title: MFI144

status: Public on Nov 01 2019

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description:
MFI144
Single-cell RNA-Seq
3' end of mRNA

data_processing:
The paired-end reads Smart-seq2 data was processed using the standard pipeline of Drop-seq_tools-2.0.0 (http://mccarrolllab.com/dropseq/) with modifications.
For read2, bases 1 to 8 were tagged with cell-barcode “XC,”and bases 8 to 16 were tagged with UMI “XM”.
Read1 was trimmed at the 5' end to remove adaptor and TSO sequence, and the 3' end was trimmed to remove poly(A) sequences of length 6 or more and then aligned to Macaca_fascicularis_5.0 genome reference using STAR aligner.
Gene expression matrix for each cell was then generated with DigitalExpression command.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: csv (Comma Separate Values) files include UMI (unique molecular identifiers ) count values for each cell

organism: Macaca fascicularis

source_name: Blastocyst

growth_protocol: Firest of all, choose the high quality blastocysts with the blastocoel occupying three-quarters or more of the embryos for culture. Remove the zona pellucida by drops of preheated 0.5% protease, and  neutralize protease by adding CMRL1066 containing 10% FBS. Culture blastocysts with 600 ml IVC day0 medium (CMRI 1066 containing 10%FBS with supplementaries N2, B27, Glumax, sodium pyruvate and penicillin as supplementaries) in 4-well plate coated with matrigel (one blastocyst per one chamber) at 37°C in a humidified atmosphere of 5% CO2 and 95% air. On the first two days, the medium was unchanged. From IVC day2 after the embryos firmly attached, the medium should be changed every day by increasing concentration of serum. Collect the embryos in different culture stage for further analysis.

extract_protocol:
Dissect the implantation site of the embryos on Matrigel and remove the extra-embryonic cells under stereo microscope remaining the bi-laminar disc-like structure visualized clearly. Put the embryonic fragment in drops with 1 X TrypLE for 15 min at 37°C and pipette the degested tissue into single cells by repeated mouth pipetting. Then collect the cells into 500 μl CRML 1066 containing 10% FBS to terminate the enzymatic reaction and centragate to collect cells at 300 g for 5 min at room temperature. Resuspend the cell pellet with 0.1% BSA/PBS and store at 4°C. Pick single cells into 2.5 µl lysis buffer in 200 µl PCR tubes.
The linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

treatment_protocol: Matrigel were coated on dishes before the culture.

tag: condition

value: in vitro

value: Embryo

tag: developmental stage

value: day 14


title: MFI142

type: SRA

city: Beijing

country: China

description:
MFI142
Single-cell RNA-Seq
3' end of mRNA

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: MFI164

description:
MFI164
Single-cell RNA-Seq
3' end of mRNA

value: day 16


title: MFI161

description:
MFI161
Single-cell RNA-Seq
3' end of mRNA


title: MFI143

description:
MFI143
Single-cell RNA-Seq
3' end of mRNA


title: MFI173

description:
MFI173
Single-cell RNA-Seq
3' end of mRNA

value: day 17


title: MFI162

description:
MFI162
Single-cell RNA-Seq
3' end of mRNA


title: MFI163

description:
MFI163
Single-cell RNA-Seq
3' end of mRNA


title: TCCSUPPi_R3

status: Public on Nov 25 2019

city: Serdang

first: Abhimanyu

last: Veerakumarasivam

state: Selangor

address: Jalan Puchong

department: Biomedical Science

country: Malaysia

institute: Universiti Putra Malaysia

description:
cDNA
processed data file: txicounts_TCCSUP.csv
processed data file: diffexpr-results_TCCSUP.csv

data_processing:
Quality control of the sequencing reads was assessed using FastQC and MultiQC analyses.
All ribosomal RNA (rRNA) sequences were filtered out using bbduk and Greengenes rRNA db.
Quality reads were mapped to a human reference genome (hg19) using HISAT2 aligner. Reads that mapped to the reference genome was used to quantify the transcriptome assembly using StringTie (Pertea et al., 2015). Quantification of the transcripts abundance was carried out using Salmon’s quasimapping strategy which count the number of reads that map to a given transcript (Patro et al., 2017) calculated in fragments per kilobase of gene model per million mapped (FPKM) of the coding genes in each samples.
Differential transcripts analysis (DEGs) was carried out using DESeq2 package (Love et al., 2014) via tximport in R environment/
Genome_build: human reference genome (hg19, GRCh37)
Supplementary_files_format_and_content: txicountsTCCSUP.csv: Comma-separated values file includes FPKM values for each sample.
Supplementary_files_format_and_content: txicounts_EJ28.csv: Comma-separated values file includes FPKM values for each sample.
Supplementary_files_format_and_content: diffexpr-results_TCCSUP.csv: Comma-separated values file includes differential expression results.
Supplementary_files_format_and_content: diffexpr-results_EJ28P.csv: Comma-separated values file includes differential expression results.

organism: Homo sapiens

source_name: Bladder cancer cells

growth_protocol: Cells were grown in a monolayer in culture flasks with normal complete growth media (RPMI1640 and MEM alpha) placed in a humidified chamber at 37°C in 5% CO2/air until confluence.

extract_protocol:
Total RNA was extracted from each of the persistently infected cells and the cell lines without NDV infection (negative control) using Qiagen RNeasy micro kit (Qiagen, Germany) following the manufacturer’s protocol. RNA quality and RNA integrity number (RIN) were assessed by spectrophotometer (NanoDrop 2000) and Bioanalyzer 21000 expert software system (Agilent Technologies, Santa Clara, CA, USA). RNA Integrity Number (RIN) were of good quality being in the range between 8.0 to 9.0.
Transcriptome library was constructed based on TruSeq Stranded mRNA library preparation kit v2 protocols (Illumina, San Diego, CA) using a total of 3 μg of RNA per sample.

treatment_protocol: EJ28 and TCCSUP cells were infected with NDV AF2240 at MOI of 1 and 0.1, respectively. Cells were incubated at 37oC and rocked at every 15 minutes interval for an hour to allow for viral absorption. Majority of the cells died leaving small subpopulation of cells which were re-infected three more times. These cells were named EJ28Pi and TCCSUPPi cell lines respectively.

tag: cell line

value: TCCSUP

tag: cell type

value: Bladder cancer cells

tag: infection

value: Newcastle disease virus


title: MFI133

description:
MFI133
Single-cell RNA-Seq
3' end of mRNA

value: day 13


title: MFI141

description:
MFI141
Single-cell RNA-Seq
3' end of mRNA


title: June28R4High2

status: Public on Nov 04 2019

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

description:
Reduced, biological replicate 2
Sample_70810

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (WS220) (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using WS220 as the reference genome sequence. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff2. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: WS220
Supplementary_files_format_and_content: raw counts, txt

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - reduced biol.replicate 2

growth_protocol: Worms were grown on standard NGM plates at 20oC

extract_protocol:
Worms were grounded in Trizol reagent (Life Technologies) with sea sand and pestle. After filtering of the sand, samples were vigorously shaken with chloroform, allowed to stand for 3 minutes at room temperature, and then centrifuged at 16,000 g at 4°C. The aqueous phase was then collected and RNA was purified using QIAGEN RNeasy RNA extraction columns as per manufacturers’ recommendations.
Total RNA was assessed for quality using the TapeStation (Agilent). Samples were prepared using the Illumina TruSeq Stranded Total RNA Library Prep kit (Illumina). 100 ng of total RNA was rRNA-depleted using Ribo-Gone (Takara Bio USA). The rRNA-depleted RNA was then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The products were purified and enriched by PCR (15 cycles) to create the final cDNA library. The 3’ prime ends of the cDNA were adenylated and ligated to adapters, including a 6-nt barcode unique for each sample. Final libraries were checked for quality and quantity by TapeStation and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems, Wilmington MA).
The samples were pooled, clustered on an Illumina cBot and sequenced on one lane of an Illumina HiSeq4000 flow cell, as paired-end 50 nt reads. The quality of the raw reads data for each sample (e.g. low-quality scores, over-represented sequences, inappropriate GC content) was checked using FastQC (version v0.11.3).

treatment_protocol: Age - synchronized eggs were extracted using alkaline hypochlorite solution and allowed to hatch by overnight incubation in M9 medium during gentle shaking. Newly hatched, arrested L1 larvae were transferred onto standard nematode growth medium (NGM) plates seeded with live E. coli OP50.

tag: redox

value: reduced

tag: source


title: MFI124

description:
MFI124
Single-cell RNA-Seq
3' end of mRNA

value: day 12


title: MFI112

description:
MFI112
Single-cell RNA-Seq
3' end of mRNA

value: day 11


title: MFI123

description:
MFI123
Single-cell RNA-Seq
3' end of mRNA


title: MFI122

description:
MFI122
Single-cell RNA-Seq
3' end of mRNA


title: MFI125

description:
MFI125
Single-cell RNA-Seq
3' end of mRNA


title: MFI111

description:
MFI111
Single-cell RNA-Seq
3' end of mRNA


title: MFI172

description:
MFI172
Single-cell RNA-Seq
3' end of mRNA

data_processing:
The paired-end reads Smart-seq2 data was processed using the standard pipeline of Drop-seq_tools-2.0.0 (http://mccarrolllab.com/dropseq/) with modifications.
For read2, bases 1 to 8 were tagged with cell-barcode “XC”, and bases 8 to 16 were tagged with UMI “XM”.
Read1 was trimmed at the 5' end to remove adaptor and TSO sequence, and the 3' end was trimmed to remove poly(A) sequences of length 6 or more and then aligned to Macaca_fascicularis_5.0 genome reference using STAR aligner.
Gene expression matrix for each cell was then generated with DigitalExpression command.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: MF438.csv: Comma Separated Values file includes UMI (unique molecular identifiers) count values for each cell.

