title: CD56+ NK cells and CD8+ T cells in blood from humanized mice

city: Singapore

first: Wai Nam

last: Liu

address: 61 Biopolis Drive

country: Singapore

institute: Agency for Science, Technology and Research

description: 10x Genomics

data_processing:
Following the subjection of paired-end sequencing reads to the Cell Ranger (version 2.02; 10x genomics pipeline), quality control and cell selection were performed in R using the standard pre-processing workflow in Seurat (version 4.3.0) with some modifications. Firstly, data from blood, spleen and tumor samples were merged into one Seurat Object. Cells with less than 250 or more than 5,500 genes were excluded from the analysis. The maximum number of unique molecular identifiers (UMI) was set at 30,000, and cells were required to have a log10 Genes per UMI score of 0.8 or higher to address cell complexity. The mitochondrial ratio was restricted to <0.1. A total of 29,283 cells and 18,467 genes were used in the study. At the gene level, only genes expressed in ten or more cells were included in the analysis.
Assembly: grcm38 and grch38
Supplementary files format and content: NKsubset_integrated_metadata.csv
Supplementary files format and content: Tsubset_integrated_metadata.csv

source_name: Humanized mice

growth_protocol: Humanized mice were intravenously injected with AAV-hIL15, followed by the transplant of HCC-PDX.

extract_protocol:
Blood, spleen and HCC-PDX were first digested to generate single-cell suspensions. After that, the cells were subjected to dead cell removal and mouse cell depletion, using the Dead Cell Removal Kit (Miltenyi Biotec) and Mouse Cell Depletion Kit (Miltenyi Biotec), respectively. Viable human CD56+ NK cells and CD8+ T cells from these samples were then selected using CD56 MicroBeads, Human (Miltenyi Biotec) and CD8 MicroBeads, Human (Miltenyi Biotec). Subsequently, the cells were resuspended in Dulbecco's Phosphate Buffered Saline without calcium and magnesium ions (STEMCELL Technologies) to reach a density of 1,200 cells/µl.
Library was performed according to the manufacturer's instructions (Chromimum Next GEM Single Cell 3' Reagent Kits v3.1).

value: Blood


title: CD56+ NK cells and CD8+ T cells in HCC-PDX from humanized mice

status: Public on Dec 28 2024

type: SRA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: HCC-PDX


title: CD56+ NK cells and CD8+ T cells in spleen from humanized mice

description: 10x Genomics

value: Spleen


title: VR06_WR_b

city: Verona

first: Davide

last: Pasini

state: VR

address: Piazzale Ludovico Antonio Scuro 10

country: Italy

institute: University of Verona

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCh38 genome using STAR v2.7 and expression quantification were performed with RSEM
Assembly: GRCh38
Supplementary files format and content: comma-delimited file containing raw counts for each sample at baseline
Supplementary files format and content: comma-delimited file containing raw counts for each sample in the adaptation experiment

molecule: polyA RNA

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
RNA from organoids were isolated using the TRIzol® Reagent (Life Technologies), followed by the column based PureLink RNA Mini Kit (Thermo Fisher Scientific). Purified RNA quality was evaluated using RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent) and only RNA with an RNA Integrity Number (RIN) greater than 9 were used.
RNA-seq library were obtained using poly(A) enrichment with TrueSeq Stranded mRNA Library Prep kit (Illumina).

tag: individual

tag: disease state

value: pancreatic cancer

value: pancreatic ductal adenocarcinoma

tag: replicate

value: b

tag: condition

value: adapted to the removal of WNT3a and RSPO1 from the normal PDO media


title: VR01_WR24h_b

value: baseline PDO grown without WNT3A and RSPO1 for 24h


title: VR23_WR24h_b


title: HCC-PDX, anti-PD-1- and anti-TIGIT-treated, #3

data_processing:
Sequencing was performed using a 2 × 150 paired-end configuration. Image analysis and base calling were conducted by NovaSeq Control Software + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument. Following quality control and adapter sequence removal using Cutadapt, the sequences were first aligned to grcm38 mouse genome using HISAT2. Subsequently, those unaligned sequences were aligned to grch38 human genome, and the reads were counted using featurecounts. Genes with transcripts per million of three or above, in at least two of the three samples in a treatment group, were included in the analysis. Differentially expressed genes were defined based on the above criteria, with Benjamini-Hochberg corrected p-values ≤ 0.05 and log2 fold change ≥ 2 or ≤ -2.
Assembly: grcm38 and grch38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
RNA was harvested using Trizol Reagent (Thermo Fisher Scientific). One μg of total RNA was used for library preparations.
RNA libraries for RNA-seq were prepared according to the manufacturer’s protocol (VAHTS mRNA-seq V3 Library Prep Kit for Illumina).

treatment_protocol: Once the tumor growth, the mice were treated with saline, anti-PD-1 and/or anti-TIGIT antibodies.

value: Tumor

tag: cell type

value: Hepatocellular carcinoma

tag: treatment

value: Anti-PD-1 and anti-TIGIT antibodies


title: VR23_WR_a

value: a


title: VR01_WR_b


title: VR40-LNO patient-derived organoid

source_name: pancreatic ductal adenocarcinoma lymph node metastasis

value: baseline


title: Sample 44986, Positive, Replicate 1

city: München

first: Robert

middle: Stefan

last: Piecyk

state: Bayern

address: Marchioninistr. 15

department: Klinik und Poliklinik für Strahlentherapie und Radioonkologie

country: Germany

institute: LMU Klinikum

description:
Library name: 44986
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44986

data_processing:
RNA-Seq data was analysed using the nf-core/rnaseq pipeline v3.14.0 with Nextflow version 23.10.1, using default parameters.
Sequence reads were trimmed for adapter/low-quality sequence using Trim Galore (v0.6.7).
Reads were aligned to mm10 reference genome using STAR (v2.6.1) approach.
Extraction of the read count matrices was performed using Salmon (v1.10.1) approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes bias-corrected counts without an offset (TPM)

organism: Mus musculus

source_name: liver

growth_protocol: Mouse liver tissue were immediately harvested and frozen in liquid nitrogen.

extract_protocol:
Animals were sacrificed and Livers were collected, snap frozed in liquid nitrogen.Total RNA isolation from snap-frozen liver tissue or cultured cells was performed with RNeasy Mini Kit (Qiagen, 74106). The on-column DNA digestion was carried out using an RNase-free DNase kit (Qiagen) or RNA samples were treated with TURBO DNase (ThermoFisher Scientific, AM1907) according to the manufacturer’s protocol to completely remove genomic DNA.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols ( TruSeq Stranded).

treatment_protocol: Mouse were feeding CD-HFD for 12 months.

value: liver

tag: cell line

value: liver tissue

value: Hepatocyte, immune cells

tag: genotype

value: 12m CD-HFD feeding


title: HCC-PDX, anti-PD-1- and anti-TIGIT-treated, #1


title: VR01_WR_a


title: VR32-O patient-derived organoid


title: HCC-PDX, anti-TIGIT-treated, #3

value: Anti-TIGIT antibody


title: HCC-PDX, anti-PD-1- and anti-TIGIT-treated, #2


title: VR29-O patient-derived organoid


title: TCR data from Tetramer negative T cells and B cells from naive mouse

city: Zwijnaarde

first: Kevin

last: Verstaen

address: Technologiepark-Zwijnaarde 71

department: VIB Single Cell Core

country: Belgium

institute: VIB

description:
Library name: Sample 3 - TCR
10X Genomics

library_source: other

data_processing:
Gene counting was done using Cell Ranger software version 6.1.1
Assembly: mm10 (GRCm38 Ensembl version 99)
Supplementary files format and content: CellRanger count filtered and raw count matrix
Supplementary files format and content: CellRanger vdj tsv and csv files

molecule: other

source_name: spleen

extract_protocol:
Cells were sorted in PBS + 0,04% BSA
scRNA-seq

value: spleen

value: T cells and B cells

value: wildtype

value: vehicle

tag: library type

value: TCR


title: TCR data from Tetramer negative T cells and B cells from immunised mice

description:
Library name: Sample 2 - TCR
10X Genomics

value: Spike immunisation


title: VR01_WR_c

value: pancreatic cancer

value: pancreatic ductal adenocarcinoma

value: c

value: adapted to the removal of WNT3a and RSPO1 from the normal PDO media


title: VR06_WR_a

value: a


title: HCC-PDX, anti-TIGIT-treated, #2

value: Tumor

value: Hepatocellular carcinoma


title: Hashing data from Tetramer positive T cells and B cells from immunised mice

description:
Library name: Sample 1 - Hashing
10X Genomics

molecule: protein

value: HTO

tag: hashing antibodies

value: TotalSeq-C301 (Mouse 1 T cells), TotalSeq-C302 (Mouse 2 T cells), TotalSeq-C303 (Mouse 1 B cells), TotalSeq-C304  (Mouse 2 B cells)


title: VR23-LNO patient-derived organoid

value: pancreatic ductal adenocarcinoma lymph node metastasis

value: baseline


title: Hashing data from Tetramer negative T cells and B cells from immunised mice

description:
Library name: Sample 2 - Hashing
10X Genomics

value: spleen


title: VR01_WR24h_a

value: baseline PDO grown without WNT3A and RSPO1 for 24h


title: FPKM.DC5 D7

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

country: USA

institute: University of Illinois

description:
Library name: Sample 22
Monocytes-derived Dendritic cells-D7 Replicate 5

data_processing:
Data normalization was performed according to manufacturer’s instructions. Briefly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Tophat to map reads to the genome of Homo sapiens (Version: ). The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from 37 samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts. Transcripts that overlapped with known lncRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs. StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown.
Assembly: not provided
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.
Supplementary files format and content: Tab-delimited text files include RPKM counts for each sample.

source_name: Healthy buffy coats

growth_protocol: Freshly prepared buffy coats were collected from healthy donors (Oklahoma Blood Institute, Oklahoma City, OK, USA) and CD14+ monocytes were obtained by density gradient centrifugation and magnetic bead isolation. Monocytes were plated at a density of 2X10^6/ml in DMEM, supplemented with penicillin (100 U/ml), streptomycin (100 mg/ml), and gentamicin (50 mg/ml). After 2 h, the media were substituted with media containing 10% heat-inactivated FBS, rhGM-CSF, and IL-4 (both 50 ng/ml; PeproTech, Rocky Hill, NJ, USA). Media were replaced every 72 hours. Cells were harvested at 18h, day 3, 5, and 7 for total RNA isolation.

