title: Sample 18_p166 NGS

description: Pig-Mike.integrations.txt

source_name: liver

extract_protocol:
(RNA-Seq samples 1-13) Total RNA was extracted from fresh frozen tissue using Qiagen RNeasy Plus Universal mini kit followed by Manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
(NGS DNA samples 14-22) Genomic DNA was isolated from snap-frozen tissue fragments using a Gentra Puregene Tissue Kit (Qiagen, Hilden, Germany).  Ligation-mediated PCR (LM-PCR) was used for efficient isolation of integration sites.  Restriction enzyme digestions with MseI were performed on genomic DNA samples; the digested DNA samples were then ligated to linkers and treated with ApoI to limit amplification of the internal vector fragment downstream of the 5' LTR.  Samples were amplified by nested PCR and and sequenced using the Illumina HiSeq 2500 Next-Generation Sequencing System (San Diego, CA).
Samples 1-13 contain paired-end reads of extracted mRNA.  Samples 14-22 contain paired end reads of DNA amplicons for mapping lentiviral integration sites.
(RNA-seq samples 1-13) RNA libraries were prepared using 200 ng of total RNA according to the manufacturer's instructions for the truSeq Stranded mRNA Sample Prep Kit (Illumina, Sna Diego, CA). The concentration and size distribution of the completed libraries were determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).  Library was sequenced at 600 million fragment reads per sample following Illumina's standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100x2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HiSeq Control Software HD 3.4.0.38 collection softward. Base-calling was performed using Illumina's RTA version 2.7.7.
(NGS DNA samples 14-22)We used Picard software’s (http://broadinstitute.github.io/picard/) insert size metrics function to calculate the average fragment length per sample. This metric averaged across all the samples was 158 base pairs (bps) long with an average standard deviation of 29bps. Since 150bp long reads were sequenced, most of the paired read one (R1) and read two (R2) reads overlapped, providing redundant information. R2 reads were therefore not considered in the analysis.


title: E08_MS273_207

status: Public on Nov 19 2021

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E08

library_source: transcriptomic

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicu;aris 5.0
Supplementary_files_format_and_content: tab-delimited text files *rpm.txt include RPM values (cufflinks) or *count.txt include Read counts (HTSeq) for each Sample

molecule: total RNA

organism: Macaca fascicularis

source_name: Cynomolgus monkey embryo E08

growth_protocol: For cultivation of CMK6 and CMK9 cyESCs, they were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).

extract_protocol: For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60; Ishikura et al. 2016, Cell Reports, 17, 2789].

tag: tissue

value: embryo

tag: developmental stage

tag: sequencer

value: Nextseq550, High, 75 cycle


title: E08_MS273_208


title: NT2

status: Public on Nov 20 2021

city: Parkville

first: Michael

middle: James

last: Haydon

state: VIC

address: BioSciences 4, Royal Parade

country: Australia

institute: University of Melbourne

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
SOAPnuke v2.1.0 (Chen et al., 2018) was used to remove adapter sequences and low-quality reads from the sequencing data.
HiSAT2 v2.2.1 (Kim et al., 2015) to align the sequencing reads to the Arabidopsis thaliana Col-0 genome (TAIR10).
RSEM v1.2.22 (Li & Dewey, 2011) to quantify the gene expression level of each replicate.
Genome_build: TAIR10
Supplementary_files_format_and_content: TAIR_gene_expression.txt: Abundance measurements matrix.

organism: Arabidopsis thaliana

source_name: 14 d old seedlings

growth_protocol: 12 h light/12 h dark, 14 d on 1/2MS media.

extract_protocol:
Total RNA extracted with ISOLATE II RNA Plant Kit (Meridian Bioscience).
NEBNext® UltraTM RNA Library Prep Kit for Illumina® and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 2.0 Fluorometer (Invitrogen). Libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument and sequenced using a 2x150bp paired-end (PE) configuration.

treatment_protocol: 1/2MS media containing DMSO, 10 µM DPI, 25 µM pentamidine isethionate, 12.5 µM AEG3482 or 2 µM Tyrphostin AG879.

tag: ecotype

value: Seedlings

tag: age

value: 14 days

tag: treatment

value: Untreated

tag: time point


title: E08_MS224_088


title: E07_MS257_208

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E07

source_name: Cynomolgus monkey embryo E07


title: E07_MS257_215


title: E07_MS257_218


title: E07_MS257_140


title: CMK9_MS009_053

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey ESC CMK9.

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfas5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs.
Mapped reads were also processed with HTSeq v0.11.0  to calculate number of read counts per gene.
For the reference gene annotations used in cufflinks and HTSeq, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicularis 5.0 (macFas5)
Supplementary_files_format_and_content: *_rpm.txt: tab-delimited text files include RPM or raw count values for each Sample.

source_name: Cynomolgus monkey ESC CMK9

tag: cell line

tag: cell type

value: Undifferentiated embryonic stem cell

value: SOLiD, 50bp, ECC


title: E08_MS273_223


title: E07_MS257_070


title: E07_MS257_132


title: E08_MS273_216


title: E07_MS257_066


title: E07_MS257_067


title: E07_MS257_058


title: E07_MS257_056


title: E07_MS257_139


title: E07_MS257_057


title: E07_MS257_055


title: E07_MS257_054


title: E07_MS257_053


title: E07_MS257_137


title: E07_MS257_052


title: E07_MS257_036


title: E07_MS257_037


title: E07_MS257_039


title: E07_MS252_124


title: E07_MS257_040


title: E07_MS257_038


title: E07_MS257_041


title: E07_MS257_044


title: E07_MS257_032


title: KAT5 KO mice_PT cells

type: RNA

city: Shinjyuku-ku,

first: Akihito

last: Hishikawa

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

description: Gene expression data from embryos proximal tubular cells isolated from proximal tubular cell-specific KAT5 knockout mice kidney

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were normalized with Transcriptome Analysis　Console (TAC) 4.0.2  using default analysis settings and global scaling as normalization method (sst-RMA). Normalized CHP files were analyzed with TAC 4.0.2.

label: biotin

organism: Mus musculus

source_name: Proximal tubular cells isolated from proximal tubular cell-specific KAT5 knockout mice kidney

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 64ng total RNA (GeneChip WT PLUS Reagent Kit User Guide , Thermo Fisher Scientific Applied Biosystems).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: 8 week old mice

extract_protocol: RNA was quantified using a NanoDrop-2000c spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: proximal tubular cells were isolated from mice kidney

value: proximal tubular cells

tag: Sex

value: male

tag: genotype

value: KAT5 knockout


title: WT_PT cells

description: Gene expression data from embryos proximal tubular cells isolated from wild type mice kidney

source_name: Proximal tubular cells isolated from wild type mice kidney

value: wild type


title: E07_MS257_045


title: E51_MS173_237

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E51

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfac5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs.
Mapped reads were also processed with HTSeq v0.11.0  to calculate number of read counts per gene.
For the reference gene annotations used in cufflinks and HTSeq, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicu;aris 5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM or raw count values for each Sample

source_name: Cynomolgus monkey embryo E51

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60; Ishikura et al. 2016, Cell Reports, 17, 2789].


title: E07_MS252_088


title: E16_MS173_235

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E16

source_name: Cynomolgus monkey embryo E16


title: E16_MS173_239


title: E16_MS173_092


title: E16_MS173_088


title: E07_MS252_075


title: E13_MS173_243

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E13

source_name: Cynomolgus monkey embryo E13


title: E16_MS127_162


title: E07_MS252_062


title: E16_MS127_160


title: E13_MS127_192


title: E13_MS132_143


title: E13_MS127_184


title: E13_MS127_182


title: E13_MS130_021


title: E13_MS127_180


title: E13_MS127_181


title: E13_MS127_178


title: E13_MS127_177


title: E13_MS127_183


title: E13_MS127_189


title: E13_MS127_174


title: E13_MS127_172


title: E13_MS127_168


title: E13_MS127_170


title: E13_MS133_056


title: E13_MS173_233


title: E13_MS107_076


title: E13_MS107_071


title: E13_MS107_069


title: E13_MS107_068


title: E13_MS107_067


title: E13_MS101_067


title: E13_MS127_176


title: E13_MS101_061


title: E13_MS127_186


title: E13_MS101_056


title: Sample 17_p167 NGS

city: Rochester

first: Joseph

middle: Benjamin

last: Lillegard

state: MN

address: 200 First St. SW

department: Surgery

country: USA

institute: The Mayo Clinic

description: Pig-Kellyanne.integrations.txt

library_source: genomic

data_processing:
RNA-seq:
The mRNA-seq data were aligned with STAR version 2.5.2b to the Sscrofa11.1 assembly of the pig genome.  Raw gene expression was quantified with the featureCounts software.  Normalization and differential expression analyses were performed using R version 3.5.3 with the edgeR version 3.24.3 and limma version 3.38.3 packages.  Network and functional term enrichment analyses were processed through Qiagen's Ingenuity application on the identified differentially expressed genes.  Heat maps visualizing the z-scores of the relevant genes' normalized expression values were created using the clustvis web tool.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The mgi GO list was used to cluster the set of genes based on their biological process and determine their statistical significance. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
NGS DNA:
Quality control of the sequenced read pairs was performed using the FASTQC software. The average base quality of the sequenced reads was >Q30 on the Phred scale. Uniform distribution of A,G,T and C nucleotides was seen across the length of the reads without bias for any specific bases. The number of unknown “N” bases was less than 1% across the length of the reads. High sequence duplication (> 80%) was observed, however, this was anticipated due to the nature of the experiment and the amplification of specific library fragments.
Reads were trimmed to remove the viral sequence in two separate steps. In step 1, the viral sequence was trimmed from the R1 reads using cutadapt84 with a mismatch rate (e=0.3) from the 5’ end of each read. In step 2, if the linker sequence was present, it was similarly trimmed from the 3’end of the read. Trimmed reads with a length less than 15bps were removed from the rest of the analysis to reduce ambiguous alignments. Untrimmed reads were also removed from the rest of the analysis because they did not contain a viral segment that could be used as evidence of a viral mediated integration.
The remaining R1 reads were aligned to the susScr11 build of the pig reference genome using BWA-MEM in single-end mode. Default BWA-MEM parameters were used. The reads used to identify genomic points of viral integrations had to be uniquely mapped to the genome with a BWA-MEM mapping quality score greater than zero.
An integration point was defined by the position of R1’s first aligned base on the susScr1 genome. Unique integration points were identified across the genome without any constraints on coverage. However, for downstream annotation and analysis, only those integration points with 5 or more supporting reads were used to minimize calling false positive integration points.
Locations of integration points were categorized into: exons, introns, 3 prime UTRs, 5 prime UTRs and intergenic regions using information extracted from the susScr11 refflat file maintained by UCSC’s Genomics Institute. To avoid conflict of feature categorization arising from multiple overlapping gene definitions, only the definition of the longest gene was used to annotate integration points. Additional features where computed including: the distance to the nearest transcription start site (TSS), makeup of CpG-rich regions of the genome (“CpG islands”), and enrichment to tumor-associated genes. This tumor gene list was comprised of 745 clinically validated tumor-associated human genes (from Mayo Clinic internal data). Those genes were related to their pig homologs based on GenBank’s gene names.
In order to look for selective enrichment of any specific biological pathways, the genes identified as integration sites were entered into the WEB-based GEne SeT AnaLysis Toolkit. Results were identified using the over-representation analysis (ORA) method with identified KEGG pathways. A false discovery rate (FDR) of <0.05 was considered significant.
Genome_build: NGS DNA: susScr11; RNA-seq: Sscrofa11.1
Supplementary_files_format_and_content: "bed" (.txt); Rawcounts