growth_protocol: First of all, choose the high quality blastocysts with the blastocoel occupying three-quarters or more of the embryos for culture. Remove the zona pellucida by drops of preheated 0.5% protease, and neutralize protease by adding CMRL1066 containing 10% FBS. Culture blastocysts with 600 ml IVC day0 medium (CMRI 1066 containing 10% FBS with supplementaries N2, B27, Glumax, sodium pyruvate and penicillin as supplementaries) in 4-well plate coated with matrigel (one blastocyst per one chamber) at 37°C in a humidified atmosphere of 5% CO2 and 95% air. On the first two days, the medium was unchanged. From IVC day2 after the embryos firmly attached, the medium should be changed every day by increasing concentration of serum. Collect the embryos in different culture stage for further analysis.

extract_protocol:
Dissect the implantation site of the embryos on Matrigel and remove the extra-embryonic cells under stereo microscope remaining the bi-laminar disc-like structure visualized clearly. Put the embryonic fragment in drops with 1 X TrypLE for 15 min at 37°C and pipette the digested tissue into single cells by repeated mouth pipetting. Then collect the cells into 500 μl CRML 1066 containing 10% FBS to terminate the enzymatic reaction and centrifuge to collect cells at 300 g for 5 min at room temperature. Resuspend the cell pellet with 0.1% BSA/PBS and store at 4°C. Pick single cells into 2.5 µl lysis buffer in 200 µl PCR tubes.
The linearized RNA molecules were released in a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with biotinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator. Enrich the cDNA fragments by Dynabeads® MyOneTM Streptavidin C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

tag: culture stage

value: Day 17


title: Ad-ctrl rep3

status: Public on Nov 02 2019

city: shanghai

first: chao

last: sun

state: shanghai

address: 320 Yueyang Road, Xuhui District, Shanghai, China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy ofSciences

description:
Ad-Ctrl-3
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx

data_processing:
RNA were pooled for deep sequencing by using Illumina Hiseq Xten (2 × 150) platforms at the CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China. Raw read qualities were evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.5). Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed. Trimmed reads were then mapped with the Hisat2 algorithm (Hisat2 v2.1.0) to target sequences. Gene expression levels were quantified by the software package HTSeq (v0.6.1p1).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA-SEQ_Ad_Ctrl_vs_378.xlsx: Excel file includes RPKM values for each Sample.

organism: Mus musculus

source_name: liver

growth_protocol: Eight-week-old male mice were injected with adenovirus 1x10^9 PFU, and liver tissue was collected two weeks later.

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

treatment_protocol: The corresponding adenovirus was injected into the tail vein, and the liver was taken two weeks later.

tag: strain/background

tag: genotype/variation

value: Control

tag: Sex

value: Male

tag: age

value: 10 weeks

value: Liver


title: MFI121

description:
MFI121
Single-cell RNA-Seq
3' end of mRNA

value: in vitro

value: Day 12


title: MFI171

description:
MFI171
Single-cell RNA-Seq
3' end of mRNA

value: Embryo


title: Peripheral-12mm-cd31-enriched-donor-7

status: Public on Oct 30 2019

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

description: Sample 14

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
Experiment 1:  Relates to donors 1-3 (Samples 1-6).  The six samples were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.  Cells were then filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 6000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). Aggregated reads were normalized and clustered in Seurat (v3.0.2) with the following commands: seurat_obj <- NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000); seurat_obj <- FindVariableFeatures(seurat_obj, selection.method = "mvp", nfeatures = 2000); all.genes <- rownames(seurat_obj); seurat_obj <- ScaleData(seurat_obj, features = all.genes); seurat_obj <- RunPCA(Seurat_obj, features = VariableFeatures(object = seurat_obj)); seurat_obj <- FindNeighbors(seurat_obj, dims = 1:14); seurat_obj <- FindClusters(seurat_obj, resolution = 0.175).
Experiment 2:   Relates to donors 4-7 (Samples 7-14).  Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). For each of the eight libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: donor_x_region <- NormalizeData(donor_x_region, normalization.method = "LogNormalize", scale.factor = 10000); donor_x_region <- FindVariableFeatures(donor_x_region, selection.method = "vst", nfeatures = 2000).  Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands: CD31.anchors <- FindIntegrationAnchors(object.list = c(donor_4_macula, donor_5_macula, donor_6_macula, donor_7_macula, donor_4_peripheral, donoro_5_peripehral, donor_6_peripheral, donor_7_peripheral), dims=1:20); CD31.combined <- IntegrateData(anchorset = CD31.anchors, dims = 1:20).  Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE); CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE); CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindClusters(CD31.combined, resolution = 0.5).
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from GetAssayData(object = seurat_object) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: RPE-choroid

extract_protocol:
In experiment 2, a 12-mm macular centered and a 12-mm peripheral punch of RPE/choroid from the inferotemporal region were acquired from four human donors (Donors 4-7). After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples from donors 1-3 were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Cryopreserved cells from donors 4-7 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) of the CD31+ cell fraction. The positive cell fraction was passed two times through a 40 mm filter to remove aggregates before immediate single cell capturing and barcoding as described above. Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: enrichment

tag: donor

value: RPE-choroid

tag: location

value: periphery

tag: punch-size


title: Peripheral-12mm-cd31-enriched-donor-6

description: Sample 13


title: THattP40_15

status: Public on Oct 23 2019

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Genetics

country: United Kingdom

institute: University of Cambridge

description:
attP40_2
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt

data_processing:
Fastq reads were aligned using tophat (v2.1.1) with Bowtie (version: 2.3.4.0) using the default parameters.
Gene counts tables across samples were created with Rsubread (1.22.3) using dmel_r6.20.gtf and options GTF.featureType="exon" and GTF.attrType="gene_id" and default parameters.
Read counts per experiment (sgg-A and sgg-B were processed independent of each other) were imported into edgeR (3.14.0) and filtered using the filterByExpr function with the default parameters (10397 genes were retained for sggA and 10693 genes for sggB).
The data was then normalised in limma (3.28.21) using limma-voom. Significant genes were identified fitting a linear model (lmFit) and empirical Bayes method (eBayes). Genes were considered significant differential expressed with fdr <= 0.05 and logFC >= |0.7|.
Genome_build: FlyBase dmel_r6.20
Supplementary_files_format_and_content: GeneCounts.txt is a tab-delimited file containing the raw counts created by Rsubread per sample (columns) for each gene (row).
Supplementary_files_format_and_content: The *_RNAseq_limma-voom_result_master.txt files contain the filtered raw counts, normalised logCPM and the limma stats columns.

organism: Drosophila melanogaster

source_name: control for sgg-A null

growth_protocol: 10-15hr embryos from a homozygous sggisoA stock and a control line were collected and processed for RNA-seq. In the case of sggisoB, non-fluorescent embryos from a cross between sggisoB/Bal X Bal/Y were collected.

extract_protocol:
Tissue was homogenised in 300 µL TRIzol with a motorised pellet pestle for 30 seconds. The sample volume was then increased to 1 mL, then 200 µL of Chloroform was added and vortexed. Samples were centrifuged at max speed for 15 minutes at room temperature and the upper phase transferred to a new 1.5 mL tube. The RNA was then precipitated with 0.8 volumes of Isopropanol and incubated at -20°C for 2 hours. The samples were then centrifuged at 4°C at maximum speed for 30 minutes to pellet the RNA. The pellet was then washed with 1 mL 70% ethanol and centrifuged cold for another 5 minutes. After complete removal of the ethanol the RNA was dried for 5 minutes and re-suspended in 20 µL DEPC-treated water. The concentration of the samples were measured using the Qubit RNA HS Assay Kit and sample quality assess with the Bioanalyzer and or 1% agarose gel.
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. For each sample 100ng total RNA were processed with the NEBNext Poly(A) mRNA Magnetic Isolation Module. For all reactions half reactions/volumes were used throughout the protocol, with exception for the AMPure bead cleanup step where washes were performed used the standard 200 µL 80% fresh Ethanol. Samples were barcoded and PCR amplification were performed for 12 cycles. After Bioanalyzer quality control equal amount of samples were pooled and submitted for Illumina single-end sequencing.

treatment_protocol: Embryos frozen in liquid nitrogen and stored at minus 80 degree Celsius until processing.

