description: Library name: Spike-in_PtetRpb_rnaseq_aTc100


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 200 ng/mL aTc

description: Library name: Spike-in_PtetRpb_rnaseq_aTc200


title: SUBJECT9 [Block_1_FOV_21]


title: SUBJECT14 [Block_1_FOV_7]

value: GG


title: BMDM, Slc7a7+/+, AcLDL, rep1

description:
BMDM_WT_acLDL_ID946_S3
salmon.merged.gene_counts.tsv


title: Young 1

description: Library name: T03


title: BMDM, Slc7a7-/-, OxLDL, rep3

description:
BMDM_Slc7a7KO_oxLDL_ID964_S11
salmon.merged.gene_counts.tsv


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 20 ng/mL aTc

description: Library name: Spike-in_PtetRpb_rnaseq_aTc20


title: Cohouse young 1

description: Library name: T02


title: SUBJECT4 [Block_1_FOV_14]


title: BMDM, Slc7a7-/-, OxLDL, rep2

description:
BMDM_Slc7a7KO_oxLDL_ID963_S14
salmon.merged.gene_counts.tsv


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 10 ng/mL aTc

description: Library name: Spike-in_PtetRpb_rnaseq_aTc10


title: SUBJECT4 [Block_1_FOV_13]


title: BMDM, Slc7a7-/-, OxLDL, rep1

description:
BMDM_Slc7a7KO_oxLDL_ID961_S17
salmon.merged.gene_counts.tsv


title: Old 1

description: Library name: T01


title: S. cerevisiae in trehalose, replicate 2 – ribosome profiling

description: Library name: SC_riboseq_trehalose_Replicate2

library_source: other

data_processing:
For ribo-seq, raw paired-end reads were first processed with Trimmomatic v0.39 to remove adapter sequences and perform quality trimming. We retained only reads ≥ 15 nt. Low-quality bases were trimmed using default parameters. Trimmed reads were then aligned against the S. cerevisiae rRNA reference sequence (SGD S288C; http://sgd-archive.yeastgenome.org/sequence/S288C_reference/rna/) using Bowtie v1.2.3 with options -f -v 2 -k 1 -p 4. Reads mapping to rRNA were discarded. The remaining non-rRNA reads were mapped to the S. cerevisiae genome (NCBI R64) with Bowtie (-m 1) to retain only uniquely aligned fragments. Finally, these uniquely mapped reads were aligned to the S. cerevisiae transcriptome (NCBI R64) to produce BAM files for subsequent analysis of ribosome footprints to calculate translation efficiency.
Assembly: R64
Supplementary files format and content: For Ribo-seq, xlsx files includes raw counts for each sample.
Library strategy: Ribo-seq

molecule: other

organism: Saccharomyces cerevisiae W303

extract_protocol:
Total RNA was purified using the Direct-zol RNA Microprep Kit (Zymo Research) following the manufacturer’s instructions.
For ribo-seq, NEBNext Small RNA Library Prep Set (E7330S) was used to build libraries for pair-end (2×150 bp) Illumina sequencing.For mRNA-seq and WGS, library was constructed by Azenta standard protocols.


title: S. cerevisiae Ptet-Rpb1 – RNA-seq at 5 ng/mL aTc

description: Library name: Spike-in_PtetRpb_rnaseq_aTc5


title: BMDM, Slc7a7+/+, AcLDL, rep3

description:
BMDM_WT_acLDL_ID969_S9
salmon.merged.gene_counts.tsv


title: SUBJECT18 [Block_2_FOV_12]


title: S. cerevisiae in trehalose, replicate 2 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_trehalose_Replicate2


title: BMDM, Slc7a7-/-, Control, rep3

description:
BMDM_Slc7a7KO_Ctrl_ID964_S10
salmon.merged.gene_counts.tsv


title: S. cerevisiae in trehalose, replicate 1 – ribosome profiling

description: Library name: SC_riboseq_trehalose_Replicate1


title: BMDM, Slc7a7-/-, Control, rep2

description:
BMDM_Slc7a7KO_Ctrl_ID963_S13
salmon.merged.gene_counts.tsv


title: S. cerevisiae in glycerol, replicate 2 – ribosome profiling

description: Library name: SC_riboseq_glycerol_Replicate2


title: BMDM, Slc7a7-/-, Control, rep1

description:
BMDM_Slc7a7KO_Ctrl_ID961_S16
salmon.merged.gene_counts.tsv


title: SUBJECT25 [Block_2_FOV_26]


title: S. cerevisiae in glycerol, replicate 1 – ribosome profiling

description: Library name: SC_riboseq_glycerol_Replicate1


title: S. cerevisiae in glycerol, replicate 1 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_glycerol_Replicate1


title: S. cerevisiae in galactose, replicate 2 – ribosome profiling

description: Library name: SC_riboseq_galactose_Replicate2


title: SUBJECT1 [Block_1_FOV_2]


title: S. cerevisiae in galactose, replicate 1 – ribosome profiling

description: Library name: SC_riboseq_galactose_Replicate1


title: S. cerevisiae in galactose, replicate 2 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_galactose_Replicate2


title: BMDM, Slc7a7-/-, AcLDL, rep1

description:
BMDM_Slc7a7KO_acLDL_ID961_S18
salmon.merged.gene_counts.tsv


title: S. cerevisiae in glucose, replicate 1 – ribosome profiling

description: Library name: SC_riboseq_glucose_Replicate1


title: SUBJECT20 [Block_2_FOV_16]


title: S. cerevisiae in glucose, replicate 2 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_glucose_Replicate2


title: SUBJECT18 [Block_2_FOV_11]


title: S. cerevisiae in galactose, replicate 1 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_galactose_Replicate1


title: S. cerevisiae in glucose, replicate 2 – ribosome profiling

description: Library name: SC_riboseq_glucose_Replicate2


title: S. cerevisiae in trehalose, replicate 1 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_trehalose_Replicate1


title: SUBJECT2 [Block_1_FOV_10]


title: S. cerevisiae in glucose, replicate 1 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_glucose_Replicate1


title: SUBJECT5 [Block_1_FOV_15]


title: NCM460-shUHRF1

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Xijing Hospital of Fourth Military Medical University

description: Gene expression in NCM460-shUHRF1 cell line

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Both NCM460-shCtrl and NCM460-shUHRF1 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in a humidified atmosphere containing 5 % CO2.

value: Human colon epithelial cells


title: SUBJECT1 [Block_1_FOV_1]


title: NSC200 CD133-

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description: Library name: SS32

data_processing:
The data files were quantified in GenomeStudio Version 2011.1 (Illumina). All samples passed Illumina sample dependent and independent QC Metrics. GSEA analysis was performed using the MySigDB oncogenic signature collection
Assembly: GRCh38
Supplementary files format and content: .txt files containing read counts of annotated genes.

source_name: Normal Neural Stem Cells

growth_protocol: Glioblastoma cells originating from primary samples were processed and maintained in Neurocult media (STEMcell Technolgies) as brain tumour initiating cells (BTICs). BTICs were grown as tumorspheres that were maintained at 37°C with a humidified atmosphere of 5% CO2

extract_protocol:
RNA was extracted from cells using the QIAGEN RNEasy kit.
Library prep was performed using the NEBNext Ultra Directional RNA Library Prep Kit along with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were subject to further BioAnalyzer QC and quantified by qPCR.

treatment_protocol: Cells were stained with anti-human CD133 antibody and were flow sorted into CD133+ and CD133- populations.

value: Normal Neural Stem Cells


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 100 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc100

data_processing:
For DNA-seq, paired-end RNA-seq reads were trimmed to remove adapters and low-quality bases using Trimmomatic (v0.39). Clean reads were quantified with Salmon (v1.10) against a combined transcriptome reference of Saccharomyces cerevisiae (sacCer3, R64) and Candida glabrata (CGD assemblies).
Assembly: For spike-in RNA and DNA sequencing, a combined S. cerevisiae (sacCer3, R64) and C. glabrata (CGD assemblies) reference genome was built.
Supplementary files format and content: For DNA-seq, xlsx files includes raw counts for each sample.

extract_protocol:
Genomic DNA was extracted using the YeaStar Genomic DNA Kit (Zymo Research) according to the manufacturer’s chloroform protocol.
For mRNA-seq and WGS, library was constructed by Azenta standard protocols.


title: SUBJECT22 [Block_2_FOV_20]


title: NCM460-shCtrl

description: Gene expression in NCM460-shCtrl cell line


title: SUBJECT3 [Block_1_FOV_12]


title: NSC200 CD133+

description: Library name: SS31


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 50 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc50


title: SUBJECT22 [Block_2_FOV_19]


title: NSC195 CD133-

description: Library name: SS28


title: SUBJECT24 [Block_2_FOV_24]


title: 200 nM OC 3

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from 200 nM of OC treated for 96 hours