molecule: genomic DNA

organism: Sus scrofa

growth_protocol: All animal procedures were reviewed and approved by Mayo Clinic’s  Institutional Animal Care and Use Committee, and all animals received humane care and husbandry for the  duration of the study.

treatment_protocol: Animals with the genotype "Fah +/+" were positive controls which did not exhibit the diseased phenotype of HT1 received no treatment. Pig number 266 was used as a negative control and received no consitant treatment, however, was treated on cycles of the drug NTBC. Animals with the genotpye "Fah -/-" which recieved the NTBC treatment were used as controls for the current standard of care of HT1 patients.  Animals with the genotype "Fah -/-" which recieved the LV-FAH treatment were the subjects of the study for the lentiviral gene therapy.

value: parenchyma

value: Fah -/-

value: LV-FAH


title: E13_MS101_053


title: E13_MS101_052


title: E13_MS101_035


title: E13_MS083_041


title: E13_MS101_036


title: E13_MS127_169


title: E13_MS101_054


title: E08_MS219_095


title: E08_MS219_097


title: E08_MS219_094


title: E08_MS219_091


title: E08_MS219_093


title: E13_MS107_070


title: E13_MS107_073


title: E08_MS219_092


title: E13_MS107_075


title: E13_MS107_074


title: Veh_2.2

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads align to mouse genome GRCm38.95 using STAR 2.6.0c
featureCounts v1.6.3
Genome_build: GRCm38.95
Supplementary_files_format_and_content: raw counts

source_name: Liver

extract_protocol: Libraries were prepared from 800ng of total RNA per sample and processed using A Kappa Hyper-prep kit (Roche cat# KR1352). Samples quality was then confirmed using a tapestation (D1000), where samples were sequenced on 2 lanes (PE 50bp reads) of a HiSeq 4000.

tag: strain

value: Liver

value: Veh

tag: batch


title: Veh_2.4


title: E08_MS219_087


title: Veh_1.3


title: Veh_2.1


title: Veh_2.3


title: E08_MS219_084


title: LBP_1.4

value: LBP


title: E13_MS101_021

value: embryo


title: LBP_1.3


title: Veh_1.4


title: FSTL3_2.3


title: Veh_1.1


title: FSTL3_2.4


title: FSTL3_2.1


title: FCN2_2.4


title: FCN2_2.3


title: FCN2_2.2


title: E06_MS099_073

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E06

source_name: Cynomolgus monkey embryo E06

value: Nextseq550, High, 75 cycle


title: LoVo control GFP cells

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

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, then mapped to hg38 whole genome using Hisat2.
Gene were quantified using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: LoVo cells

extract_protocol: RNA libraries were prepared for sequencing using polyA selection RNA-seq protocols

value: LoVo

value: control


title: LoVo CEBP4 overexpression cells

value: CEBP4 overexpression


title: EPDR1_2.4


title: T6_CD45-

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description:
10X genomics
scRNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger 10XRNA Vcellranger-3.1.0 mkfastq
cellranger 10XRNA Vcellranger-3.1.0 count
reads are mapped to hg38
UMI counts are summarized are gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: UMI counts

source_name: Ovary

growth_protocol: Single cell suspensions are made from fresh tumors

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)

treatment_protocol: samples are collected before treatment

value: Cancer cells

tag: histopathology

value: High grade serous ovarian carcinoma


title: FCN2_2.1


title: EPDR1_2.1


title: EPDR1_2.3


title: Veh_1.2


title: EPDR1_2.2


title: T1

description:
10X genomics
scRNAseq


title: Young Villous Epithelium 2

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

institute: Lancaster University

data_processing:
Reads were trimmed with Cutadapt (version cutadapt-1.9.dev2) using a quality threshold of 30 for the 3'end and the adapter sequences of the TruSeq stranded mRNA kit (AGATCGGAAGAGC). Trimmed reads with a length of less than 50 were discarded.
Read alignment was made using STAR (version 2.5.2b), with the parameters specifying paired-end reads and --outSAMtype BAM Unsorted.
FeatureCounts (version 1.5.1) was used for assigning counts.
Genome_build: Mus musculus (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text of raw gene counts for every gene for each sample
Supplementary_files_format_and_content: Tab-delimited text of FPKM values for each sample

source_name: Villous Epithelium

extract_protocol:
Portions of small intestine containing individual Peyer’s patches were removed and immersed in Hank’s balanced salt solution (HBSS) containing 30 mM EDTA at 4oC for 15 min.  Peyer’s patches domes were micro-dissected and the FAE layer then carefully teased away from the underlying tissue using fine needles under stereomicroscopy and trimmed of villi.  Sheets of conventional VE were prepared in the same manner from 5 mm portions of ileum that lacked Peyer’s patches adjacent to each dissected Peyer’s patch. Isolated FAE and VE sheets as well as 5 mm sections of whole ileum from each mouse were kept at -80oC until RNA extraction.  Total RNA was isolated from FAE, VE and ileum samples using a RNeasy Plus Kit (Qiagen).
TruSeq stranded mRNA-seq library

value: 4 months

value: Small Intestine


title: Young Villous Epithelium 4


title: T6

description:
10X genomics
scRNAseq


title: Young Villous Epithelium 1


title: OMT-3_CD45-

description:
10X genomics
scRNAseq

source_name: Omentum


title: N1_normal ovary

description:
10X genomics
scRNAseq

value: Normal cells


title: LBP_1.2


title: Young Ileum 4

source_name: Ileum


title: OMT-1_CD45-

description:
10X genomics
scRNAseq


title: Young Ileum 2


title: Young Villous Epithelium 3


title: Young Ileum 3


title: OMT-1_CD45+

description:
10X genomics
scRNAseq


title: APC T2D-FDR Pool 1 (smallRNA-seq)

city: Napoli

first: Gregory

middle: Alexander

last: Raciti

address: Via S. Pansini 5

country: Italy

institute: Università degli Studi di Napoli Federico II

data_processing:
Clean reads were generated per each sample. Trimmed and quality raw filtered reads from small RNA-Seq were aligned and assigned to human mature miRNAs (miRBase Release 20), using the CASAVA software. Within each experimental group, replicate concordance among the two anisogenic replicates was computed by Spearman’s rank-order correlation. Aligned reads were then used to estimate the expression level of each miRNA.
Differential expression analysis of read counts among the two experimental groups was performed using the Generalized Linear Model approach for multifactorial experiments implemented in the R/Bioconductor package edgeR. The expression cutoff used was 1 count per million in at least two samples. P values were adjusted for multiple testing correction according to the Benjamini-Hochberg approach. The cutoff for significance in differential expression was Q < .05.
Genome_build: Human miRBase Release 20
Supplementary_files_format_and_content: xlsx file includes for each Pool,miRNAID, CPM values, logFC, LogCPM, LR, Pvalue and FDR

source_name: SAT APC cells

extract_protocol:
Total RNA, including miRNA, was isolated from SAT APCs, using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany). Samples were quantified by using a Qubit 3 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).
Libraries were prepared using Illumina small library preparation protocols, and sequenced using the SBS sequencing protocol on Illumina Hiseq2000 platforms

value: Subcutaneous Adipose Tissue

value: Adipocyte Precursor Cells

tag: disease state

value: Healthy individuals with Family history of Type 2 diabetes (FDR)


title: FSTL3_2.2


title: Young Ileum 1


title: Young FAE 3

source_name: Peyer's patch follicle associated epithelium


title: Young FAE 1


title: APC Ctrl Pool 2 (smallRNA-seq)

value: Healthy individuals without Family history of Type 2 diabetes (Ctrl)


title: Young FAE 2


title: Aged Villous Epithelium 6

value: 26-28 Months


title: APC Ctrl Pool 2 (RNA-seq)

data_processing:
Clean reads were generated per each sample. Trimmed and quality filtered raw reads from RNA-Seq were aligned and assigned to Gencode Human release v19 transcripts and genes by using RSEM version 1.2.19 with standard parameters. Within each experimental group, replicate concordance among the two anisogenic replicates was computed by Spearman’s rank-order correlation. Aligned reads were then used to estimate the expression level of each gene.
Differential expression analysis of read counts among the two experimental groups was performed using the Generalized Linear Model approach for multifactorial experiments implemented in the R/Bioconductor package edgeR. The expression cutoff used was 1 count per million in at least two samples. P values were adjusted for multiple testing correction according to the Benjamini-Hochberg approach.39 The cutoff for significance in differential expression was Q < .05.
Genome_build: Human Release 19 (GRCh37.p13)
Supplementary_files_format_and_content: xlsx file includes for each Pool, Ens_GeneID,  Gene_Symbol, TPM values, logFC, Pvalue and FDR