extract_protocol: Approximately 1 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribo-minus RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the pair-end 2×150bp sequencing on an Illumina Hiseq 4000 platform housed in the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

value: Healthy buffy coats

value: WT

value: Monocytes-derived Dendritic cells

tag: time point

value: Day 7


title: FPKM.DC3 D7

description:
Library name: Sample 20
Monocytes-derived Dendritic cells-D7 Replicate 3


title: FPKM.DC4 D7

description:
Library name: Sample 21
Monocytes-derived Dendritic cells-D7 Replicate 4


title: TCR data from Tetramer positive T cells and B cells from immunised mice

description:
Library name: Sample 1 - TCR
10X Genomics

value: T cells and B cells

value: wildtype

value: Spike immunisation

value: TCR


title: VR23-O patient-derived organoid

value: pancreatic cancer

value: pancreatic ductal adenocarcinoma


title: HCC-PDX, anti-TIGIT-treated, #1

value: Tumor

value: Hepatocellular carcinoma

value: Anti-TIGIT antibody


title: HCC-PDX, anti-PD-1-treated, #3

value: Anti-PD-1 antibody


title: FPKM.DC2 D7

description:
Library name: Sample 19
Monocytes-derived Dendritic cells-D7 Replicate 2


title: Tetramer negative T cells and B cells from naive mouse

description:
Library name: Sample 3 - GEX
10X Genomics

value: vehicle

value: mRNA


title: VR21-O patient-derived organoid

source_name: Adenosquamous carcinoma

value: Adenosquamous carcinoma

value: baseline


title: HCC-PDX, anti-PD-1-treated, #2


title: HCC-PDX, anti-PD-1-treated, #1


title: KO_DIFF_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

data_processing:
the reads were trimmed to remove adapter sequences and low-quality ends and reads mapping to contaminating sequences (e.g., ribosomal RNA, phIX control) were filtered-out. Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq. Trimming and cleaning with bbduk. Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: C2C12 cellline

growth_protocol: Cells and myotubes are grown in DMEM with 10%FBS

extract_protocol:
Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 50ng/5 µL.
Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)1 which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).

treatment_protocol: RNA was extracted from C2C12 and differentiated myotubes

value: C2C12 cellline

value: unknown

value: Transcriptome profile of KO cells differentiated, biological rep4


title: VR11-O patient-derived organoid

source_name: pancreatic carcinoma from IPMN

value: pancreatic carcinoma from IPMN


title: KO_DIFF_3

value: Transcriptome profile of KO cells differentiated, biological rep3


title: Tetramer negative T cells and B cells from immunised mice

description:
Library name: Sample 2 - GEX
10X Genomics

value: spleen

value: T cells and B cells

value: wildtype

value: Spike immunisation


title: HCC-PDX, saline, #3

value: Tumor

value: Saline


title: HCC-PDX, saline, #2

value: Hepatocellular carcinoma


title: VR06-O patient-derived organoid

value: pancreatic cancer

value: pancreatic ductal adenocarcinoma


title: KO_DIFF_2

value: Transcriptome profile of KO cells differentiated, biological rep2


title: FPKM.DC2 D5

description:
Library name: Sample 15
Monocytes-derived Dendritic cells-D5 Replicate 2

value: Healthy buffy coats

value: WT

value: Monocytes-derived Dendritic cells

value: Day 5


title: VR19-LNO patient-derived organoid

value: pancreatic ductal adenocarcinoma lymph node metastasis

value: baseline


title: FPKM.DC1 D7

description:
Library name: Sample 18
Monocytes-derived Dendritic cells-D7 Replicate 1

value: Day 7


title: VR09-O patient-derived organoid

data_processing:
Reads were aligned to the GRCh38 genome using STAR v2.7 and expression quantification were performed with RSEM
GRCh38
tab-delimited file containing raw counts for each sample

source_name: pancreatic ductal adenocarcinoma signet ring

extract_protocol:
RNA were isolated using the TRIzol® Reagent (Life Technologies), followed by the column based PureLink RNA Mini Kit (Thermo Fisher Scientific). Purified RNA quality was evaluated using RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent) and only RNA with an RNA Integrity Number (RIN) greater than 7.5 were used.
RNA-seq library were obtained using poly(A) enrichment with TrueSeq Stranded mRNA Library Prep kit (Illumina).


title: KO_DIFF_1

value: C2C12 cellline

value: unknown

value: Transcriptome profile of KO cells differentiated, biological rep1


title: VR20-O patient-derived organoid


title: FPKM.DC1 D5

description:
Library name: Sample 14
Monocytes-derived Dendritic cells-D5 Replicate 1


title: FPKM.DC3 D5

description:
Library name: Sample 16
Monocytes-derived Dendritic cells-D5 Replicate 3


title: HCC-PDX, saline, #1


title: FPKM.DC4 D5

description:
Library name: Sample 17
Monocytes-derived Dendritic cells-D5 Replicate 4


title: Tetramer positive T cells and B cells from immunised mice

description:
Library name: Sample 1 - GEX
10X Genomics

value: spleen

value: T cells and B cells

value: wildtype

value: Spike immunisation

value: mRNA


title: FPKM.DC4 D3

description:
Library name: Sample 13
Monocytes-derived Dendritic cells-D3 Replicate 4

value: Day 3


title: T98GT3

city: Shanghai

first: Ming

last: Chen

address: 1665 Kong Jiang Road

department: Neurosurgery

country: China

institute: Xinhua Hospital of Shanghai Jiaotong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Excel format, Number of raw junction reads

growth_protocol: The culture medium for LN229 and T98G was composed of DMEM and 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
The total RNA was isolated from both normoxic and hypoxic cultured GBM cell lines using TRIzol reagent according to the manufacturer’s instructions. The RNA purity and concentration were determined with Nano-Drop ND-1000. The RNA integrity of the samples was assessed by denaturing agarose gel electrophoresis. The Ribo-Zero rRNA Removal Kit was used to remove the rRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For normoxic culture, the cells were incubated at 37 °C with 95% air, 5% CO2 and 100% humidity. For hypoxic culture, the cells were incubated at 37 °C with 1% O2, 5% CO2 and 100% humidity.

value: Glioblastoma Multiforme Cells

tag: stress

value: Hypoxia


title: KO_UNDIFF_4

description: KO cells , biological rep4

value: Transcriptome profile of KO cells , biological rep4


title: VR11-LNO patient-derived organoid

source_name: pancreatic carcinoma from IPMN lymph node metastasis

value: pancreatic cancer


title: T98GT2


title: VR02-O patient-derived organoid

value: pancreatic ductal adenocarcinoma


title: FPKM.DC3 D3

description:
Library name: Sample 12
Monocytes-derived Dendritic cells-D3 Replicate 3

value: Healthy buffy coats

value: WT

value: Monocytes-derived Dendritic cells


title: KO_UNDIFF_3

description: KO cells , biological rep3

value: C2C12 cellline

value: Transcriptome profile of KO cells , biological rep3


title: T98GT1


title: VR01-O patient-derived organoid

value: baseline


title: FPKM.DC2 D3

description:
Library name: Sample 11
Monocytes-derived Dendritic cells-D3 Replicate 2


title: FPKM.DC1 D3

description:
Library name: Sample 10
Monocytes-derived Dendritic cells-D3 Replicate 1
The R1 fastq file for this Sample is not available.


title: KO_UNDIFF_2

description: KO cells , biological rep2

value: unknown

value: Transcriptome profile of KO cells , biological rep2


title: L-6

city: Goyang

first: JAE YEON

last: MOON

address: Dongguk-ro 32

country: South Korea

institute: Dongguk university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: adipose-derived stromal/stem cells

growth_protocol: The hASCs were seeded onto 100 mm dishes at density of 1 × 10^6 cells per dish in αMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin 100X.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: phenotype

value: low osteogenic differentiation

tag: passages

value: lipoaspirate


title: T98GC3

value: Normoxia


title: KO_UNDIFF_1

description: KO cells , biological rep1

value: Transcriptome profile of KO cells , biological rep1


title: L-5


title: T98GC1

value: Glioblastoma Multiforme Cells


title: T98GC2


title: WT_DIFF_4

value: Transcriptome profile of Control cells differentiated, biological rep4


title: L-4


title: LNT3

source_name: LNT

value: Hypoxia


title: FPKM.DC2 18h

description:
Library name: Sample 7
Monocytes-derived Dendritic cells-18h Replicate 2


title: WT_DIFF_2

value: Transcriptome profile of Control cells differentiated, biological rep2


title: L-3


title: FPKM.DC1 18h

description:
Library name: Sample 6
Monocytes-derived Dendritic cells-18h Replicate 1


title: WT_UNDIFF_4

description: Control, biological rep4

value: Transcriptome profile of control cells, biological rep4


title: L-2


title: WT_DIFF_1

value: Transcriptome profile of Control cells differentiated, biological rep1


title: LNT2


title: LNT1


title: FPKM.Mon 4

description:
Library name: Sample 4
Monocytes Replicate 4

value: Healthy buffy coats

value: WT

value: pre


title: FPKM.DC4 18h

description:
Library name: Sample 9
Monocytes-derived Dendritic cells-18h Replicate 4

value: Monocytes-derived Dendritic cells


title: LNC3

source_name: LNC


title: WT_UNDIFF_3

description: Control, biological rep3

value: C2C12 cellline

value: Transcriptome profile of control cells, biological rep3


title: H-6

value: high osteogenic differentiation


title: FPKM.Mon 3

description:
Library name: Sample 3
Monocytes Replicate 3


title: WT_UNDIFF_2

description: Control, biological rep2

value: unknown

value: Transcriptome profile of control cells, biological rep2


title: FPKM.Mon 2

description:
Library name: Sample 2
Monocytes Replicate 2


title: FPKM.DC3 18h

description:
Library name: Sample 8
Monocytes-derived Dendritic cells-18h Replicate 3


title: LNC2

value: Normoxia


title: LNC1


title: H-4

value: lipoaspirate


title: FPKM.Mon 1

description:
Library name: Sample 1
Monocytes Replicate 1


title: FPKM.Mon 5

description:
Library name: Sample 5
Monocytes Replicate 5


title: L-1

value: low osteogenic differentiation


title: WT_DIFF_3

value: Transcriptome profile of Control cells differentiated, biological rep3


title: Gill, Ts12G-2

city: Gansu Province/Lanzhou City/Anning District

first: Xujuan

last: Fu

address: No.1 Yingmen Village, Anning District, Lanzhou City, Gansu Province, China

department: College of Animal Science and Technology

institute: Gansu Agricultural University

description: Library name: Sample 8

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: gill

growth_protocol: Fish weighing (130 ± 5.0) g were selected and temporarily reared for two weeks in a flow-through aquaculture system with DO of 8.5 ± 0.1 mg/L, water temperature of 12 ± 0.1℃.

