title: Formalehyde treated, FA3

description:
Library name: Sample 7
Column name in raw reads.txt = FA3


title: HUCCT1-NC

status: Public on Jan 20 2025

type: SRA

city: Wuhan

first: Fei

last: Xiong

state: Hubei

address: Jiefang Road No.1095

country: China

institute: Huazhong University of Science and Technology

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting.
Bowtie2 software was used to compare Clean Reads with the reference genome for analysis; DeepTools' computeMatrix module was used to analyze the Reads distribution in the upstream and downstream 3kb regions of transcription start sites (TSS).
MACS2 software was used to complete Peak detection in genome-wide range, and CHIPseeker software R package was used to analyze and calculate the distribution of Peak in each functional area.
MACS2 software is used to compare the Peaks of different experimental groups in two groups, so as to obtain the Peaks difference between different experimental groups. For a candidate difference peaks region, it is required to be enriched in at least one sample, and its likelihood ratio (log10 Likelihood ratio) is used to determine whether there is a difference.
Assembly: GRCh38
Supplementary files format and content: txt, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Intrahepatic cholangiocarcinoma

growth_protocol: HUCCT1 cells were cultured in RPMI-1640 medium. All cell culture media were supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
CUT & Tag assay was performed with the Hyperactive Universal CUT&Tag Assay Kit (Vazyme). 1×106 TFK-1 cells were harvested and their nuclei were extracted. The extracted nuclei were immobilized with activated concanavalin A‐coated magnetic beads and reacted with anti-Flag antibodies (1:50) in 100 μL DIG buffer overnight at 4℃. After being washed, the bound antibodies were reacted with secondary antibodies (1:50) for 1 h at room temperature and incubated with 100 μl Hyperactive pA/G-Transposon adapter complex (0.04 μM) for 1 h at room temperature. The precipitated immunocomplex was diluted in Trueprep Tagment Buffer L and after proteinase K digestion, the DNA fragments were extracted and stored at -80 ℃.
A DNA library was constructed using the TruePrep Index Kit V2 (Vazyme). The DNA fragments were mixed with N5XX and N7XX and amplified by PCR at 72 ℃ for 3 min, 95 ℃ for 3 min, and subsequent 10 cycles of 98 ℃ for 10 sec and 60 ℃ for 5 sec, 72 ℃ for 1 min and hold at 4 ℃. The library was extracted by VAHTS DNA Clean Beads (Vazyme). Average insert size of the molecules sequenced in A2 sample is 499. The specific gene sequences with paired ends were analyzed with DNA sequencing in an Illumina HiSeq 2000 platform (Illumina).

treatment_protocol: HUCCT1 cells were transfected with HP1α overexpression vector or normal control vector.

tag: tissue

value: Intrahepatic cholangiocarcinoma

tag: cell line

tag: cell type

value: Intrahepatic cholangiocarcinoma cell

tag: chip antibody

value: HA (51064-2-AP, Proteintech)

tag: treatment

value: Normal control


title: ChAP DNA associated with wildtype tRF - replicate 2

city: San Marcos

first: Hong-Gu

last: Kang

state: TX

address: 601 University Dr

country: USA

institute: Texas State University

data_processing:
Pair-end reads were adapter-trimmed (forward: GATCGGAAGAGCACACGTCTGAACT, reverse: GATCGGAAGAGCGTCGTGTA) and quality-trimmed (3:25) via cutadapt (v2.10) and trimmomatic (v0.36), respectively.
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.2.9) with the options ‘--no-unal, --no-discordant, --end-to-end, --no-mixed’. Only unique alignments aligned to the nuclear genome were retained.
Peaks were identified by MACS2 with default parameters, and filtered with p-value ≤ 0.05 using aligned reads for tRF31Asp2 and tRF31Asp2_mSS as IP and control, respectively.
Reproducible peaks found in a minimum of two independent biological replicates were merged as primary peaks.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files contain aignment information; pair-end reads were merged after alignment
Supplementary_files_format_and_content: bw files from bed files are intended for a genome browser
Supplementary_files_format_and_content: narrowPeak files contain peak position information; note that WT_tRF and Mut_tRF was used as sample and control, respectively, thus, this pair gives one narrowPeak file

organism: Arabidopsis thaliana

source_name: 3.5 wk-old leaves

growth_protocol: Plants were grown in soil at 22°C, 60% relative humidity, and in a 16 h light period.

extract_protocol:
Collected tissues were crosslinked with 1% formaldehyde at room temperature for 15 min and ground with liquid N2. Nuclei isolated as described above were lysed in the lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 25 U/ml RNase Inhibitor) and sonicated (Diagenode, Bioruptor Pico) for the 10 cycles of 30 sec on/off interval. Biotin-bound DNA was affinity-purified from nuclear lysate using Dynabeads M-280 streptavidin (ThermoFisher) at 4°C for overnight.
DNAs were recovered and used for the ChAP-seq library using NEBNext Ultra II DNA Library Prep kit (NEB).
ChAP(Chromatin-affinity precipitation)-seq

treatment_protocol: Renatured nucleotides were syringe-infiltrated into the abaxial side of the leaves.

tag: ecotype

value: treated with wildtype tRF RNA for 1 hr


title: CI4

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

library_source: transcriptomic

data_processing:
Sequencing was performed on NovaSeq 6000 (Illumina) with NovaSeq Reagent Kits v1.5 (150bp × 2 paired-end). Fastq files from each sample were analyzed using the cloud platform, RaNA-seq [Prieto C, Barrios D. Bioinformatics 2020]. Gene enrichment analyses were performed using the online tools, Enrichr, Kyoto Encyclopedia of Gene and Genomes (KEGG) and Gene Ontology [Kuleshov MV, et al. Nucleic Acids Res 2016, Kanehisa M, Goto S. Nucleic Acids Res 2000, Ashburner M, et al. Nat Genet 2000].
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Matrix table with TPM values for every gene and every sample

molecule: total RNA

source_name: iPSC-derived β-like cell spheroid

growth_protocol: iPSCs were differentiated using the modified version of the protocol published by Nair et al. [Nair GG, et al. Nat Cell Biol 2019]. Before the differentiation, ~80% confluent iPSC cultures were dissociated into single cells using Accutase (#12679-54, nacalai tesque), and seeded 6.0×106 cells per well in 6-well suspension plate in 5.5 mL StemFit with 10 µM Y-27632. The plates were incubated at 37℃ with 5% carbon dioxide on an orbital shaker at 100 rpm to form a 3D structure. After 24 hours, the cells were washed with PBS, deposited by gravity, and resuspended in Day 1 medium. Thereafter, the medium was changed every day with removing 4.5 mL (5 mL until Day 3) of medium and adding 5 mL (5.5 mL until Day 22) of fresh medium. The content of medium are as follows: Day 1: RPMI (#05176-25, nakalai tesque) containing 1:100 Glutamax (#04260-64, nakalai tesque), 0.2% FBS, 1:5000 ITS (#090-06741, FUJIFILM Wako Pure Chemical Corporation), 100 ng/mL ActivinA (#QK-035, Qkine), 3 μM CHIR99021 (#038-23101, FUJIFILM Wako Pure Chemical Corporation), and 1 μM JNJ-42041935 (#400093, Calbiochem). Day 2: RPMI containing 1:100 Glutamax, 0.2% FBS, 1:2000 ITS, 100 ng/mL ActivinA, and 1 μM JNJ-42041935. Day 3: RPMI containing 1:100 Glutamax, 0.2% FBS, 1:1000 ITS, 25 ng/mL KGF (#QK-046, Qkine), and 2.5 μM TGF-β1 Ⅳ (#039-24111, FUJIFILM Wako Pure Chemical Corporation). Day 4-5: RPMI containing 1:100 Glutamax, 0.4% FBS, 1:1000 ITS, and 25 ng/mL KGF. Day 6-7: DMEM with 25 mM glucose (#08488-55, nakalai tesque) containing 1:100 Glutamax, 1:100 B27 (#17504044, Thermo Fisher Scientific), 3 nM TTNPB (#T3757, Sigma Aldrich), and 0.5 mM Vitamin C (#13571-56, nakalai tesque). Day 8: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 B27, 3 nM TTNPB, 0.5 mM Vitamin C, and 50 ng/mL EGF (#236-EG-200, R&D systems). Day 9-10: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 B27, 0.5 mM Vitamin C, and 50 ng/mL EGF, 50 ng/mL KGF. Day 11-15: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 ITS, 1:100 NEAA (#06344-56, nakalai tesque), 1 mM pyruvate (#06977-34, nakalai tesque), 10 μg/mL Heparin sulphate (#H3149-10KU, Sigma Aldrich), 1 mM N-acetyl cysteine (#A7250-5G, Sigma Aldrich), 10 μM zinc sulphate (#Z0251-100G, Sigma Aldrich), 1.75 μL 2-mercaptoethanol (#ES-007-E, Merck Millipore), 1% BSA (#A3803-100G, Sigma Aldrich), 10 μM Repsox (#S7223, selleck), 2 μM T3 (#038-25541, FUJIFILM Wako Pure Chemical Corporation), 0.5 μM LDN-193189 (#SML0559-5MG, Sigma Aldrich), and 1 μM DBZ (#S2711, Selleck). Day 16-22: CMRL (#11530037, Thermo Fisher Scientific) containing 1:100 Glutamax, 1:100 ITS, 1:100 NEAA, 1 mM pyruvate, 10 μg/mL Heparin, 1 mM N-acetyl cysteine, 10 μM zinc sulphate, 1.75 μL 2-mercaptoethanol, 1% BSA, 1:100 HEPES (#17557-94, nakalai tesque), 10 μM Repsox, 2 μM T3, and 0.155 mM Vitamin C.

extract_protocol:
From the differentiated spheroids, RNA was extracted using TRIzol Reagent (#10296028, Thermo Fisher Scientific) and purified using isopropanol and 75% ethanol. RNA samples were depleted DNase using TURBO DNA-freeTM Kit (#AM1907, Thermo Fisher Scientific), and purified to mRNA by Poly-A selection using NEBTNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs). Only RNA samples with RIN > 6 were used to generate libraries.
Following purification of first-strand cDNA, libraries were PCR amplified in accordance with their input RNA amount and purified using NEBNext Ultra II Directional RNA Library Prep Kit (#E7760, New England Biolabs).

treatment_protocol: For the experiments, 1 mM metformin (#PHR1084, Merk), 1mM imeglimin (provided by Sumitomo Pharma Co., Ltd.), 10 ng/mL TNF-α (#570106, Biolegend), and 10 ng/mL IFN-γ (#570206, Biolegend) were added on Day 16-22.