extract_protocol:
Total RNA, including miRNA, was isolated from SAT APCs, using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany). Samples were quantified by using a Qubit 3 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced using the 90bp Paired-End sequencing protocol on Illumina Hiseq2000 platforms


title: OMT-3_CD45+

description:
10X genomics
scRNAseq


title: APC T2D-FDR Pool 1 (RNA-seq)


title: Aged Villous Epithelium 4


title: Aged Villous Epithelium 5


title: APC Ctrl Pool 1 (RNA-seq)


title: PC9 cells Etoposide 10 µM RNA-seq.rep3

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

institute: East China Normal University

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lung adenocarcinoma cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Lung adenocarcinoma

value: treated with 10 uM Etoposide for 24 hours


title: APC T2D-FDR Pool 2 (smallRNA-seq)


title: PC9 cells Etoposide 10 µM RNA-seq.rep1


title: PC9 cells control RNA-seq.rep3

value: untreated


title: Aged Villous Epithelium 1


title: Aged Villous Epithelium 3


title: APC Ctrl Pool 1 (smallRNA-seq)


title: Aged Villous Epithelium 2


title: PC9 cells control RNA-seq.rep2


title: Aged Ileum 3


title: Aged Ileum 2


title: PC9 cells control RNA-seq.rep1


title: Aged Ileum 1


title: Capan2 cells Etoposide 50 µM RNA-seq.rep3

source_name: Pancreatic adenocarcinoma cells

value: pancreatic

value: Pancreatic adenocarcinoma

value: treated with 50 uM Etoposide for 24 hours


title: Capan2 cells Etoposide 50 µM RNA-seq.rep2


title: Aged FAE 3


title: Aged FAE 1


title: Capan2 cells Etoposide 50 µM RNA-seq.rep1


title: Capan2 cells control RNA-seq.rep3


title: Capan2 cells control RNA-seq.rep2


title: Capan2 cells control RNA-seq.rep1


title: Lyz2-Cre/+-Egr2-fl/fl_3

city: Edinburgh

first: Calum

middle: C

last: Bain

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq were be converted into fastq files and de-multiplexed using Illumina bcl2fastq v. 2.17 program.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Genome_build: Mus musculus mm10 using STAR alinger v.2.5.2b
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Enzymatic digestion and FACS
Lung tissue was excised, enzymatic digested and alveolar macrophages isolated using FACS
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for cDNA synthesis and amplification and Illumina Nextera XT library was used for library preparation

value: Lyz2-Cre/+-Egr2-fl/fl (C57BL/6J)

value: Lung

tag: population

value: F


title: Lyz2-Cre/+-Egr2-fl/fl_4

description: SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for cDNA synthesis and amplification and Illumina Nextera XT library was used for library preparation


title: H661 cells Etoposide 40 µM RNA-seq.rep3

value: treated with 40 uM Etoposide for 24 hours


title: Egr2-fl/fl_4


title: H661 cells Etoposide 40 µM RNA-seq.rep1


title: H661 cells Etoposide 40 µM RNA-seq.rep2


title: Egr2-fl/fl_2


title: Lyz2-Cre/+-Egr2-fl/fl_2


title: Egr2-fl/fl_3


title: H661 cells control RNA-seq.rep1


title: BLCA_Nac_288

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials â€¢ Heat cocktails at 99Â° for 5 minutes, then 42Â° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). â€¢ Transfer 200Î¼l of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45Â° at 60rpmâ€¢ Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Raw data from RMA was quantile normalized, adjusted for labeling batch using ComBat, and merged by median probe set values per gene symbol.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit (samples 1-32) or GeneChip WT Pico kit (samples 33-149)

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

treatment_protocol: not applicable

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: induction

tag: pathologic tn stage rc specimen

tag: lundtax rna subtype

value: UroC

tag: lundtax ihc subtype

value: Uro

tag: consensus classifier subtype

value: LumNS


title: H661 cells control RNA-seq.rep2

tag: cell line

tag: tissue

tag: cell type

tag: treatment


title: Egr2-fl/fl_1

tag: strain

tag: Sex


title: H661 cells control RNA-seq.rep3


title: BLCA_Nac_201

value: UroB

value: Ba/Sq

value: BASQ


title: P8-inter_BCR-seq

city: Yokohama

first: Takashi

last: Watanabe

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN

data_processing:
Sequence read were clustered using USEARCH version 4.1.93
Data combined clustered read1 and read2
Supplementary_files_format_and_content: FASTA

source_name: B cells

extract_protocol:
All single cell-derived antibodies were expressed separately on the surface of cultured cells. Two fluorescently labeled antigens (H1 and H2) were reacted with the cells, and cells reacting with both H1 and H2, H1 alone, or H2 alone were isolated by FACS. Only the heavy chain of the antibody was amplified by PCR and the sequence was read by Miseq. The antibody sequence in each fraction was determined using the antibody sequence read by single cell as a reference.
Cells in each fraction (P5-cros, P6-H2, P7-PR8, P8-inter) were used as template for PCR using primers for heavy chains. After that, adapter primers for NGS were added and the run was performed with Miseq. The CDR3 sequence of the heavy chain, contained in each fraction, was determined. Since we had previously determined the antibody sequence from a single cell, we used that sequence as a reference sequence to identify the antibody sequence contained in each fraction.

value: Germinal Centor B cells

value: Spleen

value: BALB/c

value: After bulk sorting, the immunoglobulin sequence of each population was obtained.


title: M3

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

data_processing:
fastq read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 25 bp long were discarded.
Downstream processing was conducted with STAR v2.7.3a and its single cell seq implementation "STARsolo".
Cells being accepted had to pass the following filters: at least 750 transcripts profiled, having at least 10% of transcripts arising from intron spanning or unspliced reads, less than 15% of their transcriptome of mitochondrial origin
Genome_build: GRCm38.p6

extract_protocol:
Lungs were removed and single cells dissociated using collagenase and elastase.
Single-cell libraries were prepared using the standard 10x Genomics single cell 3' reagent kits v3 processing workflow.

tag: exposure

value: room-air

value: male

value: lung

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: Mouse_control

description:
Enzymatic digestion and FACS
10X Genomics Single cell 3' gene expression V2

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.1
Genome_build: mm10 (Ensemble 84)
Supplementary_files_format_and_content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

extract_protocol:
Lung tissue was excised, enzymatic digested and CD11c+/CD11b+ cells isolated using FACS
10X Genomics Single cell 3' gene expression V2

tag: genotype

value: Rag1-/- (Tgfbr1fl/fl)

value: Lung

tag: cell population

value: After excluding eosinophils and neutrophils, all cells expressing either CD11c or CD11b were selected

value: F


title: Aged FAE 2

tag: age

value: 26-28 Months

value: Small Intestine


title: BLCA_Nac_148

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: neoadjuvant

value: GU

value: Uro

value: LumNS


title: P7-PR8_BCR-seq

value: Germinal Centor B cells

value: Spleen

value: BALB/c

value: After bulk sorting, the immunoglobulin sequence of each population was obtained.


title: Lyz2-Cre/+-Egr2-fl/fl_1

value: Lyz2-Cre/+-Egr2-fl/fl (C57BL/6J)

tag: population


title: P6-H2_BCR-seq

tag: tissue


title: M1

value: room-air

value: male

value: lung

value: 10x Genomics

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: BLCA_Nac_146

tag: pathologic tn stage rc specimen

tag: lundtax rna subtype

tag: lundtax ihc subtype

tag: consensus classifier subtype


title: BLCA_Nac_150

value: Mes-like

value: StromaRich


title: F1

tag: exposure

tag: strain

tag: Sex

value: female


title: P5-cross_BCR-seq

tag: cell type

tag: treatment


title: F3

tag: platform

tag: technology


title: BLCA_Nac_142

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GeneChip WT Pico kit

value: neoadjuvant

value: LumP


title: Ope3

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

data_processing:
Adapters were trimmed using TrimGalore (version: 0.6.6).
The reads were mapped by the aligning software HISAT2 (version 2.2.1) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 2.0.1).
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.28.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix of RNA-seq

source_name: FAPs in overloaded plantaris muscle

extract_protocol:
The cells were sorted to each 1000 cells into tube contained lysis buffer using Cell sorter.  Libraries were constructed following the protocol as shown previously (Hashimshony et al., 2016).
Libraries were constructed as shown previously (Hashimshony et al., 2016).

value: Mesenchymal progenitors (FAPs)

value: overloaded

tag: type

value: Pdgfra+

value: plantaris muscle


title: BLCA_Nac_141

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: GU

value: LumU


title: D5

value: cigarette-smoke

tag: tissue


title: Ope2


title: D2


title: BLCA_Nac_139

tag: pathologic tn stage rc specimen

tag: lundtax rna subtype

value: Uro

value: LumNS


title: Ope1


title: Cont3

source_name: FAPs in sham plantaris muscle

value: sham


title: C5

value: male

value: lung

value: 10x Genomics

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: BLCA_Nac_131

value: GeneChip WT Pico kit

tag: lundtax ihc subtype

tag: consensus classifier subtype

value: StromaRich


title: BLCA_Nac_130

value: neoadjuvant

value: UroA

value: LumP


title: BLCA_Nac_129


title: Cont2

value: Mesenchymal progenitors (FAPs)

value: Pdgfra+

tag: strain


title: C2

tag: exposure

tag: Sex


title: BLCA_Nac_124

value: UroB


title: H2_PR8_TdT_K_p4_BCR-seq

description:
"K" indicates the kappa chain of the antibody light chain.
"TdT" refers to Terminal Deoxynucleotidyl Transferase (TdT) that is used to obtain the Immunoglobulin sequence.

data_processing:
Sequence read were clustered using USEARCH version 4.1.93
Data combined clustered read1 and read2
Supplementary_files_format_and_content: The FASTA files show the sequence of the variable region of the antibody. Since only one type of antibody is produced per single cell, the sequence is only obtained and not quantified.