tag: fly stock

value: progenitor strain

value: Control for sgg-A null

value: Embryos

value: Whole body


title: THattP40_16

description:
attP40_3
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt

tag: developmental stage


title: Peripheral-12mm-cd31-enriched-donor-4

description: Sample 11

tag: tissue


title: Peripheral-12mm-cd31-enriched-donor-5

description: Sample 12


title: control_nF_4

description:
attP40_7
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt

source_name: control for sgg-B null

value: progenitor/FM7 GFP X FM7 GFP/Y

value: Control for sgg-B null


title: BsggNull_nF_3

description:
sgg_isoB_zygotic_null_3
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt

source_name: sgg-B null

value: sggisoB/FM7 GFP X FM7 GFP/Y

value: sgg-B null


title: control_nF_1

description:
attP40_4
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: MFI132

description:
MFI132
Single-cell RNA-Seq
3' end of mRNA

tag: condition

value: Day 13


title: BsggNull_nF_4

description:
sgg_isoB_zygotic_null_4
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: THattP40_13

description:
attP40_1
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: B2

status: Public on Oct 09 2019

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

description: QN Orange scallop

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4
HTSeq v0.9.1 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.
Supplementary_files_format_and_content: tab-delimited text files include gene expression count for each Sample

organism: Mimachlamys nobilis

source_name: adductor muscle

extract_protocol:
Adductor muscle tissues were dissected and stored in liquid nitrogen individually.Total RNA from each tank was isolated by TRIzol reagent (Invitrogen, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: with RNAi

value: one year old


title: B1

description: QN Orange scallop


title: BsggNull_nF_1

description:
sgg_isoB_zygotic_null_1
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: BsggNull_nF_2

description:
sgg_isoB_zygotic_null_2
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: AsggN_4

description:
sgg_isoA_null_3
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt

source_name: sgg-A null

value: sggisoA

value: sgg-A null


title: control_nF_3

description:
attP40_6
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: AsggN_3

description:
sgg_isoA_null_2
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: A1

description: QN Orange scallop

value: without RNAi


title: MFI131

description:
MFI131
Single-cell RNA-Seq
3' end of mRNA

value: in vitro

value: Embryo


title: A3

description: QN Orange scallop


title: B3

description: QN Orange scallop


title: A2

description: QN Orange scallop


title: AsggN_2

description:
sgg_isoA_null_1
All
processed data file: SggA_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: pbmc2_repair

status: Public on Oct 02 2019

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 2 repair

library_source: genomic

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/rhumba/tree/master/haircut). Single cell RNA-Seq libraries were preprocessed using the 10x genomics software cellranger (3.0.2). The single cell DNA repair libraries were preprocessed to append the read 1 sequence to the paired read 2 read id using umi_tools extract(v 1.0.0 --bc-pattern CCCCCCCCCCCCCCCCNNNNNNNNNN)(Smith et al. 2017) followed by poly(A) tail and template switching oligo removal from read 2 using cutadapt (v. 1.8.3 -a AAAAAAAAAAA -g AAGCAGTGGTATCAACGCAGAGTACATGGG --minimum-length=2)  (Martin 2011). Reads were next aligned with bowtie2 (v 2.3.2 Langmead B, Salzberg S. 2012) to a repair substrate reference.
Following alignment, BAM files were processed to extract the alignment hairpin and position into a tag (XT) within the BAM file (tag_bam). UMI groups were identified and added as a tag (CB) using umi_tools group (--read-length = True --per-cell --output-bam = True --output-unmapped = True). BAM files were then sorted by cell barcode tag using samtools sort (v 1.5-4 -t CB -@ 23) (Li 2009). UMIs per hairpin_position were enumerated per cell using umi-tools count (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.
Count tables produced by umi_tools are then converted into sparseMatrix format using the scrunchy R package (https://github.com/hesselberthlab/scrunchy, umitools_to_mtx). Matrices are the filtered to include only the cell-associated barcodes using the scrunchy R package (filter_matrix). Cell-associated barcodes are identified from the mRNA data using cellranger (v 3.0.2) from the filtered barcodes.tsv output.
Genome_build: hg38, custom repair substrate reference
Supplementary_files_format_and_content: Text file containing cell barcodes, genes/features, and UMI counts per gene/feature per cell are provided

molecule: other

organism: synthetic construct

source_name: synthetic oligonucleotides (not of human origin) added to and recovered from Human PBMCs

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant to clean up the repair fraciton. The repair fraction was split in two to optimize the library prep. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.

tag: cell type

value: Human PBMCs


title: pbmc2_repair_pst1

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with a PST1 digestion for detection of direct reversal substrate. Fresh PBMCs were isolated from a healthy human donor.
PBMC 2 repair with PST1 digest

source_name: synthetic oligonucleotides (not of human origin) added to and recovered from Human PBMCs; PST1 digest

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant to clean up the repair fraction. The repair fraction was split in two to optimize the library prep. To remove unrepaired uracil substrate, these repair products were incubated with 20 ug (2 ul) Dynabeads™ M-270 Streptavidin (ThermoFisher 65305). The supernatant was then cleaned up via precipitation and the these repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: pbmc3_repair

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 3 repair


title: pbmc1_repair

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 1 repair

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant. These repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: pbmc2_mrna

description:
Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 2 mRNA

source_name: Human PBMCs

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 60 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: control_nF_2

description:
attP40_5
Non-fluorescent embryos
processed data file: SggB_RNAseq_limma-voom_result_master.txt
processed data file: GeneCounts.txt


title: barnyard_repair

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry). A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.
Barnyard repair

source_name: synthetic oligonucleotides (not of human origin) added to and recovered from 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
Following GEM generation, GEMs were incubated at 37 C for 60 minutes, followed by 53 C for 45 minutes for RT. GEM emulsion was broken and DNA/RNA was isolated using the 10x genomics protocol using MyOne Silane beads. Repair products were separated from mRNA using and Ampure size selection as follows: 0.6x volume of Ampure XP beads were added to the purified DNA/RNA. Following 5 minute incubation, the supernatant was collected and an additional 1.2x volume of Ampure XP was added to supernatant. These repair products were digested with Pst1 (NEB R3140) for 1 hour at 37 C. These repair products then end repaired (NEB E6050) and A-tailed. Illumina TruSeq adapters were ligated followed by Illumina barcoded TruSeq PCR. See https://www.protocols.io/run/single-cell-analysis-of-functional-heterogeneity-i-uhyet7w for more detailed library protocol. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the repair product.


title: pbmc1_mrna

description:
Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 1 mRNA


title: D_35_2

status: Public on Sep 16 2019

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

institute: Wuhan University

description:
RNA-Seq-Whole transcriptome
processed data file: Processed_data.txt

data_processing:
Raw image data file from high-throughout sequencing was transformed to sequenced reads (called raw data or raw reads) by CASAVA base recognition (Base Calling), Q30≥80%.
Raw data is stored in FASTQ (fq) format files. Fastq files were checked for quality using fastqc and fastq_screen.
Reads were quality filtered. Filtered fastq files were aligned to mouse genome using STAR (v2.5). STAR used the method of maximal mappable prefix (MMP) which can generate a precise mapping result for junction reads.
Htseq v0.6.1 was used to count the read numbers mapped of each gene.
FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effects of sequencing depth and gene length for the reads count at the same time.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_data.txt: Tab-delimited txt file that includes normalized read counts for each sample per gene.

source_name: Purified mature dermal adipocytes

extract_protocol:
Mature dermal adipocytes and inguinal adipocytes were collected from P21, P25, P29, P35, P49 mice using Collagenase IV and DispaseII digestion combined with the floating centrifuge method. RNA was harvested using Trizol reagent, and purified with the Qiagen RNA purification kit. 1 µg of total DNase treated RNA is then prepared for the library construction.
RNA libraries were prepared for sequencing using NEBNext UltraTM RNA library Prep Kit.

value: Primary purified adipocytes


title: D_49_1


title: D_35_3


title: D_49_2


title: D_29_3


title: D_29_1


title: D_35_1


title: D_21_2


title: D_21_3


title: D_25_3


title: D_21_1


title: 95T_TCCGCGAA-AGGCGAAG_L00M_R1_001

status: Public on Sep 15 2019

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

description: Brain region: Telencephalon

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina).
Read alignment: Tophat 2.0.8, default parameters.
Read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
Differential expression: Done in R using the Bioconductor package edgeR.
Genome_build: Gacu Ensembl release 75
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files include raw counts.

organism: Gasterosteus aculeatus

source_name: Telencephalon

extract_protocol:
Heads were flash frozen in liquid nitrogen and the telencephalon and diencephalon were carefully dissected and placed individually in Eppendorf tubes containing 500 μL of TRIzol Reagent (Life Technologies). Total RNA was isolated immediately using TRIzol Reagent according to the manufacturer’s recommendation and subsequently purified on columns with the RNeasy kit (QIAGEN). RNA was eluted in a total volume of 30 μL in RNase-free water. Samples were treated with DNase (QIAGEN) to remove genomic DNA during the extraction procedure. RNA quantity was assessed using a Nanodrop spectrophotometer (Thermo Scientific), and RNA quality was assessed using the Agilent Bioanalyzer 2100 (RIN 7.5-10); one sample was excluded because of low RNA quality. RNA was immediately stored at −80 °C until used in sequencing library preparation.
The RNAseq libraries were constructed with the TruSeq® Stranded mRNA HT (Illumina) using an ePMotion 5075 robot (Eppendorf). Libraries were quantified on a Qubit fluorometer, using the dsDNA High Sensitivity Assay Kit (Life Technologies), and library size was assessed on a Bioanalyzer High Sensitivity DNA chip (Agilent). Libraries were pooled and diluted to a final concentration of 10 nM. Final library pools were quantified using real-time PCR, using the Illumina compatible kit and standards (KAPA) by the W. M. Keck Center for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Center (University of Illinois). Single-end sequencing was performed on an Illumina HiSeq 2500 instrument using a TruSeq SBS sequencing kit version 3 by the W. M. Keck Center for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Center (University of Illinois). The 79 libraries were sequenced on 27 lanes.