tag: strain

value: Human iPSC line derived from healthy individual

value: Cytokine and imeglimin


title: C5

value: Cytokine


title: Phaseolus vulgaris 4004, grain,10DAF,2

city: Hangzhou

first: Yunxiu

last: Liu

address: No. 258 Xueyuan Street, Xiasha Higher Education Park

institute: China Jiliang University

data_processing:
The joint sequence in reads was removed, and the reads without inserted fragments were removed due to the joint self-connection and other reasons.
The bases with low quality (mass value less than 20) at the end of the sequence (3 'end) are pruned away. If there are still bases with mass value less than 10 in the remaining sequence, the whole sequence is eliminated, otherwise it is retained.
reads containing more than 10% N were removed.
Discard sequences less than 75bp in length after adapter removal and mass pruning.
Assembly: 3885

organism: Phaseolus vulgaris

source_name: Grain

extract_protocol:
RNA was obtained using the TRIzol® Reagent kit. 1μg total RNA was used to construct sequencing library RNA-seq.
RNA libraries for RNA-seq were prepared using SMARTER mRNA--Seq Library Prep Kit following manufacturer's protocols.

value: Grain

tag: developmental stage


title: HUCCT1-IFN-rep3

data_processing:
Raw data was pretreated by fastp 0.20.0 software. The useless sequences (e.g, adaptor sequences and low-quality sequences) were filtered.
The reads were compared with human genome sequences by HISAT2 2.1.0 software to confirm the detailed gene names and locations in the genome (e.g., promoter, UTR and intron region).
The expresion level of each gene was measured by calculating the Reads Count value by HTSeq 0.10.0 software and union model.
The Reads Count values were converted into TPM values which were used to observe the differences in gene expression under different experimental conditions.
Difference analysis was performed by DESeq2 1.18.1 software to evaluate the differences in gene expression.
Assembly: GRCh38
Supplementary files format and content: txt

extract_protocol:
Total RNA from cell samples was extracted with RNA Extraction Reagent (Vazyme, China) according to the manufacturer’s instructions. Total RNA samples were stored at -80℃.
The quality was evaluated by a 4200 TapeStation system (Agilent, USA) and quantified using a Life Invitrogen Qubit 3.0 fluorometer (Thermo Fisher Scientific). Then, the samples were used for library preparation. The mRNA with polyA structure was captured by Oligo (DT) magnetic beads. Fragmented mRNA was used as the template to synthesize the first strand of cDNA in the M-MuLV reverse transcriptase system. Then RNA was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. The double-strand cDNA was then purified and added by polyA tails and adaptors followed by PCR amplification. The product of PCR was purified by AMPure XP beads.

treatment_protocol: HUCCT1 cells were treated by IFN-α2b (60 ng/mL) or recommended solvent for 24h.


title: Formalehyde treated, FA2

city: Talas

first: Ghulam Asghar

last: Sajid

state: Kayseri

address: Yenidoğan, Turhan Baytop Sokak No:1

department: Animal Science Department

country: Turkey

institute: Erciyes University

description:
Library name: Sample 6
Column name in raw reads.txt = FA2

data_processing:
Preprocessed with FastQC; cleaned using HTStream; alignment to chicken genome using Salmon; DESeq2 for normalization and differential expression analysis.
Assembly: Chicken reference genome from Ensembl (https://www.ensembl.org/Gallus_gallus/Info/Index).
Supplementary files format and content: Tab-delimited text file contains raw reads of all samples

organism: Gallus gallus

source_name: Embryo liver tissue

growth_protocol: Tinted breed chick embryos incubated at 37.8°C with 58-63% relative humidity.

extract_protocol:
Total RNA isolated using Nucleogene RNA extraction kit (Nucleogene, Istanbul, Türkiye).
Prepared using TruSeq RNA Sample Preparation Kit v2 Guide (Illumina, San Diego, CA, USA).

treatment_protocol: Formaldehyde (FA) gas fumigation using 35 mL formalin + 17.5 g KMnO4 for FA concentration of 6 g/m³ for 25 minutes.

value: Embryo liver tissue

value: liver cells

tag: genotype

value: chicken tinted

value: formaledehyde


title: C2


title: HUCCT1-IFN-rep2


title: ChAP DNA associated with mutant tRF - replicate 1

value: treated with mutant tRF RNA for 1 hr


title: CM3

value: Cytokine and metformin


title: ChAP DNA associated with wildtype tRF - replicate 1


title: Control 3, C3, non-treated

description:
Library name: Sample 3
Column name in raw reads.txt = C3

value: control


title: HUCCT1-Normal-rep3

value: Recommended solvent


title: Formalehyde treated, FA1

description:
Library name: Sample 5
Column name in raw reads.txt = FA1


title: C1


title: Control 2, C2, non-treated

description:
Library name: Sample 2
Column name in raw reads.txt = C2


title: I5

value: Imeglimin


title: I2


title: HUCCT1-Normal-rep2

value: Intrahepatic cholangiocarcinoma

value: Intrahepatic cholangiocarcinoma cell


title: iPSC OL, Sox6, ATAC, rep2

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: Library name: 2-6_siSox6_SortedOLs

data_processing:
Adapters were trimmed with cutadapt
The data were aligned to the mouse genome (mm10) using BWA
Peak calling was performed using MACS2 and cluster plots and tracks were generated using deepTools
Assembly: mm10
Supplementary files format and content: BigWig and narrowPeaks (excluding igG input)

organism: Mus musculus

source_name: iPSC

extract_protocol:
Cells were sorted based on surface marker O1, nuclei was extracted, incubated with transposase enzyme, then DNA was column purified
ATAC libraries were prepared using Illumina Nextera DNA Library Prep Kit

value: iPSC

value: OL


title: Control 1, C1, non-treated

description:
Library name: Sample 1
Column name in raw reads.txt = C1


title: I1

value: Human iPSC line derived from healthy individual


title: iPSC OL, NTC, ATAC, rep1

description: Library name: 2-2_siNTC_SortedOLs


title: iPSC OL, Sox6, ATAC, rep1

description: Library name: 2-2_siSox6_SortedOLs


title: HUCCT1-Normal-rep1


title: M4

value: Metformin


title: HUCCT1-TSA-rep3

data_processing:
Raw data was pretreated by fastp 0.20.0 software. The useless sequences (e.g, adaptor sequences and low-quality sequences) were filtered.
The reads were compared with human genome sequences by HISAT2 2.1.0 software to confirm the detailed gene names and locations in the genome (e.g., promoter, UTR and intron region ).
The expresion level of each gene was measured by calculating the Reads Count value by HTSeq 0.10.0 software and union model.
The Reads Cound values used to observe the differences in gene expression under different experimental conditions.
Difference analysis was performed by DESeq2 1.18.1 software to evaluate the differences in gene expression.
Assembly: GRCh38
Supplementary files format and content: txt

growth_protocol: HUCCT1 cells were cultured in RPMI-1640 medium. All cell culture media were supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified incubator with 5% CO2.

treatment_protocol: HUCCT1 cells were treated by TSA (0.5 μM) or DMSO for 24h.

value: TSA Treatment


title: treatment-3

city: Haikou, China

first: Bing

last: Wang

address: No. 58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan university

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: WBcel235 release-100
Supplementary files format and content: Excel files and gene expression level information

organism: Caenorhabditis elegans

source_name: the whole worm

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: the whole worm


title: M3


title: HUCCT1-TSA-rep2


title: treatment-2


title: Control 4, C4, non-treated

description:
Library name: Sample 4
Column name in raw reads.txt = C4

value: Embryo liver tissue


title: T_2

city: Xiamen

first: Tiansheng

last: Chen

address: No. 43, Yindou Road, Jimei District, Fisheries College of Jimei University

institute: Jimei University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. 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: The PacBio Iso-Seq data from the male and female samples were merged to construct a unified reference transcriptome.（The datasets generated during the current study are available in the Sequence Read 435 Archive (SRA) repository, the accession number to datasets is PRJNA1147859.）
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for all Samples

organism: Anguilla japonica

source_name: Testis

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Testis


title: T_3


title: HUCCT1-IFN-rep1


title: treatment-1


title: iPSC OL, NTC, ATAC, rep2

description: Library name: 2-6_siNTC_SortedOLs


title: M1


title: HUCCT1-TSA-rep1


title: T_1


title: V5

value: Vehicle


title: control-3


title: O_3

source_name: Ovary

value: Ovary


title: control-2


title: V2


title: O_2


title: V3


title: HUCCT1-DMSO-rep1

value: DMSO Treatment


title: control-1


title: O_1


title: Rhesus_16-cell_3

status: Public on Jan 19 2025

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: 2x150bp reads

data_processing:
Reads were mapped to the appropriate reference genome using STAR
Internal fragments and 5' transcript ends were distinguished using a custom python script available on github
BigWig files were generated from unique mapping reads, rRNA removed and rpm normalized, using bedtools and ucsc bedGraphToBigWig
TEs and genes were quantified from unique and multimapping reads from 5' fragments using TEtranscript
For more information see (gitlab link)
Assembly: GRCm38 (Mus musculus), Sscrofa11.1 (Sus scrofa), Btau_5.0.1 (Bos taurus), OryCun2.0 (Oryctolagus cuniculus), Mmul_8.0.1 (Macaca mulatta)
Supplementary files format and content: merged bigWig files, 2 files per species/stage seperated for 5' fragments ("FivePrime") and internal fragments ("Else")
Supplementary files format and content: table txt file containing gene and TE counts for each species

organism: Macaca mulatta

source_name: 16 cell embryo

growth_protocol: Oocyte and preimplantation stages were collected from mouse, pig, cow, rabbit and rhesus.

extract_protocol:
For each library a single embryo from was used originating from the listed species and developmental stage
An adapted version of Smart-seq2 (called Smart-seq+5') was used to capture both 5' transcript information as well as internal transcript fragments

treatment_protocol: Mouse and rabbit embryos were collected after natural mating. Pig, cow and rhesus embryos were harvested by IVF. For more information see methods of accompaning paper