extract_protocol:
Germinal Center B cells (CD43 positive) from immunized mice by H1 and H2 have been collected using AutoMACS. Furthermore, the IgG1 positive-B cells were sorted with fluorescent-labeling H1 and H2 into wells of a 96-well plate as an single cell using BD FACSAria III (BD Biosciences). The single cell in lysis buffer was immediately stored at -80 degree centigrade.
Single cell was dropped in 4µL/well of lysis buffer and 1µL of 10µM Oligo(dT)18 Primer. Cell lysate was incubated at 70°C for 90 sec, at 35°C for 15 sec and then put on ice for 2min. For First-Strand cDNA Synthesis, 5µL of RT mix was added to the cell lysate and incubated consecutively at 35°C for 5min, 45°C for 20min , 70°C for 10min and 4°C for chilling. For Primer Digestion, 5µL of the Primer Digestion mix was prepared, incubated at 37°C for 30 min, 80°C for 20min and 4°C for chilling. For Poly-A tailing reaction, 5µL of the Poly-A tailing reaction mix was prepared, incubated at 37°C for 50 sec, 65°C for 10min and 4°C for chilling. For 2nd strand cDNA synthesis, 25µL of the amplification mix was prepared, incubated at 95°C for 3min, 40°C for 1min, 65°C for 10min and 72°C for 5min and chilled. For cDNA amplification by Ig-specific outer primer set, 20µL of the outer amplification mix was prepared, incubated at 94°C for 2min followed by 25 cycles of 98°C for 10sec, 60°C for 30sec, and 68°C for 45sec, then chilled. For cDNA amplification by Ig-specific inner primer set, 20L of the inner amplification mix was prepared, incubated at 94°C for 2min followed by 40 cycles of 98°C for 10sec, 60°C for 30sec, and 68°C for 45sec, then chilled. Finally, 3L of the inner cDNA amplified product was used for further plate-indexing by amplification. Finally, 3µL of the inner cDNA amplified product was used for further plate-indexing by amplification. 20µL of the plate-indexing amplification mix was prepared, incubated at 94°C for 2min followed by 25 cycles of 98°C for 10sec, 60°C for 30sec, and 68°C for 45sec, then chilled. The Libraries were sequenced on the Miseq following the manufacturer's protocols.

tag: cell type

value: Germinal Centor B cells

value: Spleen

value: BALB/c

tag: treatment

value: After single cell sorting, the immunoglobulin sequence of each well was obtained.


title: H2_PR8_TdT_G_p4_BCR-seq

description:
"G" indicates the gamma chain of the antibody heavy chain
"TdT" refers to Terminal Deoxynucleotidyl Transferase (TdT) that is used to obtain the Immunoglobulin sequence.


title: BLCA_Nac_128

value: UroC

value: Uro

value: LumNS


title: Cont1

value: sham

value: plantaris muscle


title: iEC_2

city: Boston

first: Mark

last: Feinberg

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's

description: iEC Replicate 2

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCh38

source_name: induced endothelial cells

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs, Lonza) and iECs were cultured in endothelial cell growth media (EGM-2, Lonza). Human Coronary Artery Smooth Muscle Cells (CASMCs, Lonza) were cultured in smooth muscle cell growth media (SMGM, Lonza) prior to use.

extract_protocol:
Total RNA was extracted with QIAzol reagent and miRNeasy micro kit (Qiagen)
RNA-Seq analysis was performed with polyA selection and standard library construction using Illumina HiSeq2500 V4 2x100 PE  (Genewiz, South Plainfield, NJ).

treatment_protocol: CASMCs were seeded into 6-well plates 24 hours prior to transfection at 60% confluency. Transfection was performed using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer specifications.  miR-143-3p (Ambion) and miR-145-5p (Ambion) inhibitors and miR-146a-5p (Ambion) and miR-181b-5p (Ambion) mimics were used for transfection at 50 nM.

value: Induced Endothelial Cell

value: primary, transdifferentiated

value: miR143-3p inhibitor, miR-145-5p inhibitor, miR-146a-5p mimic, miR-181b-5p mimic


title: BLCA_Nac_119

value: GeneChip WT Pico kit

value: neoadjuvant

value: GU

value: StromaRich


title: iEC_4

description: iEC Replicate 4


title: iEC_3

description: iEC Replicate 3


title: H2_PR8_TdT_K_p3_BCR-seq


title: CASMC_4

description: CASMC Replicate 4

source_name: Coronary artery smooth muscle cells

value: Smooth Muscle Cell

value: primary


title: H2_PR8_TdT_G_p3_BCR-seq

value: Germinal Centor B cells

value: Spleen


title: CASMC_3

description: CASMC Replicate 3


title: CASMC_2

description: CASMC Replicate 2


title: H2_PR8_TdT_K_p2_BCR-seq

value: BALB/c

value: After single cell sorting, the immunoglobulin sequence of each well was obtained.


title: BLCA_Nac_118

value: Ba/Sq

value: Uro

value: BASQ


title: BLCA_Nac_114

value: UroC

value: LumU


title: BLCA_Nac_117

value: LumP


title: BLCA_Nac_140


title: BLCA_Nac_115

value: UroA


title: CASMC_1

description: CASMC Replicate 1


title: H2_PR8_TdT_G_p2_BCR-seq


title: iEC_1

description: iEC Replicate 1

value: Induced Endothelial Cell

value: primary, transdifferentiated

value: miR143-3p inhibitor, miR-145-5p inhibitor, miR-146a-5p mimic, miR-181b-5p mimic


title: BLCA_Nac_113

value: GeneChip WT Pico kit

value: neoadjuvant


title: BLCA_Nac_112

value: GU


title: HUVEC_3

description: HUVEC Replicate 3

source_name: Human umbilical vein endothelial cells

value: Endothelial Cell

value: primary


title: HUVEC_4

description: HUVEC Replicate 4


title: H2_PR8_TdT_K_p1_BCR-seq

value: Germinal Centor B cells

value: Spleen

value: BALB/c


title: H2_PR8_TdT_G_p1_BCR-seq

value: After single cell sorting, the immunoglobulin sequence of each well was obtained.


title: HUVEC_2

description: HUVEC Replicate 2


title: H2_PR8_G_p4_BCR-seq

description: "G" indicates the gamma chain of the antibody heavy chain


title: APC T2D-FDR Pool 2 (RNA-seq)

value: Subcutaneous Adipose Tissue

value: Adipocyte Precursor Cells

tag: disease state

value: Healthy individuals with Family history of Type 2 diabetes (FDR)


title: BLCA_Nac_105

tag: overlap with previous submisson gse83586

value: Uro

value: LumU


title: H2_PR8_K_p3_BCR-seq

description: "K" indicates the kappa chain of the antibody light chain.


title: BLCA_Nac_102

tag: labeling kit

value: Ba/Sq

value: BASQ


title: H2_PR8_K_p4_BCR-seq


title: HUVEC_1

description: HUVEC Replicate 1


title: BLCA_Nac_96

value: induction


title: CMK9_MS130_014

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macfas5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs.
Mapped reads were also processed with HTSeq v0.11.0  to calculate number of read counts per gene.
For the reference gene annotations used in cufflinks and HTSeq, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca fascicularis 5.0 (macFas5)
Supplementary_files_format_and_content: *_rpm.txt: tab-delimited text files include RPM or raw count values for each Sample.

source_name: Cynomolgus monkey ESC CMK9

extract_protocol: For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60; Ishikura et al. 2016, Cell Reports, 17, 2789].

tag: cell line

value: Undifferentiated embryonic stem cell

tag: sequencer

value: NextSeq550, High, 75 cycle


title: H2_PR8_G_p3_BCR-seq


title: H2_PR8_K_p2_BCR-seq


title: BLCA_Nac_101

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

value: neoadjuvant

value: UroB

value: LumP


title: CMK9_MS173_015


title: H2_PR8_G_p2_BCR-seq

value: Germinal Centor B cells

tag: tissue

value: Spleen


title: CMK6_MS132_076

description: Single cell transcriptome of amplified cDNA from cynomolgus monkey ESC CMK6.

source_name: Cynomolgus monkey ESC CMK6


title: CMK6_MS132_080


title: BLCA_Nac_149

tag: neoadjuvant vs induction chemotherapy

tag: pathologic tn stage rc specimen

value: Mes-like


title: BLCA_Nac_95

tag: lundtax rna subtype

value: GU

tag: lundtax ihc subtype


title: BLCA_Nac_94

value: UroC

tag: consensus classifier subtype


title: BLCA_Nac_104

value: UroA


title: BLCA_Nac_93


title: CMK6_MS132_075


title: H2_PR8_K_p1_BCR-seq

tag: strain

value: BALB/c

value: After single cell sorting, the immunoglobulin sequence of each well was obtained.


title: H2_PR8_G_p1_BCR-seq


title: BLCA_Nac_100

value: Uro

value: LumNS


title: BLCA_Nac_90

value: Ba/Sq

value: StromaRich


title: BLCA_Nac_91


title: BLCA_Nac_92

value: LumU


title: BLCA_Nac_87

value: GeneChip WT Pico kit


title: BLCA_Nac_86

value: neoadjuvant


title: PigGeCKO_TGEV3rd

city: Wuhan

first: Shengsong

last: Xie

state: Hubei

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University

description: sequencing result of the thrid challenge round of TGEV screening

data_processing:
Mapped read counts were subsequently used as input for the MAGeCK analysis software package (version 0.5).
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sgRNAs .

source_name: PK-15-Cas9 cells

growth_protocol: Generation of PigGeCKO cells

extract_protocol:
Illumina sequencing of sgRNAs in the PigGeCKO cells.
Briefly, the genomic DNA from PigGeCKO cells  were extracted using a Blood & Cell Culture DNA Midi Kit (QIAGEN), respectively. The sgRNA-coding region was amplified by PCR using Q5 Hot Start High-Fidelity DNA Polymerase (NEB). PCR products were purified.

treatment_protocol: The PigGeCKO cells were generated by a total of ~2 × 10^8 PK-15-Cas9 cells and infected with the sgRNA library lentiviruses at an MOI of 0.3 as described in the previous publication (Zhao et al., 2020).

value: porcine kidney-15 (PK-15) cells

tag: knock-in

value: Cas9 puro

value: TGEV


title: PigGeCKO_TGEV2nd

description: sequencing result of  the second challenge round of TGEV screening

tag: cell type


title: PigGeCKO_TGEV1th

description: sequencing result of  the first challenge round of TGEV screening

tag: treatment


title: BLCA_Nac_82


title: Focused_TGEV5th

description: sequencing result of  the fifth challenge round of TGEV screening

data_processing:
Mapped read counts were subsequently used as input for the MAGeCK analysis software package (version 0.5)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sgRNAs ...

