title: Hacat cell, RR3

description: Library name: R-R3


title: RNA12

status: Public on Feb 07 2026

type: SRA

city: Hefei

first: Shuanghu

last: Yuan

address: No. 17 Lujiang Road

department: Department of Radiation Oncology,

country: China

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Tumor tissue

tag: disease

value: esophageal squamous cell carcinoma


title: NMIBC_888_URO_RNA_64

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: Library name: 888_URO_RNA_64

data_processing:
Reference genome indexing and read mapping of samples were performed using STAR software (ver. 2.6.1a).
FeatureCounsts (ver. 1.6.2) was used to calculate genereated binary alignment map (BAM) files.
The read counts per million fragments mapped (CPM) of each samples were used to estimate the expression level of each gene.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

molecule: total RNA

source_name: Male

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80°C. RNA quality and integrity were assessed using the RNA Integrity Number (RIN) and the DV200 metric, which were determined with an RNA 6000 Nano Kit and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The sequencing library was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were ligated to the cDNA, and the fragments were amplified by polymerase chain reaction (PCR). Paired-end sequencing reads (2 x 100 bp) were obtained using the Novaseq platform (Illumina, San Diego, CA).

value: Male

tag: cell line

tag: cell type

tag: grade

value: high

value: No

tag: eortc-recur score


title: NMIBC_888_URO_RNA_65

description: Library name: 888_URO_RNA_65

source_name: Female

value: Female


title: NMIBC_888_URO_RNA_60

description: Library name: 888_URO_RNA_60


title: Hacat cell, Rplam3

city: SHENZHEN

first: JIANGMING

last: ZHONG

address: Shennan rd 9996, 518000, Shenzhen, Guangdong, P.R. China.

institute: Shenzhen Hujia Technology Co., Ltd.

description: Library name: RP3

data_processing:
The raw image data of the sequencing results were subjected to Base Calling using the software Bcl2fastq (v2.20.0.422), and preliminary quality analysis (during the sequencing process, Illumina's built-in software decides whether to retain or discard the read based on the quality of the first 25 bases of each sequencing segment, i.e., the read). Pass Filter Data, the result is stored in FASTQ file format, which contains the sequencing sequence information (line 2 of FASTQ format) and its corresponding sequencing quality information (line 4 of FASTQ format).
Filtering of low quality data using Cutadapt (version 1.9.1) to remove contamination and splice sequences.
The filtered sequencing Clean Data was compared and analyzed with the reference genome, and the selection of the appropriate reference genome is crucial to the success of the project information analysis, and the data comparison rate can reflect to a certain extent the similarity relationship between the experimentally sequenced samples and the selected reference genome.
Hisat2 (v2.2.1) software was used for the comparison of short reads with default parameters.
alternative splicing analysis of RNA-Seq data using rMATS (4.1.0)，Gene expression was calculated using Htseq software (V 0.6.1), which uses the FPKM (Fragments Per Kilo bases per Million reads) (Mortazavi, 2008) method for calculating gene expressions
Assembly: mm39
Supplementary files format and content: all.fpkm_anno.txt

source_name: Hacat

growth_protocol: Hacat cell were maitained in DMEM supplemented wth 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit (Transgen).2 ug of total RNA was used for the construction of sequencing ibraries.
Library construction using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina kit

value: Hacat

value: Human Keratinocyte cell

tag: genotype

value: WT

tag: treatment

value: UVB(50 mJ/cm2) and Rpalm treated


title: spleen immune cells, Glutoborin

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: Glutoborin
10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: spleen immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

value: spleen immune cells

value: Glutoborin


title: Hacat cell, Rplam2

description: Library name: RP2


title: NMIBC_888_URO_RNA_57

description: Library name: 888_URO_RNA_57


title: NMIBC_888_URO_RNA_6

description: Library name: 888_URO_RNA_6


title: NMIBC_888_URO_RNA_55

description: Library name: 888_URO_RNA_55

value: Ta

value: low

value: Yes


title: S6k2-RK 3

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

country: USA

institute: University of Texas MD Anderson Cancer Center

description: Library name: RK3

data_processing:
fastq files were mapped to mouse genome and the count file for gene expression was generated. DESeq2 was used for analysis of the differentially experssed genes
Assembly: GRCm38/mm10
Supplementary files format and content: excel file

source_name: Pancreas

extract_protocol:
Total RNA was extracted from samples using column-based RNA isolation methods following the manufacturer’s instructions. RNA quantity and integrity were assessed prior to library preparation.
Poly(A)+ mRNA was enriched from total RNA and strand-specific sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol. Libraries were adaptor-ligated, PCR-amplified, and sequenced as paired-end 150 bp reads on an Illumina platform, generating approximately 40 million paired-end reads per sample.

value: Pancreas


title: spleen immune cells, Vehicle

description:
Library name: Vehicle
10x Genomics

value: Vehicle


title: Hacat cell, Rplam1

description: Library name: RP1


title: Hacat cell, ROL3

description: Library name: ROL3

value: UVB(50 mJ/cm2) and ROL treated


title: NMIBC_888_URO_RNA_53

description: Library name: 888_URO_RNA_53


title: S6k2-RK 2

description: Library name: RK2


title: S6k2-RK 1

description: Library name: RK1


title: Hacat cell, ROL1

description: Library name: ROL1


title: NMIBC_888_URO_RNA_44

description: Library name: 888_URO_RNA_44


title: NMIBC_888_URO_RNA_52

description: Library name: 888_URO_RNA_52


title: NMIBC_888_URO_RNA_49

description: Library name: 888_URO_RNA_49


title: NMIBC_888_URO_RNA_48

description: Library name: 888_URO_RNA_48


title: Hacat cell, ROL2

description: Library name: ROL2


title: Snd1-KI 2

description: Library name: KI2


title: NMIBC_888_URO_RNA_5

description: Library name: 888_URO_RNA_5


title: NMIBC_888_URO_RNA_54

description: Library name: 888_URO_RNA_54


title: Snd1-KI 3

description: Library name: KI3


title: Hacat cell, UVB3

description: Library name: UVB3

value: UVB(50 mJ/cm2)


title: NMIBC_888_URO_RNA_46

description: Library name: 888_URO_RNA_46

value: Male


title: NMIBC_888_URO_RNA_43

description: Library name: 888_URO_RNA_43


title: Snd1-KI 1

description: Library name: KI1


title: Hacat cell, UVB1

description: Library name: UVB1


title: NMIBC_888_URO_RNA_41

description: Library name: 888_URO_RNA_41

value: high


title: RNA3

description: Library name: Sample 3

value: Tumor tissue

value: esophageal squamous cell carcinoma


title: Hacat cell, UVB2

description: Library name: UVB2

value: Hacat


title: NMIBC_888_URO_RNA_39

description: Library name: 888_URO_RNA_39

value: No


title: NMIBC_888_URO_RNA_37

description: Library name: 888_URO_RNA_37

value: Female


title: WT 3

description: Library name: WT3


title: NMIBC_888_URO_RNA_38

description: Library name: 888_URO_RNA_38


title: Hacat cell, control 3

description: Library name: Control3

value: Human Keratinocyte cell

value: WT

value: control


title: NMIBC_888_URO_RNA_36

description: Library name: 888_URO_RNA_36


title: Hacat cell, control 2

description: Library name: Control2


title: NMIBC_888_URO_RNA_33

description: Library name: 888_URO_RNA_33


title: NMIBC_888_URO_RNA_32

description: Library name: 888_URO_RNA_32

value: Ta


title: Hacat cell, control 1

description: Library name: Control1


title: NMIBC_888_URO_RNA_30

description: Library name: 888_URO_RNA_30


title: NMIBC_888_URO_RNA_28

description: Library name: 888_URO_RNA_28


title: NMIBC_888_URO_RNA_22

description: Library name: 888_URO_RNA_22

value: low


title: NMIBC_888_URO_RNA_31

description: Library name: 888_URO_RNA_31


title: NMIBC_888_URO_RNA_27

description: Library name: 888_URO_RNA_27


title: AX-9

city: shanghai

first: qian

last: fang

address: No. 3, Pan Shan Road

institute: Changhai Hospital

description: Library name: SAMPLE-9

data_processing:
Hisat2 (version:2.0.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM counts for each sample

source_name: peritoneal lavage fluid

extract_protocol:
RNA was harvested using MJzol Animal RNA Isolation Kit（Majorivd）, and 0.6 μg RNA was used for the construction of sequencing libraries.
RNA library for RNA-sequencing were prepared using Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® )

value: peritoneal lavage fluid

value: primary cells

value: peritoneal lavage cells


title: NMIBC_888_URO_RNA_19

description: Library name: 888_URO_RNA_19


title: NMIBC_888_URO_RNA_18

description: Library name: 888_URO_RNA_18


title: AX-7

description: Library name: SAMPLE-7


title: IPFYu12

city: Bonn

first: Jiangyan

last: Yu

address: Carl-Troll-Str. 31

country: Germany

institute: University of Bonn

data_processing:
Demultiplexed fastq files from sequencer were loaded to a snakemake-based data pre-processing pipeline (v0.31) which was provided by the McCarrol lab . Reads were aligned to human reference genome (Ensembl build 38 release 91). Count matrices generated from the pipeline were imported into R (v4.1.3) for further analyses. Before data integrating cells with low quality (UMIs per cell < 700 or mitochondrial gene percentage > 40% or genes per cell < 500) were removed according to the filtering criteria previously reported in the Seq-Well paper .
Reciprocal PCA based approach wrapped in Seurat package  was used to integrate cells from present study and BALF cells from six healthy individuals generated by Seq-Well pipeline from a recently published study . For dataset from each patient or control individual, normalization and feature genes (top 2,000) determination were performed independently using default settings of NormalizaData and FindVariableFeatures, respectively. Then independent scaling and PCA analysis of each dataset were performed using features that were repeatedly variable across all datasets defined by SelectIntegrationFeatures. After identifying anchors across all datasets using FindIntegrationAnchots by setting reduction as rpca, integration was performed by IntegrateData.  Downstream dimension reduction and clustering analysis were performed on the corrected data stored in the integrated assay. In short, after scaling and PCA analysis of corrected data, first 30 PCs were used to construct a shared nearest-neighbor graph which was loaded for clustering analysis that was performed with resolution of 1 to generate 26 clusters. Two clusters (cluster 1 and 18) featured only by mitochondrial genes were removed from downstream analysis. Doublet cells (cluster 2, 3, 23 and 25) were identified using R package scDblFinder (v1.8.0) and were removed from downstream analysis. The UMAP based dimension reduction was performed to visualize cells and clusters in a low dimension, by using the first 30 PCs. To gain a better overview of macrophage subpopulations, all macrophage clusters were selected for UMAP analysis using RunUMAP with the embedding parameter b as 0.9.
Assembly: Ensembl build 38 release 91
Supplementary files format and content: R seurat object includes raw counts and normalized counts for each cell