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two weeks after rainbow trout were suspended, healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen.

value: gill

value: severe hypoxia stress

tag: time


title: H-3


title: Gill, Ts12G-3

description: Library name: Sample 9


title: liver, hypoxia_0h,2

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

institute: Hainan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Assembly: genome of Trachinotus blochii (unpublished)

organism: Trachinotus blochii

extract_protocol:
The total RNA was extracted from the liver by the Trizol Reagent (Invitrogen). RNA degradation and contamination were monitored on 1% agarose gel. The RNA purity was assessed using a NanoPhotometer® spectrophotometer (IMPLEN, München, Germany). The RNA concentration was measured using the Qubit® RNA Assay Kit in the Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). All RNA OD ratios of 260/280 and 260/230 were greater than 1.8, and the RNA integrity number (RIN) was greater than 8.0.We used Qubit 2.0 for preliminary quantification, diluted the library to 1 ng/uL, and used the highly sensitive Agilent 2100 to detect the insert size of the library.
The different libraries were pooled according to the requirements of the effective concentration and target data volume, and the Illumina SE 50 was used for sequencing.

value: liver


title: H-5


title: periodontal disease offspring 2

type: RNA

city: Bilac

first: MARIA

middle: SARA DE LIMA COUTINHO

last: MATTERA

state: SP

address: Rua Atlanta, 575

country: Brazil

institute: São Paulo State University (UNESP), School of Dentistry, Araçatuba

hyb_protocol: Hybridization to the Affymetrix® miRNA 4.1 Array strips was carried out at 48ºC for 20 hours

scan_protocol: GeneAtlas® System (Affymetrix)

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Transcriptome Analysis Console (TAC) 4.0.1 (Thermo Fisher Scientific Co.) using the Robust Multi-array Average (RMA) algorithm

label: biotin

organism: Rattus norvegicus

source_name: periodontal disease offspring

label_protocol: Total RNA (400 ng/sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Co.), according to the manufacturer’s instructions

growth_protocol: Samples were kept in RNAlater (Thermo Fisher Scientific®) before RNA extraction

extract_protocol: Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.

value: gastrocnemius muscle tissue


title: Gill, Ts12G-1

description: Library name: Sample 7


title: periodontal disease offspring 4


title: win-4

city: Sevilla

first: Alfonso

last: Rodriguez Gil

email: alfrodgil@gmail.com, arg@us.es

state: Sevilla

address: Avda. Manuel Siurot s/n

department: Oncohematology

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS)

hyb_protocol: Washing, staining (GeneChip® Fluidics Station 450, Thermo Fisher Scientific, Inc.), were performed following protocols outlined in the user manual for cartridge arrays.

scan_protocol: scanning (GeneChip® Scanner 3000, Thermo Fisher Scientific, Inc.) were performed following protocols outlined in the user manual for cartridge arrays.

data_processing: Arrays were normalized with RMA method from oligo package and differential expression analysis was performed using limma package.

source_name: HL60 AML cell line

label_protocol: RNA was amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.) Amplification was performed with 100 ng of total RNA input following procedures described in the WT PLUS Reagent Kit user manual. The amplified cDNA was quantified, fragmented, and labeled in preparation for hybridization to GeneChip® Clariom S Human Array (Thermo Fisher Scientific, Inc.) using 5.5 μg of single-stranded cDNA product and following protocols outlined in the user manual.

growth_protocol: The AML cell line HL60 was cultured in IMDM medium  suplemented wit100 units/mL penicillin, 100 µg /mL streptomycin and 10% fetal bovine serum (FBS). All cells were cultured in a humidified atmosphere of CO2/air (5%/95%) and 37ºC

extract_protocol: RNEasy

treatment_protocol: Win55 50μM for 18 h in Serumm fee medium. Control samples were treated wth DMSO as vehicle lf the drug.

value: AML


title: Gill, Tm12G-2

description: Library name: Sample 5

value: moderate hypoxia stress


title: THBS4-treated biol rep1

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CutAdapt 1.16 with Python 3.6.4.
RNA STAR (Galaxy version 2.7.7a) was used for sequence alignment to reference genome GRCh38/h38.87 and featureCounts (Galaxy version 2.0.1) was used to count the number of reads.
Differential gene expression was analysed using DESeq2 package
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include DESeq2 result values for each sample

source_name: skin

growth_protocol: Keratinocytes were cultured in Keratinocyte-SFM medium containing 50 µg/ml bovine pituitary extract, 0.5 ng/ml recombinant epidermal growth factor and 10 ng/ml recombinant keratinocyte growth factor (all from Thermo Fisher Scientific, Grand Island, NY, USA) and antibiotic-antimycotic solution (Gibco, Thermo Fisher Scientific, Grand Island, USA) with a final concentration of 100 U/ml penicillin, 100 µg/ml streptomycin and 0.25 µg/ml amphotericin B. Pooled keratinocytes from 3 donors at passages 2–4 were used in experiments. Keratinocytes were cultured on tissue culture dishes (Corning Incorporated, Corning, NY, USA) that were pre-coated with collagen type I solution (Thermo Fisher Scientific, Grand Island, NY, USA) at a concentration of 5 μg/cm2, according to the manufacturer’s instructions for thin coating procedure.

extract_protocol:
Total RNA was separated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adherent cells were treated for 4 h with THBS4-conditioned medium or control medium (from pcDNA mock-transfected HEK293 cells) in 1:4 ratio.

value: skin

value: primary cells

value: keratinocytes

value: 4 h with THBS4-conditioned medium


title: Gill, CG-3

description: Library name: Sample 3

value: control

value: 0 h


title: Gill, Tm12G-3

description: Library name: Sample 6


title: periodontal disease offspring 3


title: H-1

value: high osteogenic differentiation


title: ctr-4

value: Untreated


title: win-3


title: periodontal disease offspring 1


title: WT_UNDIFF_1

description: Control, biological rep1

value: C2C12 cellline

value: unknown

value: Transcriptome profile of control cells, biological rep1


title: Gill, Tm12G-1

description: Library name: Sample 4

value: gill


title: control offspring 4

source_name: control offspring


title: Control  biol rep3

value: 4 h with control medium


title: ctr-3


title: THBS4-treated biol rep3


title: Control  biol rep2


title: H-2

value: lipoaspirate


title: Control  biol rep1


title: mural granulosa cells, late antral follicle_5

status: Public on Dec 27 2024

city: Kobe

first: Mihoko

last: Fushii

address: Nada-ku

country: Japan

institute: Kobe University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.20.0) with ‘-w 16 --trim-poly-x --detect_adapter_for_pe_h’ options.
Trimmed sequence reads were mapped using Hisat2 (v2.1.0) with ‘-p 16 -x’ options.
Binary alignment/map (BAM) files were sorted using samtools (v1.10).
Read count extraction and normalization were performed using featureCounts (v2.0.0) tool of Subread package with ‘-T 16 -F GTF -t exon -g gene_id -p -o’ options.
Assembly: bosTau9
Supplementary files format and content: tab-delimited text files raw counts for each samples.

organism: Bos taurus

source_name: mural granulosa cells

extract_protocol:
RNA was harvested using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA).
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Preparation Kit (Illumina).

value: mural granulosa cells


title: Gill, CG-1

description: Library name: Sample 1


title: ctr-2

value: AML


title: win-1


title: Gill, CG-2

description: Library name: Sample 2


title: ctr-1


title: control offspring 2

value: gastrocnemius muscle tissue


title: win-2


title: mural granulosa cells, late antral follicle_1


title: mural granulosa cells, early antral follicle_4


title: control offspring 1


title: mural granulosa cells, early antral follicle_3


title: cumulus cells, late antral follicle_4

source_name: cumulus cells

value: cumulus cells


title: mural granulosa cells, early antral follicle_1


title: mural granulosa cells, late antral follicle_3


title: cumulus cells, early antral follicle_5


title: cumulus cells, early antral follicle_4


title: mural granulosa cells, late antral follicle_2


title: cumulus cells, late antral follicle_3


title: cumulus cells, late antral follicle_5


title: cumulus cells, late antral follicle_1


title: mural granulosa cells, early antral follicle_5


title: control offspring 3


title: cumulus cells, late antral follicle_2


title: granulosa cells, secondary follicle_3

source_name: granulosa cells

value: granulosa cells


title: granulosa cells, secondary follicle_4


title: mural granulosa cells, early antral follicle_2


title: cumulus cells, early antral follicle_2


title: mural granulosa cells, late antral follicle_4


title: granulosa cells, secondary follicle_2


title: PA_sample300

city: Ithaca

first: Hao

last: Zhou

address: 200 Kimball Hall

institute: Cornell University

description: Library name: DSP-1001660023409-D-H10_S94

data_processing:
The sequencing depth requirement was determined by aggregating the areas of illumination (measured in µm²) and multiplying the total area by a factor of 100, as recommended in the GeoMx DSP Library and Sequencing Guide (nanostring.com). Sequencing was executed using the NovaSeq 6000 System. The resultant FASTQ files were processed to Digital Count Conversion (DCC) files utilizing the GeoMxNGSPipeline v.2.3.3.10, a pipeline publicly available through NanoString Technologies. This pipeline facilitated individual probe alignment by identifying read tag sequences (RTS). Additionally, it eliminated duplicates in probe counts generated during the library preparation's polymerase chain reaction, through a meticulous analysis of the unique molecular identifiers (UMIs) associated with each probe.
Assembly: mm10
Supplementary files format and content: combined_dcc.zip
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Moderna_Pa02_v1.0.pkc
Library strategy: Spatial Transcriptomics

source_name: Cornea

growth_protocol: P. aeruginosa strains PAO1, PA14, PA14_30590_Tn (PA2590 transposon mutant) were grown in Luria–Bertoni broth (LB) broth (BD-Difco) overnight at 37°C with agitation (200rpm). Cultures were then passaged in fresh LB broth (BD-Difco) until an OD600 of 0.20 (midlog phase) was reached. The PAO1 strain was obtained from Dr. A. Rietsch (Case Western Reserve University). The PA14 and PA14_2590_Tn were generated during the PA14 transposon insertion mutant library generation ((http://ausubellab.mgh.harvard.edu/cgi-bin/pa14/home.cgi)) and obtained from Prof. G. Pier (BWH, HMS)48 . The PA2590 transposon mutant was sequence validated.

extract_protocol:
After imaging the corneas, eyes had 15µl of 4% formalin (ThermoFisher) dropped onto them and were left to fix at room temperature for 15 minutes. Eyes were then carefully resected and placed in 1ml of iced 4% formalin (ThermoFisher) and were fixed at 4°C for 48-72hrs. After fixation, formalin was removed, and tissue was washed twice with sterile 1x PBS. Samples were then placed in 2ml of 70% ethanol and were kept at 4°C until shipment to UMass Histopathology was complete. Tissue embedding was done by UMass Histopathology.  All tissues were processed using UMass Chan Medical School Morphology Core services following standard protocols.
Illumina i5 and i7 dual-indexing primers (Nanostring Technologies) were added to the collected barcodes during polymerase chain reaction (8 µl collected oligonucleotides/ROI) to uniquely index each ROI. Briefly, collected barcodes were re-suspended in 10 mL of nuclease-free water and incubated for 10min at room temperature. In a 96-well PCR plate, 2 mL of master mix (Nanostring Technologies), 4 mL of seq-code indexes (Nanostring Technologies) and 4 mL of re-suspended barcodes were mixed and placed in a thermocycler for PCR amplification using the following program. 1x UDG incubation for 30min at 37° C, 1x UDG deactivation for 10min at 50° C, 1x Initial denaturation for 3min at 95° C, 18x Denaturation for 15sec at 95° C > Anneal for 60sec at 65° C > Extend for 30sec at 68° C, Final extension for 5min at 68° C, Hold at 4° C.