growth_protocol: Construction of  Focused-library

extract_protocol:
Illumina sequencing of sgRNAs in the Focused-CRISPR  cells
Briefly, the genomic DNA from Focused-CRISPR  cells  were extracted using a Blood & Cell Culture DNA Midi Kit (QIAGEN), respectively. The sgRNA-coding region was amplified by PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR products were purified with a MinElute PCR purification Kit (QIAGEN) followed by Illumina HiSeq 3000 Next-generation sequencing. Mapped read counts were subsequently used as input for the MAGeCK analysis software package (version 0.5).

treatment_protocol: Focused-CRISPR library was synthesized using CustomArray 12K arrays (CustomArray Inc.). Oligonucleotides pool was amplified by PCR using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB). The PCR products were purified and cloned into the linearized lenti-sgRNA-EGFP vector using Gibson assembly approach. To achieve sufficient coverage, more than 200-times transformants were collected to generate plasmid library.


title: Focused_TGEV3rd

description: sequencing result of  the third challenge round of TGEV screening


title: BLCA_Nac_60


title: HEK293 cells, MOCK_RIP replica 3

city: Vienna

first: Renata

last: Kleinova

address: Schwarzspanierstrasse 17

department: CACB

country: Austria

institute: Medical University of Vienna

data_processing:
Sequenced reads were aligned to the genome (H.sapiens/GRCh38) using STAR aligner version 2.5.2a.
RIP-seq peak calling was performed with Genrich version 0.6 (https://github.com/jsh58/Genrich, parameters: -q 0.05 -a 200. The peaks were called on all replicates collectively for each ADAR1p150, ADAR1p110 and mock transfection. Respective input RNA samples were used as control samples. To allow strand-specific peak calling by Genrich, forward and reverse strands of a chromosome were treated separately.
Analysis was performed on peaks found in two or more replicas where p-values were below 0.1. Peaks appearing in MOCK control (PEI) were extracted from the final peak-set using bedtools (version 2.29.2)
Genome_build: hg38
Supplementary_files_format_and_content: csv files containg identified peaks for ADAR1p150- and ADAR1p110- RIP-seq

growth_protocol: HEK293 cells were maintained in in high-glucose Dulbecco’s Modified Eagle Medium (DMEM) supplied with 10% fetal bovine serum, pyruvate and L-glutamine.

extract_protocol:
RNA was extracted using TriFAST according to the manufacturer’s suggestions. Isolated RNA was treated with DNaseI and subsequently purified by phenol: chloroform, chloroform extraction and precipitated with ethanol.
10 ng of total RNA was subjected to rRNA depletion with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and subsequently to NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.
rRNA depleted RNA-seq

tag: transfected with plasmid

value: MOCK

tag: rip antibody

value: ANTI-FLAG antibody produced in rabbit, F7425, MERCK, lot:030M4800


title: Focused_Control

description: sequencing result of sgRNA library from sorted mutant cell populations

value: control


title: BLCA_Nac_59

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GU


title: BLCA_Nac_89

value: NE-like


title: BLCA_Nac_57

value: UroC

value: LumP


title: BLCA_Nac_58

value: BASQ


title: BLCA_Nac_54

value: UroA

value: Uro


title: PigGeCKO_Control


title: TMEM41B_KO_TGEV_2

description: RNA sequencing and transcriptome analysis data

data_processing:
Quality control and read mapping: Sequence quality was assessed using FastQC (v0.11.7) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for all samples, and quality trimming was done using FASTX-Toolkit (v 0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/) to remove bases with Phred33 score of less than 30, while retaining the resulting reads of at least 50 bases in length. The quality trimmed reads were mapped against the reference genome of Sus scrofa genome reference (v11.1)  using HISAT2 (v2.1.0).
Gene expression profiling was based on the number of reads. FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels by using samtools (v1.7) and htseq-count (v0.9.1). DEGs were obtained by DESeq2 (v1.30.1) with an P-value cutoff < = 0.05 and an absolute fold-change of >= 1.
Genome_build: Sus scrofa genome reference (v11.1)
Supplementary_files_format_and_content: Raw_gene_counts

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: HEK293 cells, MOCK_input replica 3

tag: cell line


title: HEK293 cells, ADAR1p110_RIP replica 3


title: TMEM41B_KO_TGEV_1


title: HEK293 cells, ADAR1p110_input replica 3


title: Y147F_PBS_105831

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MOE430_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned in a Genechip 3000 scanner with G7 update

data_processing: The images were analyzed with RMA using PartekGS default settings

source_name: liver, PBS, 6h

label_protocol: 200 ng of total RNA was converted into biotinylated cRNA.

growth_protocol: Mice were housed at 21 ± 1 °C on an alternating 12-h light/12-h dark cycle. Standard chow (Ssniff) and tap water were provided ad libitum, unless indicated otherwise.

extract_protocol: Total RNA was isolated from liver using the RNeasy Kit (QIAGEN) following to the mufacturer´s instructions.

treatment_protocol: Mice were rendered hypothyroid at the age of 10–11 wk with an iodine-deficient diet (TD.95007; Harlan-Teklad) with 0.05% 2-mercapto-1-methylimidazole (MMI), and 1% potassium perchlorate (Sigma-Aldrich) administered in the drinking water. After 3 wk, mice were separated into T3-treatment and control groups for each genotype. T3-treated animals received T3 (Sigma-Aldrich), 200 ng/g BW, i.p. once as a single dose.

tag: strain background

tag: genotype

value: TRbeta, Y147F

tag: Sex

value: male

tag: age

value: 10-11 weeks

value: liver


title: BLCA_Nac_51

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: induction

tag: pathologic tn stage rc specimen

tag: lundtax rna subtype

value: LumNS


title: Y147F_T3_107268

source_name: liver, T3, 6h

tag: tissue


title: Y147F_PBS_105829

tag: treatment


title: TMEM41B_KO_TGEV_3

tag: cell type

value: porcine kidney-15 (PK-15) cells

tag: knock-in

value: Cas9 puro

value: TGEV


title: Y147F_T3_89656


title: BLCA_Nac_53

tag: overlap with previous submisson gse83586

value: neoadjuvant

value: Ba/Sq

tag: lundtax ihc subtype

tag: consensus classifier subtype


title: BLCA_Nac_48

tag: labeling kit

value: NE-like

value: GU

value: StromaRich


title: HEK293 cells, ADAR1p150_RIP replica 3

tag: cell line

tag: transfected with plasmid

tag: rip antibody

value: ANTI-FLAG antibody produced in rabbit, F7425, MERCK, lot:030M4800


title: Y147F_T3_93628

tag: strain background

tag: genotype

tag: Sex

tag: age


title: BLCA_Nac_79

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

tag: pathologic tn stage rc specimen

value: Uro

value: LumP


title: TMEM41B_KO_MOCK_2

tag: cell type

tag: treatment

value: mock

tag: genotype/variation


title: HEK293 cells, MOCK_RIP replica 2

value: MOCK


title: HEK293 cells, ADAR1p150_input replica 3


title: Y147F_PBS_105830

value: TRbeta, Y147F

value: male

value: 10-11 weeks

value: control

tag: tissue

value: liver


title: TMEM41B_KO_MOCK_1

value: porcine kidney-15 (PK-15) cells

tag: knock-in

value: Cas9 puro


title: BLCA_Nac_44

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GeneChip WT Pico kit

value: neoadjuvant

tag: lundtax rna subtype

tag: lundtax ihc subtype

tag: consensus classifier subtype

value: LumU


title: PC9 cells Etoposide 10 µM RNA-seq.rep2

tag: cell line

value: lung

value: Lung adenocarcinoma

value: treated with 10 uM Etoposide for 24 hours


title: WT_TGEV_3

value: TGEV

value: WT


title: TMEM41B_KO_MOCK_3

value: mock


title: BLCA_Nac_43

value: Ba/Sq

value: Uro

value: BASQ


title: HEK293 cells, MOCK_input replica 2

tag: transfected with plasmid

value: MOCK

tag: rip antibody


title: WT_TGEV_2


title: Aged Ileum 4

data_processing:
Reads were trimmed with Cutadapt (version cutadapt-1.9.dev2) using a quality threshold of 30 for the 3'end and the adapter sequences of the TruSeq stranded mRNA kit (AGATCGGAAGAGC). Trimmed reads with a length of less than 50 were discarded.
Read alignment was made using STAR (version 2.5.2b), with the parameters specifying paired-end reads and --outSAMtype BAM Unsorted.
FeatureCounts (version 1.5.1) was used for assigning counts.
Genome_build: Mus musculus (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text of raw gene counts for every gene for each sample
Supplementary_files_format_and_content: Tab-delimited text of FPKM values for each sample

source_name: Ileum

extract_protocol:
Portions of small intestine containing individual Peyer’s patches were removed and immersed in Hank’s balanced salt solution (HBSS) containing 30 mM EDTA at 4oC for 15 min.  Peyer’s patches domes were micro-dissected and the FAE layer then carefully teased away from the underlying tissue using fine needles under stereomicroscopy and trimmed of villi.  Sheets of conventional VE were prepared in the same manner from 5 mm portions of ileum that lacked Peyer’s patches adjacent to each dissected Peyer’s patch. Isolated FAE and VE sheets as well as 5 mm sections of whole ileum from each mouse were kept at -80oC until RNA extraction.  Total RNA was isolated from FAE, VE and ileum samples using a RNeasy Plus Kit (Qiagen).
TruSeq stranded mRNA-seq library