source_name: Lung BALF

extract_protocol:
Human BALF samples were obtained from University Hospital of Bonn and Marien Hospital Bonn. All samples were processed within two hours after collection and all steps were performed at 4ºC. The fluid was filtered through a 100 μM cell strainer (Merck) and was centrifuged at 350 g for 7 min. The supernatant was immediately frozen in liquid nitrogen and was later stored in -80 ºC. BALF cell pellets were washed once with flow cytometry staining buffer (FACS buffer, PBS supplemented with 2 mM EDTA and 0.5% fetal calf serum). Erythrocytes were removed using the red blood cells lysis buffer (Biolegend). Cells were washed once and resuspended in FACS buffer for further analysis.
Seq-Well based scRNA-seq was performed as previously reported . The Seq-Well arrays were generated and functionalized in the PRECISE platform for single cell genomics and epigenetics in the Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) according to steps previously described (Bassler et al., Frontiers in Immunology, 2022). After loading 110,000 mRNA capture beads (Chemgenes Corp) to the functionalized array, 20,000 BALF cells were loaded into the array. Once cells were settled into wells, the array was washed five times with cold PBS and was subsequently sealed with hydroxylated polycarbonate membrane (Sterlitech) with a pore size of 10 nm. The sealed array with loaded cells was incubated at 37ºC for 30 min and was later placed in lysis buffer (5 M guanidine thiocyanate, 1 mM EDTA, 0.5% Sarkosyl and 1% β-mercaptoethanol in H2O) for 20 min at room temperature. After cell lysis the array was placed in hybridization buffer (2 M NaCl, 3 mM MgCl2 and 0.5% Tween-20 in PBS) at 4ºC for 40 min. The mRNA capture beads were collected by contrifudging at 2,000 g for 5 min, and was immediately subjected for reverse transcription reaction (Maxima RT buffer, 12% PEG8K, 1 mM dNTPs, 1 U/µL RNAse inhibitor, 2.5 µM template switch oligo (TSO) and 10 U/µL Maxima H-RT enzyme in H2O) for 30 min at room temperature and 90 min at 52ºC with end-over-end rotation. The obtained bead-bound cDNA product was washed once with TE-TW (0.1% Tween-20, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in H2O), once with TE-SDS (0.5% SDS, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in H2O) and twice with TE-TW, and was resuspended in TE-TW solution for following steps. A second-strand synthesis was performed before cDNA amplification and sequencing. First, to remove excess primers the bead-bound cDNA was treated with exonuclease I (Exonuclease buffer and 1 U/µL Exonuclease in H2O) for 50 min at 37ºC. After washing once with TE-SDS and twice with TE-TW, the beads were solvated in 0.1 M NaOH for 5 min at room temperature with end-over-end rotation. Following another sequential wash once with TE-TW and once with TE buffer (1 mM EDTA and 10 mM Tris-HCl pH 8.0 in H2O), beads were subjected for the second-strand synthesis reaction (Maxima RT buffer, 12% PEG8K, 1 mM dNTPs, 2 uM dN-Smart randomer and 1 U/µL Klenow Fragment in H2O) for 1 hour at 37ºC with over-end-over rotation. Next the beads were washed twice with TE-TW and once with TE, and were resuspended in water for following steps. After second-strand synthesis the beads underwent whole transcriptome amplification (WTA) reaction. Briefly, beads were first counted with Fuchs-Rosenthal cytometer (Merck). Parallel PCR reactions were performed to make sure to amplify all beads from the entire array. A portion of 5,000 beads were subjected for each reaction (KAPA HiFi Hotstart readmix and SMART primer in H2O) using cycling conditions: 95°C for 3 min, then 4 cycles of 98°C for 20 seconds, 65°C for 45 seconds, and 72°C for 3 min, followed by 12 cycles of 98°C or 20 seconds, 67°C or 20 second, and 72°C for 3 min, and lastly a final extension of 72°C for 5 min. The PCR products were combined into small pools, with each pool containing 10,000-12,000 beads. Usually an array generated 3 to 4 WTA pools, which were subjected to following purification and sequencing steps in parralel. Next the pooled products underwent two sequential purification steps using AMPure XP beads (Beckman Coulter) with 0.6x and 0.8x volumetric ratio according to the manufacture’s instruction. The quality of purified WTA products was assessed using Tapestation 2200 (Agilent) with high sensitivity D5000 assay, and WTA products were quantified using Qubit 4 Fluorometer (Thermo Fisher Scientific) with high-sensitivity dsDNA assay. Next purified WTA products were subjected for library construction and sequencing. In brief, 200 pg of purified WTA products from each pool were subjected for library construction with custom designed New-P5-SMART-PCR primer using the Nextera XT DNA library preparation kit (Illumina) following the detailed protocol provided by the manufacture. After purification and quantification the sequencing library was diluted to 1.25 nM for sequencer loading. Sequencing was performed in paired-end mode (21 cycles for read 1 using custom designed read 1 primer, 8 cycles for i7 index and 61 cycles for read 2) with Novaseq S2 flow cells (100 cycles) using Novaseq 6000 sequencer (Illumina) in the Life and Brain Center, Bonn.

value: Lung BALF

value: idiopathic pulmonary fibrosis

value: no


title: IPFYu13


title: WT 1

description: Library name: WT1

value: Pancreas


title: NMIBC_888_URO_RNA_29

description: Library name: 888_URO_RNA_29

value: Male


title: AX-10

description: Library name: SAMPLE-10


title: IPFYu10


title: NMIBC_888_URO_RNA_20

description: Library name: 888_URO_RNA_20

value: high


title: AX-6

description: Library name: SAMPLE-6


title: WT 2

description: Library name: WT2


title: NMIBC_888_URO_RNA_1

description: Library name: 888_URO_RNA_1

value: Yes


title: NMIBC_888_URO_RNA_10

description: Library name: 888_URO_RNA_10

value: No


title: IPFYu08


title: NC-5

description: Library name: SAMPLE-5


title: NMIBC_807_URO_RNA_9

description: Library name: 807_URO_RNA_9


title: NMIBC_807_URO_RNA_8

description: Library name: 807_URO_RNA_8


title: IPFYu11


title: NMIBC_888_URO_RNA_15

description: Library name: 888_URO_RNA_15


title: IPFYu07


title: NC-4

description: Library name: SAMPLE-4


title: NMIBC_807_URO_RNA_78

description: Library name: 807_URO_RNA_78


title: NMIBC_807_URO_RNA_76

description: Library name: 807_URO_RNA_76


title: NMIBC_807_URO_RNA_75

description: Library name: 807_URO_RNA_75


title: IPFYu06


title: NC-3

description: Library name: SAMPLE-3


title: NMIBC_807_URO_RNA_72

description: Library name: 807_URO_RNA_72


title: NC-2

description: Library name: SAMPLE-2


title: NMIBC_807_URO_RNA_70

description: Library name: 807_URO_RNA_70

value: CIS


title: IPFYu14


title: NC-1

description: Library name: SAMPLE-1


title: NMIBC_807_URO_RNA_7

description: Library name: 807_URO_RNA_7


title: IPFYu04


title: NMIBC_807_URO_RNA_69

description: Library name: 807_URO_RNA_69


title: AX-8

description: Library name: SAMPLE-8


title: NMIBC_807_URO_RNA_66

description: Library name: 807_URO_RNA_66


title: ControlYu06


title: NMIBC_807_URO_RNA_62

description: Library name: 807_URO_RNA_62


title: NMIBC_807_URO_RNA_58

description: Library name: 807_URO_RNA_58

value: Female


title: IPFYu02


title: NMIBC_807_URO_RNA_63

description: Library name: 807_URO_RNA_63


title: ControlYu04


title: Dox2

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

description:
Library name: sample17
Dox2_FPKM

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Ensembl
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: xls file includes FPKM values for each Sample

source_name: cell

extract_protocol:
Total RNA was isolated using the Freezol Reagent (Invitrogen Life Technologies. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare forhybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: cell

value: MOVAS

value: Smooth Muscle Cell

value: Doxorubicin


title: Dox1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample16
Dox1_FPKM


title: NMIBC_807_URO_RNA_57

description: Library name: 807_URO_RNA_57


title: IPFYu05


title: NMIBC_807_URO_RNA_55

description: Library name: 807_URO_RNA_55


title: D_I3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample15
D_I3_FPKM

value: Isoliensinine


title: ControlYu03

value: control


title: D_I2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample14
D_I2_FPKM


title: NMIBC_807_URO_RNA_5

description: Library name: 807_URO_RNA_5

value: Ta


title: Dox3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample18
Dox3_FPKM


title: ControlYu02

value: Lung BALF


title: NMIBC_807_URO_RNA_43

description: Library name: 807_URO_RNA_43


title: NMIBC_807_URO_RNA_52

description: Library name: 807_URO_RNA_52

value: low


title: NMIBC_807_URO_RNA_4

description: Library name: 807_URO_RNA_4


title: ControlYu01

value: no


title: NMIBC_807_URO_RNA_35

description: Library name: 807_URO_RNA_35


title: D_I1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample13
D_I1_FPKM


title: H2O23

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample12
H2O23_FPKM


title: NMIBC_807_URO_RNA_37

description: Library name: 807_URO_RNA_37


title: DNA methylation from lung adenocarcinoma, patient LU1158

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

department: Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan with standard recommended Illumina settings.

data_processing:
Signal intensities were obtained from GenomeStudio 2011.1 (Illumina), converted to beta values, filtered, and normalized to remove biases between Infinium I and II probes. Non-autosomal beta values were filtered out from the final data matrix. Only CpGs also present in HumanMethylation450 and used in the study were kept.
Beta values (methylated / methylated+unmethylated).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Lung tumor

label_protocol: Standard Illumina labelling protocol.

extract_protocol: The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions.