value: 16 cell embryo

value: WT


title: Rhesus_16-cell_1

description: 2x150bp reads


title: Rhesus_8-cell_3

description: 2x150bp reads

source_name: 8 cell embryo

value: 8 cell embryo


title: Rhesus_8-cell_2

description: 2x150bp reads


title: Rhesus_16-cell_2

description: 2x150bp reads


title: Rhesus_8-cell_1

description: 2x150bp reads


title: Rhesus_2-cell_2

description: 2x150bp reads

source_name: 2 cell embryo

value: 2 cell embryo


title: Rhesus_4-cell_2

description: 2x150bp reads

source_name: 4 cell embryo

value: 4 cell embryo


title: Rhesus_Zygote_4

description: 2x150bp reads

source_name: Zygote

value: Zygote


title: Rhesus_Zygote_3

description: 2x150bp reads


title: Rhesus_Zygote_2

description: 2x150bp reads


title: Rhesus_Oocyte_6

description: 2x150bp reads

source_name: Oocyte

value: Oocyte


title: Rhesus_2-cell_1

description: 2x150bp reads


title: Rhesus_Oocyte_5

description: 2x150bp reads


title: Rhesus_Zygote_1

description: 2x150bp reads


title: Rhesus_Oocyte_4

description: 2x150bp reads


title: Rhesus_Oocyte_3

description: 2x150bp reads


title: HUCCT1-DMSO-rep2

value: Intrahepatic cholangiocarcinoma

value: Intrahepatic cholangiocarcinoma cell


title: Rhesus_Oocyte_2

description: 2x150bp reads


title: hDRG_6

city: Stanford

first: Kent

last: Imaizumi

state: CA

address: 318 Campus Drive

institute: Stanford University

description: Library name: hDRG_6

library_source: transcriptomic single cell

data_processing:
UMI counting was performed by the ‘count’ function (--include-introns=TRUE) in Cell Ranger (v7.0.1 and 7.1.0 for organoids; v7.2.0 for the human DRG and organoid versus assembloid comparison) with GRCh38/Ensembl 98 reference. Further downstream analyses were performed using the R package Seurat (v4.3.0). Genes on the X or Y chromosome were removed from the count matrix to avoid biases in clustering due to the sex of the hiPS cell lines.
For the analysis of hSeO and hdSpO, cells with more than 10,000 or less than 2,500 detected genes, with less than 2,000 UMI counts, or cells with mitochondrial content higher than 15% were excluded. Genes that were not expressed in at least three cells in each library were not included. Gene expression was normalized using a global-scaling normalization method (normalization method, ‘LogNormalize’; scale factor, 10,000), and the 2,000 most variable genes were selected (selection method, ‘vst’) and scaled (mean = 0 and variance = 1 for each gene). hSeO samples (n = 4) and hdSpO samples (n = 5) were each separately integrated using ‘FindIntegrationAnchors’ and ‘IntegrateData’ functions with the default parameter. The top 10 principal components were used for clustering (resolution of 1.0) using the ‘FindNeighbors’ and ‘FindClusters’ functions, and for visualization with UMAP. The classification of dorsoventral neuronal cell types of hdSpO was performed based on the combinatorial expression of known markers as previously described by using ‘doCellPartition’ function (cell_level_min_step1 = 2, cell_level_min_step2 = 1; available at github.com/juliendelile/MouseSpinalCordAtlas).
For comparison across four region organoids, hSeO samples (n = 4) and hdSpO samples (n = 5) from this study, along with hDiO samples (n = 3; Kim et al., 2023) and hCO samples (n = 2; Khan et al., 2020), were aggregated using the 'aggr’ function in Cell Ranger. Cells with more than 7,500 or less than 2,000 detected genes, with less than 2,000 UMI counts, or with mitochondrial content higher than 15% were excluded. Normalization, variable gene detection, and scaling were performed as described above. The top 50 principal components were used for clustering (resolution of 1.0), using the ‘FindNeighbors’ and ‘FindClusters’ functions, and for visualization with UMAP.
For hASA and individual organoid comparison, cells with more than 10,000 or less than 1,000 detected genes or cells with mitochondrial content higher than 15% were excluded. Genes that were not expressed in at least three cells in each library were not included. After normalization, and variable gene detection, individual organoid samples (n = 4) and assembloid samples (n = 4) were integrated and clustered (30 PCs, resolution = 1).
For human DRG data, cells with more than 10,000 or less than 500 detected genes or cells with mitochondrial content higher than 10% were excluded. Genes that were not expressed in at least three cells in each library were not included. After normalization, and variable gene detection, human DRG samples (n = 7) were integrated. UMAP visualization and clustering (30 PCs, resolution = 1) were performed. Human DRG samples (n = 7) and hSeO samples (n = 4) were also integrated. After removing putative stressed cells using Gruffi, an additional round of integration, UMAP visualization and clustering (30 PCs, resolution = 2) were performed.
Assembly: GRCh38, Ensembl 98
Supplementary files format and content: tsv files with feature and cell barcode information corresponding to row and column indices of gene count data for each sample
Supplementary files format and content: matrix exchange format for sparse matrices of gene count data for each sample
Supplementary files format and content: aggr_SeuratObject file is a processed seurat object for comparison across four region organoids (hCO, hDiO, hdSpO, and hSeO). hCO and hDiO data are from Khan et al. (2020) and Kim et al. (2023), respectively
Supplementary files format and content: hSeO/hdSpO_integrated_SeuratObject files are processed seurat objects for hSeO/hdSpO datasets in RDS format
Supplementary files format and content: hASA_indOrg_integrated_SeuratObject file is a processed seurat object for hASA and individual organoid pool datasets in RDS format
Supplementary files format and content: HFT_SeuratObject is a processed seurat object for human fetal DRG datasets in RDS format
Supplementary files format and content: HFT_hSeO_integrated_SeuratObject is a processed seurat object for comparison between fetal DRG and hSeO in RDS format

molecule: polyA RNA

source_name: Fetal tissue

extract_protocol:
For the organoid dissociation, 4–5 randomly selected organoids were pooled to obtain single cell suspension. For assembloids, 1–2 assembloids were pooled for dissociation. To match the relative cell numbers across different regions, 1–2 organoids from each of the four regions, totaling 4–8 organoids, were pooled for dissociation only when comparing organoids to assembloids. For human primary tissue, 1–2 DRG were pooled for dissociation. Samples were incubated in 30 U/mL papain enzyme solution (Worthington Biochemical, LS003126) and 0.4% DNase (12,500 U/mL, Worthington Biochemical, LS2007) at 37°C for 45 minutes. After enzymatic dissociation, organoids were washed with a solution including protease inhibitor and gently triturated to achieve a single cell suspension. Cells were resuspended in 0.04% BSA/PBS (Millipore-Sigma, B6917-25MG) and filtered through a 70 μm Flowmi Cell Strainer (Bel-Art, H13680-0070).
To target 7,000 cells after recovery, approximately 11,600 cells were loaded onto a Chromium Single Cell 3′chip (Chromium Next GEM Chip G Single Cell Kit, 10x Genomics, PN-1000127) with Chromium Single Cell 3’ Library & Gel Bead kit v3.1 (10x Genomics, PN-1000128 and PN-1000269) and proceeded according to manufacturer’s instructions.

value: Fetal tissue

value: Human fetal DRG

tag: Stage

value: PCW 15


title: hDRG_7

description: Library name: hDRG_7


title: HUCCT1-DMSO-rep3


title: hDRG_5

description: Library name: hDRG_5


title: hDRG_1

description: Library name: hDRG_1


title: hDRG_4

description: Library name: hDRG_4


title: hDRG_2

description: Library name: hDRG_2


title: hDRG_3

description: Library name: hDRG_3


title: IndividualOrganoidPooled_2

description: Library name: IndividualOrganoidPooled_2

value: Pooled of human cortical organoids (hCO), human diencephalic organoids (hDiO), hdSpO, and hSeO

tag: differentiation day


title: IndividualOrganoidPooled_3

description: Library name: IndividualOrganoidPooled_3


title: hASA_1

description: Library name: hASA_1

value: Human ascending somatosensory assembloids (hASA)


title: hASA_2

description: Library name: hASA_2


title: IndividualOrganoidPooled_1

description: Library name: IndividualOrganoidPooled_1


title: IndividualOrganoidPooled_4

description: Library name: IndividualOrganoidPooled_4


title: hASA_3

description: Library name: hASA_3


title: pm5, scATACseq

city: Leipzig

first: Maria

last: Schmidt

address: Härtelstr. 16-18

institute: IZBI

description: 10x Genomics

library_source: other

data_processing:
Demultiplexing was done using bcl2fastq (Illumina®, v2...).
For further analysis and read alignment CellRanger software v6.1.2 and CellRanger ATAC software v2.0.0 was used with default settings as suggested by 10x Genomics.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Filtered feature-barcode matrices in Sparse Matrix Format (MTX) outputted by cellranger and cellranger atac. Each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a cell-associated barcode (column).
Supplementary files format and content: TSV files with feature and barcode sequences corresponding to row and column indices, respectively, outputted by cellranger.
Supplementary files format and content: BED (Browser Extensible Data format) file with information about the coordinates for particular genome features.

molecule: other

source_name: skin

extract_protocol:
single-cell suspension extracted using Mitlenyi Whole-Skin-Dissociation kit, human
according to manufacturers instructions (10x Genomics)

value: skin

tag: tumor stage

value: IIIB, T3a


title: pm6, scATACseq

description: 10x Genomics

value: IIB, T3b


title: hASA_4

description: Library name: hASA_4


title: nevus, scATACseq

description: 10x Genomics


title: Rhesus_Oocyte_1

description: 2x150bp reads


title: nevus2, scRNAseq

description: 10x Genomics


title: nevus3, scRNAseq

description: 10x Genomics


title: pm3, scATACseq

description: 10x Genomics

value: IIC, T4b


title: pm9, scRNAseq

description: 10x Genomics

value: IIB, T4a


title: pm1, scATACseq

description: 10x Genomics

value: IB, T2a


title: nevus1, scRNAseq

description: 10x Genomics


title: pm8, scRNAseq

description: 10x Genomics


title: pm6, scRNAseq

description: 10x Genomics

value: IIA, T3a


title: pm5, scRNAseq

description: 10x Genomics


title: pm4, scRNAseq

description: 10x Genomics


title: pm10, scRNAseq

description: 10x Genomics


title: pm3, scRNAseq

description: 10x Genomics


title: Liver sample 178

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

data_processing:
Raw sequencing data (.bcl) was converted to FASTQ with the Dragen Bio-IT platform (v3.9.5).
The quality of RNA-seq data was assessed by FastQC (v0.11.9).
Tissue bulk RNA-seq data were aligned and quantified using a standard protocol of Kallisto (v0.46.2) against the Human genome downloaded from Ensembl, GRCh38 (ensembl release 102)
The output of Kallisto, both estimated counts and TPM (transcript per kilobase million)-based transcript-level expressions were then transformed into gene-level expressions using the Bioconductor package tximport (v1.22.0) with the tx2gene option set to connect transcripts to genes.
Assembly: GRCh38 (ensembl release 102)
Supplementary files format and content: Tab-delimited Raw counts for every gene and samples

source_name: liver

extract_protocol:
RNA of the tissue homogenates was extracted by Trizol/Chloroform phase separation technique, then RNA purification was carried out with Qiagen RNeasy mini kit for explant liver samples (Catalog No.74104) and RNeasy micro kit (Catalog No.74004) for biopsy samples. The RNA integrity number (RIN) value of total RNA samples was measured with TapeStation (Agilent Tech, USA). The amount of total RNA was measured more precisely fluorometrically with the RNA Broad Range kit (Thermofisher, USA) by using Qubit (Invitrogen, USA).
RNA sequencing library was prepared with Illumina Stranded Total RNA Prep.