tag: strain

tag: age

value: 26-28 Months

value: Small Intestine


title: HEK293 cells, ADAR1p110_RIP replica 2

value: ANTI-FLAG antibody produced in rabbit, F7425, MERCK, lot:030M4800


title: HEK293 cells, ADAR1p110_input replica 2


title: BLCA_Nac_50

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: GU


title: BLCA_Nac_38

value: GeneChip WT Pico kit

tag: pathologic tn stage rc specimen

value: UroC

value: LumP


title: BLCA_Nac_40

value: induction

value: LumU


title: WT_MOCK_3

tag: cell type

value: porcine kidney-15 (PK-15) cells

value: Cas9 puro

tag: treatment

tag: genotype/variation


title: BLCA_Nac_32

tag: overlap with previous submisson gse83586

value: neoadjuvant

value: UroA


title: BLCA_Nac_37

tag: labeling kit

value: LumNS


title: HEK293 cells, ADAR1p150_RIP replica 2


title: HEK293 cells, ADAR1p150_input replica 2


title: WT_MOCK_2

tag: knock-in

value: mock

value: WT


title: BLCA_Nac_31

tag: lundtax rna subtype

tag: lundtax ihc subtype

value: Uro


title: BLCA_Nac_29

tag: consensus classifier subtype


title: WT_MOCK_1


title: BLCA_Nac_28


title: HEK293 cells, ADAR1p110_RIP replica 1

tag: cell line

tag: transfected with plasmid


title: BLCA_Nac_27


title: HEK293 cells, ADAR1p110_input replica 1

tag: rip antibody


title: SAMPLE 80: WFP-TN

city: Beijing

first: Yuntao

last: Bing

address: No.49 Huayuan North Road

department: Department of General Surgery

institute: Peking University Third Hospital

description: HCC

data_processing:
The above 40 pairs of samples were tested in 3 times due to different collection times of the samples,in cluding 10 pairs of samples once time, 17 pairs of samples once time and 13 pairs of samples once time.
Experiments from different batches were calibrated using experimental data of samples from the previous batch.
Standard curve method was used to analyze the final result.  β-actin as the house keeping gene. Three replicates for each sample.

label: SYBR Green

source_name: liver

label_protocol: The cDNAs for circRNA, mRNA, or miRNA measurement were synthesized using random, oligo(dT)18, or stem-loop primers, respectively, using a RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA). qRT-PCR was performed in triplicate using Maxima SYBR Green qPCR Master Mix (Thermo Fisher Scientific) on the CFX connect real-time system (Bio-Rad, Hercules, CA, USA).

extract_protocol: Total RNA was extracted by Trizol.

treatment_protocol: Paired tissue specimens (tumor and adjacent normal tissues) were collected from the patients, immediately frozen in liquid nitrogen, and stored at -80°C until use.

tag: tissue

value: HCC tissue

tag: paired sample

value: WFP-PN


title: WT_TGEV_1

value: TGEV


title: SAMPLE 79: GJX-TN

description: HCC

value: GJX-PN


title: BLCA_Nac_26

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

value: NE-like

value: Ba/Sq

value: BASQ


title: BLCA_Nac_34

tag: neoadjuvant vs induction chemotherapy

tag: pathologic tn stage rc specimen

value: UroB

value: LumP


title: BLCA_Nac_25


title: BLCA_Nac_24

value: GU

value: StromaRich


title: HEK293 cells, ADAR1p150_RIP replica 1

value: ANTI-FLAG antibody produced in rabbit, F7425, MERCK, lot:030M4800


title: SAMPLE 78: TYZ-TN

description: HCC

value: TYZ-PN


title: BLCA_Nac_23

value: neoadjuvant

value: UroC

value: LumNS


title: SAMPLE 77: ZZJ-TN

description: HCC

value: HCC tissue

value: ZZJ-PN


title: HEK293 cells, ADAR1p150_input replica 1


title: SAMPLE 76: HSX-TN

description: HCC

value: HSX-PN


title: BLCA_Nac_16

value: UroA

value: Uro


title: BLCA_Nac_15

value: GeneChip WT Pico kit

value: LumU


title: BLCA_Nac_18

value: Ba/Sq

value: BASQ


title: BLCA_Nac_14

value: Mes-like


title: SAMPLE 74: JM-TN

description: HCC

value: JM-PN


title: SAMPLE 75: SCL-TN

description: HCC

value: SCL-PN


title: BLCA_Nac_12

value: GU

value: LumP


title: SAMPLE 73: SCF-TN

description: HCC

value: SCF-PN


title: S50_B cell

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

institute: Weill Cornell Medicine

data_processing:
Demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files was performed by "cellranger mkfastq"  (cellranger version 3.02)
Gene counts were calculated using "cellranger count" (cellranger version 3.02) under default setting， BCR sequences were assembled using "cellranger vdj" (cellranger version 3.02) under default setting.
Genome_build: GRCh38-1.2.0 for transccriptome, cellranger-vdj-GRCh38-alts-ensembl-2.0.0 for V(D)J
Supplementary_files_format_and_content: For each dataset, there are 5 files. Using dataset R125 as an example: R125_barcodes.tsv.gz, R125_features.tsv.gz, R125_matrix.mtx.gz are gene count files for scRNA-seq data, R125_barcodes.tsv.gz contains all cell barcodes information, R125_features.tsv.gz contains all features information (including genes and ADT features), and R125_matrix.mtx.gz contains expression matrix. R125_consensus.fasta, R125_filtered_contig_annotations.csv are sequence files for single cell BCR sequencing data. R125_consensus.fasta contains all assembled BCR sequences, R125_filtered_contig_annotations.csv contains all cell barcode information.
Supplementary_files_format_and_content: For raw fastq data, we include a feature barcode file (feature_barcode.csv) of ADT features for each dataset. Fastq files for 5'prime RNA-seq are named by "5prime" or "RNA", e.g. R3_RNA_..... Fastq files for surface protein and probe binding are named by "ADT" or "probe", e.g. R3_ADT_.... For each sequence run, there are 12 fastq files: I1, R1, R2 for four lines (L001, L002, L003, L004). Notably, we sequenced some datasets twice to obtain enough reads. Users can run Cellranger on these fastq files by following offical documents: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

source_name: Convalescent patient

extract_protocol:
Cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum of 10,000 individual cells per sample.
Utilizing the Chromium Single Cell A Chip Kit(10x Genomics, PN-120236) and Chromium Single Cell 5' Library & Gel Bead Kit (10x Genomics, PN-1000006) , poly-adenylated mRNA from an individual cell was tagged with a unique 16 base pair 10x barcode and 10 base pair Unique Molecular Identifier.
Libraries were generated using the Chromium Single Cell 5' Feature Barcode Library Kit  (10x genomics, 1000080) and the Chromium Single Cell V(D)J Enrichment Kit Human B Cell (10x Genomics, PN-1000016). The cDNA amplicon size for each library was optimized using enzymatic fragmentation and size selection and the concentration and average fragment size of each library was determined using an Agilent High Sensitivity DNA Kit (Agilent). Specifically, user guide CG000186 Rev D was used for all steps. All libraries were sequenced on an Illuina NextSeq550 or an Illumina NextSeq500 with 26 cycles apportioned for read 1, 8 cycles for the i7 index, and 134 cycles for read 2 using an NextSeq 500/550 High Output Kit v2.5 (150 Cycles). Some samples were sequenced using a NextSeq 550 housed within the Pritzker School of Molecular Engineering's Chicago Immunoengineering Innovation Center (Chicago, IL) and others on a NextSeq500 belonging to the University of Chicago Genomics Facility (Chicago, IL - RRID: SCR_019196)

treatment_protocol: PBMCs were isolated from whole blood (acute samples) or leukoreduction filters (convalescent samples) by use of a Lymphoprep Ficoll gradient and any contaminating red blood cells were lysed by ACK buffer. Cells were then frozen at -80 deg C in fetal bovine serum supplemented with 10% DMSO. On the day of sorting and sequencing cells were thawed and B cell were purified by human pan B cell EasySep enrichment kit from STEMCELL technologies.

tag: strain

tag: tissue/cell type

value: Peripheral blood mononucelar cells (PBMCs)

tag: disease state

value: Convalescent


title: S407_B cell


title: S407v2_B cell

source_name: Convalescent patient - 2nd visit


title: SAMPLE 72: WLX-TN

description: HCC

value: HCC tissue

value: WLX-PN


title: S65_B cell


title: SAMPLE 71: GLX-TN

description: HCC

value: GLX-PN


title: BLCA_Nac_17

tag: overlap with previous submisson gse83586

tag: labeling kit

value: neoadjuvant

value: UroA

value: LumNS


title: BLCA_Nac_8

value: GeneChip WT Pico kit

value: induction

tag: lundtax rna subtype

value: StromaRich


title: SAMPLE 69: WHZ-TN

description: HCC

value: WHZ-PN


title: BLCA_Nac_4

tag: lundtax ihc subtype

value: LumU


title: S33_B cell


title: SAMPLE 68: ZJY-TN

description: HCC

value: ZJY-PN


title: BLCA_Nac_62

value: UroB

value: Uro

tag: consensus classifier subtype


title: SAMPLE 67: WFP-PN

description: Ctrl

value: Paracancerous tissue

value: WFP-TN


title: BLCA_Cx_305

value: SensationPlus FFPE Amplification and WT labeling kit

value: LumP


title: S266v2_B cell

value: Peripheral blood mononucelar cells (PBMCs)

value: Convalescent


title: BLCA_Cx_280

value: NE-like

value: Mes-like


title: S356_B cell


title: SAMPLE 66: GJX-PN

description: Ctrl

value: GJX-TN


title: BLCA_Cx_285

value: Ba/Sq

value: BASQ


title: S356v2_B cell


title: SAMPLE 65: TYZ-PN

description: Ctrl

value: TYZ-TN


title: BLCA_Nac_9

value: GeneChip WT Pico kit

value: neoadjuvant

value: UroA


title: BLCA_Cx_256

value: UroC

value: LumNS


title: BLCA_Cx_258

value: Uro

value: StromaRich


title: BLCA_Nac_5

value: GU


title: S210v2_B cell


title: S218_B cell


title: S281_B cell


title: BLCA_Cx_248

value: SensationPlus FFPE Amplification and WT labeling kit

value: LumP


title: BLCA_Cx_255


title: S272_B cell

value: Peripheral blood mononucelar cells (PBMCs)