value: Lung tumor

tag: Sex

tag: tumor stage

value: III

tag: patient age

tag: smoking status

value: Current


title: NMIBC_807_URO_RNA_34

description: Library name: 807_URO_RNA_34

value: Male

value: high


title: NMIBC_807_URO_RNA_31

description: Library name: 807_URO_RNA_31

value: No


title: NMIBC_807_URO_RNA_64

description: Library name: 807_URO_RNA_64


title: H2O22

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample11
H2O22_FPKM


title: NMIBC_807_URO_RNA_30

description: Library name: 807_URO_RNA_30


title: NMIBC_807_URO_RNA_3

description: Library name: 807_URO_RNA_3


title: H2O21

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample10
H2O21_FPKM


title: NMIBC_807_URO_RNA_26

description: Library name: 807_URO_RNA_26


title: DNA methylation from lung adenocarcinoma, patient LU1109


title: NMIBC_807_URO_RNA_24

description: Library name: 807_URO_RNA_24

value: Female

value: Yes


title: NMIBC_807_URO_RNA_27

description: Library name: 807_URO_RNA_27


title: NMIBC_807_URO_RNA_29

description: Library name: 807_URO_RNA_29


title: DNA methylation from lung adenocarcinoma, patient LU1150

value: Former


title: NMIBC_807_URO_RNA_22

description: Library name: 807_URO_RNA_22


title: NMIBC_807_URO_RNA_20

description: Library name: 807_URO_RNA_20


title: DNA methylation from lung adenocarcinoma, patient LU1184

value: II


title: DNA methylation from lung adenocarcinoma, patient LU1126


title: Blank4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample6
Blank4_FPKM

value: cell

value: MOVAS

value: Smooth Muscle Cell


title: NMIBC_807_URO_RNA_23

description: Library name: 807_URO_RNA_23


title: H_I3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample9
H_I3_FPKM

value: Isoliensinine


title: H_I2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample8
H_I2_FPKM


title: H_I1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample7
H_I1_FPKM


title: NMIBC_807_URO_RNA_21

description: Library name: 807_URO_RNA_21


title: DNA methylation from lung adenocarcinoma, patient LU1143


title: DNA methylation from lung adenocarcinoma, patient LU12

value: I


title: NMIBC_807_URO_RNA_16

description: Library name: 807_URO_RNA_16


title: Blank2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample5
Blank2_FPKM


title: NMIBC_807_URO_RNA_2

description: Library name: 807_URO_RNA_2


title: NMIBC_807_URO_RNA_15

description: Library name: 807_URO_RNA_15


title: DNA methylation from lung adenocarcinoma, patient LU1116


title: NMIBC_807_URO_RNA_14

description: Library name: 807_URO_RNA_14


title: Blank1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample4
Blank1_FPKM


title: DNA methylation from lung adenocarcinoma, patient LU965


title: B_I3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample3
B_I3_FPKM


title: NMIBC_807_URO_RNA_12

description: Library name: 807_URO_RNA_12


title: NMIBC_807_URO_RNA_11

description: Library name: 807_URO_RNA_11


title: NMIBC_807_URO_RNA_17

description: Library name: 807_URO_RNA_17


title: NMIBC_807_URO_RNA_10

description: Library name: 807_URO_RNA_10


title: NMIBC_807_URO_RNA_1

description: Library name: 807_URO_RNA_1


title: DNA methylation from lung adenocarcinoma, patient LU1168


title: DNA methylation from lung adenocarcinoma, patient LU1148


title: DNA methylation from lung adenocarcinoma, patient LU1130


title: NMIBC_P-48

description: Library name: P-48

value: High


title: NMIBC_807_URO_RNA_13

description: Library name: 807_URO_RNA_13


title: NMIBC_P-46

description: Library name: P-46


title: NMIBC_P-42

description: Library name: P-42

value: Ta

value: Low


title: B_I2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample2
B_I2_FPKM


title: NMIBC_P-52

description: Library name: P-52


title: DNA methylation from lung adenocarcinoma, patient LU1077

value: Lung tumor


title: P1_Rep1

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: 2507709_PAN_bATAC_Crx_GFP_P1_Rep1
ATAC-seq

library_source: genomic

data_processing:
Mouse ATAC-seq fastq files were aligned to the mouse genome using BWA and processed using the standardized PEPATAC ATAC-seq analysis.
Assembly: mm10
Supplementary files format and content: MACS2 peak calls (BED10)

source_name: pineal

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. Briefly, 50,000 dissociated cells from normal pineal gland or pineal tumor tissue were washed in cold 1× PBS and pelleted by centrifugation. Cell pellets were lysed in ice-cold lysis buffer containing Tris-HCl, NaCl, MgCl₂, NP-40, Tween-20, and digitonin, followed by incubation on ice. Nuclei were washed in resuspension buffer and pelleted prior to transposition. DNA was purified after transposition using the Qiagen MinElute Reaction Cleanup Kit according to the manufacturer’s instructions.
Purified nuclei were subjected to transposition using Tn5 transposase at 37 °C for 30 minutes with agitation. Transposed DNA fragments were PCR-amplified using Nextera i5 common and i7 indexed adapters. Libraries were size-selected by double-sided magnetic bead purification to remove primer dimers and large fragments (>1,000 bp). Library quality and insert size distribution were assessed using Agilent BioAnalyzer, TapeStation, or Fragment Analyzer systems. Libraries were quantified by PicoGreen dsDNA assay or low-pass sequencing and sequenced as paired-end 100-bp reads on an Illumina NovaSeq 6000.

value: pineal

value: Crx-GFP


title: NMIBC_P-39

description: Library name: P-39


title: NMIBC_P-40

description: Library name: P-40

value: Male


title: P1_Rep2

description:
Library name: 2507710_PAN_bATAC_Crx_GFP_P1_Rep2
ATAC-seq


title: NMIBC_P-38

description: Library name: P-38


title: NMIBC_P-37

description: Library name: P-37


title: NMIBC_P-35

description: Library name: P-35


title: PB49

description:
Library name: 2293013_ATAC-TAS_PB-49
ATAC-seq


title: PB14

description:
Library name: 2293014_ATAC-TAS_14
ATAC-seq


title: NMIBC_P-54

description: Library name: P-54

value: No


title: B_I1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample1
B_I1_FPKM


title: NMIBC_P-28

description: Library name: P-28


title: Gly + Ln, Biol Rep 2

city: Kalamazoo

first: Enish

last: Pathak

state: MI

address: 1903 W Michigan Ave

department: Biological Sciences

institute: Western Michigan University

description:
Library name: Sample 4
S4

data_processing:
For the data analysis, the sequence reads were first trimmed using Trimmomatic v.0.36. The trimmed reads were then mapped to the S. meliloti ERCC reference genome obtained from ENSEMBL using the Bowtie2 aligner v.2.2.6. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Using DESeq2, a comparison of gene expression between the two groups of samples was performed. The Wald test was used to generate p-values and log2-fold changes. Genes with an adjusted p-value <0.05 and absolute log2-fold change >1 were considered as differentially expressed genes for each comparison.
Assembly: S. meliloti ERCC reference genome, GCF_023197145.1
Supplementary files format and content: Excel file containing raw counts for all samples in a single file
Supplementary files format and content: Excel file containing TPM values for all samples in a single file

organism: Sinorhizobium meliloti

source_name: bacterial

growth_protocol: The wild-type strain was grown in a round bottom plastic Erlenmeyer’s flask (Corning, Corning, NY) in 50 ml volume of minimal media containing methanol (0.5%) and glycerol (0.1%) or methanol (0.5%) in the presence of lanthanides (30 μM).

extract_protocol:
Total RNA was extracted when the cells reached mid-log phase (OD600 = 0.4 - 0.9) using Quick-RNA™ Fungal/Bacterial Miniprep (Zymo Research, Irvine, CA) following the manufacturer’s protocol.
Library was prepared by Azenta Life Sciences. Ribosomal RNA was depleted followed by RNA fragmentation, random priming, and cDNA synthesis.

value: bacterial

value: Grown in Gly + Ln


title: MeOH + Ln, Biol Rep 2

description:
Library name: Sample 2
P4

value: Grown in MeOH + Ln


title: PB75

description:
Library name: 2324319_PAN_ATAC_PB75
ATAC-seq


title: Gly + Ln, Biol Rep 1

description:
Library name: Sample 3
S3


title: NMIBC_P-27

description: Library name: P-27

value: Yes


title: NMIBC_P-25

description: Library name: P-25


title: PB63

description:
Library name: 2324321_PAN_ATAC_PB63
ATAC-seq


title: NMIBC_P-24

description: Library name: P-24


title: PB61

description:
Library name: 2324320_PAN_ATAC_PB61
ATAC-seq


title: NMIBC_P-22

description: Library name: P-22


title: NMIBC_P-16

description: Library name: P-16


title: ASO_HELDR_REP2

city: Chicago

first: Shi-yuan

last: Cheng

state: Illinois

address: 303 E. Superior Street, The Robert H. Lurie Cancer Center

institute: Northwestern Univeristy

description: Library name: Sample 8

data_processing:
Data were aligned to the human genome reference hg38 using HISAT2 v2.0.4.
Assembly: hg38
Supplementary files format and content: Count

source_name: GBM

growth_protocol: Cells were cultured in in GSC medium. The GSC medium consists of DMEM/F12 medium (Thermo Fisher Scientific, 11320-033), 2% B27 supplement (Thermo Fisher Scientific, 17504-044), 1X antibiotic-antimycotic (Thermo Fisher Scientific, 15240062), 5 mg/mL heparin (Sigma-Aldrich, 9041-08-1), 20 ng/mL EGF (Peprotech, 100-15R), and 20 ng/mL bFGF (Peprotech, 100-18B).