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Clariom_S_Human Array. GeneChips were washed and stained in the GeneAtlas® Fluidics Station

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following single-sample robust multi-array average (SST-RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Genes with a linear fold change >1.5 and p-value < 0.05(one-way between-subjects ANOVA) were considered as differentially expressed genes(DEGs). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software.

label: biotin

source_name: cell treated with 200 nM of OC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Primary human epidermal keratinocytes were purchased from Gibco and were maintained in EpiLife mediium supplemented with EpiLife defined growth supplement

extract_protocol: not provided

treatment_protocol: HEK cells were seeded in 6-well plates. After 24 hours, cells were treated with 0 (Control), 10ng/ml KGF (Positive control), and 200 nM of OP and OC for 96 hours. To induce the differentiation, EpiLife medium with 2 mM of CaCl2 was used.

value: Primary human epidermal keratinocytes cell


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 5 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc5


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 200 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc200


title: BMDM, Slc7a7-/-, AcLDL, rep3

description:
BMDM_Slc7a7KO_acLDL_ID964_S12
salmon.merged.gene_counts.tsv


title: SUBJECT24 [Block_2_FOV_25]


title: S. cerevisiae in glycerol, replicate 2 – spike-in RNA-seq

description: Library name: Spike-in_rnaseq_glycerol_Replicate2


title: BMDM, Slc7a7-/-, AcLDL, rep2

description:
BMDM_Slc7a7KO_acLDL_ID963_S15
salmon.merged.gene_counts.tsv


title: 200 nM OC 2


title: NSC194 CD133-

description: Library name: SS26


title: 200 nM OC 1


title: NSC194 CD133+

description: Library name: SS25


title: NSC195 CD133+

description: Library name: SS27


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 20 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc20


title: NSC198 CD133+

description: Library name: SS29


title: 200 nM OP 2

description: Gene expression data from 200 nM of OP treated for 96 hours

source_name: cell treated with 200 nM of OP


title: SUBJECT13 [Block_1_FOV_6]


title: SUBJECT26 [Block_2_FOV_4]


title: 200 nM OP 3


title: BT698 CD133-

description: Library name: SS24

source_name: Brain Tumour Initiating Cells

value: Brain Tumour Initiating Cells


title: SUBJECT8 [Block_1_FOV_19]


title: KGF 2

description: Gene expression data from KGF treated for 96 hours

source_name: cell treated with 10ng/ml of KGF


title: 200 nM OP 1


title: BT698 CD133+

description: Library name: SS23


title: S. cerevisiae in glycerol, replicate 1 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_glycerol_Replicate1


title: SUBJECT8 [Block_1_FOV_20]


title: BT624 CD133-

description: Library name: SS22


title: SUBJECT6 [Block_1_FOV_16]


title: S. cerevisiae in trehalose, replicate 2 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_trehalose_Replicate2


title: SUBJECT15 [Block_1_FOV_9]


title: S. cerevisiae in galactose, replicate 1 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_galactose_Replicate1


title: S. cerevisiae in glycerol, replicate 2 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_glycerol_Replicate2


title: S. cerevisiae Ptet-Rpb1 – gDNA-seq at 10 ng/mL aTc

description: Library name: Spike-in_PtetRpb_gDNAseq_aTc10


title: S. cerevisiae in galactose, replicate 2 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_galactose_Replicate2


title: KGF 3


title: Control 3

description: Gene expression data from meduim treated for 96 hours

source_name: cell treated with meduim


title: S. cerevisiae in trehalose, replicate 1 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_trehalose_Replicate1


title: KGF 1


title: S. cerevisiae in glucose, replicate 2 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_glucose_Replicate2


title: BT458 CD133-

description: Library name: SS20


title: BT458 CD133+

description: Library name: SS19


title: Control 1


title: SUBJECT11 [Block_1_FOV_4]


title: Root_SA187_N1mM_1

status: Public on Nov 21 2025

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

description: Library name: sample 7

data_processing:
transcriptome mapping and counts of reads by gene locus are done with STAR and HTSeqcount; exact multihits are removed and count only consistent PE reads (in PE case).
Assembly: genome of TAIR10 Arabidopsis
Supplementary files format and content: tab delimited text file with raw count by gene. Column content: GeneID,RawCount stranded

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: - N depleted 1/2 MS + 20mM NO3 - 60 - 20/18 (day/night) - 16h/day

extract_protocol:
total RNA, quantity=100mg kit:MachereyNagel_NucleSpin_RNA_Plus.pdf
rna_selection:selection polyA, single, stranded:no, Protocol:PT_QuantSEQ-3_prime_mRNA_simple_indexage_B_17-11-21.docx

treatment_protocol:
LowN-mock-abiotic stress-nitrogen concentration-nitrogen quantity 1mM
NormalN-mock-abiotic stress-nitrogen-nitrogen quantity 20mM

value: wild type (Wild type)

value: rosette

tag: developmental stage

value: age=12.5day boyes:1.02

value: LowN


title: Root_SA187_N1mM_2

description: Library name: sample 8


title: Root_SA187_N1mM_3

description: Library name: sample 9


title: Control 2


title: Root_Mock_N20mM_3

description: Library name: sample 6


title: P20 cortical interneurons in control and in test condition with TeNT in Fezf2+ PNs

city: Cambridge

first: Min

last: Dai

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

description:
Library name: P20cIN_Ctrl_and_P20cIN_TeNT_OCM
Interneurons are enriched by FACS mScarlet+ neurons labeled with AAV harboring Dlx enhancer;  On-Chip Multiplexing (OCM) experiment by 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger (v7.0.0, 10x Genomics) was used with default parameters to map snRNA-seq data to the mouse reference genome (mm10) provided by 10x Genomics. The gene expression matrices output from CellRanger were then imported into Python v3.9.13 as AnnData objects (anndata v0.8.0). Scanpy v1.9.1 was used as the basic framework for snRNAseq processing. We used Scrublet v.0.2.342 to calculate the potential doublet score for each cell. Unless specified elsewhere, genes expressed in fewer than 3 cells were filtered. Cells were filtered based on the following criteria: n_counts < 15,000, 200 < n_genes < 4,000, ratio_of_mitochondria_genes < 5% (gene symbols beginning with 'mt-'), ratio_of_ribosome_genes < 5% (gene symbols beginning with 'Rpl' or 'Rps') and scrublet_score<0.25. After quality control, the raw counts were normalized using the pp.normalize_total function (counts_per_cell_after = 10,000); the normalized counts were log-transformed using the pp.log1p function. The Pearson residuals were calculated from the raw counts for selecting top 5,000 highly variable genes using experimental.pp.highly_variable_genes function (n_top_genes=5,000). The StandardScaler function (with_mean=False) of scikit-learn v.0.24.0 was then used to scale the Pearson residuals of highly variable genes, followed by the TruncatedSVD function of scikit-learn v.0.24.0 to calculate the Principal Component Analysis (PCA) embeddings for the cells. The unsupervised graph-based Leiden clustering algorithm, pp.neighbors and tl.leiden functions, was used for the clustering based on the PCA embeddings. To sub-cluster specific clusters, the piaso.tl.leiden_local function from our single-cell analysis toolkit PIASO (https://github.com/genecell/PIASO) was used. This function repeats the steps of highly variable gene selection, PCA embedding and Leiden clustering on selected cells while maintaining the clustering results for the remaining cells. After clustering, COSG v1.0.1 was used to identify top marker genes for each cluster, which were cross-compared with well-known marker genes from literature for cell type annotation. For visualization of multiple snRNA-seq datasets across different conditions, we employed the piaso.pl.plot_embeddings_split from PIASO to align cell coordinates from different conditions and scale the gene expression or cell metrics for consistency.
Assembly: mm10
Supplementary files format and content: The .h5 files are the output of CellRanger (v7.0.0), which contains the UMI counts for genes detected among cells.

source_name: Whole cortex

extract_protocol:
Brain samples were harvested from mice with specific genotypes and ages, and the cortex was carefully dissected in ice-cold Homogenization Buffer (HB) comprising 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, and 0.5 mM spermidine. The dissected brain tissue was then transferred to a 2 ml Dounce tissue grinder filled with HB supplemented with 0.15-0.25% IGEPAL-CA630 and 0.2 U/µl RNasin. Tissue homogenization was performed with 8-10 strokes of pestle A followed by 9-10 strokes of pestle B. The homogenate was filtered through a 30 μm filter into a 15 ml conical tube and centrifuged at 500 g for 5 min. at 4 °C using a swinging-bucket centrifuge. The resulting pellet was resuspended in 1X PBS containing 1% BSA + 0.2 U/µl RNasin and then passed through a 40 μm filter. DRAQ5 (BioLegend) was added to the nuclei suspension for sorting of GFP+ nuclei on a Sony MA900 cell sorter using a 70 µm nozzle. Nuclei were collected in pre-chilled 0.2 ml PCR tube and counted using a hemocytometer (INCYTO C-Chip).
snRNA-seq libraries were prepared using the Chromium Single Cell 3’ Kit v3.1 (10x Genomics), following the manufacturer’s protocol. Pooled libraries were sequenced on NovaSeq 6000 instruments (Illumina).