value: Cornea


title: PA_sample301

description: Library name: DSP-1001660023409-D-H11_S95


title: cumulus cells, early antral follicle_3


title: PA_sample296

description: Library name: DSP-1001660023409-D-H06_S90


title: PA_sample293

description: Library name: DSP-1001660023409-D-H03_S87


title: granulosa cells, secondary follicle_1


title: cumulus cells, early antral follicle_1


title: PA_sample292

description: Library name: DSP-1001660023409-D-H02_S86


title: PA_sample287

description: Library name: DSP-1001660023409-D-G09_S81


title: PA_sample290

description: Library name: DSP-1001660023409-D-G12_S84


title: PA_sample299

description: Library name: DSP-1001660023409-D-H09_S93


title: PA_sample297

description: Library name: DSP-1001660023409-D-H07_S91


title: PA_sample295

description: Library name: DSP-1001660023409-D-H05_S89


title: PA_sample298

description: Library name: DSP-1001660023409-D-H08_S92


title: PA_sample284

description: Library name: DSP-1001660023409-D-G06_S78


title: PA_sample281

description: Library name: DSP-1001660023409-D-G03_S75


title: PA_sample279

description: Library name: DSP-1001660023409-D-G01_S73


title: PA_sample283

description: Library name: DSP-1001660023409-D-G05_S77


title: PA_sample280

description: Library name: DSP-1001660023409-D-G02_S74


title: PA_sample278

description: Library name: DSP-1001660023409-D-F12_S72


title: PA_sample294

description: Library name: DSP-1001660023409-D-H04_S88


title: PA_sample276

description: Library name: DSP-1001660023409-D-F10_S70


title: PA_sample291

description: Library name: DSP-1001660023409-D-H01_S85


title: PA_sample275

description: Library name: DSP-1001660023409-D-F09_S69


title: PA_sample286

description: Library name: DSP-1001660023409-D-G08_S80


title: PA_sample274

description: Library name: DSP-1001660023409-D-F08_S68


title: PA_sample273

description: Library name: DSP-1001660023409-D-F07_S67


title: PA_sample289

description: Library name: DSP-1001660023409-D-G11_S83


title: PA_sample302

description: Library name: DSP-1001660023409-D-H12_S96


title: PA_sample285

description: Library name: DSP-1001660023409-D-G07_S79


title: PA_sample288

description: Library name: DSP-1001660023409-D-G10_S82


title: PA_sample282

description: Library name: DSP-1001660023409-D-G04_S76


title: PA_sample266

description: Library name: DSP-1001660023409-D-E12_S60


title: PA_sample268

description: Library name: DSP-1001660023409-D-F02_S62


title: PA_sample271

description: Library name: DSP-1001660023409-D-F05_S65


title: PA_sample277

description: Library name: DSP-1001660023409-D-F11_S71


title: PA_sample272

description: Library name: DSP-1001660023409-D-F06_S66


title: PA_sample262

description: Library name: DSP-1001660023409-D-E08_S56


title: PA_sample270

description: Library name: DSP-1001660023409-D-F04_S64


title: PA_sample263

description: Library name: DSP-1001660023409-D-E09_S57


title: PA_sample269

description: Library name: DSP-1001660023409-D-F03_S63


title: PA_sample260

description: Library name: DSP-1001660023409-D-E06_S54


title: PA_sample265

description: Library name: DSP-1001660023409-D-E11_S59


title: PA_sample267

description: Library name: DSP-1001660023409-D-F01_S61


title: PA_sample257

description: Library name: DSP-1001660023409-D-E03_S51


title: PA_sample264

description: Library name: DSP-1001660023409-D-E10_S58


title: PA_sample256

description: Library name: DSP-1001660023409-D-E02_S50


title: PA_sample261

description: Library name: DSP-1001660023409-D-E07_S55


title: PA_sample254

description: Library name: DSP-1001660023409-D-D12_S48


title: PA_sample259

description: Library name: DSP-1001660023409-D-E05_S53


title: PA_sample258

description: Library name: DSP-1001660023409-D-E04_S52


title: PA_sample252

description: Library name: DSP-1001660023409-D-D10_S46


title: PA_sample250

description: Library name: DSP-1001660023409-D-D08_S44


title: PA_sample251

description: Library name: DSP-1001660023409-D-D09_S45


title: PA_sample253

description: Library name: DSP-1001660023409-D-D11_S47


title: PA_sample248

description: Library name: DSP-1001660023409-D-D06_S42


title: PA_sample249

description: Library name: DSP-1001660023409-D-D07_S43


title: PA_sample247

description: Library name: DSP-1001660023409-D-D05_S41


title: PA_sample255

description: Library name: DSP-1001660023409-D-E01_S49


title: PA_sample241

description: Library name: DSP-1001660023409-D-C11_S35


title: PA_sample244

description: Library name: DSP-1001660023409-D-D02_S38


title: PA_sample243

description: Library name: DSP-1001660023409-D-D01_S37


title: PA_sample240

description: Library name: DSP-1001660023409-D-C10_S34


title: PA_sample245

description: Library name: DSP-1001660023409-D-D03_S39


title: PA_sample242

description: Library name: DSP-1001660023409-D-C12_S36


title: PA_sample238

description: Library name: DSP-1001660023409-D-C08_S32


title: PA_sample237

description: Library name: DSP-1001660023409-D-C07_S31


title: PA_sample246

description: Library name: DSP-1001660023409-D-D04_S40


title: PA_sample235

description: Library name: DSP-1001660023409-D-C05_S29


title: PA_sample234

description: Library name: DSP-1001660023409-D-C04_S28


title: PA_sample231

description: Library name: DSP-1001660023409-D-C01_S25


title: PA_sample229

description: Library name: DSP-1001660023409-D-B11_S23


title: PA_sample227

description: Library name: DSP-1001660023409-D-B09_S21


title: PA_sample233

description: Library name: DSP-1001660023409-D-C03_S27


title: PA_sample226

description: Library name: DSP-1001660023409-D-B08_S20


title: PA_sample230

description: Library name: DSP-1001660023409-D-B12_S24


title: PA_sample228

description: Library name: DSP-1001660023409-D-B10_S22


title: PA_sample225

description: Library name: DSP-1001660023409-D-B07_S19


title: PA_sample232

description: Library name: DSP-1001660023409-D-C02_S26


title: PA_sample224

description: Library name: DSP-1001660023409-D-B06_S18


title: PA_sample221

description: Library name: DSP-1001660023409-D-B03_S15


title: PA_sample223

description: Library name: DSP-1001660023409-D-B05_S17


title: PA_sample220

description: Library name: DSP-1001660023409-D-B02_S14


title: PA_sample222

description: Library name: DSP-1001660023409-D-B04_S16


title: PA_sample239

description: Library name: DSP-1001660023409-D-C09_S33


title: PA_sample216

description: Library name: DSP-1001660023409-D-A10_S10


title: PA_sample236

description: Library name: DSP-1001660023409-D-C06_S30


title: PA_sample217

description: Library name: DSP-1001660023409-D-A11_S11


title: PA_sample215

description: Library name: DSP-1001660023409-D-A09_S9


title: PA_sample214

description: Library name: DSP-1001660023409-D-A08_S8


title: PA_sample212

description: Library name: DSP-1001660023409-D-A06_S6


title: PA_sample218

description: Library name: DSP-1001660023409-D-A12_S12


title: PA_sample210

description: Library name: DSP-1001660023409-D-A04_S4


title: peripheral blood cells from CKD patient 12

type: genomic

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

institute: keio university

hyb_protocol: Bisulphite converted DNA was amlified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v4.1.1)
The FinalReport*.txt files contain Average Beta values.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: peripheral blood cells from CKD patient

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood cells using the QIAamp DNA Blood Mini 139 Kit (Qiagen, USA).

value: peripheral blood cells

tag: subject status

value: CKD patient


title: peripheral blood cells from CKD patient 11

tag: tissue


title: PA_sample211

description: Library name: DSP-1001660023409-D-A05_S5


title: PA_sample209

description: Library name: DSP-1001660023409-D-A03_S3


title: THBS4-treated biol rep2

value: skin

value: primary cells

value: keratinocytes

value: 4 h with THBS4-conditioned medium


title: peripheral blood cells from CKD patient 9


title: peripheral blood cells from CKD patient 8


title: PA_sample207

description: Library name: DSP-1001660023409-D-A01_S1


title: peripheral blood cells from CKD patient 10


title: peripheral blood cells from CKD patient 7(ESKD)

source_name: peripheral blood cells from ESKD patient(eGFR<15)

value: ESKD patient(eGFR<15)


title: PA_sample205

description: Library name: DSP-1001660019644-G-F04_S64


title: PA_sample204

description: Library name: DSP-1001660019644-G-F03_S63


title: PA_sample219

description: Library name: DSP-1001660023409-D-B01_S13


title: peripheral blood cells from CKD patient 6(ESKD)


title: peripheral blood cells from CKD patient 5(ESKD)


title: PA_sample203

description: Library name: DSP-1001660019644-G-F02_S62


title: PA_sample213

description: Library name: DSP-1001660023409-D-A07_S7


title: peripheral blood cells from CKD patient 4


title: PA_sample202

description: Library name: DSP-1001660019644-G-F01_S61


title: PA_sample201

description: Library name: DSP-1001660019644-G-E12_S60


title: PA_sample200

description: Library name: DSP-1001660019644-G-E11_S59


title: peripheral blood cells from CKD patient 3


title: peripheral blood cells from CKD patient 1


title: PA_sample198

description: Library name: DSP-1001660019644-G-E09_S57


title: PA_sample208

description: Library name: DSP-1001660023409-D-A02_S2


title: PA_sample197

description: Library name: DSP-1001660019644-G-E08_S56


title: PA_sample195

description: Library name: DSP-1001660019644-G-E06_S54


title: PA_sample206

description: Library name: DSP-1001660019644-G-F05_S65


title: PA_sample194

description: Library name: DSP-1001660019644-G-E05_S53


title: crypts isolated from Piezo double KO mice

city: Paris

first: Meryem

last: Baghdadi

address: 12 rue Lhomond

country: France

institute: Institut curie

description:
10X Genomics
Dan_H4

data_processing:
demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the mm10 mouse transcriptome was performed. The raw data for control mice generated by Cellranger were then read into the Seurat R package with at least 200 genes present in each cell and at least one cell. Quality control and normalization were then performed. For each cell, quality control metrics were calculated, including the total number of counts, the proportion of counts in mitochondrial genes, and the number of genes expressed by cell. Specifically, genes with non-zero counts in at least three cells were retained to remove any low-abundance genes that might interfere with statistical analysis. The gene expression was log-normalized, then scaled. A cell cycle score was calculated based on expression of various cell-cycle associated genes, pre-defined within Seurat. This score was treated as a regression variable upon data scaling to prevent cells from clustering together based on cell cycle phase. Principal components were then calculated on the basis of the 2000 most variable genes in the dataset (excluding those associated with the cell cycle) and a scree plot was used to determine the top principal components. Cells were then divided into unsupervised clusters using a shared-nearest-neighbour modularity optimization-based clustering algorithm (Smart local moving algorithm) and then plotted using the UMAP method. Cells were initially clustered at low resolution and immune cells were removed using Ptprc as a marker. Epithelial cells were re-clustered at high resolution and expressed genes for each cluster were identified using the Wilcox test in Seurat and the top genes (<0.05 P value and >0.25 log fold change) were used to identify different cell types. To test how single-cell clusters identified in control intestinal epithelia were altered upon Piezo deletion, scRNA-seq dataset from Piezo mutant was first processed as above by using the same parameters that were applied to process the control dataset. Next, FindTransferAnchors function within Seurat was used to compare the two datasets, where the control clusters were used as a reference map to infer clusters in the mutant dataset. A UMAP plot of the Piezo mutant cells mapped back to clusters calculated from the control data was then generated. All data plotting and analyses were done in R.
Assembly: mm10
Supplementary files format and content: wt.zeroone.RData after quality control
Supplementary files format and content: mut.zeroone.RData after quality control
Supplementary files format and content: twofive.mut.cycle.noimmune.RData after removing immune cells and cell cycle scoring
Supplementary files format and content: twofive.wt.cycle.noimmune.RData after removing immune cells and cell cycle scoring