value: Convalescent


title: BLCA_Cx_247

value: induction

value: LumU


title: SAMPLE 63: HSX-PN

description: Ctrl

value: Paracancerous tissue

value: HSX-TN


title: S201_B cell


title: BLCA_Cx_244

value: UroB

value: Ba/Sq


title: SAMPLE 62: SCL-PN

description: Ctrl

value: SCL-TN


title: S130_B cell


title: BLCA_Cx_268


title: BLCA_Cx_262

value: BASQ


title: BLCA_Cx_240

value: neoadjuvant

value: UroC


title: BLCA_Cx_241

value: UroA

value: Uro


title: BLCA_Cx_234


title: S266_B cell


title: S92_B cell


title: SAMPLE 61: JM-PN

description: Ctrl

value: JM-TN


title: SAMPLE 60: SCF-PN

description: Ctrl

value: SCF-TN


title: BLCA_Cx_212

value: SensationPlus FFPE Amplification and WT labeling kit

value: GU

value: StromaRich


title: S609_B cell

value: Peripheral blood mononucelar cells (PBMCs)

value: Convalescent


title: BLCA_Cx_204

value: induction


title: S586_B cell


title: SAMPLE 59: WLX-PN

description: Ctrl

value: Paracancerous tissue

value: WLX-TN


title: BLCA_Cx_201

value: LumU


title: SAMPLE 64: ZZJ-PN

description: Ctrl

value: ZZJ-TN


title: BLCA_Cx_200

value: NE-like


title: SAMPLE 58: GLX-PN

description: Ctrl

value: GLX-TN


title: BLCA_Cx_198

value: neoadjuvant

value: UroB

value: Ba/Sq

value: LumP


title: S564_B cell


title: SAMPLE 57: CL-PN

description: Ctrl

value: CL-TN


title: S537_B cell


title: BLCA_Cx_187

value: SensationPlus FFPE Amplification and WT labeling kit


title: BLCA_Cx_197

value: GU

value: BASQ


title: BLCA_Cx_178

value: UroA

value: Uro


title: BLCA_Cx_143

value: StromaRich


title: BLCA_Cx_156

value: induction


title: S48_B cell

value: Peripheral blood mononucelar cells (PBMCs)

value: Convalescent


title: SAMPLE 55: ZJY-PN

description: Ctrl

value: Paracancerous tissue

value: ZJY-TN


title: BLCA_Cx_134


title: BLCA_Cx_219

value: Mes-like


title: BLCA_Cx_131

value: neoadjuvant

value: LumU


title: SAMPLE 54: ZFY-TN

description: HCC

value: HCC tissue

value: ZFY-PN


title: S376_B cell


title: SAMPLE 53: YLF-TN

description: HCC

value: YLF-PN


title: BLCA_Cx_123

value: SensationPlus FFPE Amplification and WT labeling kit

value: Ba/Sq


title: S305_B cell


title: S24_B cell


title: BLCA_Cx_118

value: UroB

value: BASQ


title: SAMPLE 52: RXL-TN

description: HCC

value: RXL-PN


title: S214_B cell


title: Dro-GFP Positive carcass

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
20-PE1-DROGFP-plus-carcass-3

data_processing:
Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS and RTA software with default parameter settings.
Between 8 and 10 million (2X150) base pair reads were generated per library and mapped to the Drosophila genome (Release 6).
Expression was recorded as TPM (transcripts per kbp per million reads) followed by Log2 transformation.
Genome_build: Drosophila genome (Release 6)
Supplementary_files_format_and_content: TPM

organism: Drosophila melanogaster

source_name: carcass/fat body

growth_protocol: In order to standardize metabolic results, fifty virgins were crossed to 10 males and kept in bottles for 2-3 days to lay enough eggs. Wet folded filters (GE healthcare, CAT No.10311843) were inserted in bottles after parental flies removed. Progeny of crosses was collected for 3–4 d after initial eclosion. Collected progeny were then transferred to new bottles to allow them mate for 2 d. All these flies were reared on diet (cornmeal-based) at 25°C and 65% humidity on a 12 hr light/dark cycle, unless otherwise indicated. Around 20 female flies were then separated into each vial with diet for 10 days at 25 °C and 65% humidity on a 12 hr light/dark cycle.

extract_protocol:
Intact fly thoraces (8) or carcass/fat body (8) were dissected in PBS. Total RNA was extracted using Trizol reagent.
Total RNA was extracted using Trizol reagent and used as template to generate sample libraries for RNA sequencing (using the TruSeq Stranded Total RNA Library Prep Kit).

treatment_protocol: Bacterial strains Pseudomonas entomophila (P.e) were grown in LB medium at 29°C with shaking at 200 rpm overnight. Fresh bacterial cultures were generated daily. Pour the liquid culture into a sterile centrifuge flask and centrifuge at 4000 g at 4°C for 15 minutes. Empty the LB medium from the centrifuge flask. Resuspend the bacteria pellet in the remaining LB medium. Adjust the final bacteria concentration (OD600=50-60 for P.e) by diluted with LB medium.   Prepare 2.5% and 5% sucrose in sterile water. Mix the 5% sucrose solution with an equal volume of bacteria solution (OD600=50-60 for P.e) to create the bacterial infection mix. 10 day-old mated female flies (20 per vial) were transferred into a fly food vial containing a filter paper that totally covers the food and was soaked with a solution consisting of 185 μL either bacterial infection mix, for infections, or 2.5% sucrose, for unchallenged controls. The flies were always infected at 3:00-4:00pm and incubate at 25°C and 65% humidity on a 12 hours light/dark cycle for required infection times (16-20 hours for P.e).

value: carcass/fat body

tag: age

value: 10 days

tag: gender

value: Female

tag: treatment

value: oral infection with P.e.


title: Dro-GFP Negative carcass

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
19-PE1-DROGFP-minus-carcass-2

tag: tissue


title: Dro-GFP Sucrose carcass

description:
oral feeding with sucrose for 20hrs
18-Sucrose-DROGFP-carcass-3

value: oral feeding with sucrose


title: SAMPLE 51: WZZ-TN

description: HCC

tag: paired sample

value: WZZ-PN


title: S210_B cell

value: Peripheral blood mononucelar cells (PBMCs)

value: Convalescent


title: SAMPLE 56: WHZ-PN

description: Ctrl

value: Paracancerous tissue

value: WHZ-TN


title: BLCA_Cx_101

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Raw data from RMA was quantile normalized, adjusted for labeling batch using ComBat, and merged by median probe set values per gene symbol.

source_name: FFPE tissue specimen

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

tag: labeling batch

value: neoadjuvant

value: UroA

value: Uro

value: LumP


title: SAMPLE 50: ZYX-TN

description: HCC

value: HCC tissue

value: ZYX-PN


title: S20_B cell


title: BLCA_Cx_130

value: SensationPlus FFPE Amplification and WT labeling kit

tag: clinical tnm-staging

value: GU

value: LumNS


title: BLCA_Cx_73

tag: neoadjuvant vs induction chemotherapy

value: LumU


title: SAMPLE 49: YDC-TN

description: HCC

value: YDC-PN


title: S171_B cell


title: SAMPLE 48: PSY-TN

description: HCC

value: PSY-PN


title: P_2_CD14

city: München

first: Thomas

last: Magg

address: Lindwurmstr. 2a

institute: Dr. von Haunersches Kinderspital der LMU München

data_processing:
Raw sequence reads were demultiplexed and mapped to the human  genome (hg19 release) using Tophat 2.0 and hg19 gene annotation  obtained from iGenomes (Illumina).
Read counts for each gene  were obtained by the python script HTseq count. Read counts were  then normalized by r-log transformation with the program DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differentially expressed genes were identified by pairwise comparisons  with DESeq2 using FDR threshold of 5%.

source_name: PBMC

extract_protocol:
Total RNA was isolated from sorted cells using QIAzol (Qiagen) and  miRNeasy Mini kit (Qiagen)
Total RNA (100 ng) was treated with double-strand specific DNAse  (Thermo Fisher Scientific) to remove any traces of genomic DNA. cDNA  was synthesized and converted to Illumina-compatible sequencing libraries  with the Encore complete RNAseq kit (NuGen, San Carlos, USA).  First strand cDNA was generated by random priming with a set of selected  hexamers that avoid priming of rRNA, second strand cDNA was  synthesized with incorporation of dUTP and the double stranded cDNA  was fragmented using a Bioruptor nextgen (Diagenode, Liege, Belgium)  sonicator applying 25 cycles of low power (30 s on/off) in a cooled  water bath. cDNA was end-repaired and ligated to Illumina-adapters  and the second-strand selectively removed by uracyl deglycosylase.  After 18 cycles of PCR the final libraries were quantified on an Agilent  2100 Bioanalyzer and diluted to 10 nM prior to pooling and sequencing.
Libraries were sequenced on a single lane in 100 bp single end  mode on a HiSeq1500 instrument (Illumina, San Diego, USA).

tag: cell type

value: untreated

tag: genotype


title: P_2_CD19


title: S166_B cell

tag: strain

tag: tissue/cell type

value: Peripheral blood mononucelar cells (PBMCs)


title: ACT88FGal4>RelishRNAi sucrose carcass

description:
oral feeding with sucrose for 20hrs
15-Sucrose-Relish-GD-carcass-S3

value: carcass/fat body

value: 10 days

value: Female

value: oral feeding with sucrose


title: ACT88FGal4>W1118 PE carcass

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
16-PE53-W1118-carcass-P1

value: oral infection with P.e.