value: Telencephalon

tag: Stage

value: NOCLUTCH

tag: treatment

value: control

tag: timepoint

value: Male


title: D_25_1


title: 75T_TCCGCGAA-TATAGCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 90T_TCCGCGAA-CCTATCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 97T_TCCGCGAA-CAGGACGT_L00M_R1_001

description: Brain region: Telencephalon


title: pbmc3_mrna

description:
Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.
PBMC 3 mRNA


title: 96T_CGGCTATG-CCTATCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 94T_CGGCTATG-AGGCGAAG_L00M_R1_001

description: Brain region: Telencephalon


title: 91T_CGGCTATG-TATAGCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 72T_TAATGCGC-CAGGACGT_L00M_R1_001

description: Brain region: Telencephalon


title: 12T_TAATGCGC-AGGCGAAG_L00M_R1_001

description: Brain region: Telencephalon


title: 69T_CTGAAGCT-AGGCGAAG_L00M_R1_001

description: Brain region: Telencephalon


title: D_49_3


title: barnyard_mrna

description:
Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry). A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.
Barnyard mRNA

source_name: 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 60 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: 66T_CGGCTATG-CAGGACGT_L00M_R1_001

description: Brain region: Telencephalon


title: D_29_2


title: 74T_CTGAAGCT-CAGGACGT_L00M_R1_001

description: Brain region: Telencephalon


title: 47T_GAATTCGT-CAGGACGT_L008_R1_001

description: Brain region: Telencephalon

value: HATCHED

value: experiment


title: 7T_CTGAAGCT-CCTATCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 65T_CTGAAGCT-TATAGCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 41T_TAATGCGC-TATAGCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 15T_GAATTCGT-CCTATCCT_L007_R1_001

description: Brain region: Telencephalon


title: 32T_GAATTCGT-AGGCGAAG_L007_R1_001

description: Brain region: Telencephalon


title: D_25_2


title: 92T_ATTCAGAA-CAGGACGT_L005_R1_001

description: Brain region: Telencephalon


title: 81T_ATTCAGAA-CCTATCCT_L004_R1_001

description: Brain region: Telencephalon


title: 80T_ATTCAGAA-TATAGCCT_L003_R1_001

description: Brain region: Telencephalon


title: 86T_ATTCAGAA-AGGCGAAG_L005_R1_001

description: Brain region: Telencephalon


title: 73T_GAGATTCC-CAGGACGT_L003_R1_001

description: Brain region: Telencephalon


title: 64T_GAGATTCC-AGGCGAAG_L002_R1_001

description: Brain region: Telencephalon


title: 58T_GAGATTCC-CCTATCCT_L001_R1_001

description: Brain region: Telencephalon


title: 29T_GAGATTCC-TATAGCCT_L001_R1_001

description: Brain region: Telencephalon


title: 10T_GAATTCGT-TATAGCCT_L006_R1_001

description: Brain region: Telencephalon


title: 82T_TCCGGAGA-TATAGCCT_L003_R1_001

description: Brain region: Telencephalon

value: NEST


title: 16T_CGCTCATT-CAGGACGT_L008_R1_001

description: Brain region: Telencephalon


title: 71T_TCCGGAGA-AGGCGAAG_L005_R1_001

description: Brain region: Telencephalon

value: EGGS


title: 77T_TCCGGAGA-CAGGACGT_L005_R1_001

description: Brain region: Telencephalon


title: 60T_TCCGGAGA-CCTATCCT_L004_R1_001

description: Brain region: Telencephalon


title: 87T_CGCTCATT-TATAGCCT_L006_R1_001

description: Brain region: Telencephalon


title: 39T_TAATGCGC-CCTATCCT_L00M_R1_001

description: Brain region: Telencephalon


title: 13T_CGCTCATT-AGGCGAAG_L007_R1_001

description: Brain region: Telencephalon


title: 70T_ATTACTCG-TATAGCCT_L001_R1_001

description: Brain region: Telencephalon


title: 78T_ATTACTCG-CAGGACGT_L003_R1_001

description: Brain region: Telencephalon


title: 54T_ATTACTCG-AGGCGAAG_L002_R1_001

description: Brain region: Telencephalon


title: 75D_TCCGCGAA-ATAGAGGC_L00M_R1_001

description: Brain region: Diencephalon

source_name: Diencephalon

value: Diencephalon


title: 90D_TCCGCGAA-GGCTCTGA_L00M_R1_001

description: Brain region: Diencephalon


title: 96D_CGGCTATG-GGCTCTGA_L00M_R1_001

description: Brain region: Diencephalon


title: 97D_TCCGCGAA-GTACTGAC_L00M_R1_001

description: Brain region: Diencephalon


title: 91D_CGGCTATG-ATAGAGGC_L00M_R1_001

description: Brain region: Diencephalon


title: 41D_TAATGCGC-ATAGAGGC_L00M_R1_001

description: Brain region: Diencephalon


title: 69D_CTGAAGCT-TAATCTTA_L00M_R1_001

description: Brain region: Diencephalon


title: 88T_CGCTCATT-CCTATCCT_L007_R1_001

description: Brain region: Telencephalon


title: 12D_TAATGCGC-TAATCTTA_L00M_R1_001

description: Brain region: Diencephalon


title: 74D_CTGAAGCT-GTACTGAC_L00M_R1_001

description: Brain region: Diencephalon


title: 72D_TAATGCGC-GTACTGAC_L00M_R1_001

description: Brain region: Diencephalon


title: 95D_TCCGCGAA-TAATCTTA_L00M_R1_001

description: Brain region: Diencephalon


title: 65D_CTGAAGCT-ATAGAGGC_L00M_R1_001

description: Brain region: Diencephalon


title: 7D_CTGAAGCT-GGCTCTGA_L00M_R1_001

description: Brain region: Diencephalon


title: 39D_TAATGCGC-GGCTCTGA_L00M_R1_001

description: Brain region: Diencephalon


title: 47D_GAATTCGT-GTACTGAC_L008_R1_001

description: Brain region: Diencephalon


title: 10D_GAATTCGT-ATAGAGGC_L006_R1_001

description: Brain region: Diencephalon


title: 32D_GAATTCGT-TAATCTTA_L008_R1_001

description: Brain region: Diencephalon


title: 92D_ATTCAGAA-GTACTGAC_L006_R1_001

description: Brain region: Diencephalon


title: 33T_ATTACTCG-CCTATCCT_L001_R1_001

description: Brain region: Telencephalon


title: 66D_CGGCTATG-GTACTGAC_L00M_R1_001

description: Brain region: Diencephalon


title: 15D_GAATTCGT-GGCTCTGA_L007_R1_001

description: Brain region: Diencephalon


title: 64D_GAGATTCC-TAATCTTA_L002_R1_001

description: Brain region: Diencephalon


title: 58D_GAGATTCC-GGCTCTGA_L002_R1_001

description: Brain region: Diencephalon


title: 80D_ATTCAGAA-ATAGAGGC_L004_R1_001

description: Brain region: Diencephalon


title: 86D_ATTCAGAA-TAATCTTA_L005_R1_001

description: Brain region: Diencephalon


title: 73D_GAGATTCC-GTACTGAC_L003_R1_001

description: Brain region: Diencephalon


title: 29D_GAGATTCC-ATAGAGGC_L001_R1_001

description: Brain region: Diencephalon


title: 16D_CGCTCATT-GTACTGAC_L008_R1_001

description: Brain region: Diencephalon


title: 88D_CGCTCATT-GGCTCTGA_L007_R1_001

description: Brain region: Diencephalon


title: 77D_TCCGGAGA-GTACTGAC_L006_R1_001

description: Brain region: Diencephalon


title: 87D_CGCTCATT-ATAGAGGC_L006_R1_001

description: Brain region: Diencephalon


title: 78D_ATTACTCG-GTACTGAC_L003_R1_001

description: Brain region: Diencephalon


title: 70D_ATTACTCG-ATAGAGGC_L001_R1_001

description: Brain region: Diencephalon


title: 54D_ATTACTCG-TAATCTTA_L002_R1_001

description: Brain region: Diencephalon


title: 33D_ATTACTCG-GGCTCTGA_L002_R1_001

description: Brain region: Diencephalon


title: 82D_TCCGGAGA-ATAGAGGC_L004_R1_001

description: Brain region: Diencephalon


title: 60D_TCCGGAGA-GGCTCTGA_L004_R1_001

description: Brain region: Diencephalon


title: 81D_ATTCAGAA-GGCTCTGA_L004_R1_001

description: Brain region: Diencephalon


title: Snail1+STIM1 dOE rep1

status: Public on Aug 17 2019

type: RNA

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

data_processing:
For the normalization in this study, we useed ACTB as the housekeeping gene. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Matrix normalized worksheet reports normalized signal (against housekeeping genes, ACTB was used as housekeeping gene in this study).Fold Change worksheet reports test/control (i.e., Snail1 OE/Mock; Snai11+STIM1 dOE/Snail1 OE.

label: SYBR Green II

source_name: SMMC7721 cell line

label_protocol: Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA).3 ng cDNA was added into each 20μL reaction mix. mRNA expression was assessed by RT-quantitative PCR using TB Green® Premix Ex Taq™ II (TAKARA) on BioRad CFX386 (Bio-Rad, CA) with 40 cycles at 95 oC for 10 seconds, 59 oC for 20 seconds and 72 oC for 30 seconds.

growth_protocol: Cells  were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2.

extract_protocol: When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan).

treatment_protocol: Snail1 overexpression(Snail1 OE)- and Snail1 plus STIM1 double overexpression (Snail1+STIM1 dOE)- SMMC7721 cells were established via lentiviral Infection.

tag: cell line

tag: genotype

value: SMMC7721 infected with lentiviral of Snail1 plus STIM1 double overexpression


title: Snail1+STIM1 dOE rep3


title: Snail1 OE rep3

value: SMMC7721 infected with lentiviral of Snail1 overexpression


title: Snail1+STIM1 dOE rep2


title: 13D_CGCTCATT-TAATCTTA_L008_R1_001

description: Brain region: Diencephalon

tag: Sex


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post allogeneic HSCT -3

status: Public on Jul 27 2019

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome  (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive”
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Expression quantitation was performed with HTSeq version 0.6.1
Genome_build: ENSEMBL GRCm38
Supplementary_files_format_and_content: raw_counts.txt  tab delimited text - merged output from HTSeq

source_name: Donor Splenic Pan-T-cells from recipient spleen 7 days post HSCT

growth_protocol: Eight to 12 week-old female B6.SJL-Ptprca Pepcb/BoyJ (H-2b, CD45.1) and CByJ.SJL(B6)-Ptprca/J (H-2d, CD45.1) recipient mice were purchased from Jackson Laboratories.  Eight to twelve week-old female C57BL/6 (CD45.2) donor mice were purchased from Jackson Laboratories.  Animals were house under specific pathogen-free conditions.  All animal studies were approved by the University Committee on Use and Care of Animals of the University of Michigan, based on University Laboratory Animal Medicine guidelines.