value: Whole cortex

value: cortical interneurons

value: Emx1-Cre; Fezf2-2A-FlpO for control and Emx1-Cre; Fezf2-2A-FlpO; RC::PFtox for test condition with TeNT in Fezf2+ PNs


title: S. cerevisiae in glucose, replicate 1 – spike-in DNA-seq

description: Library name: Spike-in_gDNAseq_glucose_Replicate1


title: Root_Mock_N20mM_2

description: Library name: sample 5

value: NormalN


title: Shoot_SA187_N20mM_2

description: Library name: sample 23

source_name: aerial

value: aerial


title: Root_Mock_N20mM_1

description: Library name: sample 4


title: Root_Mock_N1mM_3

description: Library name: sample 3

value: no treatment


title: Shoot_Mock_N1mM_3

description: Library name: sample 15


title: Shoot_Mock_N20mM_3

description: Library name: sample 18


title: Shoot_SA187_N20mM_3

description: Library name: sample 24

source_name: roots

value: roots


title: Shoot_Mock_N1mM_1

description: Library name: sample 13


title: Shoot_Mock_N20mM_2

description: Library name: sample 17


title: Shoot_SA187_N1mM_2

description: Library name: sample 20


title: Shoot_SA187_N1mM_3

description: Library name: sample 21


title: Shoot_Mock_N20mM_1

description: Library name: sample 16


title: WGBS_NI_Donor4_CP

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

description: Library name: WGBS_NI_Donor4_CP

data_processing:
[scRNA-seq for embryos]The initial processing of raw single-cell RNA-seq data involved the removal of template switch oligo (TSO) and poly(A) tail sequences. Subsequently, reads containing adapters and those with low-quality bases were filtered out to yield clean reads. These clean reads were then aligned to the human reference genome (hg38) using software Tophat (version: 2.0.12). To ensure accuracy, only reads with unique mapping based on UMI counts were considered, and reads sharing the same UMI sequence were counted as a single entity using software HTSeq. Gene expression levels were quantified as transcripts per million (TPM). Specifically, the TPM value for gene g in cell c (TPMg,c) was calculated by dividing the UMI count of gene g by the total UMI count in cell c, then multiplying by 1,000,000. Given that the complexity of scRNA-seq libraries was estimated at approximately 100,000 transcripts, gene expression levels were normalized using the transformation log2(TPM/10 + 1).  [scDNAmet-seq for embryos]For PBAT DNA methylation sequencing data, raw reads were initially processed to eliminate adapter sequences and low-quality bases using software trim_galore (version: 0.3.3) with the following parameters: ‘--quality 20, --phred33, --length 50, --stringency 3, and --paired’. Quality-filtered reads were then aligned to the human reference genome (hg38) using software Bismark (version: 0.22.3) in paired-end mode, with the parameter ‘--non-directional’. To maximize read recovery, unmapped reads were re-aligned using Bismark in single-end mode. Only uniquely mapped reads were retained for downstream analysis. Following alignment, duplicate reads were removed using command rmdup in software samtools (version: 1.20). For each cytosine site (or its corresponding guanine on the opposite strand) in the reference genome, the DNA methylation level was calculated as the ratio of reads supporting methylated cytosines (C) to the total reads (methylated and unmethylated). The reads were extracted using command extract in software MethylDackel (version: 0.3.0). In this study, unless otherwise specified, the DNA methylation level of a sample or region refers specifically to the methylation level of CpG sites within that sample or region. For single-cell DNA methylome analysis, CpG sites with methylation levels exceeding 90% were classified as methylated (methylation level was quantified as 100%), while those below 10% were considered unmethylated (methylation level was quantified as 0%). The minimum read coverage required to determine methylation levels was set at 1× for single cells.  [Bulk RNA-seq library for placental tissues]Following standard quality control steps, raw bulk RNA-seq data was processed through our customized scripts. Initial preprocessing included the removal of adapter-contaminated sequences and low-quality reads to generate high-quality clean reads for downstream analysis. These processed reads were subsequently aligned to the UCSC human reference genome (hg38) using software Tophat. Following alignment, uniquely mapped reads were quantified using software HTSeq. Gene expression quantification was performed using the RPKM (reads per kilobase per million mapped reads) normalization method to account for variations in gene length and sequencing depth.  [10X for UCB]The raw scRNA-seq data were analyzed using command count in the 10× Genomics software CellRanger (version: 8.0.0). The sequencing reads were mapped to the human reference genome (GRCh38).
Assembly: Homo sapiens
Supplementary files format and content: bed

source_name: Placental tissue

extract_protocol:
[Collection of early human embryos and single cell isolation]All embryos used in this study were collected from the Reproductive Medicine Center of International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University. The donated blastocysts were cryopreserved via vitrification at the reproductive center, with each blastocyst individually frozen on a cryostorage carrier. Commercial vitrification and warming solutions kits (Kitazato Corporation, Japan) were used for blastocyst cryopreservation and thawing procedures. Post-thawing, the blastocysts were cultured in vitro using G2 Plus medium (Vitrolife, Sweden) for 2 hours (37°C, 6% CO2, 5% O2). The zona pellucida was subsequently removed through gentle pipetting with acidic Tyrode’s solution (Sigma), followed by three washes in phosphate-buffered saline (PBS) containing 0.5% bovine serum albumin (BSA). Laser-assisted ablation (RI Scientific Instruments) was utilized to release blastocoelic fluid from zona-free blastocysts, which were then transferred to a digestion medium (accutase medium: 0.25% trypsin, 1:1) and incubated at 37°C for 30-40 minutes. To facilitate physical dissociation into individual cells, the digested blastocysts were subjected to gentle mechanical pipetting using sequentially smaller-bore glass pipettes (varying inner diameters). Following complete dissociation, isolated single cells underwent two washes in PBS supplemented with 0.1% BSA. Finally, individual cells were transferred to lysis medium on ice using a mouth-controlled micropipette. All procedures were performed under a stereomicroscope.  [UCB collection and nucleated cell isolation]UCB samples were collected from eight neonates, including four neonates deriving from oocytes collected from mothers with acute SARS-CoV-2 infection and four neonates from mothers without a history of SARS-CoV-2 infection. Approximately 10 mL of UCB was collected from each donor using EDTA-containing anticoagulant tubes, with all samples transported to the laboratory within 60 minutes post-collection. Written informed consent was obtained from all participants or their legally authorized representatives prior to sample collection. UCB samples were processed using Ficoll density gradient centrifugation to isolate mononuclear cells. Briefly, anticoagulated whole blood was carefully layered onto human peripheral blood lymphocyte separation medium (TBD, LTS1077). The samples were centrifuged at 700g for 25 minutes at 25°C. Following centrifugation, the mononuclear cell layer at the plasma-separation medium interface was collected and diluted with PBS, followed by centrifugation at 250g for 10 minutes. The supernatant was discarded, and residual red blood cells were lysed using erythrocyte lysis buffer (Solarbio, R1010) with incubation on ice for 10 minutes. Cells were washed with wash buffer (PBS containing 0.04% BSA) and centrifuged at 300g for 10 minutes at 4°C. The cell pellet was resuspended, and cell counting was performed using a fluorescent cell counter. For long-term storage, cells were resuspended in freezing medium, aliquoted into cryovials, and transferred to liquid nitrogen after gradient freezing.
[scRNA-seq for embryos]The scRNA-seq libraries were prepared using a modified STRT-seq method. Individual cells were isolated using a mouth pipette and transferred into lysis buffer. mRNA from the lysate was reverse transcribed using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific, 18064022), with each cell’s cDNA being tagged with a unique 8-nucleotide (nt) cell-specific barcode. Following this, the second cDNA strand was synthesized, and the cDNA was pre-amplified. The amplified cDNA products were then pooled, purified, and fragmented. Library preparation was performed using the KAPA HyperPrep Kit (KAPA, KK8504), and sequencing was carried out on the Illumina HiSeq 4000 platform (Novogene) with 150-bp paired-end reads.  [scDNAmet-seq for embryos]The single-cell whole-genome bisulfite sequencing procedure followed the established PBAT method. Briefly, individual cells were transferred into lysis buffer by mouth pipetting. Genomic DNA was isolated through proteinase K digestion at 50°C, followed by bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, D5044) according to the manufacturer’s protocol. Then, the DNA was supplemented with the biotinylated random primer Bio-P5-N9 and 50 units of Klenow polymerase (3′ to 5′ exo–, New England BioLabs). This random priming process was carried out five times. Second strands were then synthesized using a different random primer, P7-N9, and the final libraries were created after 8 to 12 cycles of PCR amplification using the Illumina universal PCR primer and Illumina indexed primer. Finally, the constructed library was sequenced on the Illumina HiSeq 4000 platform (Novogene) with 150-bp paired-end reads.  [Bulk RNA-seq library for placental tissues]For bulk RNA sequencing, total RNA of placental tissues was isolated by RNA Extraction Kit (Vazyme, RC113-01) and library construction was performed using VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme, NR611).  [10X for UCB]Single cells were encapsulated in droplet emulsion using the 10× Genomics Chromium Single Cell Instrument according to the manufacturer’s protocol, with scRNA-seq libraries constructed using the 10× Genomics Chromium Single Cell 3' GEM Library & Gel Bead Kit v2. Briefly, cells were loaded into each channel with a target recovery of approximately 5,000 cells per sample, and cell concentration was measured using the Moxi GO II (Orflo Technologies) to ensure optimal loading density. All reactions were performed on a Bio-Rad C1000 Touch Thermal Cycler with a 96-deep well reaction module, where cDNA amplification and sample indexing were carried out using 12 cycles. Subsequently, amplified cDNA and final libraries were assessed using the Fragment Analyzer (AATI) with the High Sensitivity NGS Kit (Advanced Analytical). The average fragment length of 10x cDNA libraries was evaluated by AATI, and library quantification was performed using the Kapa Library Quantification Kit via qPCR. All libraries were diluted to a final concentration of 2 nM and pooled for each run on the NovaSeq platform. Sequencing was performed on the Illumina NovaSeq 6000 system. [WGBS forplacental tissues]Genomic DNA was extracted from placental tissues using the DNA Extraction Kit (TIANGEN Biotech, DP705). For library preparation, 2 μg of genomic DNA was fragmented to ~300 bp using the ME220 Focused-ultrasonicator (Covaris, 500217). Fragmented DNA underwent end repair, 3'-end adenylation (A-tailing), and ligation with Methylation Adapters (New England BioLabs, E7140S). Bisulfite conversion was performed using the DNA Methylation-Direct MagPrep Kit (Zymo Research, D5044) under optimized conditions: 98°C for 10 min denaturation followed by 64°C for 3.5 h conversion. Final libraries were constructed through 4-6 cycles of PCR amplification with KAPA HiFi Uracil+ DNA Polymerase (Roche, KK2801) using Illumina universal primers and indexed primers, followed by size selection using AMPure XP beads (Beckman Coulter, A63881).