source_name: intestine

extract_protocol:
crypts were isolated from mouse small intestine using 20mM EDTA/PBS1X (Gibco) for 25min at 4°C with continuous shaking. Intestines pieces were then incubated in 1.5% sucrose/1% sorbitol/PBS1X solution and crypts were dissociated by vigorous shaking. Following 70um filtering and centrifugation, crypts were incubated with TrypLE 1X at 37°C for 5min. After pipetting multiple times until the single-cell suspension was attained, the solution is passed through a 40um strainer and centrifugated
according to Manufacturer's guidelines : 10X genomics, single 3' v2 protocol

value: intestine

value: epithelial cells

value: Tamoxifen (5days)


title: KAT6B_D290A_inp_rep1

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
FastQ files were trimmed with trim_galore v0.6.6 in paired end mode using default parameters, then aligned to the mouse GRCm39 genome using bowtie2 v2.4.5 using options --no-discordant --no-mixed
BigWig files were generated from aligned BAM files using bamCoverage v3.5.1 from DeepTools using CPM (Counts per Million) normalisation.
Supplementary_files_format_and_content: bigWig files corresponding to merged replicates of spike-in normalised ChIP-seq profiles
Assembly: Mus musculus GRCm39
Supplementary files format and content: BigWig files with 50bp resolution showing CPM (counts per million) values over the whole genome

organism:
Drosophila melanogaster
Mus musculus

source_name: embryonic stem cell (E14 line) and Drosophila S2 cell line

growth_protocol: E14 ESCs were grown on plates coated with gelatin (0.1%, Sigma) in DMEM containing 4.5 g/l glucose (Gibco) supplemented with 15% fetal bovine serum (Gibco, South American, A3160802), 2 mM l-glutamine, 1 mM pyruvate, 1x MEM nonessential amino acids, 50 units/ml penicillin and 50 µg/ml streptomycin (all Gibco), 0.2 mM β-mercaptoethanol (Sigma), and heterologously expressed recombinant LIF (made in-house and batch-tested for maintenance of self-renewal) at 37°C and 5% CO2.

extract_protocol: To prepare chromatin for ChIP, crosslinking was carried out directly on 15-cm culture plates with 1% formaldehyde in fixation buffer (DMEM supplemented with 10 mM HEPES pH 7.6, 15 mM NaCl, 0.15 mM EDTA, 0.075 mM EGTA) for 10 min at room temperature with gentle rocking. Crosslinking was stopped by addition of glycine to a final concentration of 0.125 M and incubation for 3 min at room temperature with gentle rocking. Fixed cells were washed with cold PBS, scraped off the plate in cold PBS, and collected by centrifugation at 2500 g for 5 min at 4°C. To fragment chromatin, cell pellets were resuspended in lysis buffer 1 (50 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X100) and incubated with constant rotation for 10 min at 4°C. Cells were then centrifuged at 3000 g for 5 min and cell pellets resuspended in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated and centrifuged as before. Pellets were then resuspended in lysis buffer 3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.5% N-Lauryl Sarcosine) at a density of 75 mg cell pellet weight per ml. The suspension was transferred to polystyrene tubes (BD Falcon) and sonicated using a Bioruptor (Diagenode) at maximum output setting using 30 s ON, 30 s OFF cycles. Number of cycles (15–20) was experimentally determined to yield decrosslinked fragments of 250–350 bp size, verified by agarose gel electrophoresis and on a bioanalyzer 2100 (Agilent).   For ChIP, chromatin was clarified by centrifugation at 20,000 g for 10 min and incubated overnight with antibodies in 1x IP buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.25% N-Lauryl Sarcosine, 1% Triton X100) with constant rotation at 4°C. For spike-in normalised ChIP, chromatin generated as above from Drosophila S2 cells was added along with anti-Histone H2Av spike-in antibody (Active Motif, 61686). After overnight incubation, IPs were centrifuged for 10 min at 20,000 g at 4°C and the supernatants were combined with 50 μl protein A or G magnetic dynabeads (Invitrogen) pre-blocked with BSA and incubated at 4°C for 2–3 h under constant rotation. Beads were then washed 5 times in cold RIPA buffer (10 mM HEPES pH 7.6, 1 mM EDTA, 0.5 M LiCl, 1% NP-40, 0.1% N-Lauryl Sarcosine) with 2 min rotating incubation at room temperature for each wash. Beads were then washed briefly with TEN buffer (TE with 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads by addition of elution buffer (100 mM NaHCO3, 1% SDS, 200 mM NaCl, 0.4 mg/ml each proteinase K and RNAse A) and incubation overnight at 65°C with constant agitation to reverse crosslinking. The next day samples were purified using PCR cleanup kit columns (Monarch, NEB) and eluted using 50 μl kit elution buffer.  Libraries were prepared from 5 ng of ChIP or input DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and single index NEBNext multiplex oligos for Illumina (NEB). Following library preparation, library fragment size was determined using an Agilent Bioanalyzer 2100. Library concentration was assessed by qPCR using the NEBNext Library Quant kit for Illumina (NEB). Samples were sequenced on an S4 flow cell on an Illumina NovaSeq 6000 instrument as 150 bp paired-end reads (Novogene UK).

tag: chip antibody

value: none (input)

value: HA-KATB; KAT6B D290A homozygous knockin


title: PA_sample191

description: Library name: DSP-1001660019644-G-E02_S50


title: KAT6B_D290A_inp_rep2

value: embryonic stem cell (E14 line) and Drosophila S2 cell line


title: KAT6B_D290A_HA_rep3

value: HA (Cell Signaling, 3724, lot 9)


title: PA_sample190

description: Library name: DSP-1001660019644-G-E01_S49


title: PA_sample188

description: Library name: DSP-1001660019644-G-D11_S47


title: PA_sample189

description: Library name: DSP-1001660019644-G-D12_S48


title: peripheral blood cells from CKD patient 2


title: PA_sample187

description: Library name: DSP-1001660019644-G-D10_S46


title: PA_sample199

description: Library name: DSP-1001660019644-G-E10_S58


title: KAT6B_D290A_HA_rep1


title: PA_sample186

description: Library name: DSP-1001660019644-G-D09_S45


title: KAT6B_D290A_H3K23ac_rep3


title: KAT6B_D290A_H3K23ac_rep2


title: PA_sample185

description: Library name: DSP-1001660019644-G-D08_S44


title: PA_sample184

description: Library name: DSP-1001660019644-G-D07_S43


title: PA_sample193

description: Library name: DSP-1001660019644-G-E04_S52


title: crypts isolated from Control mice

description:
10X Genomics
Dan_H3


title: PA_sample192

description: Library name: DSP-1001660019644-G-E03_S51


title: KAT6A_B_dKO_inp_rep3

value: KAT6A-/-; KAT6B-/- dKO


title: KAT6B_D290A_H3K23ac_rep1


title: PA_sample183

description: Library name: DSP-1001660019644-G-D06_S42


title: PA_sample181

description: Library name: DSP-1001660019644-G-D04_S40


title: KAT6A_B_dKO_inp_rep2


title: KAT6B_D290A_HA_rep2


title: KAT6A_B_dKO_H3K4me3_rep3

value: H3K4me3 (Cell Signaling, 9751, lot 10)


title: PA_sample180

description: Library name: DSP-1001660019644-G-D03_S39

value: Cornea


title: KAT6A_B_dKO_H3K27me3_rep3

value: H3K27me3 (Cell Signaling, 9733, lot 14)


title: PA_sample178

description: Library name: DSP-1001660019644-G-D01_S37


title: KAT6A_B_dKO_H3K4me3_rep2


title: PA_sample179

description: Library name: DSP-1001660019644-G-D02_S38


title: KAT6A_B_dKO_H3K4me3_rep1


title: PA_sample177

description: Library name: DSP-1001660019644-G-C12_S36


title: KAT6A_B_dKO_H3K27me3_rep1


title: PA_sample176

description: Library name: DSP-1001660019644-G-C11_S35


title: PA_sample173

description: Library name: DSP-1001660019644-G-C08_S32


title: PA_sample172

description: Library name: DSP-1001660019644-G-C07_S31


title: KAT6A_B_dKO_H3K23ac_rep1


title: KAT6B_KO_inp_rep3

value: KAT6B-/- KO


title: PA_sample175

description: Library name: DSP-1001660019644-G-C10_S34


title: KAT6A_B_dKO_inp_rep1


title: KAT6A_B_dKO_H3K23ac_rep2


title: PA_sample174

description: Library name: DSP-1001660019644-G-C09_S33


title: PA_sample171

description: Library name: DSP-1001660019644-G-C06_S30


title: PA_sample170

description: Library name: DSP-1001660019644-G-C05_S29


title: KAT6A_B_dKO_H3K27me3_rep2


title: KAT6B_KO_inp_rep1


title: KAT6B_KO_inp_rep2


title: KAT6B_KO_H3K4me3_rep2


title: KAT6B_KO_H3K4me3_rep3


title: KAT6A_B_dKO_H3K23ac_rep3


title: PA_sample167

description: Library name: DSP-1001660019644-G-C02_S26


title: PA_sample169

description: Library name: DSP-1001660019644-G-C04_S28


title: KAT6B_KO_H3K27me3_rep2


title: KAT6B_KO_H3K27me3_rep3


title: PA_sample196

description: Library name: DSP-1001660019644-G-E07_S55


title: KAT6B_KO_H3K4me3_rep1


title: PA_sample166

description: Library name: DSP-1001660019644-G-C01_S25


title: PA_sample165

description: Library name: DSP-1001660019644-G-B12_S24


title: KAT6B_KO_H3K27me3_rep1


title: PA_sample163

description: Library name: DSP-1001660019644-G-B10_S22


title: PA_sample162

description: Library name: DSP-1001660019644-G-B09_S21


title: PA_sample164

description: Library name: DSP-1001660019644-G-B11_S23


title: KAT6B_KO_H3K23ac_rep3


title: KAT6B_KO_H3K23ac_rep2


title: KAT6B_KO_H3K23ac_rep1


title: PA_sample160

description: Library name: DSP-1001660019644-G-B07_S19


title: KAT6A_KO_inp_rep3

value: KAT6A-/- KO


title: PA_sample159

description: Library name: DSP-1001660019644-G-B06_S18


title: PA_sample158

description: Library name: DSP-1001660019644-G-B05_S17


title: KAT6A_KO_inp_rep2


title: PA_sample157

description: Library name: DSP-1001660019644-G-B04_S16


title: KAT6A_KO_H3K4me3_rep3


title: KAT6A_KO_inp_rep1


title: KAT6A_KO_H3K4me3_rep2


title: PA_sample156

description: Library name: DSP-1001660019644-G-B03_S15


title: PA_sample155

description: Library name: DSP-1001660019644-G-B02_S14


title: PA_sample154

description: Library name: DSP-1001660019644-G-B01_S13


title: KAT6A_KO_H3K27me3_rep3


title: PA_sample153

description: Library name: DSP-1001660019644-G-A12_S12


title: Genomic DNA from HCT116 cells 1

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: HCT116 wt cells

hyb_protocol: bisulphite converted DNA (Zymo Research EZ-Kit) was amplified, fragmented and hybridised to Illumina Infinium EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using a NextSeq 550 device using standard settings