extract_protocol:
On day +7 post HSCT, donor splenic T-cells were harvested and enriched using the Pan T-cell Isolation Kit II (Miltenyi Biotec).  Live donor T-cells were subsequently flow sorted (LiveDead NearIR-/CD3-PE+/CD45.2-APC+).  RNA was extracted using the AllPrep DNA/RNA Mini Kit with on-column DNaseI digestion from Qiagen.
Stranded libraries were constructed using 100ng of total RNA and the KAPA RNA HyperPrep Kit with  RiboErase per manufacturer instruction.

treatment_protocol: Murine bone marrow transplantation was performed on 8-12 week-old animals.  Splenic T-cells from donor mice were enriched using the Pan T-cell Isolation Kit II (Miltenyi Biotec), while bone marrow (BM) cells were depleted of T cells by using CD90.2 magnetic beads (Miltenyi Biotec).  B6.SJL-Ptprca Pepcb/BoyJ (syngeneic) and CByJ.SJL(B6)-Ptprca/J  (allogeneic) recipient mice were irradiated with 9.5 or 8 (dose split equally 3-4 hours apart) Gy from a 137Cs source, respectively, on day -1.  On day 0, recipient mice received via tail vein injection 5 x 10^6 T cell depleted (TCD) BM as well as 8.5 (syngeneic recipients) or 1 x 10^6 (allogeneic recipients) splenic T-cells from C57BL/6 donor mice.  All recipients received pH 3.0 water starting day -1.

tag: hsct type

value: Allogeneic

value: B6.SJL-Ptprca Pepcb/BoyJ


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post allogeneic HSCT -1


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post allogeneic HSCT -2


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post syngeneic HSCT -3

value: Syngeneic


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post syngeneic HSCT -1


title: Mock rep1

value: SMMC7721 infected with lentiviral of control


title: Donor sorted Live,CD3+,CD45.2+ Splenic T-cells 7 days post syngeneic HSCT -2


title: 71D_TCCGGAGA-TAATCTTA_L005_R1_001

description: Brain region: Diencephalon


title: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells-3

source_name: Spleen Pan-T-cells

value: Healthy control


title: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells-2


title: Snail1 OE rep2


title: Snail1 OE rep1


title: Mock rep2


title: Mock rep3


title: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells-1


title: P2509_N715-S502

status: Public on Jul 09 2019

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
Full-length RNA-seq
Single-cell RNA-seq (scRNA-seq)
Smart-Seq2 protocol
Read 1: cDNA
Read 2: Barcode (1-8)
processed data file: P2509.tsv

data_processing:
Reads were demultiplexed according to the cell barcodes.
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the STAR pipeline.
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Gencode release 28, assembly GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values (rows) as read counts for each cell (columns)

growth_protocol: hiPSC lines were differentiated via embryoid body (EB) in serum-free condition cultures with the successive addition of BMP4 50 ng/ml (d0-d3), CHIR99021 3µM (d2-d3) and hematopoietic cytokines (d3-d15; SCF 300ng/ml, Flt3 300ng/ml, IL6 and IL3 10ng/ml) and maintained at 37 ºC in 5% CO2.

extract_protocol:
Isolation of single cells with FACS into 96-well plates containing lysis buffer (triton).
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol.

treatment_protocol: Doxycycline (Dox) was added at a final concentration of 1 µg/ml to induce the expression of GATA2 transgene from days 2 to 7 of differentiation.

value: Hemato-endothelial cell

value: Dox


title: P2509_N715-S505


title: P2509_N715-S510


title: P2509_N715-S503


title: P2509_N715-S508


title: P2509_N715-S511


title: P2509_N715-S506


title: P2509_N714-S511


title: P2509_N714-S510


title: P2509_N714-S508


title: P2509_N714-S507


title: P2509_N714-S506


title: P2509_N714-S505


title: P2509_N712-S510


title: P2509_N714-S503


title: P2509_N712-S507


title: P2509_N712-S508


title: P2509_N714-S502


title: P2509_N712-S502


title: P2509_N712-S511


title: P2509_N712-S505


title: P2509_N711-S510


title: P2509_N711-S508


title: P2509_N712-S506


title: P2509_N711-S507


title: P2509_N711-S506


title: P2509_N711-S511


title: P2509_N712-S503


title: P2509_N711-S503


title: P2509_N711-S502


title: P2509_N710-S508


title: P2509_N710-S511


title: P2509_N710-S510


title: P2509_N710-S506


title: P2509_N715-S507


title: P2509_N710-S507


title: P2509_N710-S505


title: P2509_N710-S503


title: P2509_N710-S502


title: P2509_N707-S511


title: P2509_N707-S510


title: P2509_N707-S508


title: P2509_N707-S507


title: P2509_N707-S506


title: P2509_N707-S502


title: P2509_N706-S511


title: P2509_N706-S510


title: P2509_N706-S507


title: P2509_N707-S503


title: P2509_N706-S503


title: P2509_N706-S505


title: P2509_N707-S505


title: P2509_N705-S511


title: P2509_N706-S508


title: P2509_N706-S506


title: P2509_N706-S502


title: P2509_N711-S505


title: P2509_N705-S510


title: P2509_N705-S507


title: P2509_N705-S505


title: P2509_N705-S503


title: P2509_N705-S502


title: P2509_N704-S511


title: P2509_N705-S506


title: P2509_N704-S506


title: P2509_N704-S508


title: P2509_N704-S505


title: P2509_N704-S507


title: P2509_N704-S502


title: P2509_N704-S510


title: P2509_N704-S503


title: P2509_N703-S511


title: P2509_N703-S510


title: P2509_N703-S503


title: P2509_N703-S506


title: P2509_N703-S508


title: P2509_N702-S511


title: P2509_N703-S507


title: P2509_N705-S508


title: P2509_N703-S505


title: P2509_N702-S510


title: P2509_N702-S507


title: P2509_N702-S503


title: P2509_N702-S505


title: P2509_N702-S508


title: P2509_N701-S511


title: P2509_N702-S502


title: P2509_N702-S506


title: P2509_N701-S507


title: P2509_N701-S510


title: P2509_N701-S508


title: P2509_N701-S506


title: P2508_N729-S520

description:
Full-length RNA-seq
Single-cell RNA-seq (scRNA-seq)
Smart-Seq2 protocol
Read 1: cDNA
Read 2: Barcode (1-8)
processed data file: P2508.tsv

value: Untreated


title: P2508_N729-S521


title: P2509_N703-S502


title: P2508_N729-S518


title: P2509_N701-S502


title: P2508_N728-S521


title: P2508_N729-S513


title: P2508_N728-S522


title: P2508_N728-S520


title: P2508_N729-S515


title: P2508_N728-S517


title: P2508_N729-S517


title: P2508_N728-S518


title: P2508_N728-S516


title: P2508_N727-S522


title: P2508_N727-S521


title: P2508_N727-S520


title: P2508_N728-S513


title: P2508_N727-S518


title: P2508_N727-S517


title: P2509_N701-S503


title: P2508_N729-S522


title: P2509_N701-S505


title: P2508_N727-S515


title: P2508_N727-S513


title: P2508_N726-S521


title: P2508_N726-S522


title: P2508_N726-S517


title: P2508_N729-S516


title: P2508_N726-S518


title: P2508_N726-S520


title: P2508_N728-S515


title: P2508_N726-S515


title: P2508_N726-S516


title: P2508_N724-S521


title: P2508_N726-S513


title: P2508_N724-S517


title: P2508_N727-S516


title: P2508_N724-S515


title: P2508_N724-S518


title: P2508_N724-S513


title: P2508_N724-S516


title: P2508_N723-S521


title: P2508_N723-S520


title: P2508_N723-S517


title: P2508_N723-S516


title: P2508_N723-S515


title: P2508_N723-S513


title: P2508_N722-S521


title: P2508_N723-S518


title: P2508_N722-S522


title: P2508_N722-S517


title: P2508_N722-S515


title: P2508_N724-S522


title: P2508_N722-S518


title: P2508_N722-S516


title: P2508_N722-S513


title: P2508_N724-S520


title: P2508_N723-S522


title: P2508_N721-S522


title: P2508_N721-S516


title: P2508_N721-S517


title: P2508_N721-S520


title: P2508_N721-S518


title: P2508_N721-S515


title: P2508_N721-S513


title: P2508_N720-S520


title: P2508_N720-S521


title: P2508_N720-S515


title: P2508_N720-S516


title: P2508_N720-S522


title: P2508_N720-S513


title: P2508_N722-S520


title: P2508_N719-S522


title: P2508_N719-S518


title: P2508_N719-S520


title: P2508_N719-S521


title: P2508_N719-S517


title: P2508_N721-S521


title: P2508_N718-S522


title: P2508_N718-S520


title: P2508_N719-S515


title: P2508_N719-S516


title: P2508_N719-S513


title: P2508_N718-S518


title: P2508_N718-S513


title: P2508_N718-S515


title: P2508_N718-S516


title: P2508_N716-S522


title: P2508_N720-S518


title: P2508_N718-S521


title: P2508_N716-S518


title: P2508_N716-S520


title: P2508_N718-S517


title: P2508_N716-S521


title: P2508_N716-S517


title: P2508_N716-S516


title: P2508_N720-S517


title: P2508_N716-S513


title: P2507_N715-S521

description:
Full-length RNA-seq
Single-cell RNA-seq (scRNA-seq)
Smart-Seq2 protocol
Read 1: cDNA
Read 2: Barcode (1-8)
processed data file: P2507.tsv