value: liver

tag: disease group

tag: disease

value: CVH


title: pm2, scRNAseq

description: 10x Genomics

value: IA, T1a


title: pm7, scRNAseq

description: 10x Genomics


title: Liver sample 177


title: Liver sample 175


title: Liver sample 173


title: Liver sample 176


title: Liver sample 174


title: pm4, scATACseq

description: 10x Genomics


title: pm2, scATACseq

description: 10x Genomics


title: Liver sample 171


title: Liver sample 170


title: Liver sample 167


title: Liver sample 166


title: Liver sample 168


title: Liver sample 165


title: Liver sample 164


title: Liver sample 161


title: Liver sample 162


title: Liver sample 157


title: pm1, scRNAseq

description: 10x Genomics


title: Liver sample 163


title: Liver sample 159


title: Liver sample 155


title: Liver sample 156


title: Liver sample 152


title: Liver sample 154


title: Liver sample 158


title: Liver sample 150


title: Liver sample 153


title: Liver sample 160


title: Liver sample 151


title: Liver sample 148


title: Liver sample 146


title: Liver sample 169


title: Liver sample 147


title: Liver sample 149


title: Liver sample 142


title: Liver sample 141


title: Cow_Morula_11

description: 2x150bp reads

organism: Bos taurus

source_name: Morula

value: Morula

value: WT


title: Liver sample 143


title: Liver sample 172


title: Liver sample 144


title: Liver sample 140


title: Liver sample 145


title: Liver sample 139


title: Cow_Morula_8

description: 2x150bp reads


title: Liver sample 137


title: Liver sample 138


title: Cow_Morula_10

description: 2x150bp reads


title: Liver sample 136


title: Cow_Morula_7

description: 2x150bp reads


title: Cow_Morula_6

description: 2x150bp reads


title: Cow_Morula_5

description: 2x150bp reads


title: Liver sample 135


title: Cow_Morula_4

description: 2x150bp reads


title: Liver sample 133


title: Cow_Morula_3

description: 2x150bp reads


title: Liver sample 132


title: Cow_Morula_2

description: 2x150bp reads


title: Cow_Morula_1

description: 2x150bp reads


title: Liver sample 131


title: Liver sample 130


title: Cow_16-cell_12

description: 2x150bp reads

value: 16 cell embryo


title: Liver sample 129


title: Liver sample 128


title: Cow_16-cell_10

description: 2x150bp reads


title: Liver sample 127


title: Liver sample 126


title: Cow_16-cell_9

description: 2x150bp reads


title: Cow_16-cell_8

description: 2x150bp reads


title: Cow_16-cell_11

description: 2x150bp reads


title: Cow_Morula_9

description: 2x150bp reads


title: Liver sample 125


title: Cow_16-cell_7

description: 2x150bp reads


title: Cow_16-cell_6

description: 2x150bp reads


title: Liver sample 123


title: Liver sample 124


title: Cow_16-cell_5

description: 2x150bp reads


title: Liver sample 134


title: Liver sample 121


title: Liver sample 122


title: Liver sample 120

value: MASLD


title: Cow_16-cell_4

description: 2x150bp reads


title: Cow_16-cell_2

description: 2x150bp reads


title: Cow_16-cell_3

description: 2x150bp reads


title: Cow_16-cell_1

description: 2x150bp reads


title: Liver sample 118


title: Cow_8-cell_12

description: 2x150bp reads

value: 8 cell embryo


title: Liver sample 117


title: Liver sample 116


title: Cow_8-cell_11

description: 2x150bp reads


title: Cow_8-cell_9

description: 2x150bp reads


title: Liver sample 115


title: Liver sample 114


title: Cow_8-cell_7

description: 2x150bp reads


title: Cow_8-cell_8

description: 2x150bp reads


title: Liver sample 113


title: Cow_8-cell_6

description: 2x150bp reads


title: Liver sample 111


title: Liver sample 112


title: Cow_8-cell_5

description: 2x150bp reads


title: Liver sample 110


title: Cow_8-cell_4

description: 2x150bp reads


title: Liver sample 108


title: Cow_8-cell_2

description: 2x150bp reads


title: Liver sample 119


title: Cow_8-cell_3

description: 2x150bp reads


title: Cow_4-cell_12

description: 2x150bp reads

value: 4 cell embryo


title: Liver sample 105


title: Cow_8-cell_1

description: 2x150bp reads


title: Liver sample 106


title: Liver sample 104


title: Liver sample 109


title: Cow_8-cell_10

description: 2x150bp reads


title: Cow_4-cell_10

description: 2x150bp reads


title: Liver sample 103


title: Cow_4-cell_11

description: 2x150bp reads


title: Cow_4-cell_9

description: 2x150bp reads


title: Cow_4-cell_8

description: 2x150bp reads


title: Liver sample 102


title: Liver sample 101


title: Cow_4-cell_6

description: 2x150bp reads


title: Cow_4-cell_5

description: 2x150bp reads


title: Liver sample 99


title: Liver sample 100


title: Liver sample 98


title: Cow_4-cell_4

description: 2x150bp reads


title: Liver sample 107


title: Cow_4-cell_3

description: 2x150bp reads


title: Cow_4-cell_2

description: 2x150bp reads


title: Liver sample 96


title: Liver sample 94


title: Cow_4-cell_1

description: 2x150bp reads


title: NCIH1299 cells, shPRDX1, ATM inhibition, replicate 5

city: Bethesda

first: Urbain

last: Weyemi

state: Maryland

address: Bldg. 37,  Rm 4016A, 37 Convent Dr.

department: Developmental Therapeutics Branch

institute: National Institute of Health

data_processing:
Transcript abundance normalized to transcript per million expression was determined by pseudo alignment with human transcriptome (Ensembl Transcriptome v96) using Kallisto (v 0.48.0).
Read count was generated by DESeq2 package (v 1.40.2).
Assembly: Ensembl Transcriptome v96
Supplementary files format and content: Tab-separated values (TSV) files include transcript abundance for each sample
Supplementary files format and content: Comma-separated values (CSV) files include raw counts for each sample

growth_protocol: Cells were grown in a humidified incubator at 37°C under 5% CO2 in air. A549-Cas9 cells were grown in Dulbecco's Modified Eagle Medium (DMEM) (Fisher Scientific) supplemented with 10% Fetal Bovine Serum (Thermo Scientific) and 1 μg/mL puromycin to maintain PRDX1 KO. NCIH1299 cells were grown in RPMI 1640 medium (Fisher Scientific) supplemented with 10% Fetal Bovine Serum (Thermo Scientific) and 1 mM sodium pyruvate (Gibco).

extract_protocol:
Total RNA was harvested using PureLink RNA Mini Kit (Invitrogen). 800 ng of total RNA was used to generate the library.
The kits used for the library prep were NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440) as described in the manufacturer’s manual.

treatment_protocol: Cells were treated with either ATM inhibitor, AZD1390 (Selleckchem) at 1 μM or DMSO for 6 days.

value: non small cell lung cancer cells

value: PRDX1 knockdown

value: ATM inhibition


title: NCIH1299 cells, shPRDX1, ATM inhibition, replicate 4


title: NCIH1299 cells, shPRDX1, ATM inhibition, replicate 3


title: Liver sample 93


title: NCIH1299 cells, shPRDX1, ATM inhibition, replicate 1


title: NCIH1299 cells, shPRDX1, ATM inhibition, replicate 2


title: NCIH1299 cells, shPRDX1, DMSO, replicate 5

value: DMSO


title: Liver sample 92


title: Cow_4-cell_7

description: 2x150bp reads


title: Cow_2-cell_11

description: 2x150bp reads

value: 2 cell embryo


title: Liver sample 91


title: NCIH1299 cells, shPRDX1, DMSO, replicate 4


title: NCIH1299 cells, shPRDX1, DMSO, replicate 3


title: Cow_2-cell_10

description: 2x150bp reads


title: NCIH1299 cells, shPRDX1, DMSO, replicate 1


title: Liver sample 90


title: NCIH1299 cells, shPRDX1, DMSO, replicate 2


title: NCIH1299 cells, shCT, ATM inhibition, replicate 5


title: Liver sample 89


title: NCIH1299 cells, shCT, ATM inhibition, replicate 4


title: Cow_2-cell_9

description: 2x150bp reads


title: NCIH1299 cells, shCT, ATM inhibition, replicate 3


title: Liver sample 88


title: Liver sample 97


title: Cow_2-cell_8

description: 2x150bp reads


title: Cow_2-cell_12

description: 2x150bp reads


title: Liver sample 87


title: Cow_2-cell_7

description: 2x150bp reads


title: NCIH1299 cells, shCT, DMSO, replicate 5


title: NCIH1299 cells, shCT, ATM inhibition, replicate 2


title: NCIH1299 cells, shCT, DMSO, replicate 4


title: NCIH1299 cells, shCT, ATM inhibition, replicate 1


title: Cow_2-cell_6

description: 2x150bp reads


title: Cow_2-cell_5

description: 2x150bp reads


title: NCIH1299 cells, shCT, DMSO, replicate 2


title: Liver sample 85


title: A549 cells, sgPRDX1, ATM inhibition, replicate 5

value: PRDX1 knockout pool


title: NCIH1299 cells, shCT, DMSO, replicate 3


title: NCIH1299 cells, shCT, DMSO, replicate 1


title: A549 cells, sgPRDX1, ATM inhibition, replicate 3


title: Liver sample 83


title: A549 cells, sgPRDX1, ATM inhibition, replicate 2


title: Liver sample 82


title: A549 cells, sgPRDX1, ATM inhibition, replicate 1


title: A549 cells, sgPRDX1, DMSO, replicate 5


title: Liver sample 81


title: Cow_2-cell_1

description: 2x150bp reads


title: A549 cells, sgPRDX1, DMSO, replicate 4


title: A549 cells, sgPRDX1, DMSO, replicate 3


title: Liver sample 86


title: A549 cells, sgPRDX1, DMSO, replicate 1


title: Liver sample 80


title: Cow_2-cell_4

description: 2x150bp reads


title: A549 cells, sgPRDX1, DMSO, replicate 2


title: Cow_2-cell_3

description: 2x150bp reads


title: Cow_Zygote_11

description: 2x150bp reads

value: Zygote


title: Liver sample 79


title: Cow_Zygote_12

description: 2x150bp reads


title: A549 cells, sgPRDX1, ATM inhibition, replicate 4


title: Liver sample 78


title: Cow_Zygote_10

description: 2x150bp reads


title: A549 cells, sgControl, ATM inhibition, replicate 5


title: A549 cells, sgControl, ATM inhibition, replicate 3


title: Cow_2-cell_2

description: 2x150bp reads


title: A549 cells, sgControl, ATM inhibition, replicate 4


title: Liver sample 84


title: Liver sample 77


title: A549 cells, sgControl, ATM inhibition, replicate 1


title: Cow_Zygote_8

description: 2x150bp reads


title: A549 cells, sgControl, DMSO, replicate 4


title: Liver sample 76


title: A549 cells, sgControl, DMSO, replicate 3


title: Cow_Zygote_7

description: 2x150bp reads


title: A549 cells, sgControl, DMSO, replicate 2


title: A549 cells, sgControl, DMSO, replicate 1


title: Liver sample 75


title: Cow_Zygote_6

description: 2x150bp reads


title: A549 cells, sgControl, ATM inhibition, replicate 2


title: MAIT, 5-OP-RU + IL-18, D2

city: Huddinge

first: Johan

last: Sandberg

address: Alfred Nobels allé 8

department: Department of Medicine

institute: Karolinska Institutet

description: 10X Genomics

data_processing:
Sequence data were processed with the Cell Ranger pipeline (cellranger v6.0.1). The mkfastq function was used to demultiplex the data and subsequently the count function to map the fastq files and produce count matrices.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab separated values files, matrix files and h5 files

source_name: Blood

extract_protocol:
Vα7.2+ cells were isolated from fresh PBMCs. After isolation,  Vα7.2+ cells were rested for 48h at 37°C, 5%CO2. Then Vα7.2+ cells were co-culture with THP-1 pulsed 5-OP-RU alone in presence of IL-12, IL-23 or IL-18 for 14h. Unstimulated THP-1/Vα7.2+ cells co-culture was also included. After 14h of stimulation, the cells were harvested for staining and MAIT cells were sorted on a MA900 sorter (Sony).
The library was constructed using the chromium next GEM single cell 3’ reagent kit v3.1 (dual index) as per the manufacturer’s instructions.

