title: N_CPC_03

treatment_protocol:
non-CPC were the cells under inappropriate CHIR conditions on day 6
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-derived non-CPCs

value: cells under inappropriate CHIR conditions on day 6.


title: HC_BC000268_TCPY_11_rep1

status: Public on Apr 01 2023

type: SRA

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

department: Neurology

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
RNA-seq raw files in FASTQ format were processed in a customized pipeline. For each sample, we first filtered out reads that failed vendor check or are too short (<15nt) after removing the low-quality ends or possible adaptor contamination by using fastq-mcf with options of “-t 0 –x 10 –l 15 –w 4 –q 10 –u”. We then checked the quality using FastQC and generated k-mer profile using kpal for the remaining reads. Reads were then mapped to the human genome (GRCh37/hg19) using Tophat (v2.0.8) by allowing up to 2 mismatches and 100 multiple hits. Reads mapped to ribosomal RNAs or to the mitochondrial genome were excluded from downstream analysis. Gene expression levels were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Only uniquely mapped reads were used to estimate FPKM. To calculate normalized FPKM, we first ran Cuffquant (v2.2.1) with default arguments for genes annotated in GENCODE (v19), and then ran Cuffnorm with parameters of “-total-hits-norm –library-norm-method quartile” on the CBX files generated from Cuffquant
For circRNA identification, we first extracted the chimerically aligned RNAseq reads using Tophat-fusion and then called circRNAs using circExplorer (v2.0). To identify circRNAs that are not back-spliced from a canonical exon border, we ran circExplorer2 with a customized gene annotation file and the “--low-confidence” option. CircRNAs with at least two unique back-spliced reads in overall samples are categorized as “being expressed” and kept as circRNA candidates. CircRNA expression is quantified by normalized reads per million (RPM) at the back-splicing sites for each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each circRNA in each sample

molecule: total RNA

organism: Homo sapiens

source_name: Temporal cortex pyramidal neuron

extract_protocol:
Total RNA was isolated and treated with DNase (Qiagen) using the Arcturus Picopure method (Applied Biosystems), yielding approximately 7-8 ng RNA per subject. Total RNA was linearly amplified into 5~10 µg of double-stranded cDNA using the validated, precise, isothermal RNA amplification method implemented in the Ovation RNA-seq System V2 (NuGen)
Sequencing libraries were generated from 500 ng of the double-stranded (ds) cDNA using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's protocol. The cDNA was fragmented, and end repair, A-tailing, adapter ligation was performed for library construction.

tag: source sampleid

tag: source subjectid

tag: disease state

value: AD

tag: cell type

value: TCPY

tag: batch

tag: replicate


title: HC_BC000269_TCPY_11_rep1


title: Adult_nphx_1303

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

organism: Mus musculus

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: strain

value: FACS sorted


title: Donor63_Day0_Progenitors_1 [H63-d0-Un-1]

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The default RNA-seq pipeline of DolphinNext platform was used for data processing https://dolphinnext.umassmed.edu/
RSEM v1.3.1 was used to align RNA-Seq reads to reference transcripts hg19 and estimates gene and isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

source_name: subcutaneous white adipose tissue

extract_protocol:
RNA was extracted using TriPure TRIzol reagent. Chloroform was added in a 1:5 ratio by volume and phase separation was performed. The RNA-containing layer was mixed with an equal volume of 100% isopropanol and incubated overnight at -20 °C for precipitation. RNA was pelleted and washed with 80% ethanol and resuspended in nuclease-free water.
Library preparation was performed using Illumina TruSeq Stranded mRNA Low-Throughput Sample Prep Kit (Cat# 20020594) according to manufacturer’s instruction.

tag: tissue

value: subcutaneous white adipose tissue

tag: cell line

value: primary adipose-tissue derived mesenchymal progenitors

value: Progenitors

tag: treatment


title: N_CPC_02

city: Beijing

first: Xiaochun

state: China

address: Equipment No.2, Peking University, Beijing, China

department: College of Future Technology

country: China

institute: Peking University

data_processing:
Quality control: The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base 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: 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. And then 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.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two  conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler R package（3.8.1） to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis: Gene Set Enrichment Analysis (GSEA) is a computational approach to  determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were  tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、Reactome、DO and DisGeNET data sets were used for GSEA independently. SNP analysis GATK (4.1.1.0) software was used to analyse SNP calling, and SnpEff (4.3.1q) software was used to annotate SNP. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10). AS analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event. PPI analysis of differentially expressed genes PPI analysis of differentially expressed genes was based on the STRING database, which is available to known and predicted Protein-Protein Interactions.For the species that exist in the database, we build a network by extracting the list of target genes from the database. Otherwise, the Diamond software (0.9.14) was used to compare the target  gene sequence with the selected reference protein sequence, and then the network was established according to the known interaction of the selected reference species. Fusion Analysis Fusion gene refers to the chimeric gene formed by the fusion of all or part of the sequences of two genes, which is generally caused by chromosome translocation, deletion and other reasons. We used SATR-fusion software (1.9.0) to detect genes that are fused. SATR-fusion is a software package uses fusion output results of STAR alignment to detect fusion transcripts, including SATR alignment, SATR fusion. predict, SATR-fusion.filter was used to correct the predicted results of Star-fusion to ensure the accuracy of the results. Weighted correlation network analysis WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing , FPKM can be used as gene expression data.
Assembly: Homo Sapiens genome GRCh38/hg38
Supplementary files format and content: FPKM calculated from the original data were presented in Excel file (.xls and .xlsx)

growth_protocol: All pluripotent and differentiation cells were maintained at 37 °C in the cell incubator (LS-C0150, Thermo), with 5% CO2 and atmospheric (21%) O2. Human induced pluripotent stem cell (iPSC), iPS-18 (Y00300, TaKaRa), iPS-B1 (CA4025106, CELLapy), iPS-M (RC01001-A, Nuwacell), iPS-F (RC01001-B, Nuwacell), and human embryonic stem cell (ESC) lines WIBR3 (Whitehead Institute Center for Human Stem Cell Research, Cambridge, MA) and H9 were routinely cultured in PGM1 medium (CELLAPY) or mTeSR1 (Stemcell Technologies) on growth factor–reduced Matrigel-coated (Corning) plate. iPSCs and ESCs were passaged every 3-5 days using Versene (Gibco) depending on the cell density. 3-5 μM Y27632 (Selleck Chemicals) dissolved in dimethyl sulfoxide (DMSO) was added for the first 12-24h after passage. The pluripotent cells were seeded in 6-well plates.

extract_protocol:
RNA was extracted using the EasyPure® RNA Kit (TransGen). RNA quantification and qualification: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.
Clustering and sequencing: After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

tag: genotype

value: WT


title: Adult_nphx_1295


title: HC_BC000267_TCPY_11_rep1

value: HC


title: N_CPC_01


title: Adult_nphx_1296


title: Donor63_Day0_Progenitors_2 [H63-d0-Un-3]


title: Adult_nphx_1297


title: Donor48_Day3_Osteo_2 [H48-d3-Ost-3]

value: Osteogenic


title: RNA_12_36

treatment_protocol:
iPSC treated with 12 μM 0-36h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: CHIR treated iPSC

value: iPSC treated with 12 uM 0-36h CHIR


title: hiPSC_03

treatment_protocol:
iPS-B1 cultured in PGM1
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC

value: maitained iPSC


title: hiPSC_02


title: HC_BC000266_TCPY_11_rep1


title: Donor48_Day3_Adipo_2 [H48-d3-MDI-3]

value: Adipogenic


title: Donor48_Day3_Adipo_1 [H48-d3-MDI-1]


title: CPC_03

treatment_protocol:
IR-CPCs were purified through DACT-1 photoactivation method
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-derived CPCs

value: mage-recognized cells from day 6


title: HC_BC000265_TCPY_11_rep1


title: Adult_nphx_1294


title: Donor48_Day3_Osteo_1 [H48-d3-Ost-1]


title: Adult_nphx_1291


title: hiPSC_01


title: Adult_nphx_1293


title: CPC_01

value: mage-recognized CPCs from day 6


title: Donor48_Day3_Chondro_2 [H48-d3-Cho-3]

value: Chondrogenic


title: Adult_nphx_1289


title: HC_BC000260_TCPY_11_rep1

value: AD

value: TCPY


title: HC_BC000264_TCPY_11_rep1


title: Donor48_Day3_Chondro_1 [H48-d3-Cho-1]

value: subcutaneous white adipose tissue


title: Adult_nphx_1288

value: FACS sorted


title: HC_BC000263_TCPY_11_rep1


title: Adult_nphx_1292


title: Donor48_Day3_DMEM_2 [H48-d3-DM-3]

value: primary adipose-tissue derived mesenchymal progenitors

value: Non-induced

value: DMEM


title: HC_BC000262_TCPY_11_rep1


title: Donor48_Day3_DMEM_1 [H48-d3-DM-1]


title: HC_BC000261_TCPY_11_rep1


title: CM_02

treatment_protocol:
iPSC-derived CM on day 15
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-derived CMs

value: WT

value: iPSC-derived CMs on day 12


title: CM_03


title: CPC_02


title: Adult_nphx_1290


title: Adult_nphx_1287


title: HC_BC000259_TCPY_11_rep1


title: CM_01


title: Donor48_Day0_Progenitors_2 [H48-d0-Un-3]

value: Progenitors


title: 8505C_CRABP1

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

data_processing:
FastQC
Trimmomatic v0.38 (parameter: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36)
HISHAT2 v2.1.0
featureCounts v2.0.0
Assembly: GRCh38
Supplementary files format and content: a tab-delimited text file contains TPM values for each sample

source_name: Thyroid cancer cells

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. RNA QC: total >= 2 ug, concentration >= 50 ng/ul, RIN >= 6.8, RQN >= 7.6, OD260/OD230 >= 2.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection


title: Adult_nphx_1285


title: HC_BC000256_TCPY_11_rep1


title: HC_BC000258_TCPY_11_rep1


title: Adult_nphx_1286


title: Donor48_Day0_Progenitors_1 [H48-d0-Un-1]


title: Adult_nphx_1284


title: 8505C_Vector

value: empty vector


title: FTC133_CRABP1


title: HC_BC000257_TCPY_11_rep1


title: HC_BC000255_TCPY_11_rep1


title: FTC133_Vector


title: Donor45-14day-2

data_processing:
The default RNA-seq pipeline of Dolphin platform was used for data processing https://dolphin.umassmed.edu/
RSEM v1.3.1 is used to align RNA-Seq reads to reference transcripts hg19 and estimates gene and isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

tag: differentiation

value: Adipogenic


title: Adult_nphx_1283


title: HC_BC000254_TCPY_11_rep1


title: HC_BC000253_TCPY_10_rep1


title: Monocytes_control_T406

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

country: France

institute: Inserm

data_processing:
Purity-filtered reads were pre-processed using fastp (v. 0.19.11)
STAR v2.7.6a (Spliced Transcripts Alignment To a Reference) was used to align reads to the human hg38 genome and generate raw counts.
Assembly: Human Genome hg19, gencode v19
Supplementary files format and content: csv file with raw count generated by STAR

source_name: Blood

extract_protocol:
Circulating monocytes were isolated from total blood by FACS. Total RNA were purified according the miRNeasy Micro Kit (P/N 217084, Qiagen Courtaboeuf, France) including a RNAse free DNase treatment from.
RNA sequencing libraries were prepared from 100 to 200 ng of total RNA using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus library preparation kit.
Sequencing was carried out using a pair-end 2 x 100 bp mode on the NovaSeq 6000 system (Illumina), targeting between 10 and 15M clusters per sample, strandness reverse

value: Blood

value: Monocytes

value: control


title: Adult_nphx_1281


title: Monocytes_control_T404


title: Monocytes_control_T407


title: Adult_nphx_1280


title: Adult_nphx_1282


title: Donor45-7day-2


title: Donor45-3day-2


title: HC_BC000252_TCPY_10_rep1

value: HC


title: Monocytes_control_T405


title: Donor45-14day-1


title: HC_BC000250_TCPY_10_rep1


title: Donor45-3day-1


title: Donor45-7day-1


title: HC_BC000249_TCPY_10_rep1


title: Monocytes_MUT_T402

value: mutation


title: Adult_nphx_1277


title: Adipo 3d

data_processing:
The sequencing outputs were processed using the default settings of the 10X CellRanger analysis pipeline software v3.1.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw count values for each single cell

extract_protocol:
Single-cell library preparation including RNA extraction was performed using Chromium™ Single Cell 3' GEM Library & Gel Bead Kit v3 (Cat#1000092) according to manufacturer’s instruction.
Single-cell library preparation was performed using Chromium™ Single Cell 3' GEM Library & Gel Bead Kit v3 (Cat#1000092) according to manufacturer’s instruction.


title: Monocytes_MUT_T401


title: Adult_nphx_1279


title: Donor45-Control-2

value: Undifferentiated


title: Donor45-Control-1


title: Adult_nphx_1276


title: Adult_nphx_1278


title: Undifferentiated


title: HC_BC000251_TCPY_10_rep1

value: TCPY


title: Donor37-14day-2


title: HC_BC000247_TCPY_10_rep1


title: HC_BC000248_TCPY_10_rep1


title: Monocytes_MUT_T400


title: HC_BC000246_TCPY_10_rep1


title: Donor37-14day-1


title: Adult_nphx_1274

value: FACS sorted


title: Donor37-7day-2


title: Monocytes_control_T403


title: HC_BC000245_TCPY_10_rep1

value: AD


title: Adult_nphx_1273


title: Donor37-7day-1


title: HC_BC000244_TCPY_10_rep1


title: ClpP-KO SUM159, TR-57 Treatment (24 HR) (bio. rep. 3)

city: Chapel Hill

first: Lee

middle: M

last: Graves

state: NC

address: 120 Mason Farm Rd

department: Pharmacology

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were indexed and quantified in alignment-mode through Salmon using reference transcriptome [Transcript Sequences v.27] from GENCODE
Resulting quantification files were imported to R and DESeq2 was used to normalize samples and analyze differential expression
Supplementary files format and content: comma delimited files containing differential gene expression data [log2(Fold Change), p values] of WT and ClpP-KO cells treated with ONC201 or TR-57 compared to respective DMSO controls

growth_protocol: SUM159 cells were maintained in 1:1 DMEM:F12 supplemented with 5% FBS, 1% antibiotic/antimycotic, 5 ug/mL insulin, and 1 ug/mL hydrocortisone

extract_protocol:
total RNA was extracted using Qiagen RNeasy Kit (74104)
RNA libraries for RNA-seq were generated by Novogene Co. using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Cells were treated with 0.1% DMSO, 10 uM ONC201, or 150 nM TR-57

tag: time

value: 24 hour

value: triple-negative breast cancer

value: ClpP-KO


title: WT SUM159, ONC201 Treatment (24 HR) (bio. rep. 3)

value: WT

value: 10 uM ONC201


title: ClpP-KO SUM159, ONC201 Treatment (24 HR) (bio. rep. 3)


title: WT SUM159, TR-57 Treatment (24 HR) (bio. rep. 3)


title: ClpP-KO SUM159, DMSO Control (24 HR) (bio. rep. 3)

value: 0.1% DMSO


title: Adult_nphx_1271


title: HC_BC000242_TCPY_10_rep1


title: Donor37-3day-2


title: Adult_nphx_1272


title: Donor37-3day-1


title: Donor37-Control-2


title: Adult_nphx_1270


title: HC_BC000241_TCPY_10_rep1


title: WT SUM159, DMSO Control (24 HR) (bio. rep. 3)


title: Adult_nphx_1269


title: Adult_nphx_1275


title: Donor37-Control-1


title: HC_BC000240_TCPY_10_rep1


title: Adult_nphx_1268


title: HC_BC000239_TCPY_10_rep1


title: ClpP-KO SUM159, TR-57 Treatment (1 HR) (bio. rep. 3)

value: 1 hour


title: WT SUM159, TR-57 Treatment (1 HR) (bio. rep. 3)


title: Adult_nphx_1267


title: HC_BC000243_TCPY_10_rep1


title: Osteo

data_processing:
The default RNA-seq pipeline of DolphinNext platform was used for data processing https://dolphinnext.umassmed.edu/
RSEM v1.3.1 is used to align RNA-Seq reads to reference transcripts hg19 and estimates gene and isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

value: subcutaneous white adipose tissue

tag: induction

value: Osteogenic


title: HC_BC000238_TCPY_10_rep1


title: Chondro

value: Chondrogenic


title: Adult_nphx_1266


title: ClpP-KO SUM159, ONC201 Treatment (1 HR) (bio. rep. 3)


title: HC_BC000237_TCPY_10_rep1


title: WT SUM159, ONC201 Treatment (1 HR) (bio. rep. 3)


title: ClpP-KO SUM159, DMSO Control (1 HR) (bio. rep. 3)


title: HC_BC000235_TCPY_10_rep1


title: Adult_nphx_1264


title: WT SUM159, DMSO Control (1 HR) (bio. rep. 3)


title: Total RNA MDA CRISPRI Ile GAT OE Ile TAT R2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Standard Illumina RNA library prep

data_processing:
Library strategy: Ribosomal Profiling
cutadapt v1.17
Remove rRNA and tRNA contaminants, aligned against reference bowtie2.3.4.1
Align to hg38 STAR (2.5.2a)
Xtail
Genome_build: hg38
Supplementary_files_format_and_content: Count files generated using htseq-count (RNA-seq) or Xtail (RPF)

source_name: Xenograft Cell Line

growth_protocol: Cells grown in 15cm dishes in DMEM 10% FBS, sodium pyruvate and L-glutamine

extract_protocol:
Cells flash frozen in Liquid Nitrogen, Lysis buffer (20mM Tris pH 7.4, 150mM NaCl, 5mM MgCl2, 1mM DTT, 100ug/ml Cycloheximide, 1% Triton X-100, 25U/ml Turbo DNaseI); RNA extracted in Trizol
Standard Illumina RNA library prep

treatment_protocol: No treatment

value: MDA MB 231

tag: crispri targeting

value: Ile GAU

tag: oe construct

value: tRNAIleUAU

tag: molecule subtype

value: Total RNA


title: Adipo

value: Adipogenic


title: Control

value: non-induced


title: Adult_nphx_1263

value: FACS sorted


title: ClpP-KO SUM159, TR-57 Treatment (24 HR) (bio. rep. 2)

value: 24 hour


title: HC_BC000234_TCPY_10_rep1

tag: source sampleid

tag: source subjectid

value: AD

value: TCPY


title: Total RNA MDA CRISPRI Ile GAT OE Ile TAT R1

description: Standard Illumina RNA library prep


title: HC_BC000233_TCPY_10_rep1

tag: disease state

tag: cell type


title: WT SUM159, TR-57 Treatment (24 HR) (bio. rep. 2)

value: triple-negative breast cancer

value: WT


title: Adult_nphx_1261


title: Total RNA MDA CRISPRI Ile GAT Ctrl R2

description: Standard Illumina RNA library prep

value: Control


title: Adult_nphx_1262


title: Total RNA MDA CRISPRI Ile GAT Ctrl R1

description: Standard Illumina RNA library prep


title: WT SUM159, ONC201 Treatment (24 HR) (bio. rep. 2)