value: Mesodermal cell


title: P2507_N715-S522


title: P2507_N715-S520


title: P2507_N715-S518


title: P2507_N715-S516


title: P2507_N715-S515


title: P2507_N715-S513


title: P2507_N715-S517


title: P2507_N714-S522


title: P2507_N714-S520


title: P2507_N714-S518


title: P2507_N714-S521


title: P2507_N714-S516


title: P2507_N714-S515


title: P2507_N714-S517


title: P2508_N716-S515


title: P2507_N712-S522


title: P2507_N712-S517


title: P2507_N711-S522


title: P2507_N712-S515


title: P2507_N712-S520


title: P2507_N712-S521


title: P2507_N711-S521


title: P2507_N714-S513


title: P2507_N712-S513


title: P2507_N711-S516


title: P2507_N711-S520


title: P2507_N711-S515


title: P2507_N711-S517


title: P2507_N711-S513


title: P2507_N710-S520


title: P2507_N710-S522


title: P2507_N710-S516


title: P2507_N710-S517


title: P2507_N710-S515


title: P2507_N707-S522


title: P2507_N710-S513


title: P2507_N712-S518


title: P2507_N707-S521


title: P2507_N712-S516


title: P2507_N707-S520


title: P2507_N707-S518


title: P2507_N706-S521


title: P2507_N706-S520


title: P2507_N711-S518


title: P2507_N707-S515


title: P2507_N707-S513


title: P2507_N707-S517


title: P2507_N706-S522


title: P2507_N707-S516


title: P2507_N706-S517


title: P2507_N706-S518


title: P2507_N710-S518


title: P2507_N706-S516


title: P2507_N706-S515


title: P2507_N706-S513


title: P2507_N705-S522


title: P2507_N710-S521


title: P2507_N705-S521


title: P2507_N705-S520


title: P2507_N705-S516


title: P2507_N704-S522


title: P2507_N705-S515


title: P2507_N705-S518


title: P2507_N704-S521


title: P2507_N705-S513


title: P2507_N705-S517


title: P2507_N704-S520


title: P2507_N704-S516


title: P2507_N704-S518


title: P2507_N704-S513


title: P2507_N704-S515


title: P2507_N703-S522


title: P2507_N703-S521


title: P2507_N703-S520


title: P2507_N703-S516


title: P2507_N703-S517


title: P2507_N703-S515


title: P2507_N702-S522


title: P2507_N702-S521


title: P2507_N702-S518


title: P2507_N702-S520


title: P2507_N702-S517


title: P2507_N702-S516


title: P2507_N702-S513


title: P2507_N701-S522


title: P2507_N701-S518


title: P2507_N701-S521


title: P2507_N701-S520


title: P2507_N704-S517


title: P2507_N701-S517


title: P2507_N701-S516


title: P2506_N729-S511

description:
Full-length RNA-seq
Single-cell RNA-seq (scRNA-seq)
Smart-Seq2 protocol
Read 1: cDNA
Read 2: Barcode (1-8)
processed data file: P2506.tsv


title: P2506_N729-S508


title: P2507_N701-S515


title: P2506_N729-S506


title: P2507_N703-S513


title: P2506_N729-S502


title: P2506_N729-S510


title: P2506_N729-S503


title: P2507_N703-S518


title: P2506_N729-S505


title: P2506_N728-S511


title: P2506_N728-S510


title: P2506_N728-S508


title: P2506_N728-S505


title: P2506_N728-S507


title: P2506_N728-S502


title: P2506_N728-S503


title: P2506_N728-S506


title: P2507_N702-S515


title: P2506_N727-S511


title: P2506_N727-S510


title: P2506_N727-S505


title: P2507_N701-S513


title: P2506_N727-S506


title: P2506_N727-S503


title: P2506_N727-S508


title: P2506_N729-S507


title: P2506_N727-S507


title: P2506_N727-S502


title: P2506_N726-S511


title: P2506_N726-S507


title: P2506_N726-S508


title: P2506_N726-S510


title: P2506_N726-S506


title: P2506_N726-S505


title: P2506_N726-S502


title: P2506_N724-S508


title: P2506_N724-S507


title: P2506_N726-S503


title: P2506_N724-S510


title: P2506_N724-S511


title: P2506_N724-S506


title: P2506_N724-S503


title: P2506_N724-S502


title: P2506_N723-S511


title: P2506_N724-S505


title: P2506_N723-S510


title: P2506_N723-S507


title: P2506_N723-S508


title: P2506_N723-S506


title: P2506_N723-S502


title: P2506_N723-S505


title: P2506_N722-S507


title: P2506_N722-S511


title: P2506_N722-S506


title: P2506_N722-S508


title: P2506_N722-S502


title: P2506_N721-S511


title: P2506_N722-S503


title: P2506_N722-S505


title: P2506_N721-S510


title: P2506_N721-S507


title: P2506_N720-S511


title: P2506_N720-S510


title: P2506_N721-S506


title: P2506_N721-S508


title: P2506_N720-S508


title: P2506_N721-S503


title: P2506_N721-S505


title: P2506_N723-S503


title: P2506_N720-S507


title: P2506_N720-S505


title: P2506_N720-S506


title: P2506_N719-S510


title: P2506_N720-S503


title: P2506_N720-S502


title: P2506_N719-S506


title: P2506_N719-S507


title: P2506_N722-S510


title: P2506_N719-S508


title: P2506_N719-S502


title: P2506_N719-S505


title: P2506_N718-S510


title: P2506_N719-S511


title: P2506_N716-S511


title: P2506_N718-S511


title: P2506_N719-S503


title: P2506_N718-S502


title: P2506_N721-S502


title: P2506_N718-S506


title: P2506_N718-S508


title: P2506_N716-S505


title: P2506_N718-S507


title: P2506_N716-S503


title: P2506_N718-S503


title: P2506_N716-S507


title: P2506_N718-S505


title: P2505_N715-S511

description:
Full-length RNA-seq
Single-cell RNA-seq (scRNA-seq)
Smart-Seq2 protocol
Read 1: cDNA
Read 2: Barcode (1-8)
processed data file: P2505.tsv

value: EB cell


title: P2506_N716-S506


title: P2506_N716-S508


title: P2505_N715-S506


title: P2505_N715-S510


title: P2505_N715-S507


title: P2505_N715-S508


title: P2506_N716-S502


title: P2505_N715-S505


title: P2505_N715-S503


title: P2505_N714-S511


title: P2505_N714-S510


title: P2505_N714-S507


title: P2505_N714-S506


title: P2506_N716-S510


title: P2505_N714-S505


title: P2505_N714-S503


title: P2505_N714-S502


title: P2505_N712-S505


title: P2505_N712-S510


title: P2505_N712-S507


title: P2505_N712-S508


title: P2505_N712-S506


title: P2505_N712-S511


title: P2505_N712-S502


title: P2505_N712-S503


title: P2505_N711-S511


title: P2505_N711-S508


title: P2505_N711-S510


title: P2505_N715-S502


title: P2505_N711-S506


title: P2505_N714-S508


title: P2505_N710-S511


title: P2505_N711-S503


title: P2505_N710-S507


title: P2505_N710-S508


title: P2505_N710-S506


title: P2505_N710-S510


title: P2505_N710-S505


title: P2505_N710-S503


title: P2505_N710-S502


title: P2505_N707-S511


title: P2505_N707-S510


title: P2505_N707-S508


title: P2505_N711-S507


title: P2505_N707-S503


title: P2505_N706-S508


title: P2505_N706-S510


title: P2505_N706-S505


title: P2505_N706-S503


title: P2505_N707-S505


title: P2505_N707-S506


title: P2505_N705-S508


title: P2505_N707-S507


title: P2505_N707-S502


title: P2505_N706-S511


title: P2505_N711-S505


title: P2505_N705-S511


title: P2505_N705-S510


title: P2505_N711-S502


title: P2505_N705-S503


title: P2505_N704-S511


title: P2505_N706-S506


title: P2505_N705-S506


title: P2505_N704-S505


title: P2505_N705-S502


title: P2505_N705-S505


title: P2505_N705-S507


title: P2505_N704-S506


title: P2505_N704-S510


title: P2505_N706-S507


title: P2505_N704-S503


title: P2505_N703-S506


title: P2505_N704-S502


title: P2505_N702-S511


title: P2505_N703-S502


title: P2505_N703-S503


title: P2505_N703-S508


title: P2505_N703-S511


title: P2505_N703-S507


title: P2505_N702-S506


title: P2505_N704-S507


title: P2505_N702-S508


title: P2505_N702-S510


title: P2505_N702-S507


title: P2505_N702-S505


title: P2505_N706-S502


title: P2505_N704-S508


title: P2505_N701-S511


title: P2505_N702-S502


title: P2505_N703-S510


title: P2505_N701-S508


title: P2505_N701-S507


title: P2505_N701-S510


title: P2505_N701-S505


title: P2505_N701-S506


title: P2505_N703-S505


title: CH2658 Lil+P_2

status: Public on Jul 08 2019

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

source_name: clinical isolate CH2658 passaged in the presence of 5 % linolenic acid and an overlay of paraffin for four days ( 2 passages a day)