value: Blood

value: MAIT cells


title: Liver sample 74

value: liver


title: Cow_Zygote_5

description: 2x150bp reads


title: MAIT, 5-OP-RU + IL-23, D2

description: 10X Genomics


title: Cow_Zygote_9

description: 2x150bp reads


title: MAIT, 5-OP-RU + IL12, D2

description: 10X Genomics


title: Cow_Zygote_4

description: 2x150bp reads


title: Liver sample 73


title: MAIT, unstim, D2

description: 10X Genomics

value: Unstimulated


title: Liver sample 72


title: MAIT, 5-OP-RU + IL-23, D1

description: 10X Genomics


title: MAIT, 5-OP-RU, D2

description: 10X Genomics


title: Liver sample 71


title: Cow_Zygote_2

description: 2x150bp reads


title: MAIT, 5-OP-RU, D1

description: 10X Genomics


title: A549 cells, sgControl, DMSO, replicate 5


title: Liver sample 70


title: MAIT, 5-OP-RU + IL-12, D1

description: 10X Genomics


title: MAIT, unstim, D1

description: 10X Genomics


title: Liver sample 69


title: obesity5

city: jinan

first: yongjiao

last: zhang

state: shandong

address: jingshi

institute: shandong second medical university

description:
Library name: SAMPLE10
FPKM.Obesity5

data_processing:
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. After that, a total of G bp of cleaned, paired-end reads were produced.
In addition, we aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
In addition, the reconstruction of transcripts was carried out with software Stringtie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6), which together with HISAT2, allow biologists to identify new genes and new splice variants of known ones. To identify the new transcripts, all of the reconstructed transcripts were aligned to reference genome and were divided into twelve categories by using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). Transcripts with one of the classcodes “i,j,o,u,x” were defined as novel transcripts, which was then used to predict lncRNA. Transcripts that overlapped with known mRNAs, lncRNAs and transcripts shorter than 200bp were filtered. Then we utilized CPC0.9-r2 (http://cpc2.cbi.pku.edu.cn, ) and CNCI2.0 (https://github.com/www-bioinfo-org/CNCI#install-cnci) with default parameters to predict novel transcripts with coding potential. All transcripts with CPC score < 0.5 and CNCI score < 0 were retained and considered as novel lncRNAs.The remaining transcripts with class code (I, j, o, u, x) were considered as novel lncRNAs.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for transcripts by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value. FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB).
Genes/RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/mRNA/lncRNA with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes/mRNA/lncRNA. Differentially expressed coding RNAs were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes reads counts and  FPKM values for each Sample

source_name: the greater omentum adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0. Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
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. After that, a total of G bp of cleaned, paired-end reads were produced.

value: the greater omentum adipose tissue


title: obesity4

description:
Library name: SAMPLE9
FPKM.Obesity4


title: Cow_Oocyte_12

description: 2x150bp reads

value: Oocyte

value: WT


title: obesity3

description:
Library name: SAMPLE8
FPKM.Obesity3


title: Liver sample 68

value: MASLD


title: obesity2

description:
Library name: SAMPLE7
FPKM.Obesity2


title: MAIT, 5-OP-RU + IL-18, D1

description: 10X Genomics


title: Cow_Zygote_3

description: 2x150bp reads


title: Cow_Oocyte_11

description: 2x150bp reads


title: normal5

description:
Library name: SAMPLE5
FPKM.Normal5


title: normal3

description:
Library name: SAMPLE3
FPKM.Normal3


title: Cow_Oocyte_8

description: 2x150bp reads


title: Cow_Oocyte_10

description: 2x150bp reads


title: normal4

description:
Library name: SAMPLE4
FPKM.Normal4


title: normal2

description:
Library name: SAMPLE2
FPKM.Normal2


title: Liver sample 66


title: SS2_PA_sample8

description: 2x150bp reads

data_processing:
Reads were mapped to the appropriate reference genome using STAR
Internal fragments and 5' transcript ends were distinguished using a custom python script available on github. For smart-seq2 and smart-seq2-polyA libraries, reads were not seperated by 5' or internal fragments and all reads were processed together
BigWig files were generated from unique mapping reads, rRNA removed and rpm normalized, using bedtools and ucsc bedGraphToBigWig
TEs and genes were quantified from unique and multimapping reads from 5' fragments using TEtranscript
For more information see (gitlab link)
Assembly: GRCm38 (Mus musculus), Sscrofa11.1 (Sus scrofa), Btau_5.0.1 (Bos taurus), OryCun2.0 (Oryctolagus cuniculus), Mmul_8.0.1 (Macaca mulatta)
Supplementary files format and content: merged bigWig files, 2 files per species/stage seperated for 5' fragments ("FivePrime") and internal fragments ("Else")
Supplementary files format and content: table txt file containing gene and TE counts for each species using 5' fragments (Smart-seq+5') or all fragments (Smart-seq2)

source_name: Late 2 cell embryo

growth_protocol:
Oocyte and preimplantation stages were collected from mouse, pig, cow, rabbit and rhesus.
Stem cells were cultured in appropriate medium and collected at least 48hr since last cell split. rbESC were seperated from feeder cells by FACS using the Oct4-GFP marker. For more information see methods of accompaning paper

extract_protocol:
For each library a single embryo from was used originating from the listed species and developmental stage. For stem cells, RNA was extracted using the ReliaPrep kit. 250pg was used as input for the Smart-seq+5 protocol. For more information see methods of accompaning paper
An adapted version of Smart-seq2 (called Smart-seq+5') was used to capture both 5' transcript information as well as internal transcript fragments. For Smart-seq2 libraries (SS2), embryos were processed as described in published protocol (Picelli et. al. 2014). For Smart-seq2-polyA libraries (SS2-PA), an additional polyadenylation step was preformed at the start of the protocol. See methods of accompaning paper for more information
Smart-seq+5'

value: Late 2 cell embryo


title: Liver sample 65


title: Cow_Oocyte_7

description: 2x150bp reads


title: Cow_Oocyte_6

description: 2x150bp reads


title: Liver sample 64


title: Clone42_UPSEM_24H_S8

city: Paris

first: Sheerazed

last: BOULKROUN

address: 56 rue Leblanc

country: France

institute: Inserm

data_processing:
STAR (v2.7.6a), RSEM (v1.3.1), R 4.2.2, DESeq2_1.38.1
STAR --genomeDir /path/to/STAR/reference/directory --sjdbGTFfile /path/to/gtf --runThreadN 20 --readFilesIn /path/to/fastq/R1 /path/to/fastq/R2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output /path/to/AlignedToTranscriptome/file /path/to/rsem-prepare-reference/files [sample-rsem-suffix]
Deseq2 Design : ~ Clone + Condition
Assembly: Ensembl release 101, GRCh38
Supplementary files format and content: Raw counts from rsem in tabulated format, filename ending by .resultsRSEM.genes.results
Supplementary files format and content: Normalized matrix in tabulated format : NGS22-060_ensemblGRCh38r101_deseq2_NormalizedMatrix.tsv

growth_protocol: H295R-S2 adrenocortical cells were maintained in complete medium containing DMEM/Eagle's F12 medium supplemented with 2% Ultroser G, 1% insulin/trasnsferrin/selenium and 1% penicillin and streptomycin.

extract_protocol:
RNA was extracted using Trizol (Thermo Fischer Scientific). 250 ng of total RNA was used for the construction of sequecing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA Prep kit (Illumina).

treatment_protocol: 24 hours after seeding, cells were serum-deprived in DMEM/F12 containing 0.1% Ultroser G for 24 hours and then incubated for 8h or 24h with fresh serum-deprived medium with solvent (basal) or with 10-8M AngII, 12 mM K+ or 10-7M uPSEM-817.