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini Kit following the manufacturer’s instructions.
We followed the manufacturer’s instructions for preparing the library using the NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609).

value: GBM


title: Ovary_O2

city: Kansas City

first: Anna

middle: M

last: Galligos

state: KS

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: Library name: L46152

data_processing:
Raw reads were demultiplexed into Fastq format using cellranger mkfastq. Alignment, filtering, barcode counting, and UMI counting was done using Cell Ranger’s count pipeline.
Assembly: mm10
Supplementary files format and content: individual TSV files of barcodes, features, and matrices for each sample

source_name: ovary

extract_protocol:
Ovarian tissue was dissociated using the mouse and rat adult brain dissociation kit (130-107-677; Miltenyi Biotec). The single cell suspension was then loaded on a Chromium Single Cell Controller (10X Genomics; CA).
cDNA libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Chip G single Cell Kit (#1000120; 10X Genomics), the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (#1000121; 10X Genomics), the Chromium i7 Multiplex Kit (#120262; 10X Genomics) and the SPRIselect Reagent (#B23318, Beckman Coutler, Indianapolis, IN) with 12 cycles of PCR amplification to yield 150-500ng of input cDNA according to the manufacturer’s instructions. Quality control was completed via the Qubit Fluorometer and the Agilent 2100 HS Bioanalyzer. Libraries were pooled in groups at equal molar concentration and sequenced on a NovaSeq S1 flowcell on the Illumina NovaSeq 6000 instrument RTA v3.4.4, recipe v1.7.0 or v1.7.5 using v1.5 chemistry with the following paired read lengths: 28 bp Read 1, 8 bp I7 Index and 91 bp Read 2. With 12,000 to 16,000 cells per sample, libraries were sequenced to a depth necessary to achieve 53,000 to 82,000 mean reads per cell - around 900 million to 1 billion reads each -1456-2508 median genes per cells.

value: ovary


title: NMIBC_P-10

description: Library name: P-10


title: ASO_CTRL_REP2

description: Library name: Sample 6


title: NMIBC_P-11

description: Library name: P-11


title: NMIBC_P-09

description: Library name: P-09


title: Ovary_O1

description: Library name: L46151


title: NMIBC_P-03

description: Library name: P-03


title: NMIBC_P-07

description: Library name: P-07


title: Ovary_Y1

description: Library name: L44349


title: NMIBC_P-02

description: Library name: P-02


title: NMIBC_N-64

description: Library name: N-64


title: MeOH + Ln, Biol Rep 1

description:
Library name: Sample 1
P3


title: sh1_HELDR_REP2

description: Library name: Sample 4


title: NMIBC_N-60

description: Library name: N-60

value: Female


title: sh1_HELDR_REP1

description: Library name: Sample 3


title: Ovary_Y2

description: Library name: L44350


title: ASO_HELDR_REP1

description: Library name: Sample 7


title: NMIBC_N-63

description: Library name: N-63


title: Crx Rb p53_Rep22

data_processing:
RNA-seq reads had adapters trimmed using bbduk and were aligned using STAR to the mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: comma-separated files representing FPKM and count values

source_name: Pineal tumor

extract_protocol:
RNA was extracted from mice tissue using the AllPrep RNA Micro Kit for Illumina RNA-seq, following manufacturer’s instructions.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions

value: Pineal tumor

value: Crx Rb p53

value: E15 induction


title: sh1CTRL_HELDR_REP2

description: Library name: Sample 2


title: NMIBC_N-55

description: Library name: N-55

value: Ta


title: NMIBC_N-54

description: Library name: N-54

value: High


title: NMIBC_N-53

description: Library name: N-53


title: Crx Rb p53_Rep23

value: unknown


title: GSC17-KAT7-KD-B

description: Library name: Sample 4

value: KAT7 KD


title: NMIBC_N-39

description: Library name: N-39


title: ASO_CTRL_REP1

description: Library name: Sample 5


title: NMIBC_N-41

description: Library name: N-41


title: GSC17-KAT7-KD-A

description: Library name: Sample 3


title: NMIBC_N-50

description: Library name: N-50


title: NMIBC_N-31

description: Library name: N-31


title: Crx Rb p53_Rep21


title: Crx Rb p53_Rep18

value: P20 induction


title: Crx Rb p53_Rep19


title: sh1CTRL_HELDR_REP1

description: Library name: Sample 1


title: Crx Rb p53_Rep17


title: GSC17-Control-B

description: Library name: Sample 2

value: control


title: NMIBC_N-36

description: Library name: N-36

value: No


title: NMIBC_N-21

description: Library name: N-21

value: Male

value: Low


title: NMIBC_N-25

description: Library name: N-25


title: sh2_HELDR_REP1

description: Library name: Sample 3

value: HELDR KD


title: NMIBC_N-17

description: Library name: N-17

value: Yes


title: NMIBC_N-20

description: Library name: N-20


title: Crx Rb p53_Rep20


title: Crx Rb p53_Rep15


title: Crx Rb p53_Rep16


title: NMIBC_N-49

description: Library name: N-49


title: sh2_HELDR_REP2

description: Library name: Sample 4

value: GBM


title: NMIBC_N-15

description: Library name: N-15


title: GSC17-Control-A

description: Library name: Sample 1


title: sh2CTRL_HELDR_REP2

description: Library name: Sample 2


title: NMIBC_N-22

description: Library name: N-22


title: NMIBC_N-19

description: Library name: N-19


title: Crx Rb p53_Rep14

value: P1 induction


title: NMIBC_N-14

description: Library name: N-14

value: Female


title: NMIBC_N-13

description: Library name: N-13


title: NMIBC_N-11

description: Library name: N-11


title: Crx Rb p53_Rep13

value: Pineal tumor


title: sh2CTRL_HELDR_REP1

description: Library name: Sample 1


title: NMIBC_N-08

description: Library name: N-08


title: Crx Rb p53_Rep12

value: Crx Rb p53


title: Roots_SULF_1

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description: Library name: R24

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The final transcriptome was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 3 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Assembly: Pinaster_CO2_final_a.fasta
Supplementary files format and content: Tab-delimited text files include CPM normalized counts for each sample S1, S2, S3, S4, S5, S6, C7, C8, C9, C10, C11, C12, N13, N14, N15, N16, N17, N18, R19, R20, R21, R22, R23, R24).The column id is the sequence identifier.

organism: Pinus pinaster

source_name: Roots

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 23 °C and watered twice a week with distilled water until the start of treatment.

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209-214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK).
The RNA-seq was carried out by Novogen. After the QC procedures, mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The 24 samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: One month after germination, the seedlings were watered for three months with 0.3 mM KNO3 once a week to induce sulfur deficiency. The pine seedlings were then divided into two groups. The first control group (C) was watered with 1 mM KCl, while the second experimental group (S) was watered with 0.5 mM K2SO4. Twenty-four hours after watering, samples were taken from four organs: needles, cotyledons, stems, and roots. Each of these was immediately frozen in liquid nitrogen. Three biological replicates were obtained by grouping samples from 13-14 seedlings.

value: Roots

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: Four-months-old

value: 0.5 mM K2SO4

tag: biological replicate


title: Roots_SULF_2

description: Library name: R22


title: Roots_CONT_1

description: Library name: R23

value: 1 mM KCl


title: GSC11

description: Library name: Sample 1


title: Roots_CONT_2

description: Library name: R20


title: Crx Rb p53_Rep11

value: P10 induction


title: Roots_SULF_3

description: Library name: R21


title: GSC1478_Even

description: Library name: Sample 17

data_processing:
We aligned the pre-processed reads using Bowtie2 v2.5.1 with the --very-sensitive parameter against the GENCODE human release 45.Peaks were called for each replicate individually using MACS v3.0.1 with parameters --qvalue 0.05 --broad --broad-cutoff 0.05.
Assembly: hg38
Supplementary files format and content: bed
Library strategy: ChIRP-seq

extract_protocol:
Genomic DNA was isolated using a ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205) following the manufacturer’s instructions.
The library preparation was performed using the KAPA HyperPrep Kit (Roche, 07962347001) and xGen UDI-UMI adapters (IDT, 10006914) following the manufacturer’s instructions.


title: Need_SULF_2

description: Library name: N17

source_name: Needles

value: Needles


title: Need_CONT_1

description: Library name: N16


title: Need_CONT_2

description: Library name: N18


title: Antisense_Odd

description: Library name: Sample 15

value: Antisense


title: GSC34

description: Library name: Sample 2


title: Crx Rb p53_Rep8

value: E15 induction


title: Crx Rb p53_Rep10


title: Crx Rb p53_Rep9


title: Need_SULF_1

description: Library name: N15


title: Crx Rb p53_Rep6


title: GSC1478_Input

description: Library name: Sample 16


title: Need_SULF_3

description: Library name: N14


title: Cot_SULF_3

description: Library name: C12

source_name: Cotyledons

value: Cotyledons


title: Antisense_Even

description: Library name: Sample 14


title: GBM6

description: Library name: Sample 1

data_processing:
ONT reads were base-called and demultiplexed using Guppy. The sequencing data was analyzed using Porechop and FLAIR according to the tools' standard workflows.
Assembly: hg38
Supplementary files format and content: bed

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini Kit following the manufacturer’s instructions.
Long-reads RNA-seq; The SQK-DCS109 kit (ONT) was used to prepare the library according to the manufacturer's instructions.


title: Roots_CONT_3

description: Library name: R19


title: Cot_SULF_1

description: Library name: C11


title: Need_CONT_3

description: Library name: N13


title: GSC1478_Odd

description: Library name: Sample 18


title: Crx Rb p53_Rep7


title: Crx Rb p53_Rep1

value: Crx MycT


title: Cot_SULF_2

description: Library name: C10


title: Antisense_Input

description: Library name: Sample 13


title: RNAse_Odd

description: Library name: Sample 12

value: RNAse


title: Cot_CONT_2

description: Library name: C9


title: Young_3

description:
Library name: L46344
Index-sequence: CGTACTAG

data_processing:
Syrah35 was downloaded from GitHub (https://github.com/0x644BE25/Syrah) (version 480d2da, which was private at the time, used with “vs2” bead oligo version and maxLinkDist=5). After running Syrah, DigitalExpression from the dropseq (2.3.0) pipeline was used to generate digital expression matrices from the Syrah bam files (arguments MIN_NUM_TRANSCRIPTS_PER_CELL=10 and READ_MQ=10).
Assembly: mm10
Supplementary files format and content: individual TSV files of barcodes, features, and matrices for each sample
Library strategy: Spatial Transcriptomics