data_processing: minfi-package for R

label: Cy3 / Cy5

label_protocol: The standard Illumina protocol was applied as provided with the Infinium MethylationEPIC Kit

growth_protocol: McCoy’s 5A, 10% Fetal Bovine Serum, 20 mM L-glutamate and 100 U/ml penicillin/streptomycin and cells were grown at 37°C and 5% CO2

extract_protocol: Genomic DNA was extracted using QIAmp DNA Mini Kit (Qiagen)

treatment_protocol: No Treatment

value: WT


title: KAT6A_KO_H3K27me3_rep2


title: KAT6A_KO_H3K4me3_rep1


title: PA_sample152

description: Library name: DSP-1001660019644-G-A11_S11


title: KAT6A_KO_H3K27me3_rep1


title: KAT6A_KO_H3K23ac_rep3


title: PA_sample150

description: Library name: DSP-1001660019644-G-A09_S9


title: KAT6A_KO_H3K23ac_rep2


title: KAT6A_KO_H3K23ac_rep1


title: PA_sample148

description: Library name: DSP-1001660019644-G-A07_S7


title: ING5_Y188A_inp_rep3

value: HA-KATB; ING2 Y188A homozygous knockin


title: ING5_Y188A_inp_rep2


title: PA_sample151

description: Library name: DSP-1001660019644-G-A10_S10


title: Genomic DNA from HCT116 cells 2

description: HCT116 wt cells


title: ING5_Y188A_inp_rep1


title: PA_sample145

description: Library name: DSP-1001660019644-G-A04_S4


title: PA_sample146

description: Library name: DSP-1001660019644-G-A05_S5


title: PA_sample147

description: Library name: DSP-1001660019644-G-A06_S6


title: ING5_Y188A_HA_rep3


title: PA_sample149

description: Library name: DSP-1001660019644-G-A08_S8


title: PA_sample143

description: Library name: DSP-1001660019644-G-A02_S2


title: ING5_Y188A_H3K23ac_rep3


title: PA_sample142

description: Library name: DSP-1001660019644-G-A01_S1


title: ING5_Y188A_H3K23ac_rep2


title: Genomic DNA from SETDB1 KO HCT116 cells 1

description: HCT116 cells with SETDB1 knock out

value: SETDB1 KO


title: Genomic DNA from SETDB1 KO HCT116 cells 2

description: HCT116 cells with SETDB1 knock out


title: PA_sample141

description: Library name: DSP-1001660018950-B-H12_S198


title: ING5_Y188A_H3K23ac_rep1


title: PA_sample139

description: Library name: DSP-1001660018950-B-H10_S196


title: HA-KAT6B_mutant_control_inp_rep3

value: HA-tagged endogenous KAT6B, homozygous tag knockin


title: PA_sample138

description: Library name: DSP-1001660018950-B-H09_S195


title: PA_sample144

description: Library name: DSP-1001660019644-G-A03_S3


title: HA-KAT6B_mutant_control_inp_rep2


title: ING5_Y188A_HA_rep2


title: HA-KAT6B_mutant_control_inp_rep1


title: ING5_Y188A_HA_rep1


title: PA_sample136

description: Library name: DSP-1001660018950-B-H07_S193


title: HA-KAT6B_mutant_control_HA_rep3


title: HA-KAT6B_mutant_control_HA_rep2


title: PA_sample134

description: Library name: DSP-1001660018950-B-H05_S191


title: HA-KAT6B_mutant_control_H3K23ac_rep2


title: PA_sample133

description: Library name: DSP-1001660018950-B-H04_S190


title: HA-KAT6B_mutant_control_H3K23ac_rep3


title: HA-KAT6B_mutant_control_HA_rep1


title: PA_sample140

description: Library name: DSP-1001660018950-B-H11_S197


title: PA_sample135

description: Library name: DSP-1001660018950-B-H06_S192


title: PA_sample132

description: Library name: DSP-1001660018950-B-H03_S189


title: PA_sample130

description: Library name: DSP-1001660018950-B-H01_S187


title: HA-KAT6B_mutant_control_H3K23ac_rep1


title: PA_sample128

description: Library name: DSP-1001660018950-B-G11_S185


title: HA-KAT6B_MLL2Y2688A_inp_rep2

value: HA-KATB; MLL2 Y2688A homozygous knockin


title: HA-KAT6B_MLL2Y2688A_inp_rep3


title: PA_sample129

description: Library name: DSP-1001660018950-B-G12_S186


title: HA-KAT6B_MLL2Y2688A_HA_rep3


title: PA_sample131

description: Library name: DSP-1001660018950-B-H02_S188


title: PA_sample137

description: Library name: DSP-1001660018950-B-H08_S194


title: PA_sample127

description: Library name: DSP-1001660018950-B-G10_S184


title: PA_sample126

description: Library name: DSP-1001660018950-B-G09_S183


title: HA-KAT6B_MLL2Y2688A_inp_rep1


title: PA_sample125

description: Library name: DSP-1001660018950-B-G08_S182


title: PA_sample123

description: Library name: DSP-1001660018950-B-G06_S180


title: PA_sample124

description: Library name: DSP-1001660018950-B-G07_S181


title: HA-KAT6B_MLL2Y2688A_HA_rep2


title: HA-KAT6B_MLL2Y2688A_HA_rep1


title: HA-KAT6B_MLL2Y2688A_H3K4me3_rep3


title: HA-KAT6B_MLL2Y2688A_H3K4me3_rep2


title: PA_sample122

description: Library name: DSP-1001660018950-B-G05_S179


title: HA-KAT6B_MLL2Y2688A_H3K4me3_rep1


title: HA-KAT6B_MLL2Y2688A_H3K27me3_rep2


title: PA_sample119

description: Library name: DSP-1001660018950-B-G02_S176


title: PA_sample118

description: Library name: DSP-1001660018950-B-G01_S175


title: HA-KAT6B_MLL2Y2688A_H3K27me3_rep1


title: PA_sample182

description: Library name: DSP-1001660019644-G-D05_S41


title: HA-KAT6B_MLL2Y2688A_H3K27me3_rep3


title: HA-KAT6B_inp_rep3


title: PA_sample116

description: Library name: DSP-1001660018950-B-F11_S173


title: PA_sample117

description: Library name: DSP-1001660018950-B-F12_S174


title: HA-KAT6B_inp_rep2


title: HA-KAT6B_inp_rep1


title: HA-KAT6B_HA_rep3


title: PA_sample115

description: Library name: DSP-1001660018950-B-F10_S172


title: PA_sample114

description: Library name: DSP-1001660018950-B-F09_S171


title: PA_sample113

description: Library name: DSP-1001660018950-B-F08_S170


title: HA-KAT6B_HA_rep2


title: HA-KAT6B_HA_rep1


title: PA_sample112

description: Library name: DSP-1001660018950-B-F07_S169


title: PA_sample121

description: Library name: DSP-1001660018950-B-G04_S178


title: PA_sample120

description: Library name: DSP-1001660018950-B-G03_S177


title: HA-KAT6B_H3K4me3_rep2


title: HA-KAT6B_H3K4me3_rep3


title: PA_sample111

description: Library name: DSP-1001660018950-B-F06_S168


title: PA_sample110

description: Library name: DSP-1001660018950-B-F05_S167


title: PA_sample109

description: Library name: DSP-1001660018950-B-F04_S166


title: HA-KAT6B_H3K4me3_rep1


title: PA_sample107

description: Library name: DSP-1001660018950-B-F02_S164


title: HA-KAT6B_H3K27me3_rep2


title: HA-KAT6B_H3K27me3_rep3


title: HA-KAT6B_H3K27me3_rep1


title: PA_sample106

description: Library name: DSP-1001660018950-B-F01_S163


title: HA-KAT6B_EZH1_2_dKO_inp_rep3

value: HA-KATB; EZH1/2 dKO (EZH2-/-; EZH1-/-)


title: PA_sample104

description: Library name: DSP-1001660018950-B-E11_S161


title: PA_sample161

description: Library name: DSP-1001660019644-G-B08_S20


title: HA-KAT6B_EZH1_2_dKO_HA_rep3


title: HA-KAT6B_EZH1_2_dKO_inp_rep1


title: HA-KAT6B_EZH1_2_dKO_HA_rep2


title: PA_sample102

description: Library name: DSP-1001660018950-B-E09_S159


title: PA_sample103

description: Library name: DSP-1001660018950-B-E10_S160


title: PA_sample101

description: Library name: DSP-1001660018950-B-E08_S158


title: Hepatocyte, HAMP-/-_olive oil, rep2

city: Beijing

first: Changying

last: Li

address: Panjiayuan Street 17, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hepatocyte

extract_protocol:
The liver of WT and HAMP-/- mice were digested by using two step collagenase, and then primary hepatocytes were isolated. Pronase E was purchased from Merck (Germany). Type IV collagenase, trypsin inhibitor, 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid (HEPES), dimethylsulfoxide andlipopolysaccharide were purchased from Sigma (USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hepatocyte

value: Olive oil


title: Hepatocyte, HAMP-/-_ccl4, rep2


title: Hepatocyte, HAMP-/-_olive oil, rep1


title: PA_sample108

description: Library name: DSP-1001660018950-B-F03_S165


title: HA-KAT6B_EZH1_2_dKO_HA_rep1


title: Hepatocyte, HAMP-/-_ccl4, rep1


title: HA-KAT6B_EZH1_2_dKO_H3K4me3_rep3


title: PA_sample100

description: Library name: DSP-1001660018950-B-E07_S157


title: PA_sample105

description: Library name: DSP-1001660018950-B-E12_S162


title: PA_sample99

description: Library name: DSP-1001660018950-B-E06_S156


title: HA-KAT6B_EZH1_2_dKO_inp_rep2

value: none (input)