tag: library

value: WGBS

value: Placental tissue

tag: donor

tag: group

value: Non-infected (NI)


title: Root_SA187_N20mM_2

description: Library name: sample 11


title: Shoot_SA187_N20mM_1

description: Library name: sample 22


title: WGBS_NI_Donor3_CP

description: Library name: WGBS_NI_Donor3_CP


title: Shoot_Mock_N1mM_2

description: Library name: sample 14


title: WGBS_NI_Donor2_CP

description: Library name: WGBS_NI_Donor2_CP


title: WGBS_NI_Donor1_CP

description: Library name: WGBS_NI_Donor1_CP


title: Root_Mock_N1mM_1

description: Library name: sample 1


title: WGBS_IS_Donor4_CP

description: Library name: WGBS_IS_Donor4_CP

value: Infected SARS-CoV-2 (IS)


title: BT428 CD133-

description: Library name: SS18


title: WGBS_IS_Donor3_CP

description: Library name: WGBS_IS_Donor3_CP


title: WGBS_IS_Donor2_CP

description: Library name: WGBS_IS_Donor2_CP


title: Root_SA187_N20mM_1

description: Library name: sample 10


title: Root_SA187_N20mM_3

description: Library name: sample 12


title: Shoot_SA187_N1mM_1

description: Library name: sample 19


title: Root_Mock_N1mM_2

description: Library name: sample 2


title: WGBS_IS_Donor1_CP

description: Library name: WGBS_IS_Donor1_CP


title: PBAT.NI_Embryo9_sc.61

description: Library name: PBAT.NI_Embryo9_sc.61

source_name: Embryo (blastocyst)

value: PBAT (scDNAme-seq)

value: Embryo (blastocyst)