value: a7-5HT3 Knock In

value: UPSEM

tag: time

value: 24 hours


title: normal1

description:
Library name: SAMPLE1
FPKM.Normal1


title: Cow_Zygote_1

description: 2x150bp reads


title: Liver sample 63


title: SS2_PA_sample7

description: 2x150bp reads


title: Cow_Oocyte_5

description: 2x150bp reads


title: SS2_sample6

description: 2x150bp reads


title: Liver sample 62


title: Clone42_K_24H_S6

value: K


title: Cow_Oocyte_4

description: 2x150bp reads


title: SS2_sample5

description: 2x150bp reads


title: Clone42_AngII_24H_S7

value: AngII


title: Liver sample 61


title: obesity1

description:
Library name: SAMPLE6
FPKM.Obesity1


title: Clone42_Basal_24H_S5

value: Solvent


title: Liver sample 67


title: Cow_Oocyte_3

description: 2x150bp reads


title: mESC_R7

description: 2x150bp reads

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: Clone42_UPSEM_8H_S4

value: 8 hours


title: mESC_R6

description: 2x150bp reads


title: Liver sample 59


title: mESC_R5

description: 2x150bp reads


title: Cow_Oocyte_2

description: 2x150bp reads


title: Clone42_AngII_8H_S3


title: mESC_R4

description: 2x150bp reads


title: Cow_Oocyte_1

description: 2x150bp reads


title: Pig_Morula_12

description: 2x150bp reads

organism: Sus scrofa

value: Morula


title: Liver sample 56


title: mESC_R3

description: 2x150bp reads


title: Clone42_K_8H_S2


title: Clone42_Basal_8H_S1


title: Liver sample 57


title: Pig_Morula_11

description: 2x150bp reads


title: Liver sample 55


title: Clone24_UPSEM_24H_S16


title: Pig_Morula_9

description: 2x150bp reads


title: mESC_R2

description: 2x150bp reads


title: mESC_R1

description: 2x150bp reads


title: Clone24_AngII_24H_S15


title: Liver sample 60


title: Clone24_K_24H_S14


title: Liver sample 54


title: Liver sample 58


title: Mouse_16-cell_12

description: 2x150bp reads

value: 16 cell embryo


title: Pig_Morula_8

description: 2x150bp reads


title: Clone24_Basal_24H_S13


title: Mouse_16-cell_11

description: 2x150bp reads


title: Pig_Morula_6

description: 2x150bp reads


title: Pig_Morula_7

description: 2x150bp reads


title: Mouse_16-cell_10

description: 2x150bp reads


title: Clone24_UPSEM_8H_S12


title: Liver sample 52

value: liver


title: Clone24_AngII_8H_S11


title: Liver sample 51


title: Pig_Morula_5

description: 2x150bp reads


title: Pig_Morula_10

description: 2x150bp reads


title: Liver sample 50


title: Mouse_16-cell_9

description: 2x150bp reads


title: Pig_Morula_4

description: 2x150bp reads


title: Clone24_K_8H_S10


title: Mouse_16-cell_8

description: 2x150bp reads


title: Clone24_Basal_8H_S9


title: Liver sample 49


title: Liver sample 48

value: ARLD


title: Pig_Morula_2

description: 2x150bp reads


title: Clone17_UPSEM_24H_S8


title: Mouse_16-cell_6

description: 2x150bp reads


title: Liver sample 47


title: Clone17_AngII_24H_S7


title: Mouse_16-cell_5

description: 2x150bp reads


title: Pig_Morula_1

description: 2x150bp reads


title: Liver sample 46


title: Pig_Day3_12

description: 2x150bp reads

source_name: Day3/8-16 cell embryo

value: Day3/8-16 cell embryo


title: Clone17_K_24H_S6


title: Liver sample 45


title: Pig_Day3_11

description: 2x150bp reads


title: Liver sample 44


title: Mouse_16-cell_3

description: 2x150bp reads


title: Clone17_Basal_24H_S5


title: Clone17_UPSEM_8H_S4


title: Pig_Morula_3

description: 2x150bp reads


title: Mouse_16-cell_2

description: 2x150bp reads


title: Pig_Day3_10

description: 2x150bp reads


title: Pig_Day3_8

description: 2x150bp reads


title: Mouse_16-cell_7

description: 2x150bp reads


title: Clone17_AngII_8H_S3


title: Liver sample 43


title: Pig_Day3_7

description: 2x150bp reads


title: Clone17_K_8H_S2


title: Mouse_16-cell_1

description: 2x150bp reads


title: Mouse_8-cell_12

description: 2x150bp reads

value: 8 cell embryo


title: Liver sample 41


title: Pig_Day3_6

description: 2x150bp reads

value: WT


title: Mouse_8-cell_11

description: 2x150bp reads


title: Mouse_16-cell_4

description: 2x150bp reads


title: Rabbit_Morula_12

description: 2x150bp reads

organism: Oryctolagus cuniculus

value: Zika


title: Mouse_8-cell_10

description: 2x150bp reads


title: Liver sample 39


title: Pig_Day3_4

description: 2x150bp reads


title: Pig_Day3_5

description: 2x150bp reads


title: Mouse_8-cell_9

description: 2x150bp reads


title: Liver sample 53

value: MASLD


title: Rabbit_Morula_9

description: 2x150bp reads


title: Liver sample 40


title: Liver sample 42


title: Pig_Day3_3

description: 2x150bp reads


title: Rabbit_Morula_11

description: 2x150bp reads


title: Liver sample 37


title: Pig_Day3_2

description: 2x150bp reads


title: Mouse_8-cell_8

description: 2x150bp reads


title: Rabbit_Morula_8

description: 2x150bp reads


title: Mouse_8-cell_7

description: 2x150bp reads


title: Liver sample 36


title: Rabbit_Morula_7

description: 2x150bp reads


title: Clone17_Basal_8H_S1

value: a7-5HT3 Knock In


title: Liver sample 35


title: Pig_Day3_1

description: 2x150bp reads


title: Rabbit_Morula_6

description: 2x150bp reads


title: Pig_Day2_12

description: 2x150bp reads

source_name: Day2/5-8 cell embryo

value: Day2/5-8 cell embryo


title: Mouse_8-cell_6

description: 2x150bp reads


title: Liver sample 34

value: CVH


title: Rabbit_Morula_5

description: 2x150bp reads


title: Pig_Day2_11

description: 2x150bp reads


title: Mouse_8-cell_4

description: 2x150bp reads


title: Rabbit_Morula_4

description: 2x150bp reads


title: Liver sample 33


title: Mouse_8-cell_3

description: 2x150bp reads


title: Pig_Day2_10

description: 2x150bp reads


title: Rabbit_Morula_3

description: 2x150bp reads


title: Liver sample 38


title: Liver sample 32


title: Mouse_8-cell_2

description: 2x150bp reads


title: Liver sample 31


title: Pig_Day2_9

description: 2x150bp reads


title: Pig_Day2_8

description: 2x150bp reads


title: Rabbit_Morula_2

description: 2x150bp reads


title: Rabbit_Morula_1

description: 2x150bp reads


title: Mouse_4-cell_12

description: 2x150bp reads

value: 4 cell embryo


title: Pig_Day2_7

description: 2x150bp reads


title: Liver sample 30


title: Mouse_8-cell_1

description: 2x150bp reads


title: Rabbit_16-cell_12

description: 2x150bp reads


title: Mouse_8-cell_5

description: 2x150bp reads


title: Pig_Day2_6

description: 2x150bp reads


title: Liver sample 29


title: Mouse_4-cell_11

description: 2x150bp reads


title: Liver sample 28


title: Mouse_4-cell_9

description: 2x150bp reads


title: Pig_Day2_5

description: 2x150bp reads


title: Liver sample 27


title: Rabbit_16-cell_10

description: 2x150bp reads


title: Pig_Day2_4

description: 2x150bp reads


title: Pig_Day2_3

description: 2x150bp reads


title: Liver sample 25


title: Liver sample 26


title: Pig_Day2_1

description: 2x150bp reads


title: Mouse_4-cell_5

description: 2x150bp reads


title: Liver sample 23


title: Liver sample 24


title: Rabbit_16-cell_9

description: 2x150bp reads


title: Pig_Day2_2

description: 2x150bp reads


title: Mouse_4-cell_8

description: 2x150bp reads


title: Rabbit_16-cell_11

description: 2x150bp reads


title: Mouse_4-cell_7

description: 2x150bp reads


title: Rabbit_16-cell_7

description: 2x150bp reads


title: Rabbit_16-cell_8

description: 2x150bp reads


title: Mouse_4-cell_6

description: 2x150bp reads


title: Mouse_4-cell_4

description: 2x150bp reads


title: Liver sample 22


title: Rabbit_16-cell_5

description: 2x150bp reads


title: Pig_4-cell_12

description: 2x150bp reads

source_name: 4-cell embryo

value: 4-cell embryo


title: Mouse_4-cell_3

description: 2x150bp reads


title: Liver sample 21


title: Pig_4-cell_11

description: 2x150bp reads


title: Mouse_4-cell_2

description: 2x150bp reads


title: Liver sample 20


title: Rabbit_16-cell_3

description: 2x150bp reads

source_name: 16 cell embryo


title: Pig_4-cell_9

description: 2x150bp reads


title: Rabbit_16-cell_6

description: 2x150bp reads


title: Mouse_4-cell_1

description: 2x150bp reads


title: Mouse_Late-2-cell_10

description: 2x150bp reads

value: Late 2 cell embryo


title: Liver sample 19


title: Rabbit_16-cell_2

description: 2x150bp reads


title: Pig_4-cell_7

description: 2x150bp reads


title: Pig_4-cell_8

description: 2x150bp reads


title: Liver sample 18


title: Mouse_Late-2-cell_9

description: 2x150bp reads


title: Rabbit_16-cell_1

description: 2x150bp reads


title: Mouse_Late-2-cell_7

description: 2x150bp reads


title: Pig_4-cell_5

description: 2x150bp reads


title: Rabbit_16-cell_4

description: 2x150bp reads


title: Mouse_Late-2-cell_8

description: 2x150bp reads


title: Pig_4-cell_10

description: 2x150bp reads


title: Liver sample 17


title: Pig_4-cell_4

description: 2x150bp reads


title: Rabbit_8-cell_15

description: 2x150bp reads

source_name: 8 cell embryo


title: Pig_4-cell_6

description: 2x150bp reads


title: Liver sample 16


title: Rabbit_8-cell_12

description: 2x150bp reads


title: Rabbit_8-cell_14

description: 2x150bp reads


title: Mouse_Late-2-cell_6

description: 2x150bp reads


title: Pig_4-cell_3

description: 2x150bp reads


title: Liver sample 15


title: Liver sample 14


title: Liver sample 13


title: Rabbit_8-cell_11

description: 2x150bp reads


title: Pig_4-cell_2

description: 2x150bp reads


title: Mouse_Late-2-cell_4

description: 2x150bp reads


title: Liver sample 12


title: Liver sample 11


title: Mouse_Late-2-cell_3

description: 2x150bp reads


title: Rabbit_8-cell_13

description: 2x150bp reads


title: Pig_4-cell_1

description: 2x150bp reads


title: Rabbit_8-cell_9

description: 2x150bp reads


title: Rabbit_8-cell_8

description: 2x150bp reads


title: Mouse_Late-2-cell_2

description: 2x150bp reads


title: Pig_2-cell_12

description: 2x150bp reads

source_name: 2 cell embryo

value: 2 cell embryo


title: Liver sample 9


title: Rabbit_8-cell_6

description: 2x150bp reads


title: Pig_2-cell_10

description: 2x150bp reads


title: Liver sample 8


title: Rabbit_8-cell_7

description: 2x150bp reads


title: Rabbit_8-cell_5

description: 2x150bp reads


title: Mouse_Late-2-cell_5

description: 2x150bp reads


title: Pig_2-cell_8

description: 2x150bp reads


title: Pig_2-cell_11

description: 2x150bp reads


title: Liver sample 7


title: Mouse_Early-2-cell_12

description: 2x150bp reads

source_name: Early 2 cell embryo

value: Early 2 cell embryo


title: Mouse_Early-2-cell_11

description: 2x150bp reads


title: Rabbit_8-cell_4

description: 2x150bp reads


title: Mouse_Early-2-cell_10

description: 2x150bp reads


title: Liver sample 10


title: Rabbit_8-cell_3

description: 2x150bp reads


title: Pig_2-cell_6

description: 2x150bp reads


title: Mouse_Early-2-cell_9

description: 2x150bp reads


title: Pig_2-cell_7

description: 2x150bp reads


title: Liver sample 6


title: Liver sample 5


title: Pig_2-cell_5

description: 2x150bp reads


title: Rabbit_8-cell_1

description: 2x150bp reads


title: Mouse_Late-2-cell_1

description: 2x150bp reads


title: Liver sample 4


title: Mouse_Early-2-cell_7

description: 2x150bp reads


title: Liver sample 3


title: Liver sample 2


title: Liver sample 1


title: Mouse_Early-2-cell_3

description: 2x150bp reads


title: Rabbit_4-cell_11

description: 2x150bp reads

source_name: 4 cell embryo


title: Pig_2-cell_2

description: 2x150bp reads


title: Pig_2-cell_1

description: 2x150bp reads


title: Mouse_Early-2-cell_1

description: 2x150bp reads


title: Rabbit_4-cell_8

description: 2x150bp reads


title: Mouse_Early-2-cell_4

description: 2x150bp reads


title: Rabbit_4-cell_9

description: 2x150bp reads


title: Mouse_Zygote_12

description: 2x150bp reads

source_name: Zygote

value: Zygote


title: 70-M-Pt-K4

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

data_processing:
Basecalls were performed for Illumina NovaSeq 6000 output.
ChIP-seq reads were trimmed using Trimmomatic v0.38.
ChIP-seq reads were aligned to the Homo sapiens reference genome GRCh38 using BowTie v1.1.2.
Peaks were called using MACS2 v2.1.1.20160309 and duplicate reads were processed using Picard v0.118.
Peaks annotated using ChIPseeker 1.16.1.
Normalized bedGraph files were generated using MACS2 and converted to bigwig files using bedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: eye

extract_protocol:
Tissues were fixed with 1% formaldehyde for 15min. After quenching and cell lysis, chromatin sheared via sonication and incubated with protein A agarose beads conjugated with anti-H3K4me3 and anti-H3K9me3. The DNA was extracted with QIAquick PCR purification kits.
ChIP-seq libraries were constructed using TruSeq DNA Sample prep kits and sequenced on an Illumina Novaseq 6000.