extract_protocol:
Ovaries were washed in cold PBS and individually submerged in optimal cutting temperature compoud (OCT). Tissues were moved to a cryo-mold with fresh OCT and oriented for sagittal tissue sectioning. Tissue blocks were then flash frozen at -70°C. After freezing, tissue blocks were acclimated to -13°C in a Cryostat NX70 (Thermo Fisher Scientific) for 30 minutes prior to sectioning. Tissue blocks were then mounted on a cutting block with OCT and sectioned at a 5° cutting angle with 10-μm section thickness. Regions of interest (multiple oocytes on the same plain) were identified prior to tissue capture. Four histological cryo-sections sections from 2 female mice for each age cohort were individually placed on the slide-seq puck slides. Pucks with adhered tissue were then removed from the cryostat and placed into a 1.5-ml Eppendorf tube containing 200 µL hybridization buffer (6X SSC, 2 unit/µL Lucigen RNase inhibitor) for 30 minutes at room temperature to facilitate the binding of mRNA to the spatially barcoded beads of the puck.
First strand cDNA synthesis was performed in RT solution (115 µL water, 40 µL 5X Maxima RT buffer, 20 µL 10 mM dNTPs, 5 µL RNase Inhibitor, 10 µL 50 uM Template Switch Oligo, 10 µL Maxima H-RTase) for 30 minutes at room temperature, followed by 1.5 hours at 52°C. After reverse transcription, the tissue was removed by adding 200 µL 2X Tissue Digestion Buffer (100 mM Tris pH 8.0, 200 mM NaCl, 2% SDS, 5 mM EDTA, 32 unit/µL Proteinase K) and incubating at 37°C for 30 minutes. Following this incubation, 200 µL wash buffer (10 mM Tris pH 8.0, 1mM EDTA, 0.01% Tween-20) was then added and the mixture pipetted to remove the beads from the coverslip. A series of 3 washes was performed on the beads using 200 µL wash buffer for the first two washes and 200 µL 10mM Tris-HCl (pH 8.0) for the last wash, pelleting for 3 minutes at 3000 RCF, removing the supernatant, and resuspending beads. Samples were then treated with exonuclease I solution (170 µL water, 20 µL ExoI buffer, 10 µL ExoI) for 50 minutes at 37°C. A series of 2 washes was performed on the beads using 200 µL wash buffer and pelleting for 3 minutes at 3000 RCF, removing the supernatant and resuspending. Samples were then resuspended in 0.1N NaOH and incubated for 5 minutes at room temperature followed by a series of 2 washes in 200 µL wash buffer. The beads were resuspended in 200 µL TE, pelleted, the supernatant removed, resuspended in Second Strand Mix (133 µL water, 40 µL 5X Maxima RT buffer, 20 µL 10 mM dNTPs, 2 µL 1mM dN-SMRT oligo, 5 µL Klenow Enzyme) and incubated for 1 hour at 37°C. The beads were washed 3 times with 200 µL wash buffer, resuspended with 200 µL water, and then pelleted for 3 minutes at 3000 RCF. The final resuspension of the tissue digestion was in 200 uL of 10mM Tris-HCl (pH 8.0). The final resuspension prior to Second Strand Synthesis was in TE.  The 200 uL cDNA PCR master mix consisted of  88µL H2O, 100uL Terra PCR Direct Buffer, 4uL Terra Polymerase (Takara, 639270), 4 µL 100 uM Truseq PCR handle primer, and 4 µL 100 µM SMART PCR primer. The final cDNA purification was eluted in 20µL of H2O. Subsequent library preparation was performed using the Nextera XT kit (Illumina, FC-131-1096), starting with 600pg of cDNA using a specific P5-Truseq PCR hybrid oligo in place of the Nextera XT i5 adapter, according to manufacturer’s instructions. The PCR product was purified twice with 0.6X AMPure XP beads (Beckman Coulter, A63881), resuspended in 20 µL water, and checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Thermo Fisher Scientific). Libraries were pooled and sequenced as 42-bp pair-end reads on four Illumina NextSeq 500 flow cells on the NextSeq 500 instrument using NextSeq Control Software 2.2.0.4 with the following paired read length: 42 bp Read1, 8 bp i7 Index and 42 bp Read2. Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.4.11 and cellranger mkfastq (4.0.0) were run to demultiplex reads for all libraries and generate FASTQ files. Alignment, filtering, barcode, and unique molecular identifier (UMI) counts were done using cellranger count (4.0.0). The barcode-gene matrices were filtered with >=10 unique molecular identifier (UMI) counts using the unique barcode list. Each puck received approximately 400,000 to 500,000 spatial beads, corresponding to 175 genes per bead.

value: ovary


title: islets, Isl1CKO,6

city: Vestec

first: Valéria

last: Fabríciová

address: Průmyslová 595

country: Czech Republic

institute: Institute of biotechnology CAS

data_processing:
Fastq_screen v0.11.1 was used for quality control of sequenced reads. STARsolo (STAR version 2.7.3a) alignment tool was used for mapping sequences to the reference genome GRCm38 (GENCODE version M8 annotation) . Empty droplets were filtered out using R package DropletUtils(version 4.1.1), with set threshold of 100 UMIs and FDR <= 0.001, which lead to final number of 1316 control cells and 1025 mutant cells. Seurat (4.3.0.1) package was used for further data analysis. Data were SCTransfromed (package sctransform 0.3.5) and integrated (excluding mitochondrial and ribosomal genes with prefix mt- or Rps/Rpl). SoupX (1.6.2) package was used to remove background from ambient RNA. To identify potential clusters enriched with doublets we used DoubletFinder package.
Assembly: GRCm38.p6
Supplementary files format and content: bardcodes.tsv: list of cell barcodes
Supplementary files format and content: genes.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format

source_name: islets of Langerhans, tdTomato+ cells

extract_protocol:
P9 mice were sacrificed, and pancreas was perfused by Collagenase I (1mg/ml) with Actinomycin D (25µg/ml) and dissected. Tissue was enzymatically digested with 1mg/ml collagenase and incubated at 37°C for 10-12mins. Digested tissue was washed with 1% FBS in Hank's salt solution 3x. Dissociation of the tissue with 0,05% trypsin/0.53 mM EDTA supplemented with Actinomycin D (25 µg/ ml) at 37°C for 5 mins helped further release endocrine cells. FACS buffer (2% FBS and 10 mM EGTA in PBS) was used to stop digestion and to wash cells 1x. Cell suspension was filtered using 40µm nylon mesh and  tdTomato+ cells were sorted on  FACSAria™ Fusion flow cytometer.
According to manufacturer protocol, sorted single cell suspension was loaded to Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10 × Genomics, Pleasanton, CA) to prepare cDNA libraries. Individual cells were encapsulated into droplets with barcoded gel beads, unique molecular identifiers, and poly(dT) sequences. Reversely transcribed cDNA was amplified (1-14 cycles), fragmented and ligated to sequencing adaptors. Purification of cDNA and size selection of fragment was done with SPRISelect magnetic beads. Libraries were pair-end sequenced Illumina NovaSeq 6000 SP Reagent Kit.

value: islets of Langerhans, tdTomato+ cells

value: Neurod1 Cre/+; Isl1f/f


title: Crx Rb p53_Rep5

value: Pineal tumor


title: Old_1

description:
Library name: L46338
Index-sequence: CGGAGCCT


title: MALAT1_Odd

description: Library name: Sample 9

value: GBM


title: Cot_CONT_3

description: Library name: C7


title: Crx Rb p53_Rep2


title: WtE13.5MDM#3

description: Library name: SAMPLE 24

data_processing:
Fastq files from the sequencing output are converted to DCC file. NanoString GeoMx® Digital RNA Spatial Profiling is then utilized for data analysis
Assembly: GRCm38.p6
Supplementary files format and content: DCC

source_name: embryonic day E13.5 Mullerian duct

extract_protocol:
Wild-type and Wnt7a null female embryos were collected at E13.5 and E14.5. Three biological replicates for each timepoint were obtained, for a total of 12 biological samples. Tissue samples were fixed in 4% PFA overnight at 4oC, embedded in paraffin, sectioned at 5 um, and a section from each sample was placed on a single Fisherbrand ColorFrost Plus microscope slide in an area that was 35.3 mm by 14.1 mm. The slide was sent to NanoString Technologies, Inc. (Seattle, WA).
NanoString GeoMx® Digital RNA Spatial Profiling hybridize to mRNA with DNA probes that are conjugated to unique photo-cleavable oligonucleotides barcodes by controlled ultraviolet illumination. The released barcode oligonucleotides are subject to the sequencing

value: embryonic day E13.5 Mullerian duct

value: Wild Type


title: islets, control, 6

value: Neurod1 Cre/+; Isl1f/+


title: MALAT1_Even

description: Library name: Sample 8


title: Cot_CONT_1

description: Library name: C8

value: Segura-Alcaraz

value: Four-months-old


title: Stem_CONT_3

description: Library name: S6

source_name: Stem

value: Stem

value: 1 mM KCl


title: RNAse_Input

description: Library name: Sample 10


title: Crx MycT_P1_PB_Rep6

value: P10 induction


title: Crx MycT_P1_PB_Rep5


title: Crx MycT_P1_PB_Rep4


title: RNAse_Even

description: Library name: Sample 11


title: WtE13.5MDE#3

description: Library name: SAMPLE 23


title: Stem_SULF_2

description: Library name: S5

value: 0.5 mM K2SO4


title: Crx MycT_P1_PB_Rep3


title: NEAT1_Odd

description: Library name: Sample 6


title: WtE13.5MDE#2

description: Library name: SAMPLE 21


title: MALAT1_Input

description: Library name: Sample 7


title: WtE13.5MDM#2

description: Library name: SAMPLE 22


title: Crx MycT_P1_PB_Rep2


title: NEAT1_Even

description: Library name: Sample 5


title: WtE13.5MDM#1

description: Library name: SAMPLE 20


title: Stem_CONT_1

description: Library name: S4


title: Crx MycT_P1_PB_Rep1


title: Stem_SULF_1

description: Library name: S3


title: Crx GFP_P21_Rep2

source_name: Pineal gland

value: Pineal gland

value: Crx GFP

value: P21 dissection


title: Stem_CONT_2

description: Library name: S2


title: WtE13.5MDE#1

description: Library name: SAMPLE 19


title: Wnt7anullE13.5MDM#3

description: Library name: SAMPLE 18


title: Stem_SULF_3

description: Library name: S1


title: HELDR_KD_Even

description: Library name: Sample 2

data_processing:
We aligned the pre-processed reads using Bowtie2 v2.5.1 with the --very-sensitive parameter against the GENCODE human release 45.Peaks were called for each replicate individually using MACS v3.0.1 with parameters --qvalue 0.05 --broad --broad-cutoff 0.05.
For HELDR_KD* samples, differential binding analysis was conducted using the DiffBind R package, in which BAM files were imported and even/odd probe sets were !Sample_data_processing = Assembly: hg38
Supplementary files format and content: HELDR_KD_coverage.csv
Library strategy: ChIRP-seq