title: Hepatocyte, C57BL/6_olive oil, rep1


title: Hepatocyte, C57BL/6_CCl4, rep2


title: Hepatocyte, C57BL/6_olive oil, rep2


title: HA-KAT6B_EZH1_2_dKO_H3K4me3_rep2

value: embryonic stem cell (E14 line) and Drosophila S2 cell line


title: PA_sample97

description: Library name: DSP-1001660018950-B-E04_S154


title: HA-KAT6B_EZH1_2_dKO_H3K4me3_rep1


title: PA_sample168

description: Library name: DSP-1001660019644-G-C03_S27


title: PA_sample96

description: Library name: DSP-1001660018950-B-E03_S153


title: HA-KAT6B_EZH1_2_dKO_H3K27me3_rep3


title: PA_sample98

description: Library name: DSP-1001660018950-B-E05_S155


title: HA-KAT6B_EZH1_2_dKO_H3K27me3_rep2


title: PA_sample95

description: Library name: DSP-1001660018950-B-E02_S152


title: Hepatocyte, C57BL/6_CCl4, rep1


title: HA-KAT6B_EZH1_2_dKO_H3K27me3_rep1


title: PA_sample94

description: Library name: DSP-1001660018950-B-E01_S151


title: E14_inp_rep3

value: E14 wildtype


title: PA_sample93

description: Library name: DSP-1001660018950-B-D12_S150


title: E14_inp_rep2


title: PA_sample92

description: Library name: DSP-1001660018950-B-D11_S149


title: E14_inp_rep1


title: PA_sample91

description: Library name: DSP-1001660018950-B-D10_S148


title: CT_19

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2,0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: subcutaneous adipose tissue at basal state_CT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

extract_protocol: Qiagen extraction of total RNA was performed according to the manufacturer's instructions.

tag: bmi

value: Constitutive Thin (CT) women


title: CT_17

value: subcutaneous adipose tissue at basal state


title: MD55A3_Leucine_depletion_1

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

data_processing:
RiboSeq: Adaptors were removed from FASTQ files using cutadapt with parameters (-quality-base=33 -O 7 -e 0.15 -m 20 -q 5). Ribosomal RNA (rRNA) and tRNA contaminants were removed by aligning FASTQ reads with Bowtie2 and parameters ( -seed 42 -p1 -local) against a reference library (rRNA reference was obtained from GENCODE v19: rRNA, MT_RNA, rRNA_pseudogene, and tRNA reference data was obtained from GtRNAdb). Preprocessed FASTQ files were then aligned with TopHat2 and Bowtie2 against GRCh37/hg19 and GENCODE v19/BASIC transcripts with Ensembl coordinates using the parameters (seed 41 -n 2-m 1 -novel-juncs -- no-novel-indels –no-coverage-search –segment-length 25). Aligned reads were then filtered for minimum mapping quality of 10. Quality control of frames and periodicity of RPFs were performed using the RiboWaltz package.
HTSEQ was used to coun reads at exons of genes. Normalization was done using the TMM method from edgeR.
Assembly: hg19
Supplementary files format and content: Tab delimited text file containing readcounts normalized with TMM as decsribed in data processing steps
Library strategy: Ribo-Seq

source_name: Melanoma

growth_protocol: PC3 and MD55A3 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI 1640, Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/ml penicillin–streptomycin (Gibco). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin. All cell lines were maintained in a humidified atmosphere containing 5% CO2 at 37 °C and were regularly tested by PCR analysis and were found negative for mycoplasma contamination.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Rapid gel extraction was used, followed by overnight precipitation at −20 °C for RNA extraction from the polyacrylamide gels. Ribosomal RNA depletion was not performed. Prepared RPF libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA) and quantified by qPCR (Cat.no. 07960140001, Roche, Switzerland) and subsequently diluted to a 10 nM concentration. Next, the libraries were pooled and loaded with 1.5 pM on a NextSeq550Dx system (RUO mode) and sequenced with 75-base single-read using a 75 Cycles High Output Kit v2.5 (Illumina Inc., San Diego).

treatment_protocol: Leucine-free medium was prepared by adding glucose (Gibco), sodium pyruvate (Sigma) and all amino acids except for L-Leucine to RPMI 1640 Medium without amino acids (US Biologicals). Etoposide (Selleckchem), was dissolved in DMSO and used at a final concentration of 10 μM, unless stated otherwise. For t-RNA expression samples, oligonucleotides coding for tRNA-Leu-CAA-6-1 or tRNA-Leu-TAA-1-1 were annealed and phosphorylated. Next, a ligation reaction was performed with the annealed oligos and the digested vector using T4 DNA ligase (Thermo Scientific) for 1 hour at room temperature. The ligation products were subsequently transformed to DH5α competent cells. All resulting plasmids were sequence verified by Sanger sequencing. pLKO.1-puro vectors for expression of tRNA-Leu-CAG-1-7, tRNA-Leu-CAG-1-7-to-TAA and tRNA-TAA-3-1 were a kind gift from Heidi Greulich (PMID: 36302897).

value: Melanoma

value: Melanoma cancer

value: Leucine depletion


title: MD55A3_WT_1


title: E14_H3K4me3_rep3

value: H3K4me3 (Cell Signaling, 9751, lot 10)


title: CT_14


title: CT_18


title: CT_16


title: PA_sample90

description: Library name: DSP-1001660018950-B-D09_S147

value: Cornea


title: Ctrl_13

source_name: subcutaneous adipose tissue at basal state_control

value: Control woman


title: MCF7_miR-24-2-5p_3

city: Genova

first: Davide

last: Ceresa

state: APO/FPO EUROPE / ATLANTIC

address: Largo R. Benzi, 10

department: Cellular Oncology

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
Aligment to GRCh38 human genome assembly using STAR v2.7.5c
Transcript quantification using RSEM v1.3.1
Assembly: GRCh38
Supplementary files format and content: csv file containing raw counts of all samples, arranged by columns
Supplementary files format and content: csv file containing FPKM values of all samples, arranged by columns

source_name: cell line

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) 4.5 g/L glucose GlutaMAX (Gibco, UK), ZR-75-1 in RPMI 1640 medium (Gibco,UK), SK-BR3 in McCoy’s 5A medium (Sigma), supplemented with 10% (v/v) FCS (Life Technologies, Paisley, UK /Invitrogen) and 100 U/mL penicillin/streptomycin, at 37 °C, 5% CO2

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen), according to the manufacturer’s recommendations and performing the optional DNase digestion using RNase-free DNase I Kit (Qiagen).
PolyA enrichment

treatment_protocol: 2’O-methylated miRNA mimics for hsamiR-662 (MIMIC-miR-662), negative control (MIMIC-negCTRL), and FAMlabelled negative control (MIMIC-negCTRL-FAM+), were purchased from GenePharma, Shanghai. An optimised concentration of 50 nM of miRNA mimic was transfected into cells (MDA-MB-231, NW1, 4T1-luc2), using Lipofectamine 2000 (Invitrogen) as transfecting agent. Evaluation of transfection efficiency has been routinely performed by flow-cytometry (BD LSR II Flow Cytometer) followed analysis with Flowing Software 2.5.1 (Perttu Terho, University of Turku), and by real-time qPCR, using specific primers. Cell collections were performed 36 h post-transfection.

value: cell line

value: Breast cancer

value: MIMIC-miR-24-2-5p transfection


title: MCF7_negCTRL_3

value: MIMIC-negCTRL transfection


title: Ctrl_11


title: Ctrl_2


title: E14_H3K4me3_rep2


title: Ctrl_1


title: Ctrl_12


title: MDA_miR-24-2-5p_3


title: Ctrl_7


title: MDA_miR-662_3

value: MIMIC-miR-662 transfection


title: CT_4


title: PA_sample88

description: Library name: DSP-1001660018950-B-D07_S145


title: E14_H3K4me3_rep1


title: MCF7_negCTRL_2


title: MCF7_miR-24-2-5p_2


title: MDA_negCTRL_3


title: PA_sample89

description: Library name: DSP-1001660018950-B-D08_S146


title: MDA_miR-662_2


title: PA_sample86

description: Library name: DSP-1001660018950-B-D05_S143


title: E14_H3K27me3_rep3

value: H3K27me3 (Cell Signaling, 9733, lot 14)


title: PA_sample87

description: Library name: DSP-1001660018950-B-D06_S144


title: E14_H3K27me3_rep1


title: MDA_miR-24-2-5p_2


title: MCF7_miR-24-2-5p_1


title: MDA_negCTRL_2


title: E14_H3K27me3_rep2


title: PA_sample85

description: Library name: DSP-1001660018950-B-D04_S142


title: PA_sample84

description: Library name: DSP-1001660018950-B-D03_S141


title: E14_H3K23ac_rep3


title: MDA_negCTRL_1


title: MDA_miR-24-2-5p_1


title: APOE3-PSEN1

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

description: APOE3 microglia in PSEN1 mutatn neuron

data_processing:
Basecalls performed using RTA workflow version 3.4.4
Sequenced reads were trimmed for adaptor sequence,  low-complexity or low-quality sequence using trimmomatic v0.39 and fastp v0.20.1, then mapped to hg38 whole genome using STAR v2.7.4a with parameters --twopassMode Basic --outSAMstrandField intronMotif
Raw counts of sequencing reads for genes were perfomred using featureCounts method in Rsubread V2.8.2.
Read counts normalization, Reads Per Kilobase of exon per Megabase of library size (RPKM), and detection of differentailly expressed genes were processed using edgeR v3.36.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw counts of sequencing reads per gene for each Sample

source_name: microglia

growth_protocol: To set up the N-MG co-cultures, neurons were differentiated from the WT and PSEN1 mutant iPSCs for 21 days(Wang et al., 2021). Microglia were harvested at differentiation day 25 and seeded onto day-21 neuronal cultures  at  the ratio of N:MG= 5:2. The culture medium was gradually changed from neuronal medium into co-culture medium (Advanced F12, 1×N2, 1×Glutamax, 0.4556 µM 2-mercaptoethanol, 50 ng/ml IL-34), 10 ng/ml M-CSF, 10 ng/ml TGF-β1, 20 ng/ml BDNF and 20 ng/ml GDNF). N-MG co-cultures were maintained for 10 days before analysis.