title: ACT88FGal4>RelishRNAi PE carcass

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
17-PE53-Relish-GD-carcass-P1


title: P_2_CD3


title: SAMPLE 47: YW-TN

description: HCC

value: YW-PN


title: S155_B cell

tag: disease state

value: Convalescent


title: SAMPLE 46: HWC-TN

description: HCC

value: HCC tissue

value: HWC-PN


title: S144_B cell


title: P_1_CD19


title: SAMPLE 45: LDG-TN

description: HCC

value: LDG-PN


title: P_1_CD14


title: P_1_CD3


title: SAMPLE 44: LXT-TN

description: HCC

value: LXT-PN


title: S116_B cell


title: R6_B cell

source_name: Acute patient

value: Acute


title: R478910_B cell

description: Five acutely-infected patients' cells pooled together post-sort and hasthagged


title: SAMPLE 43: HWP-TN

description: HCC

value: HWP-PN


title: HD3_1_CD19

value: WT


title: ACT88FGal4>RelishRNAi  PE muscle

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
10-PE53-Relish-GD-Thorax-P1

source_name: thoraces/muscle

value: thoraces/muscle


title: ACT88FGal4>W1118 sucrose carcass

description:
oral feeding with sucrose for 20hrs
14-Sucrose-W1118-carcass-S3


title: Dro-GFP Negative muscle

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
12-PE1-DROGFP-minus-Thorax-2


title: Dro-GFP Positive muscle

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
13-PE1-DROGFP-plus-Thorax-3


title: Dro-GFP Sucrose muscle

description:
oral feeding with sucrose for 20hrs
11-Sucrose-DROGFP-Thorax-3


title: HD3_1_CD14

value: untreated


title: R3_B cell

value: Peripheral blood mononucelar cells (PBMCs)


title: ACT88FGal4>W1118  PE muscle

description:
oral feeding with P.e. at OD600=50-60 for 20hrs
09-PE53-W1118-Thorax-P1


title: SAMPLE 42: ZFP-TN

description: HCC

value: ZFP-PN


title: HD3_1_CD3


title: SAMPLE 41: RBM-TN

description: HCC

value: RBM-PN


title: ACT88FGal4>W1118  sucrose muscle

description:
oral feeding with sucrose for 20hrs
07-Sucrose-W1118-Thorax-S3

value: 10 days

value: Female


title: SAMPLE 40: JLN-TN

description: HCC

value: JLN-PN


title: R125_B cell

description: Three acutely-infected patients' cells pooled together post-sort and hashtagged


title: HD2_2_CD19


title: HD2_2_CD14


title: slan_plus_tonsil_3

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline,
Adapters and base quality trimming were performed using Trim Galore script with parameters -length 50, then to improve the quality of the mapping, reads were further trimmed at the 3’ to a length of 72bp using fastx_trimmer from the FASTX-toolkit
reads were mapped onto the Ensembl human transcriptome (version 84) and quantified at the transcript level using Salmon (--validateMappings flag)
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2 package
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analyzed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Genome_build: Ensembl human transcriptome (version 84)
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample

source_name: Tonsil

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

value: Freshly isolated cells

value: tonsil

value: slan+-cells


title: slan_plus_tonsil_2


title: SAMPLE 39: WJX-TN

description: HCC

value: HCC tissue

value: WJX-PN


title: SAMPLE 38: JEH-TN

description: HCC

value: JEH-PN


title: HD2_2_CD3


title: Wild type E14 embryonic stem cells

city: Houston

first: Muhammad

middle: Saad

last: Shamim

address: 6100 Main Street

department: Bioengineering

institute: Rice University

data_processing:
Juicer v1.5.7
Juicer Tools v1.9.9
Genome_build: mm10
Supplementary_files_format_and_content: hic files generated from Juicer

source_name: E14 embryonic stem cells

growth_protocol: Embryonic stem cells were grown in ES media and replated on tissue culture dishes pre-treated with gelatin two days before the experiment as described in the manuscript.

tag: cell line

value: Embryonic stem cells

value: Wild type


title: Mcph1 deleted homozygous E14 embryonic stem cells

value: Mcph1 deleted homozygous


title: SAMPLE 37: ZFY-PN

description: Ctrl

value: Paracancerous tissue

value: ZFY-TN


title: HD2_1_CD14

value: untreated

value: WT


title: MΦ_tonsil_3

value: CD11b+ CD14+macrophages


title: SAMPLE 35: RXL-PN

description: Ctrl

value: RXL-TN


title: HD2_1_CD19


title: MΦ_tonsil_2


title: ACT88FGal4>RelishRNAi  sucrose muscle

description:
oral feeding with sucrose for 20hrs
08-Sucrose-Relish-GD-Thorax-S3

value: thoraces/muscle

value: 10 days

value: Female

value: oral feeding with sucrose


title: HD2_1_CD3


title: slan_plus_tonsil_1

value: Freshly isolated cells

value: tonsil

value: slan+-cells


title: SAMPLE 34: WZZ-PN

description: Ctrl

value: WZZ-TN


title: MΦ_tonsil_1


title: mESCs, P53_ChIP_lnc956_kd_rep1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 2.19
For RNA-Seq, reads were mapped to mm10 genome using tophat2 (version 2.0.8) with default parameters. Differentialy expressed genes were determined using cuffdiff (version 2.1.1);ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 2.1.0.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1
Peaks were called using MACS version 2.2.7.1 with the following setting: qvalue=0.01.
Genome_build: mm10
Supplementary_files_format_and_content: gene_expression_FPKM.xlsx includes FPKM values for each RNA-seq Sample
Supplementary_files_format_and_content: peak text files for ChIP-seq Samples

source_name: mouse embryonic stem cells (mESC)

growth_protocol: Mouse ESCs were routinely maintained in DMEM/F12 supplemented with 20% Knockout serum replacement (Thermo Fisher,, A3181502), 104 unit/mL recombinant mouse leukemia inhibitory factor (Millipore, ESG1107), 2mM L-glutamine (Sigma; G8540-25g), penicillin (100 U/mL)/streptomycin (100 μg/mL) (Gibco; 15140-122), 100 μM beta-mercaptoethanol (Sigma; M7522), 1×MEM non-essential amino acids solution (Gibco; 11140-035).

extract_protocol:
For RNA-Seq, RNA were isolated using Trizol. For ChIP-Seq,cell lysates were clarified from sonicated nuclei and KLF4 or P53-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols;For ChIP-Seq, Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cells were treated or untreated with 10 uM etoposide.

value: mouse embryonic stem cells (mESC)

value: Lnc956 knockdown

tag: chip antibody


title: HD1_2_CD19


title: mESCs, P53_ChIP_etop_lnc956_kd_rep2

value: 10 μM etoposide


title: mESCs, P53_ChIP_etop_lnc956_kd_rep1


title: mESCs, P53_ChIP_lnc956_kd_rep2


title: mESCs, P53_ChIP_etop_rep2

value: wild type


title: DC2_tonsil_1


title: DC2_tonsil_2


title: mESCs, P53_ChIP_etop_rep1


title: SAMPLE 32: YDC-PN

description: Ctrl

value: Paracancerous tissue

value: YDC-TN


title: HD1_2_CD3

value: untreated

value: WT


title: mESCs, P53_ChIP_wt_rep2


title: SAMPLE 31: PSY-PN

description: Ctrl

value: PSY-TN


title: HD1_1_CD19


title: SAMPLE 29: HWC-PN

description: Ctrl

value: HWC-TN


title: HD1_1_CD3


title: mESCs, P53_ChIP_wt_rep1


title: TDCM_slan_plus_mono_1

source_name: Blood

value: tonsil-derived conditioned medium

value: blood

value: slan+-monocytes


title: SAMPLE 33: ZYX-PN

description: Ctrl

value: ZYX-TN


title: SAMPLE 30: YW-PN

description: Ctrl

value: YW-TN


title: SAMPLE 28: LDG-PN

description: Ctrl

value: LDG-TN


title: HD1_2_CD14


title: mESCs, Lnc956_kd_etop_rep1


title: mESCs, Lnc956_kd_etop_rep2


title: HD1_1_CD14


title: SAMPLE 27: LXT-PN

description: Ctrl

value: LXT-TN


title: SAMPLE 70: CL-TN

description: HCC

value: HCC tissue

value: CL-PN


title: slan_plus_mono_4

value: Freshly isolated cells


title: mESCs, Lnc956_kd_rep2

value: mouse embryonic stem cells (mESC)

value: Lnc956 knockdown


title: slan_plus_mono_5


title: SAMPLE 26: HWP-PN

description: Ctrl

value: Paracancerous tissue

value: HWP-TN


title: mESCs, Lnc956_kd_rep1

value: untreated


title: slan_plus_mono_2


title: SAMPLE 36: YLF-PN

description: Ctrl

value: YLF-TN


title: slan_plus_mono_3


title: TDCM_slan_plus_mono_3


title: mESCs, WT_etop_rep2

value: wild type

value: 10 μM etoposide


title: TDCM_slan_plus_mono_2

value: tonsil-derived conditioned medium

value: blood


title: AC093797_1

city: Luzhou

first: Cunliang

last: Deng

state: Sichuan

address: Taiping street No.25

department: Department of infectious diseases

institute: The affiliated hospital of southwest medical university

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, remove reads containing N (N means that the base information cannot be determined), remove low-quality reads (reads whose base number of Qphred <=20 accounts for more than 50% of the entire read length) , then mapped to hg38 whole genome using HISAT2
FeatureCounts (version 1.5.0-p3) was used to count the numbers of reads mapped to each gene, and FPKM values were calculated based on the length of each gene and the read count mapped to the gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Nude mice in OE-AC093797 group

extract_protocol:
Removed the subcutaneous tumor from those mouse and flash frozend on -80℃. Then RNA used the RNA Nano 6000 Assay Kit and Agilent 5400 to quality control，and used the TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions to perfore the clustering of the index-coded samples, and used NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® to construct the sequencing librariers.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Subcutaneous tumor

value: BALB/c nude

value: HCCLM3 cells stably transfected with overexpression vector OE-AC093797.1


title: AC093797_2


title: AC093797_3


title: SAMPLE 25: ZFP-PN

description: Ctrl

value: ZFP-TN


title: mESCs, WT_etop_rep1


title: NC_3

source_name: Nude mice in NC group

value: HCCLM3 cells stably transfected with control vector pcDNA3.1


title: NC_2


title: SAMPLE 23: JLN-PN

description: Ctrl

value: JLN-TN


title: SAMPLE 24: RBM-PN

description: Ctrl

value: RBM-TN


title: mESCs, WT_rep2

value: mouse embryonic stem cells (mESC)


title: slan_plus_mono_1

value: Freshly isolated cells

value: slan+-monocytes


title: SAMPLE 21: JEH-PN

description: Ctrl

value: Paracancerous tissue

value: JEH-TN


title: mESCs, WT_rep1

value: untreated


title: SAMPLE 22: WJX-PN

description: Ctrl

value: WJX-TN


title: NC_1


title: SAMPLE 19: 000021-TN-1

description: HCC

value: HCC tissue