value: 10 uM ONC201


title: Adult_nphx_1260


title: Total RNA MDA CRISPRi eGFP OE Ile TAT R2

description: Standard Illumina RNA library prep

value: eGFP


title: Adult_nphx_1259


title: HC_BC000236_TCPY_10_rep1

tag: batch

tag: replicate


title: HC_BC000230_TCPY_10_rep1


title: HC_BC000231_TCPY_10_rep1


title: Adult_nphx_1265

tag: strain


title: Total RNA MDA CRISPRi eGFP OE Ile TAT R1

description: Standard Illumina RNA library prep

tag: cell line


title: HC_BC000229_TCPY_10_rep1

value: HC


title: WT SUM159, DMSO Control (24 HR) (bio. rep. 2)

tag: treatment

value: 0.1% DMSO


title: HC_BC000228_TCPY_10_rep1


title: ClpP-KO SUM159, TR-57 Treatment (1 HR) (bio. rep. 2)

value: 1 hour

tag: genotype

value: ClpP-KO


title: Total RNA MDA CRISPRi eGFP Ctrl R2

description: Standard Illumina RNA library prep

value: MDA MB 231


title: Total RNA MDA CRISPRi eGFP Ctrl R1

description: Standard Illumina RNA library prep

value: Total RNA


title: Adult_nphx_1256


title: HC_BC000227_TCPY_10_rep1


title: Adult_nphx_1255


title: RPF MDA CRISPRi Ile GAT OE Ile TAT R2

description: Ribosomes pelleted in 1M Sucrose 100,000RPM 1hr, extracted in Trizol

molecule: polyA RNA

value: Ile GAU

value: tRNAIleUAU

value: Ribosome protected fragments (RPF)


title: ClpP-KO SUM159, ONC201 Treatment (1 HR) (bio. rep. 2)


title: HC_BC000232_TCPY_10_rep1


title: HC_BC000226_TCPY_10_rep1


title: WT SUM159, TR-57 Treatment (1 HR) (bio. rep. 2)


title: Adult_nphx_1254

value: FACS sorted


title: ClpP-KO SUM159, ONC201 Treatment (24 HR) (bio. rep. 2)

value: 24 hour


title: HC_BC000225_TCPY_10_rep1

value: AD

value: TCPY


title: ClpP-KO SUM159, DMSO Control (24 HR) (bio. rep. 2)

value: triple-negative breast cancer


title: WT SUM159, ONC201 Treatment (1 HR) (bio. rep. 2)

value: WT


title: RPF MDA CRISPRI Ile GAT Ctrl R2

value: Control


title: Adult_nphx_1258


title: Adult_nphx_1252


title: ClpP-KO SUM159, DMSO Control (1 HR) (bio. rep. 2)


title: Adult_nphx_1253


title: RPF MDA CRISPRI Ile GAT Ctrl R1


title: WT SUM159, DMSO Control (1 HR) (bio. rep. 2)


title: Adult_nphx_1257


title: HC_BC000223_TCPY_10_rep1


title: RPF MDA CRISPRi eGFP OE Ile TAT R2

value: eGFP


title: ClpP-KO SUM159, TR-57 Treatment (24 HR) (bio. rep. 1)


title: Adult_nphx_1250


title: HC_BC000221_TCPY_10_rep1

value: HC


title: RPF MDA CRISPRI Ile GAT OE Ile TAT R1


title: RPF MDA CRISPRi eGFP Ctrl R1


title: ClpP-KO SUM159, ONC201 Treatment (24 HR) (bio. rep. 1)

value: 10 uM ONC201


title: HC_BC000224_TCPY_10_rep1


title: RPF MDA CRISPRi eGFP Ctrl R2


title: WT SUM159, ONC201 Treatment (24 HR) (bio. rep. 1)


title: Adult_nphx_1249


title: HC_BC000219_TCPY_10_rep1


title: HC_BC000218_TCPY_10_rep1


title: HC_BC000130_FB_6_rep1

source_name: Fibroblasts

value: FB


title: Adult_nphx_1246


title: High Translating MDA CRISPRI Ile GAT OE Ile TAT C

description: High Translating (>2 polys)

data_processing:
Library strategy: Polysome Profiing
Reads mapped to hg38 with STAR
Reads tabulated using featureCounts
Bioconductor package DESeq2 used to compare fractions
Genome_build: hg38
Supplementary_files_format_and_content: count file

extract_protocol:
425uL Lysis Buffer (5mM Tris HCl pH 7.5, 2.5mM MgCl2, 1.5mM KCL, 100ug/mL cycloheximide, 2mM DTT, 0.5% Triton X-100, 0.5% sodium deoxycholate, 100units SUPERase*In Rnase Inhibitor, 1x Protease Inhibitors EDTA-free); RNA extracted with 3:1 Trizol LS Reagent after polysome fractioning
Lexogen QuantSeq 3' mRNA-Seq Library Prep kit, 500ng RNA used as Input

treatment_protocol: 100ug/mL Cycloheximide for 5mins at 37oC, then washed 2x with ice cold 1x PBS with 100ug/mL Cycloheximide. Cells were then flash frozen in liquid nitrogen.


title: High Translating MDA CRISPRI Ile GAT OE Ile TAT A

description: High Translating (>2 polys)


title: HC_BC000220_TCPY_10_rep1


title: WT SUM159, DMSO Control (24 HR) (bio. rep. 1)

value: 0.1% DMSO


title: Adult_nphx_1251


title: Adult_nphx_1245


title: ClpP-KO SUM159, DMSO Control (24 HR) (bio. rep. 1)

value: ClpP-KO


title: HC_BC000222_TCPY_10_rep1


title: RPF MDA CRISPRi eGFP OE Ile TAT R1

value: MDA MB 231


title: High Translating MDA CRISPRI Ile GAT Ctrl C

description: High Translating (>2 polys)

value: Ile GAU


title: HC_BC000129_FB_6_rep1


title: Adult_nphx_1244


title: Adult_nphx_1248


title: High Translating MDA CRISPRI Ile GAT OE Ile TAT B

description: High Translating (>2 polys)

value: tRNAIleUAU


title: Adult_nphx_1247


title: ClpP-KO SUM159, TR-57 Treatment (1 HR) (bio. rep. 1)

value: 1 hour


title: WT SUM159, TR-57 Treatment (24 HR) (bio. rep. 1)


title: WT SUM159, TR-57 Treatment (1 HR) (bio. rep. 1)


title: ClpP-KO SUM159, ONC201 Treatment (1 HR) (bio. rep. 1)


title: HC_BC000127_PBMC_6_rep1

source_name: Peripheral blood mononuclear cell

value: PBMC


title: High Translating MDA CRISPRI Ile GAT Ctrl A

description: High Translating (>2 polys)


title: HC_BC000128_FB_6_rep1


title: High Translating MDA CRISPRI Ile GAT Ctrl B

description: High Translating (>2 polys)


title: Adult_nphx_1242

value: FACS sorted


title: WT SUM159, ONC201 Treatment (1 HR) (bio. rep. 1)


title: Adult_nphx_1241


title: ClpP-KO SUM159, DMSO Control (1 HR) (bio. rep. 1)


title: Adult_nphx_1240


title: HC_BC000124_PBMC_6_rep1.amplified


title: Adult_nphx_1239


title: HC_BC000125_PBMC_6_rep1


title: WT SUM159, DMSO Control (1 HR) (bio. rep. 1)


title: HC_BC000112_SNDA_6_rep2

source_name: Substantial nigra dopamine neuron

value: PD

value: SNDA


title: HC_BC000111_SNDA_4_rep1


title: High Translating MDA CRISPRi eGFP Ctrl C

description: High Translating (>2 polys)


title: Adult_nphx_1243


title: High Translating MDA CRISPRi eGFP OE Ile TAT A

description: High Translating (>2 polys)


title: 22Rv1 DTXR_Dic2

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

description:
rsem_count_DicvsVeh
TMM_normalized_reads_count_per_million_DicvsVeh
Dic2

data_processing:
Bowtie2 version 2.4.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.3.3 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene  expression normalization.
Assembly: hg19
Supplementary files format and content: TMM normalized reads count per million

growth_protocol:
Cell culture
22Rv1 DTXR cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 3 nM DTX while 22Rv1 DTXS cells were maintain in complete medium with ethonal in parallel. Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
The total RNA was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed on an Illumina instrument for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: 22Rv1 DTXR cells were treated with ethanol or 25 µM Dic for 72 hrs.

value: Human prostate cancer cell line

tag: phenotype

value: DTXR

value: 25 uM Dic


title: Adult_nphx_1238


title: High Translating MDA CRISPRi eGFP Ctrl B

description: High Translating (>2 polys)

value: eGFP

value: Control


title: HC_BC000126_PBMC_6_rep1

value: HC


title: HC_BC000110_SNDA_4_rep2


title: Adult_nphx_1236


title: High Translating MDA CRISPRi eGFP Ctrl A

description: High Translating (>2 polys)


title: 22Rv1 DTXR_Veh1

description:
rsem_count_DicvsVeh
TMM_normalized_reads_count_per_million_DicvsVeh
Veh1

value: Ethanol


title: Adult_nphx_1235


title: Adult_nphx_1237


title: 22Rv1 DTXR_Veh2

description:
rsem_count_DicvsVeh
TMM_normalized_reads_count_per_million_DicvsVeh
Veh2


title: Low Translating MDA CRISPRI Ile GAT OE Ile TAT C

description: Low Translating (80S & 1st Poly Peak)


title: 22Rv1 DTXR

description:
rsem_count_DTXRvsDTXS
TMM_normalized_reads_count_per_million_DTXRvsDTXS
Riz_91


title: HC_BC000107_SNDA_5_rep1


title: High Translating MDA CRISPRi eGFP OE Ile TAT C

description: High Translating (>2 polys)


title: HC_BC000109_SNDA_4_rep2


title: HC_BC000106_SNDA_5_rep1


title: High Translating MDA CRISPRi eGFP OE Ile TAT B

description: High Translating (>2 polys)


title: 22Rv1 DTXS

description:
rsem_count_DTXRvsDTXS
TMM_normalized_reads_count_per_million_DTXRvsDTXS
Riz_RV