extract_protocol:
total RNA isolation with Trizol
KAPA mRNA HyperPrep kit was used for RNA sequencing library preparation according to kit user manual
PolyA enriched, stranded RNA sequencing library

treatment_protocol: cocultured with neurons

value: microglia

value: co-culture with PSEn1 mutant neuron


title: PA_sample83

description: Library name: DSP-1001660018950-B-D02_S140


title: E14_H3K23ac_rep2

value: E14 wildtype

value: embryonic stem cell (E14 line) and Drosophila S2 cell line


title: PA_sample82

description: Library name: DSP-1001660018950-B-D01_S139


title: E14_H3K23ac_rep1


title: APOE3CH-PSEN1

description: APOE3Christchurch microglia in PSEN1 mutatn neuron


title: APOE3CH-WT

description: APOE3Christchurch microglia in WTneuron

value: co-culture with wild type neuron


title: BRPF2_D212_214A_inp_rep3

value: none (input)

value: HA-KATB; BRPF2 D212/214A homozygous knockin


title: PA_sample80

description: Library name: DSP-1001660018950-B-C11_S137


title: Mutant_8dpf_5

city: Greenwood

first: Heather

last: Flanagan-Steet

state: SC

address: 101 Gregor Mendel circle

institute: Greenwood Genetic Center

data_processing:
FASTQ QC by fastp
adapter trimming and assessment of ribo-depletion by bbduk
alignment by STAR
BAM indexing by samtools
counting of reads in each gene by subread
Assembly: GRCz11
Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file

organism: Danio rerio

source_name: whole body

growth_protocol: Animals were maintained according to standard protocols

extract_protocol:
Direct zol RNA microprep kit
KTC UNIV RNA-Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit

treatment_protocol: For the sample preparation, 3dpf larvae were genotyped using the assay described (see the qRT-PCR analyses and genotyping section), subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.

value: whole body

value: Mutant

tag: age

tag: replicate


title: Mutant_8dpf_4


title: Mutant_8dpf_2


title: PA_sample81

description: Library name: DSP-1001660018950-B-C12_S138

value: Cornea


title: BRPF2_D212_214A_HA_rep3

value: HA (Cell Signaling, 3724, lot 9)

tag: cell type


title: MCF7_negCTRL_1

value: cell line

tag: treatment


title: PA_sample78

description: Library name: DSP-1001660018950-B-C09_S135


title: PA_sample79

description: Library name: DSP-1001660018950-B-C10_S136


title: BRPF2_D212_214A_inp_rep1


title: Mutant_8dpf_1


title: MDA_miR-662_1

tag: cell line

value: Breast cancer


title: APOE3-WT

description: APOE3 microglia in WTneuron

tag: genotype


title: Mutant_5dpf_5

value: WT


title: BRPF2_D212_214A_HA_rep2


title: PA_sample77

description: Library name: DSP-1001660018950-B-C08_S134


title: d52 biological replicate 3 irradiated

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

data_processing:
Sequences were trimmed with TrimGalore and standard settings
Sequences were aligned with hisat2 (standard settings) on grch38
Reads were counted by summarizeOverlaps
Assembly: grch38
Supplementary files format and content: semicolon separated file contains the raw transcript counts

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: iPSC-derived lung organoids were cultured under standard conditions, irradiated and total RNA was isolated prior RNAseq, for scRNAseq lung organoids were enzymatically digested and sc analyses were perfomed (non-irradiated and irradiated condition) and

value: lung

value: iPSC

value: various lung cell types

value: unknown


title: HCC827 Gefitinib resistant cells

city: Guangzhou

first: Xiaoting

last: Jia

address: Hengzhigang Road 78#

institute: Affiliated tumor hospital of GZMU

description: Gene expression in HCC827/GR cells

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

scan_protocol: Scanned on an Agilent G2565CA scanner.

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

source_name: cells

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

growth_protocol: These cells were routinely cultured at 37 °C in a humidified incubator (5% CO2) in RPMI-1640 medium containing 10% fetal bovine serum.

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

treatment_protocol: HCC827 cells were treated with a stepwise dose escalation of Gefitinib (ranging from 0.1 to 5 μM) over for 1 year to establish resistant cell lines HCC827/GR.

tag: cells

value: NSCLC


title: BRPF2_D212_214A_HA_rep1


title: Mutant_5dpf_3


title: BRPF2_D212_214A_inp_rep2


title: Mutant_8dpf_3


title: PA_sample75

description: Library name: DSP-1001660018950-B-C06_S132


title: Mutant_5dpf_4


title: d52 biological replicate 2 irradiated


title: BRPF2_D212_214A_H3K23ac_rep3


title: BRPF2_D212_214A_H3K23ac_rep2


title: d52 biological replicate 3 non (control)  irradiated

value: control (d52)


title: PA_sample73

description: Library name: DSP-1001660018950-B-C04_S130


title: Mutant_5dpf_1


title: Mutant_5dpf_2


title: BRPF1_D270_272A_inp_rep3

value: HA-KATB; BRPF1 D270/272A homozygous knockin

value: embryonic stem cell (E14 line) and Drosophila S2 cell line


title: BRPF2_D212_214A_H3K23ac_rep1


title: d52 biological replicate 2 non (control)  irradiated


title: PA_sample72

description: Library name: DSP-1001660018950-B-C03_S129


title: HCC827 cells

description: Gene expression in HCC827 cells


title: PA_sample76

description: Library name: DSP-1001660018950-B-C07_S133


title: BRPF1_D270_272A_inp_rep2

value: none (input)


title: WT_8dpf_4


title: PA_sample71

description: Library name: DSP-1001660018950-B-C02_S128


title: d52 biological replicate 1 non (control)  irradiated


title: d35 biological replicate 3 non (control)  irradiated

value: control (d35)


title: WT_8dpf_3

value: whole body


title: d35 biological replicate 2 non (control)  irradiated


title: BRPF1_D270_272A_inp_rep1


title: BRPF1_D270_272A_HA_rep3


title: d52 biological replicate 1  irradiated


title: WT_8dpf_2

value: Mutant


title: PA_sample70

description: Library name: DSP-1001660018950-B-C01_S127

value: Cornea


title: PA_sample69

description: Library name: DSP-1001660018950-B-B12_S126


title: d35 biological replicate 1 non (control)  irradiated


title: PA_sample74

description: Library name: DSP-1001660018950-B-C05_S131


title: PA_sample68

description: Library name: DSP-1001660018950-B-B11_S125


title: BRPF1_D270_272A_HA_rep2

value: HA (Cell Signaling, 3724, lot 9)


title: WT_8dpf_1


title: BRPF1_D270_272A_HA_rep1


title: PA_sample67

description: Library name: DSP-1001660018950-B-B10_S124


title: iPSC biological replicate 7 non (control)  irradiated

value: control (d0)


title: iPSC biological replicate 6 non (control)  irradiated


title: BRPF1_D270_272A_H3K23ac_rep3


title: WT_8dpf_5


title: WT_5dpf_4


title: BRPF1_D270_272A_H3K23ac_rep2


title: PA_sample66

description: Library name: DSP-1001660018950-B-B09_S123


title: PA_sample65

description: Library name: DSP-1001660018950-B-B08_S122


title: WT_5dpf_3


title: iPSC biological replicate 5 non (control)  irradiated


title: BRPF1_D270_272A_H3K23ac_rep1


title: WT_5dpf_2


title: PA_sample64

description: Library name: DSP-1001660018950-B-B07_S121


title: WT_5dpf_1


title: MDA-MB-231_tRNA_CAA_overexpression_Leu_depletion_2

source_name: Breast

value: Breast

value: Breast cancer


title: KAT6B_D290A_inp_rep3

value: HA-KATB; KAT6B D290A homozygous knockin


title: H3tKO_plus_rep01-03

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
Cell barcode and UMI in Read1 was extracted by using UMI-tools with following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC”. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore, and reads were mapped to the GRCm38 reference using HISAT2. Read counts for each gene were obtained by featureCounts and UMI duplications were removed by UMI-tools.
Assembly: GRCm38
Supplementary files format and content: gzipped tab delimited raw count matrix for each sample
Supplementary files format and content: gzipped tab delimited sample : Cell Barcode list.

source_name: testis

extract_protocol:
Sliced tissue section(10um) was lysed with proK/PBS and purified cDNA with ZYMO DCC5 (ZYMO reserch).
PIC library preparation protocol (Honda et al.,2021)

value: testis

value: H3t KO

value: PIC UV irradiated (entire section)


title: PA_sample63

description: Library name: DSP-1001660018950-B-B06_S120


title: MDA-MB-231_tRNA_CAA_overexpression_Leu_depletion_1


title: MDA-MB-231_tRNA_CAA_overexpression_WT_2


title: iPSC biological replicate 8 non (control)  irradiated

value: lung

value: iPSC

value: unknown


title: WT_5dpf_5

value: WT


title: young_plus_rep01-03

value: wild-type


title: PA_sample62

description: Library name: DSP-1001660018950-B-B05_S119


title: MDA-MB-231_tRNA_TAA_overexpression_Leu_depletion_2


title: MDA-MB-231_tRNA_CAA_overexpression_WT_1


title: PA_sample60

description: Library name: DSP-1001660018950-B-B03_S117


title: ParishinB-3

city: Changsha

first: Xiongtao

last: Cheng

address: Graduate School, Hunan University of Chinese Medicine, Changsha, Hunan 410208, P. R. China

institute: Department of Oncology, The First Hospital of Hunan University of Chinese Medicine

description: Library name: sample 6

data_processing:
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.
Assembly: hg38

source_name: Cell

extract_protocol:
Then libraries with different indexs were multiplexed and loaded on an Illumina Novaseq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Cell

value: Breast cancer cell


title: ParishinB-2

description: Library name: sample 5


title: PA_sample59

description: Library name: DSP-1001660018950-B-B02_S116

source_name: Cornea


title: MDA-MB-231_tRNA_TAA_overexpression_Leu_depletion_1


title: ParishinB-1

description: Library name: sample 4


title: PA_sample58

description: Library name: DSP-1001660018950-B-B01_S115


title: Control-3

description: Library name: sample 3


title: MDA-MB-231_tRNA_TAA_overexpression_WT_2


title: PA_sample57

description: Library name: DSP-1001660018950-B-A12_S114


title: Control-2

description: Library name: sample 2


title: PA_sample61

description: Library name: DSP-1001660018950-B-B04_S118


title: MDA-MB-231_tRNA_TAA_overexpression_WT_1


title: CCL+IL_1b_3

city: Osaka

first: Minami

last: Hikida

state: Chuou-Ku

address: 1-17 Machikaneyama-tyo

institute: Medicine for Sports and Performing Arts, Dept. of Health and Sport Sciences, Osaka University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: human knee articular chondrocytes, 3D constructs, IL-1β10ng/mL stimulation and cyclic compressive loading (CCL), 40kPa 0.5Hz 1h, 12h after loading

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: human knee articular cartilage

value: knee articular chondrocytes

tag: disease state

value: OA


title: Control-1

description: Library name: sample 1


title: PA_sample56

description: Library name: DSP-1001660018950-B-A11_S113

value: Cornea


title: CCL+IL_1b_2

value: IL-1β10ng/mL stimulation and cyclic compressive loading (CCL), 40kPa 0.5Hz 1h, 12h after loading


title: MDA-MB-231_Leucine_depletion_2

value: Breast

value: Breast cancer

value: Leucine depletion