title: PBAT.NI_Embryo9_sc.57

description: Library name: PBAT.NI_Embryo9_sc.57


title: PBAT.NI_Embryo9_sc.60

description: Library name: PBAT.NI_Embryo9_sc.60


title: PBAT.NI_Embryo9_sc.55

description: Library name: PBAT.NI_Embryo9_sc.55


title: PBAT.NI_Embryo9_sc.53

description: Library name: PBAT.NI_Embryo9_sc.53


title: PBAT.NI_Embryo9_sc.52

description: Library name: PBAT.NI_Embryo9_sc.52


title: PBAT.NI_Embryo9_sc.56

description: Library name: PBAT.NI_Embryo9_sc.56


title: PBAT.NI_Embryo9_sc.54

description: Library name: PBAT.NI_Embryo9_sc.54


title: PBAT.NI_Embryo9_sc.51

description: Library name: PBAT.NI_Embryo9_sc.51


title: PBAT.NI_Embryo9_sc.49

description: Library name: PBAT.NI_Embryo9_sc.49


title: PBAT.NI_Embryo9_sc.47

description: Library name: PBAT.NI_Embryo9_sc.47


title: PBAT.NI_Embryo9_sc.50

description: Library name: PBAT.NI_Embryo9_sc.50


title: PBAT.NI_Embryo9_sc.48

description: Library name: PBAT.NI_Embryo9_sc.48


title: PBAT.NI_Embryo9_sc.43

description: Library name: PBAT.NI_Embryo9_sc.43


title: PBAT.NI_Embryo9_sc.44

description: Library name: PBAT.NI_Embryo9_sc.44


title: PBAT.NI_Embryo9_sc.45

description: Library name: PBAT.NI_Embryo9_sc.45


title: PBAT.NI_Embryo9_sc.46

description: Library name: PBAT.NI_Embryo9_sc.46


title: PBAT.NI_Embryo8_sc.40

description: Library name: PBAT.NI_Embryo8_sc.40


title: PBAT.NI_Embryo8_sc.41

description: Library name: PBAT.NI_Embryo8_sc.41


title: PBAT.NI_Embryo8_sc.39

description: Library name: PBAT.NI_Embryo8_sc.39


title: PBAT.NI_Embryo8_sc.35

description: Library name: PBAT.NI_Embryo8_sc.35


title: PBAT.NI_Embryo8_sc.38

description: Library name: PBAT.NI_Embryo8_sc.38


title: PBAT.NI_Embryo8_sc.36

description: Library name: PBAT.NI_Embryo8_sc.36


title: PBAT.NI_Embryo9_sc.58

description: Library name: PBAT.NI_Embryo9_sc.58


title: PBAT.NI_Embryo8_sc.34

description: Library name: PBAT.NI_Embryo8_sc.34


title: PBAT.NI_Embryo8_sc.32

description: Library name: PBAT.NI_Embryo8_sc.32


title: PBAT.NI_Embryo8_sc.33

description: Library name: PBAT.NI_Embryo8_sc.33


title: PBAT.NI_Embryo8_sc.29

description: Library name: PBAT.NI_Embryo8_sc.29


title: PBAT.NI_Embryo8_sc.30

description: Library name: PBAT.NI_Embryo8_sc.30


title: PBAT.NI_Embryo8_sc.28

description: Library name: PBAT.NI_Embryo8_sc.28


title: PBAT.NI_Embryo8_sc.25

description: Library name: PBAT.NI_Embryo8_sc.25


title: PBAT.NI_Embryo8_sc.27

description: Library name: PBAT.NI_Embryo8_sc.27


title: PBAT.NI_Embryo8_sc.26

description: Library name: PBAT.NI_Embryo8_sc.26


title: PBAT.NI_Embryo8_sc.24

description: Library name: PBAT.NI_Embryo8_sc.24


title: PBAT.NI_Embryo8_sc.23

description: Library name: PBAT.NI_Embryo8_sc.23


title: PBAT.NI_Embryo8_sc.19

description: Library name: PBAT.NI_Embryo8_sc.19


title: PBAT.NI_Embryo7_sc.9

description: Library name: PBAT.NI_Embryo7_sc.9


title: PBAT.NI_Embryo8_sc.21

description: Library name: PBAT.NI_Embryo8_sc.21


title: PBAT.NI_Embryo8_sc.20

description: Library name: PBAT.NI_Embryo8_sc.20


title: PBAT.NI_Embryo8_sc.37

description: Library name: PBAT.NI_Embryo8_sc.37


title: PBAT.NI_Embryo7_sc.8

description: Library name: PBAT.NI_Embryo7_sc.8


title: PBAT.NI_Embryo7_sc.7

description: Library name: PBAT.NI_Embryo7_sc.7


title: PBAT.NI_Embryo7_sc.4

description: Library name: PBAT.NI_Embryo7_sc.4


title: PBAT.NI_Embryo7_sc.5

description: Library name: PBAT.NI_Embryo7_sc.5


title: PBAT.NI_Embryo7_sc.6

description: Library name: PBAT.NI_Embryo7_sc.6


title: PBAT.NI_Embryo7_sc.2

description: Library name: PBAT.NI_Embryo7_sc.2


title: PBAT.NI_Embryo7_sc.1

description: Library name: PBAT.NI_Embryo7_sc.1


title: PBAT.NI_Embryo7_sc.3

description: Library name: PBAT.NI_Embryo7_sc.3


title: PBAT.NI_Embryo8_sc.31

description: Library name: PBAT.NI_Embryo8_sc.31


title: PBAT.NI_Embryo6_sc.5

description: Library name: PBAT.NI_Embryo6_sc.5


title: PBAT.NI_Embryo6_sc.2

description: Library name: PBAT.NI_Embryo6_sc.2


title: PBAT.NI_Embryo6_sc.4

description: Library name: PBAT.NI_Embryo6_sc.4


title: PBAT.NI_Embryo7_sc.10

description: Library name: PBAT.NI_Embryo7_sc.10


title: PBAT.NI_Embryo6_sc.1

description: Library name: PBAT.NI_Embryo6_sc.1


title: PBAT.NI_Embryo6_sc.3

description: Library name: PBAT.NI_Embryo6_sc.3


title: PBAT.IS_Embryo2_sc.9

description: Library name: PBAT.IS_Embryo2_sc.9


title: PBAT.NI_Embryo8_sc.22

description: Library name: PBAT.NI_Embryo8_sc.22


title: PBAT.IS_Embryo2_sc.28

description: Library name: PBAT.IS_Embryo2_sc.28


title: PBAT.IS_Embryo2_sc.27

description: Library name: PBAT.IS_Embryo2_sc.27


title: PBAT.IS_Embryo2_sc.23

description: Library name: PBAT.IS_Embryo2_sc.23


title: PBAT.IS_Embryo2_sc.25

description: Library name: PBAT.IS_Embryo2_sc.25


title: PBAT.IS_Embryo2_sc.24

description: Library name: PBAT.IS_Embryo2_sc.24


title: PBAT.IS_Embryo2_sc.21

description: Library name: PBAT.IS_Embryo2_sc.21


title: PBAT.IS_Embryo2_sc.17

description: Library name: PBAT.IS_Embryo2_sc.17


title: PBAT.IS_Embryo2_sc.20

description: Library name: PBAT.IS_Embryo2_sc.20


title: PBAT.IS_Embryo2_sc.18

description: Library name: PBAT.IS_Embryo2_sc.18


title: PBAT.IS_Embryo2_sc.19

description: Library name: PBAT.IS_Embryo2_sc.19


title: PBAT.IS_Embryo2_sc.15

description: Library name: PBAT.IS_Embryo2_sc.15


title: PBAT.IS_Embryo2_sc.14

description: Library name: PBAT.IS_Embryo2_sc.14


title: PBAT.IS_Embryo2_sc.13

description: Library name: PBAT.IS_Embryo2_sc.13


title: PBAT.IS_Embryo2_sc.12

description: Library name: PBAT.IS_Embryo2_sc.12


title: PBAT.IS_Embryo2_sc.11

description: Library name: PBAT.IS_Embryo2_sc.11


title: PBAT.IS_Embryo2_sc.10

description: Library name: PBAT.IS_Embryo2_sc.10


title: PBAT.IS_Embryo1_sc.8

description: Library name: PBAT.IS_Embryo1_sc.8


title: PBAT.IS_Embryo1_sc.4

description: Library name: PBAT.IS_Embryo1_sc.4


title: PBAT.IS_Embryo2_sc.26

description: Library name: PBAT.IS_Embryo2_sc.26


title: PBAT.IS_Embryo1_sc.5

description: Library name: PBAT.IS_Embryo1_sc.5


title: PBAT.IS_Embryo1_sc.2

description: Library name: PBAT.IS_Embryo1_sc.2


title: PBAT.IS_Embryo1_sc.3

description: Library name: PBAT.IS_Embryo1_sc.3


title: PBAT.IS_Embryo1_sc.1

description: Library name: PBAT.IS_Embryo1_sc.1


title: PBAT.IS_Embryo2_sc.22

description: Library name: PBAT.IS_Embryo2_sc.22


title: PBAT.IS_Embryo2_sc.16

description: Library name: PBAT.IS_Embryo2_sc.16


title: TEC_rep1

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

institute: INSERM _ Université de Nantes

description: Library name: TEC_1

data_processing:
Read pairs were processed as follows: only read 1 sequences with all 16 bases having a quality score ≥ 10 and exact matches to a designed 6-base well-specific barcode were retained. Read 2 sequences were aligned to human RefSeq mRNA sequences (hg19) using BWA version 0.7.17. Reads mapping to transcripts from different genes or containing more than three mismatches were excluded. DGE profiles were generated by counting, for each sample, the number of unique UMIs associated with each RefSeq gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with gene counts for each sample

source_name: Thymus

extract_protocol:
Total RNA was extracted using RLT buffer and the RNeasy Micro Kit (Qiagen) from differentiatimg iPSc harvested at days 0, 1, 2, 3, 7, 9, 10, 14, 15, 17, 22 of the differentiation protocol, and primary TECs.
For 3′ Digital Gene Expression (DGE) bulk RNA sequencing, library preparation was performed according to the authors’ implementation of a previously published protocol (Kilens et al., Nat. Commun. 2018). A total of 10 ng of total RNA was used as input. Polyadenylated transcripts were tagged using adapters specific to poly(A) tails, well-specific barcodes, and unique molecular identifiers (UMIs) during template-switching reverse transcription. cDNAs were pooled and PCR-amplified using the Advantage 2 PCR Enzyme System (Clontech, 639206), then tagmented using the Nextera DNA kit (FC-121-1031) to enrich 3′ ends. Purification and size selection were performed using the Zymo purification kit (D4004-1-L), QIAquick Gel Extraction Kit, and Agencourt AMPure XP magnetic beads. Sequencing was carried out on an Illumina NovaSeq 6000 platform.

value: Thymus

value: primary TEC

value: WT


title: iPSc_to_TEP_J14_rep1

description: Library name: J14_1

source_name: iPSc-to-TEP

value: iPSc-to-TEP

value: LON71 iPSc

value: iPSc-derived

tag: timepoint

value: day 14


title: iPSc_to_TEP_J14_rep2

description: Library name: J14_2


title: iPSc_to_TEP_J22_rep1

description: Library name: J22_1

value: day 22


title: iPSc_to_TEP_J15_rep1

description: Library name: J15_1

value: day 15


title: iPSc_to_TEP_J10_rep4

description: Library name: J10_4

value: day 10


title: iPSc_to_TEP_J10_rep3

description: Library name: J10_3


title: iPSc_to_TEP_J10_rep2

description: Library name: J10_2


title: SUBJECT20 [Block_2_FOV_15]

data_processing: Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. After removing low quality cells and unexpressed features, 104,504 cells and 984 features remained. The rescaled log2-transformed counts per million (logCPM) of the data is provided as inputs for cell type annotation. InSituType was used to identify cell types from a reference dataset (Habermann, A. C. et al. Science Advances 2020) while incorporating additional data types through building “cohorts” based on spatial information.  Following anchor identification, “cohorts” were established using cell area, cell aspect ratio, and mean intensity of morphology markers.  Semi-supervised clustering allowing for 2-6 novel clusters yielded cell annotations.  Novel clusters were evaluated manually and grouped into identified cell populations based on their gene expression profile.