title: Wnt7anullE13.5MDE#3

description: Library name: SAMPLE 17


title: Crx GFP_P21_Rep1


title: HELDR_KD_Input

description: Library name: Sample 1

data_processing:
We aligned the pre-processed reads using Bowtie2 v2.5.1 with the --very-sensitive parameter against the GENCODE human release 45.Peaks were called for each replicate individually using MACS v3.0.1 with parameters --qvalue 0.05 --broad --broad-cutoff 0.05.
For HELDR_KD* samples, differential binding analysis was conducted using the DiffBind R package, in which BAM files were imported and even/odd probe sets were treated as biological replicates.
Assembly: hg38
Supplementary files format and content: HELDR_KD_coverage.csv
Library strategy: ChIRP-seq


title: Wnt7anullE13.5MDM#2

description: Library name: SAMPLE 16


title: ASK_78_41422

description: PB GEM model

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data processing involved reading IDAT files using the minfi (v1.44) and sesame (v1.61) packages, with normalization steps including quality masking, inferring Infinium I channel, dye bias correction, and PooBah adjustment to generate beta values for methylation levels

label: Cy5 and Cy3

source_name: tumor,mouse

label_protocol: Standard Illumina Protocol

growth_protocol: Crx-CreERT2 (RBRC05559) strain developed by Dr. Takahisa Furukawa (Osaka Bioscience Institute) provided by the RIKEN BRC through the National BioResource Project of the MEXT/AMED, Japan. These Cre positive males were bred to transgenic mice (Rb1fl/fl, RRID:IMSR_JAX:008186; Trp53fl/fl, Jax stock RRID:IMSR_JAX:008462; MycT58aLSL/LSL, from Dr. Rob Wechsler-Reya1; Dgcr8fl/fl, from Rockefeller (RRID:MMRRC_032051-JAX);  Droshafl/fl RRID:IMSR_JAX:008592;  Dicerfl/fl, RRID:IMSR_JAX:012284) over many generations until homozygosity was achieved with transgenic alleles on the heterozygous Cre line. When induced with Tamoxifen, these Cre recombinase-expressing alleles resulted in either non-functioning or over-expression of genes of interest in CRX expressing cells. Mice that were Rb1fl/fl;Trp53fl/fl;Crx-Cre+/-, Dgcr8fl/fl;Trp53fl/fl;Crx-Cre+/-, Droshafl/fl;Trp53fl/fl;Crx-Cre+/-, or Dicer fl/fl;Trp53fl/fl;Crx-Cre+/- were induced at embryonic day 15 by oral gavage of pregnant female. Embryonic gestation as determined by timed pregnancies with plug date as embryonic day 0. Tamoxifen stock was 20mg/mL/g body weight.  Rb1fl/fl;Trp53fl/fl;Crx-Cre+/- mice were induced at E15, P0, P10, P21, P30, or P60 to assess induction window. Pups that were MycT58aLSL/LSL;Crx-Cre+/- were induced at P10 by intraperitoneal injections. Tamoxifen stock for P10 pups was 10mg/mL given as a dose of 7.5uL/g body weight. Crx-GFP (PMID: 19882727) were obtained from the Jackson Laboratory (RRID:IMSR_JAX:007066).

extract_protocol: Genomic DNA from mouse pineal tumors was profiled on the Infinium Mouse Methylation BeadChip, respectively, based on the manufacturer’s instructions.

treatment_protocol: Mice were monitored for signs of tumor growth with biweekly MRI imaging. Mice were observed daily and euthanized at the onset of signs of sickness including lethargy and neurological abnormalities.


title: Crx GFP_P1_Rep2

value: P1 dissection


title: NEAT1_Input

description: Library name: Sample 4


title: Crx GFP_E15_Rep3

value: E15 dissection


title: ASK_3_40322

description: PB GEM model


title: Crx GFP_E15_Rep2


title: HELDR_Odd

description: Library name: Sample 3

data_processing:
We aligned the pre-processed reads using Bowtie2 v2.5.1 with the --very-sensitive parameter against the GENCODE human release 45.
Assembly: hg38
Supplementary files format and content: bw


title: Crx GFP_P1_Rep1


title: Wnt7anullE13.5MDE#2

description: Library name: SAMPLE 15


title: HELDR_Even

description: Library name: Sample 2


title: ASK_76_41422

description: PB GEM model


title: Wnt7anullE13.5MDM#1

description: Library name: SAMPLE 14


title: ASK_5_40322

description: PB GEM model


title: Wnt7anullE13.5MDE#1

description: Library name: SAMPLE 13


title: ASK_14_22822

description: PB GEM model


title: HELDR_KD_Odd

description: Library name: Sample 3

data_processing:
We aligned the pre-processed reads using Bowtie2 v2.5.1 with the --very-sensitive parameter against the GENCODE human release 45.Peaks were called for each replicate individually using MACS v3.0.1 with parameters --qvalue 0.05 --broad --broad-cutoff 0.05.
For HELDR_KD* samples, differential binding analysis was conducted using the DiffBind R package, in which BAM files were imported and even/odd probe sets were !Sample_data_processing = Assembly: hg38
Supplementary files format and content: LDR_KD_coverage.csv
Library strategy: ChIRP-seq


title: Rt88_high nitrogen_acetate_88h_biol rep 3

city: Urbana

first: Christopher

middle: V.

last: Rao

state: IL

address: 600 S Mathews Ave

department: Chemical and Biomolecular Engineering

institute: University of Illinois

description:
Library name: 36
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

data_processing:
Raw .fastq files were trimmed of their adapters using Trimmomatic (0.39-Java-1.8.0_201) and quality was evaluated with FastQC (v0.11.9) and MultiQC(v1.9). Alignment was performed using STAR (v2.7.10a) using an index built from a reference .gff obtained from Mycocosm. Read counts were calculated using featureCounts from the Subread package (v2.0.4). The raw read counts are under the "processed data file" column.
Assembly: No genome assembly was required
Supplementary files format and content: First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

organism: Rhodotorula toruloides

growth_protocol: Three colonies of Rhodotorula toruloides IFO0880 were seeded in 3 mL of yeast nitrogen base without amino acids with 5 g/L ammonium sulfate and 20 g/L D-glucose buffered at 25 mM phosphates pH = 7. After two days the spent media was removed and each of the three cell pellets (35-45 OD600 of cells) was resuspended in 0.5 mL of MilliQ water. The resulting inoculum was distributed amongst four flasks across the experimental design described below.

extract_protocol:
Beaten with 0.5 mL of glass beads, acid-washed 425-600 um (30-40 U.S. Sieve) in a 1.5 mL RNAse-free tube using Qiagen RNEasy kit on a Tissue-Lyser II at 30 Hz for 60 s three times.  Turbo DNAse treatment for 30 minutes followed by a second RNEasy kit purification step.
RNA-Seq libraries were prepared with the Stranded mRNA library kit (Watchmaker). The libraries were pooled; quantitated by qPCR and sequenced on one 10B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits (Illumina). Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Low-nitrogen control {0.1 g/L ammonium sulfate, no acetate}, high-nitrogen control {5 g/L ammonium sulfate, no acetate}, low-nitrogen acetate treatment {0.1 g/L ammonium sulfate, 2 g/L acetate}, high-nitrogen treatment {5 g/L ammonium sulfate, 2 g/L acetate}

value: high nitrogen_acetate_88h


title: HELDR_Input

description: Library name: Sample 1


title: ASK_67_30822

description: PB GEM model


title: WtE14.5MDM#3

description: Library name: SAMPLE 12

source_name: embryonic day 14.5 Mullerian duct

value: embryonic day 14.5 Mullerian duct


title: Crx GFP_E15_Rep1


title: Rt88_high nitrogen_acetate_88h_biol rep 2

description:
Library name: 35
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: WtE14.5MDM#2

description: Library name: SAMPLE 10


title: Crx Dgcr8 p53_Rep3

value: Pineal tumor

value: Crx Dgcr8 p53

value: E15 induction


title: Crx Dgcr8 p53_Rep4


title: Crx Dgcr8 p53_Rep5


title: ASK_35_40922

description: PB GEM model


title: ASK_22_22822

description: PB GEM model


title: WtE14.5MDE#2

description: Library name: SAMPLE 9

value: Wild Type


title: WtE14.5MDE#3

description: Library name: SAMPLE 11


title: Crx Dgcr8 p53_Rep2


title: Rt88_low nitrogen_acetate_88h_biol rep 3

description:
Library name: 33
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_acetate_88h


title: Rt88_high nitrogen_acetate_88h_biol rep 1

description:
Library name: 34
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_83_031521

description: PB GEM model


title: Rt88_low nitrogen_acetate_88h_biol rep 1

description:
Library name: 31
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Crx Dgcr8 p53_Rep1


title: Rt88_low nitrogen_acetate_88h_biol rep 2

description:
Library name: 32
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: CrxGFP_P21