value: DTXS


title: Low Translating MDA CRISPRI Ile GAT OE Ile TAT A

description: Low Translating (80S & 1st Poly Peak)


title: Adult_nphx_1233


title: Low Translating MDA CRISPRI Ile GAT OE Ile TAT B

description: Low Translating (80S & 1st Poly Peak)


title: Adult_nphx_1234


title: HC_BC000103_SNDA_5_rep1


title: Low Translating MDA CRISPRI Ile GAT Ctrl B

description: Low Translating (80S & 1st Poly Peak)


title: HC_BC000105_SNDA_5_rep1


title: HC_BC000104_SNDA_5_rep1


title: Adult_nphx_1230


title: Low Translating MDA CRISPRI Ile GAT Ctrl C

description: Low Translating (80S & 1st Poly Peak)


title: 22Rv1 DTXR_Dic1

description:
rsem_count_DicvsVeh
TMM_normalized_reads_count_per_million_DicvsVeh
Dic1


title: HC_BC000102_SNDA_5_rep1


title: Low Translating MDA CRISPRi eGFP OE Ile TAT C

description: Low Translating (80S & 1st Poly Peak)


title: Low Translating MDA CRISPRI Ile GAT Ctrl A

description: Low Translating (80S & 1st Poly Peak)


title: Adult_nphx_1229


title: Adult_nphx_1228


title: Low Translating MDA CRISPRi eGFP OE Ile TAT B

description: Low Translating (80S & 1st Poly Peak)


title: HC_BC000101_SNDA_5_rep1


title: HC_BC000100_SNDA_5_rep1


title: HC_BC000099_SNDA_5_rep1


title: HC_BC000098_SNDA_5_rep1


title: Adult_nphx_1226


title: Low Translating MDA CRISPRi eGFP OE Ile TAT A

description: Low Translating (80S & 1st Poly Peak)


title: Low Translating MDA CRISPRi eGFP Ctrl C

description: Low Translating (80S & 1st Poly Peak)


title: Adult_nphx_1225


title: Low Translating MDA CRISPRi eGFP Ctrl A

description: Low Translating (80S & 1st Poly Peak)


title: Adult_nphx_1227


title: Adult_nphx_1232


title: Adult_nphx_1224


title: HC_BC000097_SNDA_4_rep1


title: Adult_nphx_1223


title: HC_BC000096_SNDA_5_rep1


title: Total RNA MDA CRISPRI Ile GAT OE Ile TAT B

description: Input RNA


title: Total RNA MDA CRISPRI Ile GAT OE Ile TAT C

description: Input RNA


title: Total RNA MDA CRISPRI Ile GAT OE Ile TAT A

description: Input RNA


title: HC_BC000095_SNDA_5_rep1


title: Low Translating MDA CRISPRi eGFP Ctrl B

description: Low Translating (80S & 1st Poly Peak)


title: Total RNA MDA CRISPRI Ile GAT Ctrl C

description: Input RNA


title: HC_BC000094_SNDA_5_rep1


title: HC_BC000092_SNDA_3_rep1

value: ILB


title: Adult_nphx_1219


title: Adult_nphx_1221


title: HC_BC000091_SNDA_2_rep1


title: HC_BC000093_SNDA_2_rep1


title: Adult_nphx_1220


title: Total RNA MDA CRISPRI Ile GAT Ctrl B

description: Input RNA

value: MDA MB 231


title: Adult_nphx_1218


title: Total RNA MDA CRISPRi eGFP OE Ile TAT C

description: Input RNA


title: Total RNA MDA CRISPRI Ile GAT Ctrl A

description: Input RNA

value: Ile GAU


title: HC_BC000090_SNDA_2_rep1


title: HC_BC000089_SNDA_4_rep1


title: HC_BC000087_SNDA_2_rep1


title: Adult_nphx_1222


title: Total RNA MDA CRISPRi eGFP Ctrl C

description: Input RNA


title: Adult_nphx_1217


title: PK44

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

data_processing:
Mapping - HISAT2 v2.1.0 Default
Quantification - featureCounts v1.6.4
Differential Analysis - DESeq2 v2_1.6.3 or EdgeR v3.16.5 (For sample with bio-replicate using DESeq2, samples without bio-replicate using EdgeR.
Enrichment Analysis ClusterProfiler v2.4.3
Protein-Protein Interaction Analysis NCBI BLAST v2.2.28 e-value=1e-10, Using blast, String database
Supplementary files format and content: excel file include FPKM values for each Sample

source_name: Colon Biopsy

extract_protocol:
AllPrep DNA/RNA FFPE kit (Qiagen) is used for FFPE RNA isolation
Illumina TruSeq RNA Exome, 12Gb (40 million reads) raw data, Q30≥80%

tag: tissue

value: Colon Biopsy

value: GVHD

value: GI mucosal tissue

value: FFPE


title: Adult_nphx_1214

value: FACS sorted


title: Total RNA MDA CRISPRi eGFP OE Ile TAT B

description: Input RNA

value: tRNAIleUAU


title: HC_BC000088_SNDA_4_rep1

value: SNDA


title: Adult_nphx_1216


title: HC_BC000085_SNDA_5_rep1


title: Adult_nphx_1215


title: Total RNA MDA CRISPRi eGFP Ctrl A

description: Input RNA


title: smeb-2 Salt rep2

city: Hefei

first: Zhen

last: Wang

state: Anhui

address: 130 Changjiangxilu

institute: Anhui Agricultural University

description: smeb-2 Cd-rep2

data_processing:
RNA-seq raw reads were processed with the Trimmomatic v0.32 and PRINSEQ v0.20.4 programs
Trimmomatic was used to remove the potential Illumina adapter contamination and conduct read trimming and clipping the low-quality bases.
PRINSEQ was subsequently employed to mainly remove low-complexity reads. The remaining reads were aligned to the Col-0 reference genome (version TAIR10) using the TopHat v2.0.13 program (D. Kim et al., 2013) with customized parameters.
A series of python scripts from juncBASE v0.6 were employed to deﬁne alternative 5' splice site, alternative 3' splice site, exon skipping, mutually exclusive exon, and intron retention events, qualify the events and generate signiﬁcantly differentially splicing events (P value < 0.05 and abs (delta_val) > 5) between pairwise samples.
The genes with alternative splicing patterns in all biological replicates of both smeb-1 and smeb-2 mutant plants are enrolled as differentially alternatively spliced genes.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample. Matrix table with raw gene counts for every gene and every sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Twelve-day-old smeb-1, smeb-2, and Col-0 seedlings grown on 0.5× MS medium.

extract_protocol:
Total RNA was isolated with the Total RNA Extraction Kit (Hua Yue Yang) and disposed with TURBO DNA-free Kit (Ambion) to remove any potential genomic DNA.
The libraries were constructed following the standard Illumina protocols.

treatment_protocol: Treatment with 200 mM NaCl for 0 or 6 h.

value: seedlings

tag: age

value: 12-day old seedlings

value: Salt for 6 h


title: Total RNA MDA CRISPRi eGFP OE Ile TAT A

description: Input RNA

value: eGFP


title: Adult_nphx_1211


title: PK43


title: Total RNA MDA CRISPRi eGFP Ctrl B

description: Input RNA

value: Control


title: PK42


title: HC_BC000084_SNDA_5_rep1


title: HC_BC000082_SNDA_4_rep1


title: PK41


title: PK38


title: PK40


title: smeb-2 Salt rep1

description: smeb-2 Cd-rep1


title: Adult_nphx_1210


title: HC_BC000080_SNDA_3_rep1


title: Adult_nphx_1207


title: PK36


title: Col-0 Salt rep1

description: Col-0 Cd-rep1

value: wild-type


title: HC_BC000083_SNDA_5_rep1


title: PK39


title: Adult_nphx_1209


title: smeb-1 Salt rep2

description: smeb-1 Cd-rep2


title: HC_BC000081_SNDA_3_rep1


title: HC_BC000086_SNDA_2_rep1


title: HC_BC000078_SNDA_5_rep1


title: Adult_nphx_1213


title: Adult_nphx_1205


title: PK34


title: smeb-2 control rep1

value: untreated for 6 h


title: HC_BC000076_SNDA_3_rep1

value: ILB


title: smeb-1 Salt rep1

description: smeb-1 Cd-rep1


title: Adult_nphx_1208


title: HC_BC000075_SNDA_2_rep1


title: Col-0 Salt rep2

description: Col-0 Cd-rep2


title: HC_BC000074_SNDA_3_rep1


title: HC_BC000079_SNDA_5_rep1


title: PK37


title: Adult_nphx_1231


title: Adult_nphx_1206


title: Col-0 control rep2


title: smeb-2 control rep2


title: Col-0 control rep1


title: PK35


title: Adult_nphx_1199


title: Adult_nphx_1204


title: Adult_nphx_1203


title: HC_BC000069_SNDA_3_rep1


title: PK27


title: PK33


title: smeb-1 control rep2


title: smeb-1 control rep1

description: smeb-1- rep1


title: PK32


title: PK29


title: Adult_nphx_1202


title: HC_BC000073_SNDA_4_rep1


title: PK31


title: Adult_nphx_1201


title: HC_BC000072_SNDA_5_rep1


title: Adult_nphx_1200


title: PK30


title: HC_BC000071_SNDA_3_rep1


title: HC_BC000067_SNDA_5_rep1


title: HC_BC000070_SNDA_3_rep1


title: PK24

value: No GVHD


title: Adult_nphx_1198


title: FRDA_EPO7

city: Innsbruck

first: Alexander

last: Kirchmair

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

data_processing:
Sequencing reads were trimmed  with CUTADAPT 4.0 using parameters -q 20, -O 10, -e 0.15, -m 10 and -a A{100}.
The nf-core rnaseq preprocessing pipeline version 3.6 (10.5281/zenodo.6327553) was used without trimming for alignment with STAR 2.7.9a to GRCh38 and for quantification with SALMON 1.5.2.
Assembly: GRCh38
Supplementary files format and content: CSV file with raw counts

source_name: Skeletal muscle

extract_protocol:
Total RNA was extracted using Trizol (ThermoFisher #15596026) with the PureLink RNA Micro Scale Kit (ThermoFisher #12183016) according to the manufacturer’s protocol. RNA integrity was analysed on an Agilent Tapestation with the High Sensitivity RNA Screen Tapes (Agilent #5067-5579).
The Lexogen Quantseq 3'mRNA kit was used for library preparation. Libraries were multiplexed and sequenced using Ion Hi-Q chemistry with an Ion Proton Sequencer (Ion torrent/Fisher Scientific, Austria).