source_name: lung tissue FFPE

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

value: IPF

value: GT


title: iPSc_to_TEP_J10_rep1

description: Library name: J10_1


title: iPSc_to_TEP_J9_rep6

description: Library name: J9_6

value: day 9


title: iPSc_to_TEP_J9_rep4

description: Library name: J9_4


title: PBAT.IS_Embryo1_sc.6

description: Library name: PBAT.IS_Embryo1_sc.6


title: iPSc_to_TEP_J9_rep5

description: Library name: J9_5


title: PBAT.IS_Embryo1_sc.7

description: Library name: PBAT.IS_Embryo1_sc.7


title: iPSc_to_TEP_J9_rep3

description: Library name: J9_3


title: TEC_rep4

description: Library name: TEC_4


title: iPSc_to_TEP_J7_rep3

description: Library name: J7_3

value: day 7


title: iPSc_to_TEP_J9_rep1

description: Library name: J9_1


title: TEC_rep3

description: Library name: TEC_3


title: iPSc_to_TEP_J7_rep4

description: Library name: J7_4


title: iPSc_to_TEP_J7_rep2

description: Library name: J7_2


title: TEC_rep2

description: Library name: TEC_2


title: iPSc_to_TEP_J9_rep2

description: Library name: J9_2


title: iPSc_to_TEP_J7_rep5

description: Library name: J7_5


title: iPSc_to_TEP_J17_rep1

description: Library name: J17_1

value: day 17


title: SUBJECT26 [Block_2_FOV_3]

value: Control

value: GG


title: iPSc_to_TEP_J7_rep1

description: Library name: J7_1


title: iPSc_to_TEP_J3_rep4

description: Library name: J3_4

value: day 3


title: iPSc_to_TEP_J2_rep1

description: Library name: J2_1

value: day 2


title: iPSc_to_TEP_J1_rep1

description: Library name: J1_1

value: WT

value: day 1


title: iPSc_rep3

description: Library name: J0_3

source_name: iPSc

value: iPSc

value: LON71 iPSc

value: day 0


title: iPSc_to_TEP_J3_rep2

description: Library name: J3_2

value: iPSc-to-TEP

value: iPSc-derived


title: iPSc_rep1

description: Library name: J0_1


title: Donor 3, IL9

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

description:
Library name: Sample 9
10X Genomics

data_processing:
Barcode correction, GEM selection, QC, removal of cancer cells, and normalization for the processed data.
Assembly: GRCh38 2022 with our CAR sequence inserted
Supplementary files format and content: RDS

source_name: t cells

extract_protocol:
RNA extraction was done per manufacturers instructions 10x Genomics Library Preparation kit (10X Genomics)
cDNA synthesis and amplification, library preparation and indexing were performed using the 10x Genomics Library Preparation kit (10x Genomics), according to manufacturer’s instructions. Overall library size was determined using the Agilent TapeStation 4200 with the High Sensitivity DNA 5000 ScreenTape (Agilent, Santa Clara, CA) and libraries were quantitated using KAPA real-time PCR (Roche, Wilmington, MA)

value: t cells

tag: patient


title: Donor 2, Day 0

description:
Library name: Sample 4
10X Genomics

value: Day 0


title: Donor 2, IL9

description:
Library name: Sample 6
10X Genomics


title: Donor 3, Day 0

description:
Library name: Sample 7
10X Genomics


title: Donor 1, Mock

description:
Library name: Sample 2
10X Genomics

value: Mock


title: Donor 3, Mock

description:
Library name: Sample 8
10X Genomics


title: Donor 1, IL9

description:
Library name: Sample 3
10X Genomics


title: Donor 2, Mock

description:
Library name: Sample 5
10X Genomics


title: Donor 1, Day 0

description:
Library name: Sample 1
10X Genomics


title: iPSc_to_TEP with DOE[3PPE to TEP]22

description: Library name: 34_22

source_name: Thymic Epithelium Progenitor (TEP)

extract_protocol:
Total RNA was extracted using RLT Lysis buffer and RNAeasy mini kit (Qiagen) from cells harvested at day 7 (AFE stage), day 11 (3PPE stage), and day 13 (TEP stage) of the differentiation protocol. RNA extraction was performed prior to transcriptomic analyses.
For 3′ Digital Gene Expression (DGE) bulk RNA sequencing, library preparation was performed according to the authors’ implementation of a previously published protocol (Kilens et al., Nat. Commun. 2018). A total of 10 ng of total RNA was used as input. Polyadenylated transcripts were tagged using adapters specific to poly(A) tails, well-specific barcodes, and unique molecular identifiers (UMIs) during template-switching reverse transcription. cDNAs were pooled and PCR-amplified using the Advantage 2 PCR Enzyme System (Clontech, 639206), then tagmented using the Nextera DNA kit (FC-121-1031) to enrich 3′ ends. Purification and size selection were performed using the Zymo purification kit (D4004-1-L), QIAquick Gel Extraction Kit, and Agencourt AMPure XP magnetic beads. Sequencing was carried out on an Illumina NovaSeq 6000 platform.

value: Thymic Epithelium Progenitor (TEP)

value: Retinoic Acid_J5:0.0075uM

value: Retinoic Acid_J7:0.1uM

value: Retinoic Acid_J9:0.1uM


title: iPSc_to_TEP with DOE[3PPE to TEP]24

description: Library name: 34_24


title: iPSc_to_TEP with DOE[3PPE to TEP]20

description: Library name: 34_20


title: iPSc_to_TEP with DOE[3PPE to TEP]21

description: Library name: 34_21


title: iPSc_to_TEP with DOE[3PPE to TEP]19

description: Library name: 34_19


title: iPSc_to_TEP with DOE[3PPE to TEP]23

description: Library name: 34_23


title: iPSc_to_TEP with DOE[3PPE to TEP]16

description: Library name: 34_16


title: iPSc_to_TEP_J3_rep1

description: Library name: J3_1


title: iPSc_to_TEP with DOE[3PPE to TEP]14

description: Library name: 34_14


title: iPSc_to_TEP with DOE[3PPE to TEP]17

description: Library name: 34_17


title: iPSc_to_TEP with DOE[3PPE to TEP]13

description: Library name: 34_13


title: iPSc_rep2

description: Library name: J0_2


title: iPSc_to_TEP_J3_rep3

description: Library name: J3_3


title: iPSc_to_TEP with DOE[3PPE to TEP]15

description: Library name: 34_15


title: iPSc_to_TEP with DOE[3PPE to TEP]12

description: Library name: 34_12


title: iPSc_to_TEP with DOE[3PPE to TEP]8

description: Library name: 34_8


title: iPSc_to_TEP with DOE[3PPE to TEP]9

description: Library name: 34_9


title: iPSc_to_TEP with DOE[3PPE to TEP]11

description: Library name: 34_11


title: iPSc_to_TEP with DOE[3PPE to TEP]10

description: Library name: 34_10


title: iPSc_to_TEP with DOE[3PPE to TEP]6

description: Library name: 34_6


title: iPSc_to_TEP with DOE[3PPE to TEP]3

description: Library name: 34_3


title: iPSc_to_TEP with DOE[3PPE to TEP]2

description: Library name: 34_2


title: iPSc_to_TEP with DOE[3PPE to TEP]4

description: Library name: 34_4


title: iPSc_to_TEP with DOE[3PPE to TEP]5

description: Library name: 34_5


title: iPSc_to_TEP with DOE[3PPE to TEP]18

description: Library name: 34_18


title: iPSc_to_TEP with DOE[3PPE to TEP]1

description: Library name: 34_1


title: iPSc_to_AFE with DOE[DE to AFE]34

description: Library name: 28_34

source_name: Anterior Foregut Endoderm (AFE)

value: Anterior Foregut Endoderm (AFE)

value: Retinoic Acid_J5:0.75uM


title: iPSc_to_AFE with DOE[DE to AFE]33

description: Library name: 28_33


title: iPSc_to_AFE with DOE[DE to AFE]35

description: Library name: 28_35


title: diabetic patients with MASH, patient 13

city: Wuhan

first: Wenxi

last: He

address: No.1095, Jiefang Ave.

department: Department of Pharmacy

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: MASH_13

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.1 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
Assembly: miRBase 22.1
Supplementary files format and content: excel,expression profiles

source_name: Serum exosome

extract_protocol:
Serum was collected from all 10 subjects and stored at -80°C.  Exosomes were isolated from plasma samples using a commercial kit according to the manufacturer's instructions.
Load 1 µl ofthe resuspended construct on an Agilent Technologies 2100 Bioanalyzer  using a DNA specific chip such as the DNA-1000 or High Sensitivity DNA chip.  Samples prepared without ethanol precipitation should be run on a High Sensitivity  DNAchip due to their low concentration.

value: Serum exosome

tag: subject status

value: diabetic patients with MASH

tag: subject id

value: patient 13


title: diabetic patients with MASH, patient 12

description: Library name: MASH_12

value: patient 12


title: iPSc_to_AFE with DOE[DE to AFE]36

description: Library name: 28_36

value: LON71 iPSc

value: WT


title: iPSc_to_AFE with DOE[DE to AFE]31

description: Library name: 28_31


title: diabetic patients with MASH, patient 11

description: Library name: MASH_11

value: patient 11


title: diabetic patients without MASH, patient 16

description: Library name: DIA_16

value: diabetic patients without MASH

value: patient 16


title: iPSc_to_AFE with DOE[DE to AFE]32

description: Library name: 28_32

value: iPSc-derived


title: iPSc_to_AFE with DOE[DE to AFE]30

description: Library name: 28_30


title: iPSc_to_AFE with DOE[DE to AFE]28

description: Library name: 28_28


title: diabetic patients without MASH, patient 14

description: Library name: DIA_14

value: patient 14


title: diabetic patients with MASH, patient 7

description: Library name: MASH_7

value: patient 7


title: iPSc_to_TEP with DOE[3PPE to TEP]7

description: Library name: 34_7

value: Thymic Epithelium Progenitor (TEP)

value: Retinoic Acid_J5:0.0075uM


title: HCC827_METTL3i_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

description: Gene expression twelve days after shRNA lentivirus infection.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HCC827, METTL3 knocked down cell, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS

extract_protocol: Total RNA was extracted with RNAiso Plus (TAKARA Bio, Japan) according to the manufacturer's instructions.