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger (v6.0.0)
Assembly: mm10
Supplementary files format and content: R data serilazation (RDS) file containg normalized pineal gland atlas

source_name: pineal gland

extract_protocol:
Single cells from developing mouse pineal gland tissue were processed using the microfluidics-based 10x Chromium protocol, according to manufacturer instructions
mouse pineal tissue  were isolated and processed using the 10x Chromium technology

value: pineal gland

tag: time point

value: Crx-GFP

value: single index 10x


title: WtE14.5MDE#1

description: Library name: SAMPLE 7


title: ASK_81_031521

description: PB GEM model


title: ASK_75_090821

description: PB GEM model


title: Rt88_high nitrogen_no acetate_88h_biol rep 3

description:
Library name: 30
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: high nitrogen_no acetate_88h


title: Wnt7anullE14.5MDE#3

description: Library name: SAMPLE 5


title: Rt88_high nitrogen_no acetate_88h_biol rep 1

description:
Library name: 28
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: WtE14.5MDM#1

description: Library name: SAMPLE 8


title: CrxGFP_P01

description: 10x Genomics


title: ASK_65_081721

description: PB GEM model


title: ASK_90_031721

description: PB GEM model


title: Wnt7anullE14.5MDM#3

description: Library name: SAMPLE 6


title: ASK_98_031721

description: PB GEM model


title: CrxGFP_P16

description: 10x Genomics


title: Wnt7anullE14.5MDM#2

description: Library name: SAMPLE 4


title: CrxGFP_E16

description: 10x Genomics


title: Rt88_high nitrogen_no acetate_88h_biol rep 2

description:
Library name: 29
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_63_081721

description: PB GEM model


title: Rt88_low nitrogen_no acetate_88h_biol rep 3

description:
Library name: 27
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_no acetate_88h


title: CrxGFP_E14

description: 10x Genomics


title: Rt88_low nitrogen_no acetate_88h_biol rep 2

description:
Library name: 26
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Wnt7anullE14.5MDM#1

description: Library name: SAMPLE 2


title: CrxGFP_E15_Rep1

description: 10x Genomics


title: ASK_61_100321

description: PB GEM model


title: CrxGFP_E13

description: 10x Genomics


title: Rt88_low nitrogen_no acetate_88h_biol rep 1

description:
Library name: 25
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, newly diagnosed NKTCL, 52

city: Shanghai

first: Xiaozhen

last: Liang

address: Life Science Research Building 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Materia Medica Chinese Academy of Sciences

description: Library name: patient52

data_processing:
Raw scRNA-seq data were initially pre-processed using CellRanger (version 8.0.1, 10x Genomics) to align reads to the human genome (GRCh38, 2024-A from 10x Genomics) and count the unique molecular identifiers (UMIs) for each gene to generate specific gene cell count tables. For each scRNA-seq sample, the count tables were filtered to retain the genes detected in at least 10 cells and cells with a minimum gene count of 300.
Assembly: GRCh38
Supplementary files format and content: barcodes, features, and matrix files for each samples

source_name: blood

extract_protocol:
Isolated PBMCs were loaded into a 10× Chromium Chip (v3.1 PN:1000120) and barcoded using a 10x Chromium Controller.
RNA from the barcoded cells was then reverse-transcribed, amplified, and prepared into sequencing libraries with the 10× Library Construction Kit (v3.1 PN:1000190) according to the manufacturer’s instructions.

value: blood

value: PBMCs

value: Peripheral blood immune cells


title: ASK_89_031721

description: PB GEM model


title: Rt88_high nitrogen_acetate_64h_biol rep 3

description:
Library name: 24
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: high nitrogen_acetate_64h


title: CrxGFP_P10

description: 10x Genomics


title: Wnt7anullE14.5MDE#2

description: Library name: SAMPLE 3


title: ASK_54_080921

description: PB GEM model


title: Wnt7anullE14.5MDE#1

description: Library name: SAMPLE 1


title: ASK_49_081021

description: PB GEM model


title: Rt88_high nitrogen_acetate_64h_biol rep 2

description:
Library name: 23
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: CrxGFP_P05_Rep1

description: 10x Genomics


title: PBMC, newly diagnosed NKTCL, 44

description: Library name: patient44


title: CrxGFP_P05_Rep2

description: 10x Genomics


title: Rt88_high nitrogen_acetate_64h_biol rep 1

description:
Library name: 22
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_31_080221

description: PB GEM model


title: PBMC, newly diagnosed NKTCL, 41

description: Library name: patient41


title: PG-Crx82-31521

description: PB GEM model


title: CrxGFP_E18

description: 10x Genomics


title: PBMC, newly diagnosed NKTCL, 39

description: Library name: patient39


title: CrxGFP_E17

description: 10x Genomics


title: ASK_78_103022

description: PB GEM model

value: Crx-Cre;LSL-Myc


title: PBMC, newly diagnosed NKTCL, 51

description: Library name: patient51


title: Rt88_low nitrogen_acetate_64h_biol rep 1

description:
Library name: 19
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_acetate_64h


title: ASK_70_41522

description: PB GEM model


title: Rt88_high nitrogen_no acetate_64h_biol rep 3

description:
Library name: 18
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: high nitrogen_no acetate_64h


title: PBMC, newly diagnosed NKTCL, 37

description: Library name: patient37


title: Rt88_low nitrogen_acetate_64h_biol rep 3

description:
Library name: 21
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_59_041522

description: PB GEM model


title: CrxGFP_E15_Rep2

description: 10x Genomics


title: Rt88_high nitrogen_no acetate_64h_biol rep 1

description:
Library name: 16
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, newly diagnosed NKTCL, 31

description: Library name: patient31


title: Central memory T cells

first: Zeliang

last: Yang

address: No.38 Xueyuan Road,Haidian

institute: Peking University Health Science Center

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Spleen

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000

value: Spleen

value: CD8+ T cells

value: WT

value: Untreated


title: PBMC, newly diagnosed NKTCL, 36

description: Library name: patient36


title: ASK54_060524

description: PB GEM model


title: PBMC, newly diagnosed NKTCL, 38

description: Library name: patient38


title: Rt88_low nitrogen_no acetate_64h_biol rep 3

description:
Library name: 15
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_no acetate_64h


title: ASK_67_42522

description: PB GEM model


title: Naïve T cells


title: Rt88_low nitrogen_acetate_64h_biol rep 2

description:
Library name: 20
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_68_102422

description: PB GEM model


title: Rt88_high nitrogen_no acetate_64h_biol rep 2

description:
Library name: 17
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, newly diagnosed NKTCL, 30

description: Library name: patient30


title: Effector memory T cells


title: OT-I + TAMo, rep2

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD8+ T cells

treatment_protocol: Cells were cocultured with vehicle, TANs or TAMos and treated with OVA257-264 peptides for forty-eight hours

value: cocultured with TAMos under OVA257-264 stimulation


title: ASK12_050323

description: PB GEM model


title: PBMC, newly diagnosed NKTCL, 27

description: Library name: patient27


title: Rt88_low nitrogen_no acetate_64h_biol rep 1

description:
Library name: 13
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: OT-I + TAN, rep2

value: cocultured with TANs under OVA257-264 stimulation


title: ASK14_041223

description: PB GEM model


title: Rt88_low nitrogen_no acetate_64h_biol rep 2

description:
Library name: 14
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, newly diagnosed NKTCL, 22

description: Library name: patient22


title: OT-I + TAMo, rep1


title: ASK50_040523

description: PB GEM model


title: OT-I + TAN, rep1


title: Rt88_high nitrogen_acetate_48h_biol rep 2

description:
Library name: 11
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: high nitrogen_acetate_48h


title: PBMC, newly diagnosed NKTCL, 20

description: Library name: patient20


title: ASK_97_41223

description: PB GEM model


title: OT-I + Vehicle, rep2

value: cocultured with vehicle under OVA257-264 stimulation


title: Rt88_high nitrogen_acetate_48h_biol rep 1

description:
Library name: 10
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Rt88_high nitrogen_acetate_48h_biol rep 3

description:
Library name: 12
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK94_091222

description: PB GEM model


title: OT-I + Vehicle, rep1


title: ASK_04_41223

description: PB GEM model


title: PBMC, newly diagnosed NKTCL, 19

description: Library name: patient19


title: Rt88_low nitrogen_acetate_48h_biol rep 2

description:
Library name: 08
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_acetate_48h


title: PBMC, newly diagnosed NKTCL, 16

description: Library name: patient16

value: blood


title: ASK93_091222

description: PB GEM model


title: ASK24_020123

description: PB GEM model


title: Rt88_low nitrogen_acetate_48h_biol rep 1

description:
Library name: 07
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, newly diagnosed NKTCL, 25

description: Library name: patient25

value: PBMCs


title: PBMC, newly diagnosed NKTCL, 18

description: Library name: patient18

value: Peripheral blood immune cells


title: PBMC, healthy, 12

description: Library name: HD12


title: Rt88_low nitrogen_acetate_48h_biol rep 3

description:
Library name: 09
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Senp1 CKO 48h-3

first: Cen

last: Jiang

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University

description: Library name: Sample12

data_processing:
Sequencing raw data filtered by Cutadapt（version 1.9.1）was mapped the GRCm39.107 reference genome using Hisat2(v2.2.1). Gene expression was normalized with DESeq2 and indicated by FPKM.
Assembly: GRCm39.107
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: CD8+ T cell

value: Senp1 CKO


title: Senp1 CKO 48h-2

description: Library name: Sample11


title: Senp1 CKO 0h-3

description: Library name: Sample9


title: Rt88_high nitrogen_no acetate_48h_biol rep 3

description:
Library name: 06
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: high nitrogen_no acetate_48h


title: ASK35_020123

description: PB GEM model


title: Senp1 CKO 48h-1

description: Library name: Sample10


title: Rt88_high nitrogen_no acetate_48h_biol rep 2

description:
Library name: 05
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: PBMC, healthy, 10

description: Library name: HD10


title: Senp1 CKO 0h-2

description: Library name: Sample8


title: ASK68_031523

description: PB GEM model


title: Senp1 CKO 0h-1

description: Library name: Sample7


title: PBMC, healthy, 11

description: Library name: HD11


title: PBMC, healthy, 9

description: Library name: HD9


title: ask41_021223

description: PB GEM model


title: ASK67_031523

description: PB GEM model


title: PBMC, healthy, 8

description: Library name: HD8


title: Rt88_low nitrogen_no acetate_48h_biol rep 2

description:
Library name: 02
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million

value: low nitrogen_no acetate_48h


title: Senp1 WT 48h-2

description: Library name: Sample5

value: Spleen

value: Senp1 WT


title: PBMC, healthy, 7

description: Library name: HD7


title: Rt88_high nitrogen_no acetate_48h_biol rep 1

description:
Library name: 04
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Rt88_low nitrogen_no acetate_48h_biol rep 3

description:
Library name: 03
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: ASK_4_60822

description: PB GEM model


title: Senp1 WT 0h-3

description: Library name: Sample3


title: ASK15_013123

description: PB GEM model


title: ASK73_031523

description: PB GEM model


title: PBMC, healthy, 6

description: Library name: HD6


title: PBMC, healthy, 5

description: Library name: HD5


title: Senp1 WT 0h-2

description: Library name: Sample2


title: PBMC, healthy, 4

description: Library name: HD4


title: Diet containing 1% of LB-GREENboost additive

type: RNA

city: Almería

first: Alba

last: Galafat Díaz

state: Almería

address: Carr. Sacramento s/n

institute: University of Almería

description: SAMPLE 3 (GB10)

data_processing:
For each primer pair, linearity (R2 > 0.98) and amplification efficiency (90-110%) were confirmed. Gene expression was quantified by using the ΔΔCT method (Livak and Schmittgen, 2001), normalised by geometric averaging of a couple of reference genes (eef1a and 18S)
Control reactions, consisting of RNase-free water (NTC) and RNA (NRT), were included to confirm the absence of genomic DNA contamination and primer dimers
Matrix normalized worksheet reports normalized signal (against housekeeping genes). Fold Change worksheet reports control ratios.