value: Skeletal muscle

tag: donor

tag: disease

value: Friedreich's Ataxia

value: rhuEPO


title: FRDA_EPO5


title: FRDA_EPO3


title: FRDA_EPO6


title: Aged_nphx_1152

description:
Aged_nphx_lec
Aged_nphx_normalized_expression_matrix.csv


title: PK28

value: Colon Biopsy

value: GVHD

value: GI mucosal tissue


title: HC_BC000065_SNDA_6_rep1

value: HC


title: FRDA_EPO4


title: Aged_nphx_1151

value: FACS sorted


title: PK26

value: FFPE


title: Aged_nphx_1148


title: FRDA_EPO1


title: PK25


title: PK22


title: FRDA7

value: control


title: FRDA_EPO2


title: HC_BC000064_SNDA_6_rep1

value: SNDA


title: Aged_nphx_1150


title: PK21


title: Aged_nphx_1146


title: Aged_nphx_1149


title: HC_BC000068_SNDA_3_rep1


title: PK23


title: Aged_nphx_1145


title: HC_BC000062_SNDA_2_rep1


title: HC_BC000061_SNDA_4_rep1


title: Aged_nphx_1144


title: PK19


title: HC_BC000060_SNDA_4_rep1


title: Aged_nphx_1147


title: HC_BC000066_SNDA_5_rep1


title: Aged_nphx_1143


title: FRDA6


title: HC_BC000063_SNDA_2_rep1


title: PK20


title: HC_BC000058_SNDA_4_rep1


title: PK16


title: Aged_nphx_1142


title: HC_BC000056_SNDA_4_rep2


title: FRDA5


title: Aged_nphx_1140


title: FRDA4


title: PK18


title: CTRL6

value: healthy


title: CTRL5


title: PK17


title: HC_BC000059_SNDA_4_rep1


title: FRDA2


title: FRDA3


title: FRDA1


title: PK15


title: PK13


title: HC_BC000054_SNDA_2_rep1


title: Aged_nphx_1137


title: Aged_nphx_1139


title: PK14


title: CTRL4


title: PK12


title: HC_BC000052_SNDA_2_rep1


title: Aged_nphx_1138


title: HC_BC000055_SNDA_2_rep1


title: CTRL2


title: CTRL3


title: Aged_nphx_1141


title: cDNA library from gRNA of hiPSC at day5 after transduction

city: Kyoto

first: Mototsugu

last: Eiraku

address: 53 Kawahara-chi, Sakyo-ku

country: Japan

institute: Kyoto University

description:
10x Genomics
sample4_gRNA

library_source: transcriptomic single cell

data_processing:
GRCh38
10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

growth_protocol: Human iPSC line was obtained from the Wellcome Sanger Institute and cultured in StemFlex medium (Thermo Fisher) on Vitronectin (ThermoFisher)-coated culture dishes. Cells were detached using TrypLE (Thermo Fisher) and re-seeded at 4 × 104 cells per well into 6-well plates for routine maintenance. For the first 24 h after passaging, cells were treated with 10µM Y-27632 (Wako).

extract_protocol: single-cell RNA-seq library preparation using a 363 Chromium Next GEM Single Cell 5’Library & Gel Bead Kit following the manufacturers’proto364 col with minor modifications to simultaneously capture guide RNA molecules

tag: library type

value: gRNA

value: human iPSC


title: cDNA library from mRNA of hiPSC at day5 after transduction

description:
10x Genomics
sample4_mRNA

value: mRNA


title: CTRL1


title: Aged_nphx_1135


title: Adult_nphx_1212


title: Aged_nphx_1134


title: cDNA library from gRNA of hiPSC at day4 after transduction

description:
10x Genomics
sample3_gRNA


title: Lung, Knockout, Replicate 2

city: Milwaukee

first: Adeleye

middle: J.

last: Afolayan

state: Wisconsin

address: 8701 Watertown Plank Rd., PD278, CRI TBRC, Rm C3278

institute: Medical College of Wisconsin

description:
mouse_gene_exp.diff
CHUP-hete-KO-comparison.xlsx
Mouse_KO_2

data_processing:
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
Assembly: UCSC hg37, GRCm39
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: Lung

growth_protocol: Pulmonary-derived arterial endothelial cells or smooth muscle cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

extract_protocol:
Cells were collected using trypsin and RNA was gathered using the Qiagen RNeasy kit (cat. 74004)
Libraries were prepared according to Lexogen's instruction accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Cat. 015). Briefly, total RNA was reverse transcribed by oligodT priming, RNA template was removed, and the second strand was synthesized by random priming using DNA polymerase. After bead purification, library is amplified by PCR and sequences required for cluster generation are introduced. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were transfected at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest.

value: Lung

value: Knockout (Stub1-K287R mutant)


title: cDNA library from mRNA of hiPSC at day4 after transduction

description:
10x Genomics
sample3_mRNA


title: Aged_nphx_1133

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs


title: cDNA library from gRNA of hiPSC at day3 after transduction

description:
10x Genomics
sample2_gRNA


title: HC_BC000048_TCPY_11_rep1

data_processing:
RNA-seq raw files in FASTQ format were processed in a customized pipeline. For each sample, we first filtered out reads that failed vendor check or are too short (<15nt) after removing the low-quality ends or possible adaptor contamination by using fastq-mcf with options of “-t 0 –x 10 –l 15 –w 4 –q 10 –u”. We then checked the quality using FastQC and generated k-mer profile using kpal for the remaining reads. Reads were then mapped to the human genome (GRCh37/hg19) using Tophat (v2.0.8) by allowing up to 2 mismatches and 100 multiple hits. Reads mapped to ribosomal RNAs or to the mitochondrial genome were excluded from downstream analysis. Gene expression levels were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Only uniquely mapped reads were used to estimate FPKM. To calculate normalized FPKM, we first ran Cuffquant (v2.2.1) with default arguments for genes annotated in GENCODE (v19), and then ran Cuffnorm with parameters of “-total-hits-norm –library-norm-method quartile” on the CBX files generated from Cuffquant
For circRNA identification, we first extracted the chimerically aligned RNAseq reads using Tophat-fusion and then called circRNAs using circExplorer (v2.0). To identify circRNAs that are not back-spliced from a canonical exon border, we ran circExplorer2 with a customized gene annotation file and the “--low-confidence” option. CircRNAs with at least two unique back-spliced reads in overall samples are categorized as “being expressed” and kept as circRNA candidates. CircRNA expression is quantified by normalized reads per million (RPM) at the back-splicing sites for each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each circRNA in each sample

value: TCPY


title: HC_BC000049_SNDA_5_rep1


title: HC_BC000048_SNDA_4_rep1


title: Lung, Heterozygous, Replicate 2

description:
mouse_gene_exp.diff
CHUP-hete-KO-comparison.xlsx
Mouse_Het_2

value: Heterozygous (Stub1-K287Q mutant)


title: Lung, Knockout, Replicate 1

description:
mouse_gene_exp.diff
CHUP-hete-KO-comparison.xlsx
Mouse_KO_1


title: HC_BC000051_SNDA_3_rep1


title: Aged_nphx_1132


title: Aged_nphx_1136


title: HC_BC000050_SNDA_4_rep1


title: cDNA library from gRNA of hiPSC at day2 after transduction

description:
10x Genomics
sample1_gRNA


title: Aged_nphx_1131


title: cDNA library from mRNA of hiPSC at day3 after transduction

description:
10x Genomics
sample2_mRNA


title: CKO3

city: Guangzhou

first: WU

middle: CHENG

last: ZHI

address: Zhongshan 2nd Road

institute: Sun Yat-sen University

description:
primary chondrocyte
CKO3

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM and read counts value of each transcript was calculated using bowtie2 and eXpress
DEGs were identified using the DESeq2 functions estimateSizeFactors and nbinomTest.
P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern.GO enrichment and KEGG pathway enrichment of differentially expressed genes were analyzed using the online tool of DAVID Bioinformatics Resources 2021z
Assembly: mm10
Supplementary files format and content: xls files include counts value for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: vertebral growth plate, Col2a1cre;Mapk7f/f, day7

extract_protocol:
Total RNA was extracted from the growth plate using TRIzol regent (Invitrogen, Carlsbad, CA)
We constructed libraries using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, USA) and sequenced them on the Illumina sequencing platform according to the manufacturer's instructions

value: vertebral growth plate

value: chondrocyte

value: MAPK7 knockdown

tag: developmental stage

value: postnatal day7


title: HC_BC000046_SNDA_3_rep1

extract_protocol:
Total RNA was isolated and treated with DNase (Qiagen) using the Arcturus Picopure method (Applied Biosystems), yielding approximately 7-8 ng RNA per subject. Total RNA was linearly amplified into 5~10 µg of double-stranded cDNA using the validated, precise, isothermal RNA amplification method implemented in the Ovation RNA-seq System V2 (NuGen)
Sequencing libraries were generated from 500 ng of the double-stranded (ds) cDNA using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's protocol. The cDNA was fragmented, and end repair, A-tailing, adapter ligation was performed for library construction.