value: Cancer cell


title: iPSc_to_AFE with DOE[DE to AFE]27

description: Library name: 28_27

value: Anterior Foregut Endoderm (AFE)


title: HCC827_METTL3i_rep1

source_name: HCC827, METTL3 knocked down cell, replicate 1


title: HCC827_nonTi_rep2

source_name: HCC827, non-targeting control cell, replicate 2


title: HCC827_nonTi_rep1

source_name: HCC827, non-targeting control cell, replicate 1


title: iPSc_to_AFE with DOE[DE to AFE]26

description: Library name: 28_26

value: Retinoic Acid_J5:0.75uM


title: diabetic patients without MASH, patient 6

description: Library name: DIA_6

value: Serum exosome

value: patient 6


title: iPSc_to_AFE with DOE[DE to AFE]25

description: Library name: 28_25


title: diabetic patients without MASH, patient 4

description: Library name: DIA_4

value: patient 4


title: iPSc_to_AFE with DOE[DE to AFE]24

description: Library name: 28_24


title: diabetic patients without MASH, patient 2

description: Library name: DIA_2

value: patient 2


title: mRNA_Melanoma_rep111

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Read count extraction and calculation of TPM and FPKM were performed by RSEM 1.3.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM, FPKM and expected count values for each Sample

source_name: Melanoma

extract_protocol:
RNA was extracted from FF tumour specimens using RNeasy Micro Kit (Qiagen).
mRNA libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

value: Melanoma

tag: age

value: UNKNOWN

tag: Sex


title: iPSc_to_AFE with DOE[DE to AFE]23

description: Library name: 28_23

value: LON71 iPSc

value: WT


title: mRNA_Melanoma_rep110

value: male


title: diabetic patients with MASH, patient 1

description: Library name: MASH_1

value: diabetic patients with MASH

value: patient 1


title: iPSc_to_AFE with DOE[DE to AFE]29

description: Library name: 28_29

value: iPSc-derived


title: mRNA_Melanoma_rep109


title: iPSc_to_AFE with DOE[DE to AFE]22

description: Library name: 28_22


title: iPSc_to_AFE with DOE[DE to AFE]21

description: Library name: 28_21


title: mRNA_Melanoma_rep108

value: female


title: mRNA_Melanoma_rep107


title: mRNA_Melanoma_rep106


title: iPSc_to_AFE with DOE[DE to AFE]18

description: Library name: 28_18

value: Retinoic Acid_J5:0.0075uM


title: mRNA_Melanoma_rep104


title: mRNA_Melanoma_rep103


title: iPSc_to_AFE with DOE[DE to AFE]20

description: Library name: 28_20


title: iPSc_to_AFE with DOE[DE to AFE]16

description: Library name: 28_16


title: iPSc_to_AFE with DOE[DE to AFE]19

description: Library name: 28_19


title: iPSc_to_AFE with DOE[DE to AFE]15

description: Library name: 28_15


title: iPSc_to_AFE with DOE[DE to AFE]13

description: Library name: 28_13


title: mRNA_Melanoma_rep100


title: mRNA_Melanoma_rep102


title: mRNA_Melanoma_rep98


title: iPSc_to_AFE with DOE[DE to AFE]12

description: Library name: 28_12


title: iPSc_to_AFE with DOE[DE to AFE]14

description: Library name: 28_14


title: iPSc_to_AFE with DOE[DE to AFE]11

description: Library name: 28_11


title: iPSc_to_AFE with DOE[DE to AFE]10

description: Library name: 28_10


title: mRNA_Melanoma_rep97


title: mRNA_Melanoma_rep96


title: mRNA_Melanoma_rep95


title: iPSc_to_AFE with DOE[DE to AFE]9

description: Library name: 28_9


title: iPSc_to_AFE with DOE[DE to AFE]8

description: Library name: 28_8


title: iPSc_to_AFE with DOE[DE to AFE]7

description: Library name: 28_7


title: mRNA_Melanoma_rep105


title: mRNA_Melanoma_rep94


title: iPSc_to_AFE with DOE[DE to AFE]5

description: Library name: 28_5


title: mRNA_Melanoma_rep92


title: mRNA_Melanoma_rep93


title: mRNA_Melanoma_rep91


title: iPSc_to_AFE with DOE[DE to AFE]4

description: Library name: 28_4


title: iPSc_to_AFE with DOE[DE to AFE]17

description: Library name: 28_17


title: iPSc_to_AFE with DOE[DE to AFE]6

description: Library name: 28_6


title: iPSc_to_AFE with DOE[DE to AFE]3

description: Library name: 28_3


title: mRNA_Melanoma_rep99


title: mRNA_Melanoma_rep89


title: mRNA_Melanoma_rep90


title: iPSc_to_AFE with DOE[DE to AFE]2

description: Library name: 28_2


title: mRNA_Melanoma_rep101


title: mRNA_Melanoma_rep88


title: iPSc_to_3PPE with DOE[AFE to 3PPE]36

description: Library name: 27_36

source_name: 3rd Pharyngeal Pouch Endoderm (3PPE)

value: 3rd Pharyngeal Pouch Endoderm (3PPE)

value: Retinoic Acid_J7:0.07uM


title: mRNA_Melanoma_rep85


title: mRNA_Melanoma_rep86


title: iPSc_to_3PPE with DOE[AFE to 3PPE]34

description: Library name: 27_34


title: iPSc_to_AFE with DOE[DE to AFE]1

description: Library name: 28_1

value: Anterior Foregut Endoderm (AFE)

value: Retinoic Acid_J5:0.75uM


title: mRNA_Melanoma_rep87


title: iPSc_to_3PPE with DOE[AFE to 3PPE]33

description: Library name: 27_33


title: mRNA_Melanoma_rep84


title: iPSc_to_3PPE with DOE[AFE to 3PPE]32

description: Library name: 27_32


title: mRNA_Melanoma_rep83


title: iPSc_to_3PPE with DOE[AFE to 3PPE]31

description: Library name: 27_31


title: mRNA_Melanoma_rep81


title: mRNA_Melanoma_rep82


title: iPSc_to_3PPE with DOE[AFE to 3PPE]30

description: Library name: 27_30


title: mRNA_Melanoma_rep80


title: iPSc_to_3PPE with DOE[AFE to 3PPE]29

description: Library name: 27_29


title: iPSc_to_3PPE with DOE[AFE to 3PPE]28

description: Library name: 27_28


title: iPSc_to_3PPE with DOE[AFE to 3PPE]27

description: Library name: 27_27


title: iPSc_to_3PPE with DOE[AFE to 3PPE]26

description: Library name: 27_26


title: mRNA_Melanoma_rep78


title: iPSc_to_3PPE with DOE[AFE to 3PPE]25

description: Library name: 27_25


title: iPSc_to_3PPE with DOE[AFE to 3PPE]35

description: Library name: 27_35


title: mRNA_Melanoma_rep77


title: mRNA_Melanoma_rep75


title: iPSc_to_3PPE with DOE[AFE to 3PPE]24

description: Library name: 27_24


title: mRNA_Melanoma_rep74


title: iPSc_to_3PPE with DOE[AFE to 3PPE]23

description: Library name: 27_23


title: iPSc_to_3PPE with DOE[AFE to 3PPE]22

description: Library name: 27_22


title: mRNA_Melanoma_rep73


title: mRNA_Melanoma_rep72


title: iPSc_to_3PPE with DOE[AFE to 3PPE]20

description: Library name: 27_20


title: mRNA_Melanoma_rep71


title: mRNA_Melanoma_rep79


title: iPSc_to_3PPE with DOE[AFE to 3PPE]19

description: Library name: 27_19


title: mRNA_Melanoma_rep70


title: iPSc_to_3PPE with DOE[AFE to 3PPE]18

description: Library name: 27_18


title: Human HIC bladder, biol rep 10

city: Chengdu

first: Lede

last: Lin

state: Sichuan

address: No.37 Guoxue Lane, Wuhou District, Chengdu, Sichuan, P. R. China

institute: West China Hospital of Sichuan University

description: Library name: HIC_10

data_processing:
The FASTQ files were aligned to the human GRCh38 reference genome using the Cell Ranger toolkit from 10X Genomics. Following this, the scRNA-seq data underwent quality control (QC) analysis using the Seurat package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bladder

extract_protocol:
The procedure initiated with the fastidious creation of a single-cell suspension, succeeded by a rigorous assessment of its viability. It was ascertained that the cells exhibited a remarkable degree of activity, surpassing the 85% threshold, and were distinguished by their excellent uniformity and minimal impurities. To augment the efficiency of isolating individual cells, the cell concentration was carefully fine-tuned to an exact range of 700 to 1200 cells per microliter.
During the construction of the single-cell RNA sequencing (scRNA-seq) library, each cell, along with its associated cellular enzymes, was attached to a gel bead. This assembly was subsequently encapsulated within an oil droplet, forming a single-cell gel bead-in-emulsion (GEM). Each gel bead was uniquely labeled with a distinct barcode, incorporated a unique molecular identifier (UMI) sequence, and was equipped with a poly-dT primer sequence designed to initiate reverse transcription. The GEM droplets were then collected in Eppendorf tubes, where cell membranes were lysed using specifically designed recovery reagents, releasing the mRNA. The liberated mRNA interacted with the enzymes, dNTP substrates, and the poly-dT primer sequence within the droplets. Under precisely controlled conditions in a polymerase chain reaction (PCR) apparatus, reverse transcription was initiated, resulting in the synthesis of complementary DNA (cDNA). In the final step, the cDNA underwent PCR amplification, thereby completing the construction of the scRNA-seq library.