growth_protocol: cell were grown in LB to an OD600 =2

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C

tag: isolate

tag: replica

value: Replica 2

tag: growth condition

value: RNA derived from liquid culture (OD600 =2)


title: P2505_N701-S503


title: CH2658 Lil+P_1

value: Replica 1


title: P2505_N701-S502


title: CH2658 Lil_2

source_name: clinical isolate CH2658 passaged in the presence of 5 % linolenic acid for four days ( 2 passages a day)


title: CH2658 LB+P_1

source_name: clinical isolate CH2658 passaged in LB and an overlay of paraffin as control for four days (two passages a day)


title: CH2658 Lil_1


title: CH2658 LB+P_2


title: P2505_N702-S503


title: CH2658 LB_1

source_name: clinical isolate CH2658 passaged in LB as control for four days (two passages a day)


title: CH2658 Rev3_1

source_name: Fourth G. mellonella Passage of CH2658 cultivated in LB  (day 3; 6 passages)


title: CH2658 Rev1_2

source_name: Fourth G. mellonella Passage of CH2658 cultivated in LB  (day 1; 2 passages)


title: CH2658 Rev2_2

source_name: Fourth G. mellonella Passage of CH2658 cultivated in LB  (day 2; 4 passages)


title: CH2658 Rev3_2


title: CH2658 LB_2


title: CH2658 Rev4_1

source_name: Fourth G. mellonella Passage of CH2658 cultivated in LB  (day 4; 8 passages)


title: CH2658 Rev4_2


title: CH2658 Rev1_1


title: CH2658 IV_2

source_name: clinical isolate CH2658 passaged in G. mellonella (fourth passage)


title: CH2658 III_2

source_name: clinical isolate CH2658 passaged in G. mellonella (third passage)


title: CH2658 IV_1


title: CH2658 II_1

source_name: clinical isolate CH2658 passaged in G. mellonella (second passage)


title: CH2658 II_2


title: CH2658 III_1


title: CH2658 I_1

source_name: clinical isolate CH2658 passaged in G. mellonella (first passage)


title: CH2658_1

source_name: clinical isolate derived from Charité Berlin


title: CH2658_2


title: CH2658 I_2


title: invitro_LLC

status: Public on Jul 04 2019

description:
LLC = lower lobe central, close to bronchus
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PAO1 whole genome using a Stampy pipeline with default parameters.
Genome_build: PAO1 NC_002516
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

source_name: Pool of Pseudomonas strains isolated from the lung of a CF subject and grown in LB medium

tag: growth medium

value: grown in LB medium


title: invitro_ULC

description:
ULC = lower lobe central, close to bronchus
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.


title: spp381_37_rep1

status: Public on Jul 05 2019

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

data_processing:
Raw reads were filtered and trimmed with FASTQ toolkit 1.0.0 by BaseSpace Sequence Hub Illumina website
Mapped to sacCer3 with the HISAT2 aligner and filtered for MapQuality ≥ 30 using BAM tools
Counts were generated using Feature Counts v1.6.2  and Differential expression analysis was performed using limma pipeline.
Data was further annotated for functional classification using DAVID bioinformatics resources 6.8
Genome_build: sacCer3
Supplementary_files_format_and_content: Coverage bigWig file provided for each sample were generated by deeptools

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in rich media YPAD.

extract_protocol:
RNA was extracted with the RNeasyMini Kit (Qiagen, Hilden, Germany)  and treated with the RNase-Free DNase Set (Qiagen) to remove any contaminating genomic DNA
RNA libraries for sequencing were performed from 150 ng RNA samples using the TruSeq® Stranded mRNA Library preparation kit (20020594, Illumina )

treatment_protocol: 1h heat-shock at 37ºC to induce the spp381-ts mutation.

value: YPH2622-2D-4B (BY4741 background)

value: MAT{alpha} his3{delta}1 leu2{delta}0  trp1{delta}::KanMX4 spp381-ts::URA3


title: spp381_37_rep2


title: invitro_ULP

description:
ULP = upper lobe periphery
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.


title: invitro_LLP

description:
LLP = lower lobe periphery
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.


title: CH2658 Rev2_1


title: invivo_LLP

description:
LLP = lower lobe periphery
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: Pool of Pseudomonas strains directly extracted from the lung of a CF subject


title: invivo_ULP

description:
ULP = upper lobe periphery
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

value: directly extracted from the lung of a CF subject


title: ALYREF_PARCLIP_rep2

status: Public on Jul 02 2019

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: PARCLIP-seq for ALYREF replicate 2 in T24 cell

data_processing:
Library strategy: PAR-CLIP.
Only the forward reads were used in the data analysis and uploaded.
Bowtie was applied to map sequencing reads against hg19 genome.
PARalyzer software was used to define proteins binding clusters.
Genome_build: hg19.
Supplementary_files_format_and_content: txt. Binding clusters for YBX1, ELAVL1 and ALYREF.

source_name: T26 cell line

extract_protocol:
The PAR-CLIP sample was separated by SDS-PAGE, RNA were recovered from the gel by D-tubeTM Dialyzer Midi(Millipore).The mixture were digested by 4 μg/μl proteinase K (Roche, 03115828001) and precipitated in ethanol with the help of glycogen (Thermo, R0551).
RNAs in ethanol were used for the small RNA library construction (NEB, E7300L). Finally, the library was sequenced on the Illumina HiSeq X-Ten platform with paired-end 150 bp (PE150) kits.

value: T24 cell line


title: ALYREF_PARCLIP_rep1

description: PARCLIP-seq for ALYREF replicate 1 in T24 cell

source_name: T25 cell line


title: YBX1_PARCLIP_rep1

description: PARCLIP-seq for YBX1 replicate 1 in T24 cell

source_name: T24 cell line


title: YBX1_PARCLIP_rep2

description: PARCLIP-seq for YBX1 replicate 2 in T24 cell

data_processing:
Library strategy: PAR-CLIP.
Only the forward reads were used in the data analysis and uploaded.
Bowtie was applied to map sequencing reads against hg19 genome.
PARalyzer software was used to define proteins binding clusters.
Genome_build: hg19
Supplementary_files_format_and_content: txt. Binding clusters for YBX1, ELAVL1 and ALYREF.


title: ELAVL1_PARCLIP_rep1

description: PARCLIP-seq for ELAVL1 replicate 1 in T24 cell


title: ELAVL1_PARCLIP_rep2

description: PARCLIP-seq for ELAVL1 replicate 2 in T24 cell


title: invivo_ULC

description:
ULC = lower lobe central, close to bronchus
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.


title: LHX4::GFP+

status: Public on Jun 06 2019

city: New York

first: Mark

middle: Monroe

last: Emerson

state: NY

address: 160 Convent Ave

department: Biology

institute: The City College of New York

description: PolyA RNAseq

data_processing:
Sequencing and alignment were provided by the Columbia Genome Center Single Cell Core. In brief, raw sequencing data from NovaSeq6000 were processed using the 10x Genomics Cell Ranger pipeline (v2.1.1) using default parameters and the reference genome was refdata-cellranger-mm10-2.1.0, distributed by 10X.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Files include barcode.tsv, genes.tsv and matrix.mtx that are produced as CellRanger output.

source_name: Retinal cells

extract_protocol:
Live cells were collected after dissociation and flow sorting for GFP signal. 3 Samples were extracted from 2 litters of E14.5 LHX4::GFP mice, pooled into one sorting solution during dissociation.
For each sample (GFP+ and GFP-), approx. 4000 cells were individually lysed, and their RNA transcribed and sequenced by the Columbia University Single Cell Analysis Core.
They were prepared using the 10X Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer's instructions (cDNA amplification cycles = 12, library amplification cycles = 12).

value: Cone photoreceptors (LHX4::GFP+)


title: LHX4::GFP-

description: PolyA RNAseq

value: Retinal cells (LHX4::GFP-)


title: invivo_BR

description:
BR = bronchus
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.


title: CBFb CD8+ T input

status: Public on May 01 2019

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Input DNA

data_processing:
ChIP-seq sequences were aligned to mouse reference genome release mm10 using bowtie (v1.1.2) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: Aligned BAM files were transformed to bigwig files.

molecule: genomic DNA

source_name: Mouse CD8+ T cells

extract_protocol:
For ChIP-seq using CBFb Ab, 0.5x10^7 T cells were washed with ice-cold PBS three times and were crosslinked by incubation with 1% formaldehyde containing 0.5 mM PMSF and protease inhibitor cocktail (Roche, 4693116001) on ice for 10 minutes. The crosslinking reaction was stopped by the addition of glycine to 0.125 M. Cells were incubated on ice for 5 minutes and then washed three times with ice-cold PBS. Cells were lysed by the incubation for 10 min on ice in 0.5 ml of 50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100 containing protease inhibitor cocktail. Nuclei were pelleted and lysed by resuspending in 10 mM Tris-Cl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA containing protease inhibitor cocktail. Pelleted chromatin was resuspended in 400 μl of 10 mM Tris-Cl (pH 8.0), 300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate and 0.5% N-laurylsarcosine containing protease inhibitor cocktail, and was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON) to approximately 350 bp of DNA fragments. Sonicated chromatin was incubated at 4°C overnight with anti-CBFb antibody preconjugated to magnetic beads (Dynabeads). Beads were washed by RIPA buffer 6 times and DNA was eluted and reverse-crosslinked at 65 °C in 50 mM Tris-Cl (pH 8.0), 10 mM EDTA, 1% SDS overnight.
Library construction was conducted by using NEBNext ChIP-seq Library Prep Reagent Set for Illumina according to the manufacturer’s protocol. Libraries were sequenced to 50 bp read length on a HiSeq2000 (Illumina).