tag: source sampleid

value: HC


title: Aged_nphx_1130

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: FACS sorted


title: CKO2

description:
primary chondrocyte
CKO2


title: HC_BC000047_SNDA_5_rep1

tag: source subjectid


title: cDNA library from mRNA of hiPSC at day2 after transduction

description:
10x Genomics
sample1_mRNA


title: HC_BC000044_SNDA_4_rep1

tag: disease state


title: HC_BC000045_SNDA_5_rep1

tag: cell type


title: Aged_nphx_1129


title: Low Density Layer

data_processing:
The default RNA-seq pipeline of DolphinNext platform was used for data processing https://dolphinnext.umassmed.edu/
RSEM v1.3.1 was used to align RNA-Seq reads to reference transcripts hg19 and estimates gene and isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

extract_protocol:
RNA was extracted using TriPure TRIzol reagent. Chloroform was added in a 1:5 ratio by volume and phase separation was performed. The RNA-containing layer was mixed with an equal volume of 100% isopropanol and incubated overnight at -20 °C for precipitation. RNA was pelleted and washed with 80% ethanol and resuspended in nuclease-free water.
Library preparation was performed using Illumina TruSeq Stranded mRNA Low-Throughput Sample Prep Kit (Cat# 20020594) according to manufacturer’s instruction.

value: subcutaneous white adipose tissue

value: primary adipose-tissue derived mesenchymal progenitors

value: Progenitors

value: 7-day adipogenic induction

tag: population

value: LowDensity


title: CKO1

description:
primary chondrocyte
CKO1


title: Aged_nphx_1128


title: HC_BC000043_SNDA_3_rep1

value: SNDA

tag: batch

tag: replicate


title: High Density Layer

tag: cell line

value: HighDensity


title: HC_BC000042_SNDA_3_rep1


title: Aged_nphx_1127

tag: strain


title: WT3

description:
primary chondrocyte
WT3

source_name: vertebral growth plate, WT, day7

tag: genotype

value: WT


title: WT2

description:
primary chondrocyte
WT2


title: Lung, Heterozygous, Replicate 1

description:
mouse_gene_exp.diff
CHUP-hete-KO-comparison.xlsx
Mouse_Het_1

value: Lung


title: HC_BC000042_TCPY_11_rep1

value: TCPY


title: nc-YY1 M2 macrophages CM treated LNCaP

city: Nanjing

first: Bin

last: Xu

address: Dingjiaqiao 87

institute: Southeast University

data_processing:
StringTie v2.1.0 and Ballgown
Gene expression caculated with Ballgown and gene level higher than FPKM>= 0.5 was included.
Differentially expressed genes were screened by setting the threshold as 1.5 times the difference, p<=0.05 and the mean intra-group FPKM > =0.5.
Read count extraction and normalization were performed using StringTie
Assembly: mm10
Supplementary files format and content: Excel files including gene expression and differentially expressed genes in each compared samples

source_name: LNCaP

growth_protocol: RPMI Medium1640, 10% fetal bovine serum,  1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted by the RNA extraction kit (Takara Kusatsu, Shiga, Japan) according to the manufacturer’s protocol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), RiboZero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre, an Illumina Company) and KAPA Stranded RNA-Seq Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: LNCaP

value: Human prostate cancer cells

tag: treatment

value: nc-YY1 M2 macrophages CM cocultured

tag: time

value: Day 0


title: oe-YY1 M2 macrophages CM treated LNCaP

value: oe-YY1 M2 macrophages CM cocultured


title: WT1

description:
primary chondrocyte
WT1

tag: tissue

value: vertebral growth plate

value: chondrocyte

value: postnatal day7


title: HC_BC000041_SNDA_3_rep1

value: HC


title: M2, Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: hg19

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. 10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit. Sequencing was carried out by running 2×150 cycles on Illumina NovaSeq 6000 according to the manufacturer’s instructions.

value: M2 macrophages

tag: chip antibody


title: Aged_nphx_1124

value: FACS sorted


title: THP-1, Input

value: Human monocytes


title: HC_BC000040_SNDA_3_rep1

value: SNDA


title: HC_BC000040_TCPY_11_rep1


title: M2, H3K27ac, CST

value: H3K27ac (CST, D5E4)


title: Day4_creAF10_DMSO_rep2

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Reads were processed with the FASTX-toolkit: fastq_quality_trimmer (-Q33 -t 28 -l 20), fastx_clipper (-Q33 -a adapter_sequence), and fastx_trimmer (-Q33 -f 11).
Reads were aligned to mm9 with RSEM: rsem-calculate-expression -bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28
Differentially expressed (DE) genes were called with "expected count" output from RSEM using EBSeq in R: MedianNorm, 5 iterations, target FDR = 0.05, and posterior probability of being DE (PPDE) > 0.95. Genes with 2-fold or greater posterior FC (PostFC) relative to the control sample were considered DE.
Relative expression was assessed with the "TPM" output from RSEM
Assembly: mm9
Supplementary files format and content: tab-delimited text files include expected count, TPM, and FPKM values for each sample

source_name: Mouse embryonic fibroblast

growth_protocol: MEFs were maintained in MEF media (DMEM, 10% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, and 2-Mercaptoethanol - 4 μl/500ml) and reprogramming cells were grown in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol - 4 μl/525ml, and leukemia inhibitory factor) on plates coated with 0.1% porcine gelatin and DR4 feeder MEFs. All cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested in TRIzol and extracted with chloroform. The aqueous phase was isolated after spinning the samples at 21xg for 15 min at 4°C. 0.53 volumes of ethanol was added, mixed, and spun through Qiagen RNeasy column at 21xg for 30 seconds. DNA was digested on the column with 10 μL RNAse free DNase mixed with 70 μL RDD buffer (Qiagen, 79254) for 30 min at room temperature. The RNA was washed with 500 μL of buffer RW1 and RPE, each. RNA was eluted with 30 μL of water. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq RNA Sample Prep Kit V2 (Illumina, RS-122-2002) following the manufacturer’s instructions.

treatment_protocol: Cells were infected with Cre recombinase (Ad5-CMV-Cre) and empty control (Ad5-CMV-Empty) purchased from the Vector Development Lab (Baylor College of Medicine) to delete AF10. 2.4e9 pfu of virus was resuspended in 5 mL of serum-free DMEM and added to 1-2 million MEFs in a 10-cm dish. Virus containing media was removed after 1 hour and replaced with MEF media. Reprogramming was initiated 2 days post-transduction with with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891) in media containing vehicle (DMSO) control or 5 μM SGC0946 (ApexBio, A4167). Media with fresh doxycycline and drugs was replaced every 48 hours.

value: Mouse embryonic fibroblast

value: Conditional AF10

value: Day 4 reprogramming

value: AF10 -/-, OSKM, rtTA

value: CRE, DMSO, dox


title: Day4_creAF10_SGC_rep1

value: CRE, SGC0946, dox


title: Aged_nphx_1122


title: M2, YY1, CST

value: YY1 (CST, D5D9Z)


title: Day4_creAF10_DMSO_rep1


title: Aged_nphx_1121


title: THP-1, H3K27ac, CST


title: Day4_fl_SGC_rep2

value: AF10 fl/fl, OSKM, rtTA

value: Control, SGC0946, dox


title: Aged_nphx_1120


title: Aged_nphx_1126


title: HC_BC000037_SNDA_3_rep1

city: Boston

first: Xianjun

institute: Brigham and Women's Hospital


title: THP-1, YY1, CST


title: Aged_nphx_1119

city: Daejeon

first: Myung Jin

institute: Institute for Basic Science


title: Day4_fl_SGC_rep1


title: HC_BC000036_SNDA_3_rep1


title: Day4_creAF10_SGC_rep2


title: Aged_nphx_1125


title: CRC_liver_metastasis_3

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description:
liver metastatic colorectal tumors
3LM

library_source: genomic single cell

data_processing:
All preprocessing steps were performed using Cell Ranger ATAC processing pipeline (version 1.1.0) provided by 10x Genomics.  Basecalls from the sequencer were first converted into the FASTQ format by using the bcl2fastq tool wrapped in “cellranger-atac mkfastq”. Raw sequencing reads were trimmed using cutadapt tool to remove adapter sequences. Clean FASTQ files were aligned to either 1) the human and mouse reference (refdata-cellranger-atac-GRCh38 and mm10, references-2020-A), or 2) human reference (refdata-cellranger-atac-GRCh38, references-2020-A), by using the modified version of BWA aligner with the manufacturer’s recommended settings. Two mapped results including: 1) results from both human and mouse references, reads that from human tumor cells and mouse cells will be aligned, 2) results from human reference, only reads that from human cells will be aligned, were generated by “cellranger-atac count”. The first result was used to evaluate the quality of all cells we sequenced. Only the second result from human cells was used for all downstream analysis (Figure 1C), we applied this method to filter non-human tumor cells. Five “cellranger-atac count” output files including fragments.tsv.gz, peaks.bed, singlecell.csv, filtered_peak_bc_matrix.h5, and fragments.tsv.gz.tbi were used for downstream analysis with Seurat v3.2.2 and its companion package Signac v1.1.0.
Assembly: refdata-cellranger-atac-GRCh38, references-2020-A

source_name: colorectal cancer cells

growth_protocol: Intracecal injection was performed as previously described. Generally, a mini laparotomy incision was made on the lower right abdomen of mice that were anesthetized with avertin. The cecum was found and carefully located out on a sterile field. After injecting CRC cells(5x10^6) into the outer wall tissue layer of the cecum of mice, the cecum was relocated into the abdomen. Mice were sacrificed 7 weeks later and paired tumors from primary site and liver metastasis sites in 3 mice were collected for Sc-ATAC-seq.

extract_protocol:
Nuclei Isolation and all procedures were performed as described in the manufacturer’s protocol (Nuclei Isolation for Single-Cell ATAC-Sequencing, CG000168 Chromium Single-Cell ATAC Reagent Kits User Guide ,10X Genomics).
Following the 10x Genomics single cell ATAC solution, by using Chromium Chip E Single Cell Kit(Product Code 1000086 ) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nucleus in bulk sample are partitioned into nanoliter-scale Gel Beads-in- emulsion (GEMs), a pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus, and libraries are generated(performed by CapitalBio Technology, Beijing). The libraries was sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nucleus.