label: EvaGreen

organism: Sparus aurata

source_name: Proximal intestine

label_protocol: Real-time qPCR amplifications were conducted in duplicates, in 6 μL, containing 3 μL of SsoFast EvaGreen Supermix (Bio-Rad, UK) and 0.25-6.25 ng of total cDNA. Prior to the experiment, optimal primer concentrations (150 nM for 18S; 250 nM for others) and annealing temperatures (58 ºC for 18S; 60 ºC for others) were determined.

extract_protocol: Anterior intestines were processed to extract RNA using the Total RNA Kit I (ENZA, Omega Bio-Tek), incorporating a Dnase tratment with the DNA free Kit (Rnase-Free Dnase I Set, Omea Bio-tek).

value: Proximal intestine


title: Senp1 WT 48h-1

description: Library name: Sample4


title: Rt88_low nitrogen_no acetate_48h_biol rep 1

description:
Library name: 01
First column is the mRNA_xxxx listed as Parent in Rhoto_IFO0880_4.FrozenGeneCatalog.gtf reference file, second column is raw counts per million


title: Diet containing 0.5% of LB-GUThealth additive

description: SAMPLE 4 (GH5)


title: Senp1 WT 48h-3

description: Library name: Sample6


title: Senp1 WT 0h-1

description: Library name: Sample1


title: Diet containing 1% of LB-GUThealth additive

description: SAMPLE 5 (GH10)


title: PBMC, healthy, 3

description: Library name: HD3


title: ASK_1_60822

description: PB GEM model


title: ASK_43_51822

description: PB GEM model


title: ASK_6_60822

description: PB GEM model


title: OT-I + TAMo

data_processing:
Raw data were stored in FASTQ format, including the base sequence and corresponding quality information.
Trimmomatic (v0.36) was used to remove adaptor-polluted or low-quality bases, and reads considered too short (< 36 nt) were filtered out to obtain clean data.
Clean data were then mapped to the reference genome (mm10) by Bowtie2, and visualized by IGV (Integrative Genomics Viewer).
Peaks corresponding to open genomic regions were detected by MACS2, and significantly differential peaks between samples were acquired using MAnorm.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
Approximately 50,000 viable CD8+ T cells sorted from cocultures were used for each library preparation. Cells were lysed in 1 × Lysis Buffer and nuclei were isolated by centrifugation.
A TruePrep™ DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) was used to construct transposase-treated libraries. Qualified libraries were sequenced using an Illumina HiSeq X ten platform in pair-end 150 bp style.

treatment_protocol: Cells were cocultured with vehicle or TAMos and treated with OVA257-264 peptides for forty-eight hours

value: CD8+ T cells

value: WT


title: CT diet

description: SAMPLE 1 (CT)

value: CT diet


title: OT-I + Vehicle


title: ASK_44_51822

description: PB GEM model


title: F-D01

status: Public on Feb 06 2026

city: Kensington

first: Orazio

last: Vittorio

address: High St

department: School of Biomedical Sciences, Faculty of Medicine

country: Australia

institute: UNSW Sydney

description: Library name: F-D01

data_processing:
The tissues were hybridized with the GeoMx Mouse Whole Transcriptome Atlas (~18,000 targets) to generate FASTQ files.
Assembly: mm10
Supplementary files format and content: *.dcc = digital count conversion files
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc = NanoString Probe Kit Configuration file
Library strategy: Spatial Transcriptomics

source_name: conjunctiva

extract_protocol:
Eyes (n=3) were fixed in 4% paraformaldehyde (PFA) overnight. The superior nasal (SN) quadrant was dissected and paraffin-embedded. Sections (5µm) were mounted onto glass slides within a 35.3mm x 14.1mm area, dried at 58°C for 3 hrs.
The tissues were subjected to the GeoMx DSP workflow (Bruker Spatial Biology, San Jose, CA). Prior to selecting ROIs, serial sections were stained with hematoxylin or double immunostained for K8 and K12 to identify tissue boundaries. ROIs included corneal, transitional (containing some limbus and cornea), limbal and bulbar conjunctival epithelia.

value: conjunctiva


title: F-C12

description: Library name: F-C12

source_name: limbus

value: limbus


title: F-C11

description: Library name: F-C11

source_name: transitional

value: transitional


title: F-C07

description: Library name: F-C07


title: F-C09

description: Library name: F-C09


title: PBMC, healthy, 1

description: Library name: HD1


title: F-C10

description: Library name: F-C10

source_name: cornea

value: cornea


title: Diet containing 0.5% of LB-GREENboost additive

description: SAMPLE 2 (GB5)


title: F-C05

description: Library name: F-C05


title: PBMC, healthy, 2

description: Library name: HD2

value: blood


title: F-C04

description: Library name: F-C04


title: F-C06

description: Library name: F-C06


title: F-C08

description: Library name: F-C08


title: F-C03

description: Library name: F-C03


title: F-C02

description: Library name: F-C02


title: F-B12

description: Library name: F-B12


title: F-C01

description: Library name: F-C01


title: F-B10

description: Library name: F-B10


title: F-B11

description: Library name: F-B11


title: F-B08

description: Library name: F-B08


title: F-B06

description: Library name: F-B06


title: F-B04

description: Library name: F-B04


title: F-B05

description: Library name: F-B05


title: F-B02

description: Library name: F-B02


title: F-B01

description: Library name: F-B01


title: F-B09

description: Library name: F-B09


title: F-B07

description: Library name: F-B07


title: F-B03

description: Library name: F-B03


title: F-A10

description: Library name: F-A10


title: F-A11

description: Library name: F-A11


title: F-A07

description: Library name: F-A07


title: F-A09

description: Library name: F-A09


title: F-A05

description: Library name: F-A05


title: F-A06

description: Library name: F-A06


title: F-A12

description: Library name: F-A12


title: F-A08

description: Library name: F-A08


title: Heart, WT-2

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

description: Library name: Sample 5

data_processing:
Raw RNA-seq reads for each sample were originally aligned with TopHat (Version 2.1.1) to the zebrafish genome assembly (Zv9) using the Ensembl annotation Zv9 (Danio_rerio.Zv9.79.gtf) and later with the updated genome assembly GRCz11 (Genome assembly GRCz11). Gene expression was quantified by using Cufflinks (Version 2.2.1). Differential gene expression expressed across different groups was determined based on fold change and a false discovery rate of less than 0.05 according to the Cuffdiff script from Cufflinks.
Assembly: Zv9 (Danio_rerio.Zv9.79.gtf)
Supplementary files format and content: tsv (est_counts, tpm)

organism: Danio rerio

source_name: Heart

extract_protocol:
Total RNA was extracted from dissected ventricular tissue of 6 months old ttnaA fish, which harbors a truncational mutation in exon 201 of ttna and corresponding WT siblings.
Six ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform (Illumina) with a 50-bp paired-end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility.

value: Heart


title: Heart, WT-1

description: Library name: Sample 4


title: Heart, ttna+/-3

description: Library name: Sample 3


title: F-A02

description: Library name: F-A02


title: F-A03

description: Library name: F-A03


title: Heart, ttna+/-1

description: Library name: Sample 1


title: Heart, ttna+/-2

description: Library name: Sample 2


title: Heart, WT-3

description: Library name: Sample 6


title: P3_383

city: Bethesda

first: Lingling

last: Miao

address: 9000 Rockville Pike

department: NIAMS

institute: National Institutes of Health

data_processing:
Sequencing reads were demultiplexed using Bcl2fastq. Adaptors were trimmed and 125bp sequencing reads were trimmed to 100bp using Trimmomatic. Reads were aligned to mouse reference genome Ensembl GRCm38.p6 using STAR 2.5.2b. Expression values for individual genes and transcripts were estimated and quantified with RSEM 1.3.0. Expression values of TPM (transcripts per million) were used for further analysis. 1057 cells passed quality control and were included in this study.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files at gene and transcript expression levels

source_name: skin

extract_protocol:
Neonatal or postnatal epidermal cells and embryonic skin cells were disscociated from Sox2-GFP or Gfi1-GFP reporter mice. Cells were stained with DAPI for viability prior to cell sorting. Single GFP+ live cells were sorted into a 96 well plate preloaded with lysis buffer using Beckman MoFlo Astrios or BD Influx Cell Sorter. Lysis buffer was prepared following Smart-seq2 protocol (Picelli et al., 2014). Single GFP- live cells were sorted from the neonatal epidermal cells as controls.
Single-cell cDNA libraries were prepared following Smart-seq2 protocol (Picelli et al., 2014) with minor modifications. Briefly, single-cell RNA transcripts were reverse-transcribed using SuperScript II Reverse Transcriptase, following by pre-amplification of 21 cycles. cDNA concentration and quality were assessed using PicoGreen dsDNA Assay kit and Agilent bioanalyzer analysis with High sensitivity DNA kit, respectively. Single-cell cDNA libraries with high quality were selected for further processing. The cDNA was diluted and the concentration was normalized. 1152 single-cell cDNA libraries were generated using Illumina Nextera XT library preparation kit and were indexed using Illumina Nextera XT index kit v2.
cDNA libraries for each of the 384 cells was pooled together for sequencing in a way that each pooled library contained cells sourced from all different time points and both reporter mice. A total of three pooled cDNA libraries were prepared. Each pooled library was pair-end sequenced on 4 lanes of Hiseq3000 with 125bp or 100bp read length.

value: Merkel cell

value: skin

tag: strain

tag: age


title: P3_378

value: dermal papilla cell

tag: tissue


title: P3_382

value: hematopoietic cell


title: P3_381


title: F-A04

description: Library name: F-A04


title: P3_379


title: P3_377


title: P3_375


title: P3_371


title: P3_372


title: P3_380


title: P3_368


title: P3_367


title: P3_366


title: P3_365


title: P3_376


title: P3_363


title: P3_364


title: P3_374


title: P3_369


title: P3_360


title: P3_373


title: P3_362


title: P3_357


title: P3_354


title: P3_370


title: P3_355


title: P3_359


title: P3_356


title: P3_358


title: P3_350


title: P3_353


title: P3_349