value: eye

value: pterygium

value: stage 3


title: Pig_Zygote_12

description: 2x150bp reads


title: Rabbit_4-cell_6

description: 2x150bp reads


title: 70-M-Pt-K9


title: Pig_Zygote_11

description: 2x150bp reads


title: Mouse_Zygote_11

description: 2x150bp reads


title: 70-M-Pt-H3


title: Rabbit_8-cell_2

description: 2x150bp reads


title: Pig_2-cell_4

description: 2x150bp reads


title: Pig_Zygote_10

description: 2x150bp reads


title: Mouse_Zygote_10

description: 2x150bp reads


title: Pig_Zygote_9

description: 2x150bp reads


title: Rabbit_4-cell_4

description: 2x150bp reads


title: 70-M-Ct-K9

value: conjunctiva


title: Mouse_Early-2-cell_6

description: 2x150bp reads


title: Pig_2-cell_3

description: 2x150bp reads


title: Rabbit_4-cell_10

description: 2x150bp reads


title: Mouse_Zygote_8

description: 2x150bp reads


title: 70-M-Ct-K4


title: Rabbit_4-cell_3

description: 2x150bp reads


title: Pig_Zygote_8

description: 2x150bp reads


title: Mouse_Zygote_7

description: 2x150bp reads


title: Rabbit_4-cell_2

description: 2x150bp reads


title: Mouse_Zygote_6

description: 2x150bp reads


title: Rabbit_4-cell_1

description: 2x150bp reads


title: 70-F-Pt-K9


title: 70-F-Pt-K4


title: Mouse_Zygote_5

description: 2x150bp reads


title: Rabbit_2-cell_12

description: 2x150bp reads


title: Mouse_Zygote_4

description: 2x150bp reads


title: Rabbit_4-cell_5

description: 2x150bp reads


title: 70-F-Pt-H3


title: Pig_Zygote_4

description: 2x150bp reads


title: Rabbit_2-cell_10

description: 2x150bp reads


title: 70-F-Ct-K9


title: Mouse_Zygote_3

description: 2x150bp reads


title: Pig_Zygote_3

description: 2x150bp reads


title: 70-F-Ct-K4


title: Rabbit_2-cell_9

description: 2x150bp reads


title: Mouse_Zygote_2

description: 2x150bp reads


title: Pig_Zygote_7

description: 2x150bp reads


title: Rabbit_2-cell_8

description: 2x150bp reads


title: 70-M-Ct-H3


title: Pig_Zygote_2

description: 2x150bp reads


title: Mouse_Zygote_1

description: 2x150bp reads


title: Rabbit_2-cell_7

description: 2x150bp reads


title: Rabbit_2-cell_6

description: 2x150bp reads


title: Pig_Zygote_6

description: 2x150bp reads


title: Pig_Zygote_1

description: 2x150bp reads


title: 60-M-Pt-K9


title: Mouse_Oocyte_12

description: 2x150bp reads

source_name: Oocyte

value: Oocyte


title: 60-M-Pt-K4


title: Pig_Zygote_5

description: 2x150bp reads

value: WT


title: Rabbit_2-cell_5

description: 2x150bp reads

value: Zika


title: Rabbit_2-cell_4

description: 2x150bp reads


title: 60-M-Ct-K9


title: Rabbit_2-cell_3

description: 2x150bp reads


title: 60-M-Pt-H3


title: Mouse_Oocyte_10

description: 2x150bp reads


title: 70-F-Ct-H3


title: Mouse_Oocyte_11

description: 2x150bp reads


title: 60-M-Ct-K4


title: Pig_Oocyte_10

description: 2x150bp reads


title: Mouse_Oocyte_8

description: 2x150bp reads


title: Mouse_Oocyte_7

description: 2x150bp reads


title: Rabbit_2-cell_1

description: 2x150bp reads


title: 60-F-Pt-K9


title: 60-M-Ct-H3


title: Mouse_Oocyte_4

description: 2x150bp reads


title: Rabbit_Zygote_10

description: 2x150bp reads


title: Mouse_Oocyte_5

description: 2x150bp reads


title: Pig_Oocyte_11

description: 2x150bp reads


title: Pig_Oocyte_12

description: 2x150bp reads


title: Pig_Oocyte_6

description: 2x150bp reads


title: Rabbit_Zygote_11

description: 2x150bp reads


title: Pig_Oocyte_7

description: 2x150bp reads


title: Mouse_Oocyte_3

description: 2x150bp reads


title: Pig_Oocyte_9

description: 2x150bp reads


title: Rabbit_2-cell_2

description: 2x150bp reads


title: Pig_Oocyte_8

description: 2x150bp reads


title: Mouse_Oocyte_6

description: 2x150bp reads


title: Pig_Oocyte_5

description: 2x150bp reads


title: 60-F-Pt-K4


title: 60-F-Pt-H3


title: Rabbit_Zygote_9

description: 2x150bp reads


title: Rabbit_Zygote_8

description: 2x150bp reads


title: Mouse_Oocyte_2

description: 2x150bp reads


title: 60-F-Ct-K9


title: Pig_Oocyte_3

description: 2x150bp reads


title: 60-F-Ct-K4


title: Mouse_Oocyte_1

description: 2x150bp reads


title: Rabbit_Zygote_7

description: 2x150bp reads


title: Pig_Oocyte_1

description: 2x150bp reads


title: Zn15_Brain

city: Wuxi

first: Fan

last: Yu

address: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China

data_processing:
Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.
Generation and Analysis of Single-Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings
Genome_build: GRCz11
Supplementary_files_format_and_content: barcodes counts, barcodes and gene files

organism: Danio rerio

source_name: Zn15_Brain Single cell

extract_protocol:
Single brain cell were prepared
libraries were prepared for sequencing using standard 10Xgenomic protocols

value: Brain


title: Rabbit_Zygote_4

description: 2x150bp reads


title: DOCA_salt-2

city: Jinan

last: Yi

address: Wenhua Road

institute: Shandong University

description:
Library name: sample8
10X Genomics

data_processing:
Illumina platform sequencing was used to obtain Raw off-machine sequences (Raw reads), and data interception was performed to obtain sequences to be analyzed (Clean reads). All subsequent analyses were based on Clean reads with GRCm38 genome compilation as a reference and the corresponding GENCODE annotation file (version 25). The count matrix was screened, only protein-coding genes, long noncoding genes and antisense genes were retained, and the Ensembl ID was replaced with Mouse Genome Informatics (MGI) symbols.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Mouse kidney cells treated with CART cells and each control group were isolated. After grinding, cells from each group were dissociated into single-cell suspension.
The freshly prepared single-cell suspension was adjusted to 700-1200 cell/μl according to the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (No. 1000268) Operation manual for computer and library construction. After reverse transcription, Qubit3.0 was used for preliminary quantification, and the library was diluted to 1ng/ul. Then, Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, Q-PCR was performed using StepOnePlus Real-Time PCR System to accurately quantify the effective concentration of the library (the effective concentration of the library was required to be > 10nM) and ensure the quality of the library. Qualified libraries were sequenced using theIllumina Nova 6000 PE150 platform.

value: Kidney


title: Rabbit_Zygote_2

description: 2x150bp reads


title: Rabbit_Zygote_5

description: 2x150bp reads


title: HEK293, Iso-Dyngo, Riboseq, rep3 [ISODYNGO3.RIBO]

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description:
Novogene
MK24

data_processing:
*library strategy: RIBO-seq
Samples were trimmed with BBDuk (BBMap version #38.63) to remove adaptors.
Sequences aligning to ncRNA, tRNA, and rRNA were removed using Bowtie (version 2.3.5)
Cleaned files were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) using STARaligner (version 2.7.5)
FeatureCounts (Subread version 1.6.3) was used to align and quantify coding sequences, with RPF reads being narrowed to reads of length 26 to 34 nucleotides.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw reads for each Sample

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS. For the experiment, cells were cultured in DMEM without FBS

extract_protocol:
All samples were lysed in Riboseq lysis buffer (20 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100ug/mL cyclohexamide, 25 u/mL DNase I). RNAseq samples were purified with Qiagen RNeasy Plus Mini Kit. Ribo-seq samples were purified on Zymo-Spin IIC columns, then ribosome protected fragments were size-selected on 15% TBE-Urea gels. rRNA for Ribo-seq samples was depleted with Galen Molecular Human riboPOOL for Ribosome Profiling RNA kit.
RNAseq samples were prepared the NEBNext Ultra II RNA Library Prep Kit for Illumina. Riboseq samples were prepared with NEBNext Multiplex Small RNA Library Prep Kit for Illumina

treatment_protocol: 20 minutes of DMSO or 30uM Dyngo, then 2 hours of 1 uM isoproterenol or left untreated

value: Human embryonic kidney cell

value: 30uM Dyngo (20 min), 1uM Isoproterenol (2 hr)


title: HEK293T cells, NT, rep1

city: Changchun

first: Tao

last: Zhang

address: Xinzhu Road

institute: Jilin University

description:
1
NSUN6_vs_NT_DMC_p_0.05_d_0.05.xls

data_processing:
Trimmomatic，PE150
Sequence reads were trimmed for adaptor sequence/low-qualty sequence using Trimmomatic software (parameter- Quality limit: 0.05）
Software BS-RNA performs data preprocessing, pairing, and annotation.
MetalKit software was used to identify inter group DMC(Differential methylation  m5C sites).
Assembly: hg38
Supplementary files format and content: xls file includes pvalue  and qvalue of each sample
Supplementary files format and content: xls file includes meth.diff of each sample
Library strategy: RNA-BSPseq

extract_protocol:
The total RNA of each sample was extracted using Invitrogen TRIzol® Reagent. After quality testing, the RNA-BS libraries were constructed by E-GENE Co.
Briefly, the extracted total RNA was firstly subjected to DNase I (NEB) treatment at 37℃ for 30min to remove residual DNA. After purification, mRNA was isolated using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA bisulfite conversion of the isolated RNA samples was conducted using EZ RNA Methylation Kit (Zymo Research) with two cycles of 70 ℃ for 5min followed by 54℃ for 45min incubation and then purified using the provided Zymo-Spin IC Column according to the manufacturer’s instructions. Bisulfite converted RNA reverse transcription was carried out using ACT random hexamers and Superscript II Reverse Transcriptase (Invitrogen), the synthesized cDNA was then used for the final library construction.