tag: host mouse strain

value: Balb/c nude

value: liver

value: liver metastatic colorectal tumors


title: Aged_nphx_1118


title: HC_BC000035_SNDA_3_rep1

last: Dong

value: HC


title: Aged_nphx_1123

last: Yang

value: FACS sorted


title: CRC_liver_metastasis_2

description:
liver metastatic colorectal tumors
2LM


title: HC_BC000034_SNDA_5_rep1


title: Aged_nphx_1117


title: HC_BC000039_SNDA_3_rep1


title: HC_BC000033_SNDA_5_rep1


title: MEF_creAF10_rep2

value: CRE


title: Day4_fl_DMSO_rep1

value: Control, DMSO, dox


title: Aged_nphx_1116


title: CRC_liver_metastasis_1

description:
liver metastatic colorectal tumors
1LM


title: HC_BC000038_SNDA_2_rep1

value: SNDA


title: MEF_creAF10_rep1

value: Mouse embryonic fibroblast


title: CRC_primary_3

description:
primary colorectal tumors
3P

value: colon

value: primary colorectal cancer


title: Aged_nphx_1114


title: Aged_nphx_1115


title: HC_BC000031_SNDA_5_rep1


title: Day4_fl_DMSO_rep2

value: Conditional AF10

value: Day 4 reprogramming


title: CRC_primary_1

description:
primary colorectal tumors
1P


title: Aged_nphx_1113


title: HC_BC000030_SNDA_4_rep1


title: TE5 cells, shNUP153, rep2

city: kanazawa city

first: Masaharu

last: Hazawa

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

description:
TE5sh153g2
FPKM_RNAseq_TE5_shNUP153.txt

data_processing:
Paired end fastq files were pseudoaligned to Ensembl (hg19, v82) transcripts using Kallisto.
Transcript level abundances and counts were summarized to gene level using the TxImport bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Reads were aligned to the hg19 genome assembly using Bowtie2 with the default parameters. Only tags that uniquely mapped to the genome were used for further analysis.
Bigwig files were generated using the deepTools bamCoverage function with --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --binSize 1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: bigwig files representing signal normalized to per million reads

growth_protocol: TE5 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin. KYSE150 cells were RPMI-1640 medium supplemented with 5% FBS, 1% Penicillin and Streptomycin.

extract_protocol:
RNA was harvested usingTotal RNAs were extracted with NucleoSpin RNA (MACHERY-NAGEL). Initial RNA quality were checked by electrophoresis and sent to NOVOGENE for sequencing. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using 250-300 bp insert cDNA library following manufacturer's protocols.

treatment_protocol: shRNA were introduced to TE5 cells by lenti-virus infection. After puromycin selection, those cells were further maintained in growth medium for 7 days.

value: Esophageal squamous cell carcinoma

value: NUP153 knockdown

tag: time point

value: Day 7


title: Aged_nphx_1112


title: TE5 cells, shNUP153, rep1

description:
TE5sh153g1
FPKM_RNAseq_TE5_shNUP153.txt


title: H1975 + HCC4210F + Mouse Macrophages

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCm38 (mouse) or GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Human reads were filtered out in the co-culture samples.
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: Genome_build: GRCm38 (mouse) or GRCh38 (human)

growth_protocol: See publication

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

value: NSCLC

tag: co-culture

value: Yes


title: Aged_nphx_1111


title: H1993 + HCC4210F + Mouse Macrophages biol rep 1


title: HC_BC000028_SNDA_3_rep1

address: 60 Fenwood Rd

tag: source sampleid


title: Aged_nphx_1110


title: HC_BC000032_SNDA_3_rep1

tag: source subjectid


title: TE5 cells, shControl, rep2

description:
TE5shCtl2
FPKM_RNAseq_TE5_shNUP153.txt

value: WT


title: H596 + HCC4210F + Mouse Macrophages


title: HC_BC000026_SNDA_3_rep1

tag: disease state


title: H1666 + HCC4210F + Mouse Macrophages biol rep 1

tag: cell type


title: HC_BC000027_SNDA_3_rep1


title: MEF_fl_rep2

value: AF10 fl/fl, OSKM, rtTA

value: Control


title: S4144F

value: Cancer-associated-Fibroblast

value: No


title: MEF_fl_rep1


title: CRC_primary_2

description:
primary colorectal tumors
2P

value: Balb/c nude


title: HC_BC000025_SNDA_5_rep1

value: HC

value: SNDA


title: Aged_nphx_1108

value: FACS sorted


title: Aged_nphx_1109


title: HCC4218F


title: A427 + HCC4210F + Mouse Macrophages biol rep 1


title: HC_BC000024_SNDA_5_rep1


title: Aged_nphx_1107


title: LPS + Mouse Macrophages

source_name: Mouse Macrophage

value: Mouse Macrophage


title: HC_BC000029_SNDA_3_rep1


title: Aged_nphx_1106


title: HCC4215F


title: HC_BC000023_SNDA_5_rep1


title: Aged_nphx_1105


title: HCC4210F


title: IL4 + Mouse Macrophages


title: HC_BC000022_SNDA_5_rep1


title: HCC4209F


title: TE5 cells, shControl, rep1

description:
TE5shCtl1
FPKM_RNAseq_TE5_shNUP153.txt


title: H650 + HCC4210F + Mouse Macrophages


title: Aged_nphx_1104


title: HC_BC000021_SNDA_5_rep1


title: HC_BC000020_SNDA_4_rep1


title: Mouse Macrophages biol rep 3


title: Aged_nphx_1103


title: CD19 CAR-T

city: Beijing

first: Shuai

last: Tong

address: No.10 Yangfangdian Road

institute: Beijing Shijitan Hospitol

description: CD19 CAR-T

data_processing:
Raw data were first processed through custom Perl a scripts. Clean data (clean reads) were read by removing reads containing poly-N with 5′-adapter contaminants, without 3′ adapter or the insert tag, or containing poly-A or -T or -G or -C from raw data, as well as low-quality reads.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs). DESeq2 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
Assembly: ensemble release-80
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: peripheral blood

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were separated from healthy donors by gradient centrifugation

extract_protocol:
Total RNA was extracted from cell using Trizol Reagent (Invitrogen) following the manufacturer’s instructions. The quantity and purity of RNA were measured on a Nanodrop Technologies ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc.). Only samples with the appropriate absorbance measurements (A260/A280 of ~2.0, and A260/A230 of 1.9-2.2) were considered for inclusion in the present study
A total amount of 2 µg total RNA per sample was used as input material for generating the sequencing libraries using NEBNext®Ultra™ RNA Library Prep Kit (#E7530L, NEB, USA) following the manufacturer’s. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: T cells in PBMCs were isolated and stimulated with anti-CD3 and anti-CD28 beads, and then transduced with retrovirus. On day 5, the transduced T cells were subjected to CAR expression detection and then expanded in X-VIVOTM15 serum-free medium which containing 10% GemCellTM Human Serum AB(Gemini Bio) and IL-2. One day 7, the cells were subjected to cytotoxicity assay and in vivo tumor treatment.

value: peripheral blood

value: CD19 CAR transduced T cell

value: untreated


title: OTULIN HI patient 4

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Sequenced reads were processed using CellRanger 3.1.0 to generate gene count matrix
Gene count data were further processed with R ver.4 to perform batch correction, clustering, cell type annotation, and differential expression analyses.
Assembly: GRCh38
Supplementary files format and content: Gene-cell count matrix generated via CellRanger

source_name: PBMC

extract_protocol:
Thawed PBMCs were washed and captured via 10X Genomics Chromium. Reverse transcription was performed per manufacturer's guideline.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Single cell RNA sequencing, 3' gene expression

tag: cells

value: Blood


title: Aged_nphx_1101


title: HC_BC000019_SNDA_3_rep1

tag: batch


title: HC_BC000018_SNDA_5_rep1

tag: replicate


title: iOvCa147 DYRK1A knockout final condition (reattached spheroid) replicate 3 RNA-seq

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

country: Canada

description:
RNA-seq sample
iOvCa147_WTSph_vs_DYRK1AKOSph_RNAseq.csv

data_processing:
Raw read files (FASTQ) from GO-CRISPR screen were anlayzed using TRACS 1.1.3
TRACS 1.1.3 automatically does the following: FASTQ files are trimmed with Cutadapt 1.15; the reference sgRNA CSV file is converted to FASTA format; A Bowtie2 index is constructed using Bowtie 2.3.4.1; the initial plasmid library (L0) is aligned to the index and a BAM file is generated using Bowtie 2.3.4.1 and Samtools 1.7; Read counts are generated using MAGeCK 0.5.6; TRACS then runs the TRACS algorithm to determine gene essentiality.
Raw read files (FASTQ) from RNA-seq experiments were mapped using STAR 2.6.1 to get read counts. Then, differential expression was analyzed using BEAVR 1.0.9
Genome_build: Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary_files_format_and_content: For GO-CRISPR, CSV files containing Enrichment Scores (ES) and Enrichment Ratios (ER) for each gene
Supplementary_files_format_and_content: For RNA-seq, CSV files containing transcript/gene read counts and metadata (sample info)

source_name: High-grade serous ovarian cancer

extract_protocol:
Cells were harvested and total RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB #T2010S). Samples were submitted to the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada) for quantification using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and quality control analysis using Agilent 2100 Bioanalyzer (Agilent Technologies #G2939BA) and RNA 6000 Nano Kit (Agilent Technologies #5067-1511). Ribosomal RNA removal and library preparation was performed using ScriptSeq Complete Gold Kit (Illumina #BEP1206). High-throughput sequencing was performed on an Illumina NextSeq 500 platform (mid-output, 150-cyclekit).
Ribosomal RNA removal and library preparation was performed using ScriptSeq Complete Gold Kit (Illumina #BEP1206). High-throughput sequencing was performed on an Illumina NextSeq 500 platform (mid-output, 150-cyclekit). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample.