value: Bladder


title: mRNA_Melanoma_rep76


title: Human HIC bladder, biol rep 9

description: Library name: HIC_9


title: iPSc_to_3PPE with DOE[AFE to 3PPE]16

description: Library name: 27_16


title: iPSc_to_3PPE with DOE[AFE to 3PPE]17

description: Library name: 27_17


title: mRNA_Melanoma_rep69


title: mRNA_Melanoma_rep67


title: Human HIC bladder, biol rep 8

description: Library name: HIC_8


title: iPSc_to_3PPE with DOE[AFE to 3PPE]15

description: Library name: 27_15


title: iPSc_to_3PPE with DOE[AFE to 3PPE]12

description: Library name: 27_12


title: mRNA_Melanoma_rep68


title: iPSc_to_3PPE with DOE[AFE to 3PPE]10

description: Library name: 27_10


title: Human HIC bladder, biol rep 7

description: Library name: HIC_7


title: iPSc_to_3PPE with DOE[AFE to 3PPE]13

description: Library name: 27_13


title: iPSc_to_3PPE with DOE[AFE to 3PPE]21

description: Library name: 27_21


title: iPSc_to_3PPE with DOE[AFE to 3PPE]11

description: Library name: 27_11


title: mRNA_Melanoma_rep65


title: Human HIC bladder, biol rep 5

description: Library name: HIC_5


title: iPSc_to_3PPE with DOE[AFE to 3PPE]14

description: Library name: 27_14


title: Human HIC bladder, biol rep 4

description: Library name: HIC_4


title: iPSc_to_3PPE with DOE[AFE to 3PPE]8

description: Library name: 27_8


title: mRNA_Melanoma_rep64


title: iPSc_to_3PPE with DOE[AFE to 3PPE]9

description: Library name: 27_9


title: Human HIC bladder, biol rep 3

description: Library name: HIC_3


title: iPSc_to_3PPE with DOE[AFE to 3PPE]3

description: Library name: 27_3


title: iPSc_to_3PPE with DOE[AFE to 3PPE]5

description: Library name: 27_5


title: iPSc_to_3PPE with DOE[AFE to 3PPE]6

description: Library name: 27_6


title: iPSc_to_3PPE with DOE[AFE to 3PPE]4

description: Library name: 27_4


title: iPSc_to_3PPE with DOE[AFE to 3PPE]2

description: Library name: 27_2


title: mRNA_Melanoma_rep62


title: Human HIC bladder, biol rep 2

description:
Library name: HIC_2
R2 file was corrupt


title: mRNA_Melanoma_rep63


title: mRNA_Melanoma_rep66


title: H460 cells, CDDP-resistant-3

city: tianjin

first: meixi

last: wang

address: Tianjin Sports Institute North Road Huanhu West Road

institute: Tianjin Medical University Cancer Hospital

description: Library name: H460-CDDP-3

data_processing:
Differential expression analysis was performed using DESeq2, and an adjusted p-value threshold of 0.05 was applied to filter differentially expressed genes
Assembly: hg38
Supplementary files format and content: For RNA-seq, an XLS file includes raw counts for each sample.

source_name: Lung

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol reagent kit according to the manufacturer’s protocol.
For RNA-seq, mRNA was enriched with magnetic beads containing Oligo (dT). Subsequently, a fragmentation buffer was added to break the mRNA into short fragments. Using mRNA as a template, a single strand of cDNA was synthesized using six base random primers. Then, buffer, dNTPs, and DNA polymerase I and RNase H were added to synthesize a double stranded cDNA. The double stranded cDNA was purified using AMPure XP beads. The purified double stranded cDNA is first subjected to end repair, followed by adding an A-tail and connecting to a sequencing adapter, followed by AMPure XP beads for fragment size selection. Finally, PCR amplification was performed and the PCR product was purified using AMPure XP beads to obtain the final sequencing library.

value: Lung

value: large cell lung cancer cells

value: CDDP


title: Human HIC bladder, biol rep 1

description: Library name: HIC_1


title: mRNA_Melanoma_rep61

value: Melanoma


title: Human HIC bladder, biol rep 6

description: Library name: HIC_6


title: iPSc_to_3PPE with DOE[AFE to 3PPE]7

description: Library name: 27_7

value: LON71 iPSc


title: mRNA_Melanoma_rep60


title: H460 cells, CDDP-resistant-2

description: Library name: H460-CDDP-2


title: H460 cells, CDDP-resistant-1

description: Library name: H460-CDDP-1


title: iPSc_to_3PPE with DOE[AFE to 3PPE]1

description: Library name: 27_1

value: WT


title: mRNA_Melanoma_rep59

value: male


title: Human control bladder, biol rep 7

description: Library name: Control_7


title: H460 cells, WT-3

description: Library name: H460-WT-3


title: H460 cells, WT-2

description: Library name: H460-WT-2


title: Human control bladder, biol rep 6

description: Library name: Control_6


title: mRNA_Melanoma_rep58


title: Human control bladder, biol rep 5

description: Library name: Control_5


title: Human control bladder, biol rep 4

description: Library name: Control_4


title: H460 cells, WT-1

description: Library name: H460-WT-1


title: HTO multiplex TotalSeqB (3HTO)

description:
Library name: Orga3D_late_D28_HTO
10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the cellranger v6.1.2 software. HTO2 (sample: Orga3D_late_D28_2) was considered and used for scSplit SNP analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files and feature_README.txt

molecule: protein

source_name: thymic organoid

extract_protocol:
Cells were detached by soft mechanical dissociation from hTOs seeded with primary early thymic progenitors (ETPs) at late phase of maturation (D28)
Three cell samples were incubated with TotalSeq‐B antibodies (HTO1,2,3) prior to droplet generation on the Chromium Instrument (10x Genomics). cDNA synthesis was conducted to simultaneously capture both mRNA (GEX) and HTO sequences. A targeted PCR amplification of the HTO-derived cDNA was then performed to generate a discrete HTO library, which was pooled with the GEX library for subsequent Illumina sequencing.The GEX library was prepared with Chromium Single-Cell 3′ Reagent v2 Kit (10× Genomics) as per the manufacturer’s protocol. Illumina adapters were incorporated during library preparation.

value: thymic organoid

value: hematopoietic cells


title: Rem-3

city: Hefei

first: Chenyang

address: 443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: sample7

data_processing:
Raw reads were processed using fastp v0.18.0 to remove adapter-containing reads, reads with >10% unknown bases (N), and reads with >50% low-quality bases (Q ≤ 20).
Clean reads were aligned to an rRNA database using Bowtie2 v2.2.8. Reads mapping to rRNA were removed.
Remaining reads were aligned to the reference genome using HISAT2 v2.1.0 with default parameters.
Aligned reads were assembled using StringTie v1.3.1, and gene expression levels (FPKM and TPM) were quantified using RSEM.
Assembly: mm10
Supplementary files format and content: Processed data files include gene-level and transcript-level expression matrices generated by RSEM, reported as  TPM values. Differential expression result tables include log2 fold change, p-value, and FDR values generated by DESeq2 or edgeR.

source_name: Liver

extract_protocol:
Total RNA was extracted from samples using standard procedures. mRNA was enriched with Oligo(dT) beads (mRNA Capture Beads), followed by bead-based purification. The enriched mRNA was fragmented at high temperature and used as the template for first-strand cDNA synthesis using a reverse transcription enzyme mix.
After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the MGI DNBSEQ-T7 or Illumina Novaseq X Plus.

value: Liver


title: Rem-4

description: Library name: sample8


title: mRNA_Melanoma_rep56

value: female


title: Rem-2

description: Library name: sample6


title: mRNA_Melanoma_rep57


title: Human control bladder, biol rep 3

description: Library name: Control_3


title: Detaching hematopoietic cell fraction from hTOs at D28

description:
Library name: Orga3D_late_D28_GEX
10x Genomics


title: Rem-1

description: Library name: sample5