value: Human Embryonic Kidney 293 Cells

value: Methylation differentiation by RCMS Editors


title: Sham-3

description:
Library name: sample12
10X Genomics


title: Sham-2

description:
Library name: sample11
10X Genomics


title: HEK293T cells, NT, rep3

description:
3
NSUN6_vs_NT_DMC_p_0.05_d_0.05.xls


title: 60-F-Ct-H3


title: HEK293, Iso-Dyngo, Riboseq, rep1 [ISODYNGO1.RIBO]

description:
Novogene
MK22


title: Ctrl_Brain

institute: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization

source_name: Ctrl_Brain Single cell

value: Ctrl


title: Rabbit_Zygote_6

description: 2x150bp reads


title: Zn10_Brain

source_name: Zn10_Brain Single cell


title: HEK293T cells, NT, rep2

description:
2
NSUN6_vs_NT_DMC_p_0.05_d_0.05.xls


title: HEK293T cells, dCasRx-NSUN6, rep2

description:
8
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: DOCA_salt-1

description:
Library name: sample7
10X Genomics


title: DOCA_salt+Vec-T-3

description:
Library name: sample6
10X Genomics


title: HEK293, Dyngo, Riboseq, rep2 [DYNGO2.RIBO]

description:
Novogene
MK20

value: 30uM Dyngo (20 min), no drug


title: Sham-1

description:
Library name: sample10
10X Genomics


title: HEK293T cells, dCasRx-NSUN6, rep1

description:
7
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: Rabbit_Oocyte_13

description: 2x150bp reads


title: HEK293, Dyngo, Riboseq, rep3 [DYNGO3.RIBO]

description:
Novogene
MK21


title: Rabbit_Zygote_1

description: 2x150bp reads


title: HEK293T cells, dCasRx-dNSUN6, rep3

description:
6
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: Pig_Oocyte_4

description: 2x150bp reads


title: HEK293, Iso-Dyngo, Riboseq, rep2 [ISODYNGO2.RIBO]

description:
Novogene
MK23


title: Rabbit_Zygote_3

description: 2x150bp reads


title: DOCA_salt-3

description:
Library name: sample9
10X Genomics


title: HEK293T cells, dCasRx-NSUN6, rep3

description:
9
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: Rabbit_Oocyte_12

description: 2x150bp reads


title: HEK293, Dyngo, Riboseq, rep1 [DYNGO1.RIBO]

description:
Novogene
MK19


title: Rabbit_Oocyte_11

description: 2x150bp reads


title: HEK293T cells, dCasRx-dNSUN6, rep2

description:
5
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: DOCA_salt+mPDGFRβ_CAR-T-3

description:
Library name: sample3
10X Genomics


title: HEK293, Iso, Riboseq, rep2 [ISO2.RIBO]

description:
Novogene
MK17

value: DMSO, 1uM Isoproterenol (2 hr)


title: Rabbit_Oocyte_9

description: 2x150bp reads


title: hdSpO5

value: Human dorsal spinal cord organoids (hdSpO)


title: HEK293, Iso, Riboseq, rep3 [ISO3.RIBO]

description:
Novogene
MK18


title: DOCA_salt+mPDGFRβ_CAR-T-2

description:
Library name: sample2
10X Genomics


title: HEK293T cells, dCasRx-dNSUN6, rep1

description:
4
NSUN6_vs_dNSUN6_DMC_p_0.05_d_0.05.rename.xls


title: Rabbit_Oocyte_10

description: 2x150bp reads


title: DOCA_salt+Vec-T-1

description:
Library name: sample4
10X Genomics


title: hdSpO4


title: HEK293, no drug, Riboseq, rep3 [ND3.RIBO]

description:
Novogene
MK15

value: DMSO, no drug


title: Rabbit_Oocyte_7

description: 2x150bp reads


title: HEK293, no drug, Riboseq, rep2 [ND2.RIBO]

description:
Novogene
MK14


title: HEK293, Iso, Riboseq, rep1 [ISO1.RIBO]

description:
Novogene
MK16


title: Spleen, CD8 (HTO)

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: E1002 Biomedical Science Tower,  200 Lothrop Street

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Library strategy: CITE-seq
For demultiplexing of samples, cellranger (v6.0.0; 10X Genomics) was used with the defualt settings.
CellRanger was used to align gene expression data to the mm10 reference and generate feature barcode expression matrices using the default settings.
cite-seq-count was(v1.4.3) used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 -trim 10.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression feature barcode matrices.  CITEseq feature barcode matrices.  The cite seq hash tags to distinguish different experimental settings.

molecule: protein

source_name: spleen

extract_protocol: Splenocytes were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with Cl. 13. for 16d. T cells were enriched by negative selection. Briefly, single cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with a uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration.A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population. Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: LCMV infected only

value: spleen


title: hdSpO3


title: Rabbit_Oocyte_6

description: 2x150bp reads

value: Oocyte


title: Spleen, Tregs (HTO)

value: naïve or LCMV infected


title: HEK293, no drug, Riboseq, rep1 [ND1.RIBO]

description:
Novogene
MK13

value: WT


title: Spleen, CD8 (GEX)


title: Rabbit_Oocyte_5

description: 2x150bp reads

value: Zika


title: hdSpO1


title: DOCA_salt+Vec-T-2

description:
Library name: sample5
10X Genomics

value: Kidney


title: Rabbit_Oocyte_4

description: 2x150bp reads


title: Rabbit_Oocyte_3

description: 2x150bp reads


title: DOCA_salt+mPDGFRβ_CAR-T-1

description:
Library name: sample1
10X Genomics


title: HEK293, Iso-Dyngo, RNAseq, rep2 [ISODYNGO2.RNA]

description:
Novogene
MK11

data_processing:
Samples were trimmed with BBDuk (BBMap version #38.63) to remove adaptors.
Sequences aligning to ncRNA, tRNA, and rRNA were removed using Bowtie (version 2.3.5)
Cleaned files were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) using STARaligner (version 2.7.5)
FeatureCounts (Subread version 1.6.3) was used to align and quantify coding sequences, with RPF reads being narrowed to reads of length 26 to 34 nucleotides.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw reads for each Sample

value: Human embryonic kidney cell


title: hSeO_4

value: Human sensory organoids (hSeO)


title: rbESC_R3T2S2

description: 2x150bp reads

source_name: rabbit embryonic stem cells

value: rabbit embryonic stem cells


title: Spleen, Tregs (GEX)


title: rbESC_R3T2

description: 2x150bp reads


title: Rabbit_Oocyte_2

description: 2x150bp reads


title: Rabbit_Oocyte_8

description: 2x150bp reads


title: hdSpO2


title: HEK293, Iso-Dyngo, RNAseq, rep1 [ISODYNGO1.RNA]

description:
Novogene
MK10

value: 30uM Dyngo (20 min), 1uM Isoproterenol (2 hr)


title: hSeO_1


title: Rabbit_Oocyte_1

description: 2x150bp reads


title: hSeO_3


title: HEK293, Dyngo, RNAseq, rep2 [DYNGO2.RNA]

description:
Novogene
MK8


title: hSeO_2


title: irradiated_patient_blood

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

description: mRNA Expression Profiling

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: blood

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: sample preparation

value: scRNA-seq

value: blood


title: HEK293, Dyngo, RNAseq, rep3 [DYNGO3.RNA]

description:
Novogene
MK9

value: 30uM Dyngo (20 min), no drug


title: MEF_WT2

city: Dallas

first: Yingfei

last: Wang

address: 5323 Harry Hines BLVD

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Assembly: hg19
Supplementary files format and content: TXT

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a Kapa mRNA Hyper Prep kit (Roche).

value: MEF


title: rbESC_R3T1S2

description: 2x150bp reads

tag: tissue


title: rbESC_R3T1

description: 2x150bp reads


title: HEK293, Dyngo, RNAseq, rep1 [DYNGO1.RNA]

description:
Novogene
MK7

tag: cell line


title: OS cell lines-143B shBIP_3

city: shanghai

first: tao

address: 650 new songjiang road

institute: Department of Orthopedics,Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using HISAT2 soft
HTSeq statistics were used to compare the Read Count value of each gene as the original expression level of the gene, and the expression level was standardized by the number of fragments per million from a gene per thousand base length (FPKM).
We adopt DESeq for differences in gene expression analysis, screening of differentially expressed genes conditions as follows: the expression differences multiples | log2FoldChange | > 1, significant P - value < 0.05.  The differential genes were analyzed by ggploT2 and Pheatmap, and the protein network interaction was mapped by Cytoscape.
Genome_build: Ensembl Homo_sapiens（102.38）
Supplementary_files_format_and_content: The Expression file provides the normalized Expression data (FPKM) for each sample
Supplementary_files_format_and_content: The DESeq file provided the differential expression multiple and P value of each gene in different comparison groups.

source_name: osteosarcoma

extract_protocol:
Total RNA of Cells was isolated using the Trizol Reagent (Invitrogen Life Technologies) and quantified in a NanoDrop (ThermoFisher). 3 μg of total RNA were used for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was sequenced on a Hiseq platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

tag: cell type

value: osteosarcoma cell line

value: specific targeting  BIP-shRNA

value: BIP KD

tag: cell  line


title: rbESC_R2T2S2

city: München

address: Feodor-Lynen-Strasse 21

institute: Helmholtz Zentrum München

description: 2x150bp reads


title: HEK293, Iso, RNAseq, rep3 [ISO3.RNA]

description:
Novogene
MK6

tag: treatment

value: DMSO, 1uM Isoproterenol (2 hr)


title: MEF_WT1


title: HEK293, Iso-Dyngo, RNAseq, rep3 [ISODYNGO3.RNA]

description:
Novogene
MK12


title: OS cell lines-143B shBIP_2


title: C3WT_2


title: OS cell lines-143B shBIP_1

value: specific targeting BIP-shRNA


title: OS cell lines-143B NC3

value: Targeting NC-shRNA


title: C3WT_1


title: AIF3_2


title: OS cell lines-143B NC2


title: HEK293, no drug, RNAseq, rep3 [ND3.RNA]

description:
Novogene
MK3

value: WT

value: DMSO, no drug


title: rbESC_R2T1S2

description: 2x150bp reads


title: AIF3_1


title: HEK293, Iso, RNAseq, rep2 [ISO2.RNA]

description:
Novogene
MK5