value: iOvCa147 DYRK1A-/-

tag: cas9 status

tag: go-crispr time point

tag: plate condition

value: Reattached (Ultra low attachment)


title: iOvCa147 DYRK1A knockout final condition (reattached spheroid) replicate 2 RNA-seq


title: iOvCa147 DYRK1A knockout final condition (reattached spheroid) replicate 1 RNA-seq


title: iOvCa147 DYRK1A knockout adherent condition replicate 3 RNA-seq

value: Adherent


title: Aged_nphx_1099

tag: strain


title: iOvCa147 DYRK1A knockout adherent condition replicate 2 RNA-seq


title: HC_BC000017_SNDA_5_rep1


title: OTULIN HI patient 3

tag: genotype


title: Aged_nphx_1100


title: OTULIN HI patient 2


title: Aged_nphx_1102


title: HC_BC000016_SNDA_5_rep1


title: OTULIN HI patient 1


title: iOvCa147 DYRK1A knockout adherent condition replicate 1 RNA-seq


title: HC_BC000015_SNDA_5_rep1


title: Healthy control 4

value: WT/WT


title: Aged_nphx_1098


title: iOvCa147 final condition (reattached spheroid) 3 RNA-seq

description:
RNA-seq sample
iOvCa147_WTAdh_vs_WTSph_RNAseq.csv


title: NMN treated CD19 CAR-T

description: NMN treated CD19 CAR-T

tag: tissue

tag: treatment

value: NMN


title: Aged_nphx_1097


title: HC_BC000014_SNDA_4_rep1


title: Healthy control 3


title: iOvCa147 final condition (reattached spheroid) 2 RNA-seq


title: Aged_nphx_1096


title: Healthy control 2


title: HC_BC000013_SNDA_4_rep1


title: iOvCa147 final condition (reattached spheroid) 1 RNA-seq


title: HC_BC000013_TCPY_11_rep1

source_name: Temporal cortex pyramidal neuron

value: TCPY


title: iOvCa147 adherent condition replicate 3 RNA-seq


title: Aged_nphx_1094


title: Aged_nphx_1095


title: HC_BC000012_SNDA_3_rep1


title: iOvCa147 adherent condition replicate 2 RNA-seq


title: HC_BC000012_TCPY_11_rep1


title: Aged_nphx_1093


title: iOvCa147 adherent condition replicate 1 RNA-seq

extract_protocol:
Cells were harvested and total RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB #T2010S). Samples were submitted to the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada) for quantification using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and quality control analysis using Agilent 2100 Bioanalyzer (Agilent Technologies #G2939BA) and RNA 6000 Nano Kit (Agilent Technologies #5067-1511).
Ribosomal RNA removal and library preparation was performed using ScriptSeq Complete Gold Kit (Illumina #BEP1206). High-throughput sequencing was performed on an Illumina NextSeq 500 platform (mid-output, 150-cyclekit). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample.


title: PC3_Control shRNA

city: Shanghai

first: Wandong

last: Yu

address: No. 801, Heqing Road, Minhang District, Shanghai

institute: The Fifth People’s Hospital of Shanghai, Fudan University

data_processing:
CASAVA used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 in the human genome using HISAT2
The gene transcript expression count was performed by Hiseq RNA-seq to generate a matrix of transcripts per kilobase of exon model per million mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: PC3 cells

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruseqTM RNA sample prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: HC_BC000011_SNDA_3_rep1


title: Aged_nphx_1092


title: 22RV1_DDX52 shRNA

source_name: 22RV1 cells


title: TOV1946 Cas9-negative final (reattached spheroid) condition replicate 3

description:
GO-CRISPR screen sample
TOV1946_TRACS.csv

data_processing:
Library strategy: GO-CRISPR
Raw read files (FASTQ) from GO-CRISPR screen were anlayzed using TRACS 1.1.3
TRACS 1.1.3 automatically does the following: FASTQ files are trimmed with Cutadapt 1.15; the reference sgRNA CSV file is converted to FASTA format; A Bowtie2 index is constructed using Bowtie 2.3.4.1; the initial plasmid library (L0) is aligned to the index and a BAM file is generated using Bowtie 2.3.4.1 and Samtools 1.7; Read counts are generated using MAGeCK 0.5.6; TRACS then runs the TRACS algorithm to determine gene essentiality.
Raw read files (FASTQ) from RNA-seq experiments were mapped using STAR 2.6.1 to get read counts. Then, differential expression was analyzed using BEAVR 1.0.9
Genome_build: Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary_files_format_and_content: For GO-CRISPR, CSV files containing Enrichment Scores (ES) and Enrichment Ratios (ER) for each gene
Supplementary_files_format_and_content: For RNA-seq, CSV files containing transcript/gene read counts and metadata (sample info)

extract_protocol:
Cells were harvested and genomic DNA was extracted using QIAmp Blood Maxi Kits (QIAGEN #51194). Genomic encoded sgRNA sequences were PCR amplified with two rounds of PCR to increase abundance of the initial sgRNA population and insert sample barcodes necessary for identification of condition and replicate number. PCR products were gel purified, quantitated by Qubit (Invitrogen) and pooled prior to high throughput sequencing.
Pooled preparation containing all barcoded samples were sequenced using an Illumina NextSeq 550 75-cycle high output kit (#20024906). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample: one initial pooled sgRNA library file (L0), 3x Cas9-positive initial condition replicates (T0), 3x Cas9-positive final condition replicates (Tf), 3x Cas9-negative initial condition replicates (T0), 3x Cas9-negative final condition replicates (Tf).

value: Cas9 negative

value: Tf


title: HC_BC000011_TCPY_11_rep1


title: Aged_nphx_1091


title: 22RV1_Control shRNA


title: TOV1946 Cas9-negative final (reattached spheroid) condition replicate 2


title: Aged_nphx_1090


title: HC_BC000010_SNDA_3_rep1

source_name: Substantial nigra dopamine neuron


title: Aged_nphx_1089


title: Syn-HighFK506-Rep3

city: Chicago

first: Marc

middle: L

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC.  Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.  The cleaned reads were aligned to rat genome assembly rn6 using Tophat.  Gene counts were quantified from BAM files using htseq-counts.
Assembly: rn6
Supplementary files format and content: htseq counts tables provide normalized count estimates of uniquely mapped RNAseq reads

organism: Rattus norvegicus

source_name: brain, cerebral cortex

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to supplied protocol.
Llibraries were prepared from 150 ng RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, according to supplied protocol.

value: brain, cerebral cortex

value: primary glutamatergic  neurons and astrocytes

value: Alpha-Synuclein A53T


title: TOV1946 Cas9-negative final (reattached spheroid) condition replicate 1


title: HC_BC000009_SNDA_2_rep1

value: HC

value: SNDA


title: Healthy control 1


title: PC3_DDX52 shRNA


title: Aged_nphx_1088

value: FACS sorted


title: TOV1946 Cas9-negative initial (adherent) condition replicate 3


title: Syn-HighFK506-Rep2


title: Syn-HighFK506-Rep1


title: HC_BC000008_SNDA_4_rep1


title: Aged_nphx_1087


title: Syn-LowFK506-Rep3


title: Syn-LowFK506-Rep2


title: TOV1946 Cas9-negative initial (adherent) condition replicate 1


title: TOV1946 Cas9-positive final (reattached spheroid) condition replicate 3

value: Cas9 positive


title: HC_BC000007_SNDA_4_rep1


title: HC_BC000008_TCPY_11_rep1


title: Aged_nphx_1085


title: Syn-DMSO-Rep2

value: DMSO


title: Aged_nphx_1084


title: TOV1946 Cas9-positive final (reattached spheroid) condition replicate 1


title: Syn-LowFK506-Rep1


title: TOV1946 Cas9-positive final (reattached spheroid) condition replicate 2


title: Aged_nphx_1083


title: HC_BC000007_TCPY_11_rep1


title: Aged_nphx_1082


title: Syn-DMSO-Rep1


title: TOV1946 Cas9-positive initial (adherent) condition replicate 3


title: Control-HighFK506-Rep3

value: Empty Vector


title: HC_BC000006_SNDA_4_rep1


title: HC_BC000006_TCPY_11_rep1


title: TOV1946 Cas9-negative initial (adherent) condition replicate 2


title: HC_BC000005_SNDA_4_rep1


title: Aged_nphx_1081


title: Control-HighFK506-Rep2


title: HC_BC000009_TCPY_11_rep1


title: Aged_nphx_1086


title: Aged_nphx_1080


title: HC_BC000005_TCPY_11_rep1


title: TOV1946 Cas9-positive initial (adherent) condition replicate 2


title: TOV1946 Cas9-positive initial (adherent) condition replicate 1


title: Aged_nphx_1079


title: Aged_nphx_1078


title: Control-LowFK506-Rep3


title: HC_BC000004_TCPY_11_rep1


title: Control-HighFK506-Rep1


title: HC_BC000003_MCPY_4_rep1

source_name: Motor cortex pyramidal neuron

value: MCPY


title: OVCAR8 Cas9-negative final (reattached spheroid) condition replicate 3

description:
GO-CRISPR screen sample
OVCAR8_TRACS.csv

value: Reattached (Ultra low attachment)


title: Control-LowFK506-Rep2


title: HC_BC000002_MCPY_4_rep1


title: OVCAR8 Cas9-negative final (reattached spheroid) condition replicate 1


title: OVCAR8 Cas9-negative initial (adherent) condition replicate 3

value: Adherent


title: Control-LowFK506-Rep1


title: Aged_nphx_1077


title: Aged_nphx_1076


title: OVCAR8 Cas9-negative initial (adherent) condition replicate 2