tag: strain/background

value: CD8+ T cells

tag: chip antibody


title: ZG8525123

status: Public on Apr 08 2019

description:
Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
ProcessedDataMatrix_clinical_isolates.xlsx
geographical location: not determined

source_name: clinical isolate

tag: sample type

value: clinical isolate

tag: infection side

value: urinary tract


title: CBFb CD4+ T input

description: Input DNA

source_name: Mouse CD4+ T cells

value: CD4+ T cells


title: CBFb CD8+ T ip

description: ChIP DNA

value: Anti-CBFb


title: ZG8510487

description:
Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
ProcessedDataMatrix_clinical_isolates.xlsx

tag: geographical location


title: ZG8038581181

value: respiratory tract


title: invitro_BR

description:
BR = bronchus
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.


title: ZG5089456


title: ZG5051896

value: wound infection


title: ZG5021922


title: ZG5048010


title: invivo_LLC

description:
LLC = lower lobe central, close to bronchus
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.


title: ZG5003493


title: B3-406Nf2Cdkn2aBap1

status: Public on May 30 2019

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description:
SN935
406
mRNA enriched

data_processing:
Alignment to mm10.
Count with HTseq.
DE analysis with DEseq2.
Pathway analysis with ConcensusPathDb.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *tsv: Tab-separated text files include HTseq results.
Supplementary_files_format_and_content: Double-vs-Triple-tumors.xlsx: Excel file includes DEseq2 results.

source_name: Mouse MM

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS, 1x Penicillin/Streptomycin, 2mM L-Glutamine, and 5 ug/mL Insulin in a 37C incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using a Trizol and RNA min-prep Purification Kit (Zymo Research) according to manufacturer's instructions.
NEBNext® Ultra™ II RNA Library Prep (Cat#E7775L).

tag: tissue

value: MM

value: Triple knockout


title: ZG316722

value: ulcer


title: ZG316716

value: ear infection


title: ZG314777


title: CBFb CD4+ T ip

description: ChIP DNA

tag: cell type


title: ZG316704

value: nd/other


title: ZG316694


title: ZG302451


title: ZG314738


title: ZG302383


title: ZG302367


title: pbcm3_repair_pst1

description:
Single cell DNA repair activity library from the 10X genomics 3´ end kit (v2 chemistry) with a PST1 digestion for detection of direct reversal substrate. Fresh PBMCs were isolated from a healthy human donor.
PBMC 3 repair withi PST1 digest

source_name: synthetic oligonucleotides (not of human origin) added to and recovered from Human PBMCs; PST1 digest

value: Human PBMCs


title: ZG302432


title: ZG302442


title: ZG302431


title: ZG314696


title: ZG302359


title: ZG205864


title: ZG302368


title: ZG302370


title: ZG301975


title: ZG8006959


title: ZG205710


title: ZG205694


title: ZG205565


title: ZG02512057


title: spp381_37_rep3

tag: strain

value: YPH2622-2D-4B (BY4741 background)

value: MAT{alpha} his3{delta}1 leu2{delta}0  trp1{delta}::KanMX4 spp381-ts::URA3


title: ZG02420619


title: ZG02488718


title: ZG322541


title: Vb3320

value: Germany:University hospital Essen


title: PSAE2139

value: Germany:University of Freiburg


title: PSAE2126


title: PSAE2127


title: PSAE1970


title: PSAE1975


title: PSAE2325


title: PSAE1934


title: PSAE1872


title: PSAE1912


title: PSAE1837


title: PSAE1656


title: PSAE1984


title: PSAE2125


title: PSAE1649


title: PSAE1742


title: PSAE1647


title: PSAE1903


title: PSAE1745


title: PSAE1654


title: PSAE1651


title: PSAE1635


title: PSAE1439


title: PSAE1438


title: PSAE1642


title: PSAE1401


title: Vb20477


title: MS5

value: Germany:University hospital Muenster


title: MS2

value: clinical isolate


title: MS1


title: MHH2419

value: Germany:Hannover Medical School


title: MHH1883


title: MHH17783


title: MHH17767


title: MHH17501


title: PSAE1641


title: PSAE1645


title: MHH17247

value: sepsis


title: MHH16563


title: MHH16459


title: MHH16513


title: MHH16951


title: MHH16379


title: MHH17233


title: MHH17441

value: urinary tract


title: PSAE1630


title: MHH16530

value: respiratory tract


title: MHH16798


title: MHH16727

value: wound infection


title: MHH16208


title: MHH16050


title: MHH16610


title: MHH15817


title: MHH15280

value: rectal infection


title: MHH16371


title: MHH15275


title: MHH1525


title: MHH15204


title: MHH15187


title: MHH17546


title: MHH15151


title: MHH15083


title: MHH15015


title: MHH16427


title: MHH14911


title: MHH14929


title: MHH0927


title: MHH14990


title: M70656672


title: MHH0985


title: M70663247


title: M70646077


title: M70652746


title: MHH0147


title: MHH0426


title: M70640096


title: M70639645


title: M70641593


title: M70638412


title: M70647319


title: M70608424


title: M70649365


title: M70604538


title: M70646050


title: M70635118


title: M70565897


title: MHH15103


title: M70565254


title: M70564993


title: M70563004


title: F2240

value: Germany:University hospital Frankfurt


title: F2236


title: F2234


title: F2230


title: F2199


title: F2205


title: F2208


title: F2172


title: F2176


title: F2137


title: F2166


title: F2148


title: F2128


title: F2098


title: F2165


title: F2119


title: F2084


title: F2093


title: F2081


title: F2064


title: F2065


title: F2075


title: F2056


title: F2055


title: F2054


title: F2235


title: F2097


title: F2045


title: F2044


title: F2073


title: F2035


title: F2167


title: F2040


title: F2034


title: F2059


title: F2020


title: F2017


title: F2006


title: F1997


title: F2005


title: F2030


title: F1983


title: F2000


title: F2010


title: F1968


title: F2029


title: F1894


title: F1864


title: F1883


title: F1880


title: F1823


title: F1862


title: F1853


title: F1979


title: F1812


title: F1957


title: F1801


title: F1800


title: F1796


title: F1810


title: F1821


title: F1798


title: F1795


title: F2003


title: F1787


title: F1775


title: F1789


title: F1758


title: F1760


title: F1764


title: F1869


title: F1757


title: F1752


title: F1754


title: F1748


title: F1746


title: F1747


title: F1741


title: F1727


title: F1745


title: F1724


title: F1706


title: F1712


title: F1697


title: F1688


title: ESP084

value: Spain:University hospital Palma de Mallorca

value: nd/other, acute


title: ESP088


title: F1659

value: nd/other


title: ESP083


title: ESP091


title: ESP082


title: F1759


title: ESP077


title: ESP078


title: ESP075


title: F1763


title: ESP076


title: ESP081


title: ESP074


title: ESP079


title: ESP072


title: ESP069


title: ESP068


title: ESP064


title: ESP067


title: ESP063


title: ESP066


title: F1689


title: ESP060


title: ESP059


title: ESP058


title: ESP057


title: ESP053


title: ESP046

value: nd/other, chronic


title: ESP050


title: ESP043


title: ESP044


title: ESP038


title: ESP070


title: ESP040


title: ESP039


title: ESP073


title: ESP036


title: ESP035


title: ESP071


title: ESP033


title: ESP061


title: ESP029


title: ESP031


title: ESP028


title: ESP027


title: ESP024


title: ESP025


title: ESP032


title: ESP055


title: ESP047


title: ESP023


title: ESP022


title: ESP020


title: ESP021


title: ESP013


title: ESP037


title: ESP012


title: ESP015


title: ESP004


title: ESP034


title: ESP006


title: ESP003


title: CH5666

value: Germany:Charite Berlin


title: ESP002


title: CH5638


title: CH5688


title: ESP009


title: CH5695


title: CH5621


title: CH5596


title: CH5591


title: CH5548


title: CH5551


title: CH5597


title: CH5550


title: CH5531


title: CH5432


title: CH5528

value: ear infection


title: CH5464


title: CH5363


title: CH5387


title: CH5356


title: CH5334


title: ESP011


title: CH5291


title: CH5262


title: CH5267


title: CH5353


title: CH5182


title: CH5193


title: CH5362


title: CH5206


title: CH5174


title: CH5052


title: CH5022


title: CH5066


title: CH4914


title: CH4878


title: CH4916


title: CH5462


title: CH4891


title: CH4877


title: CH4862


title: CH4840


title: CH4860


title: CH4785


title: CH5478


title: CH4780


title: CH4757


title: CH4704


title: CH4703


title: CH4745


title: CH5159


title: CH4755


title: CH4681


title: CH4766


title: CH4733


title: CH4992


title: CH4634


title: CH4990


title: CH4584


title: CH4591


title: CH4560


title: CH4528


title: CH4509


title: CH4549


title: CH4443


title: CH4433


title: CH4446


title: CH4438


title: CH4520


title: CH4411


title: CH4418


title: CH4684


title: CH4083


title: CH3648


title: CH3797


title: CH3570


title: CH3906


title: CH3882


title: CH3613


title: CH3549


title: CH4602


title: CH3484


title: CH3466


title: CH4548


title: CH4489


title: CH4035


title: CH3462


title: CH3325


title: CH2939


title: CH3173


title: CH2922


title: CH3290


title: CH3177


title: CH2875


title: CH2860


title: CH2829


title: CH2824


title: CH2764


title: CH2748


title: CH2680


title: CH2687


title: CH2747


title: CH2672


title: CH2674


title: CH2706


title: CH2724


title: CH2734


title: CH2699


title: CH2735


title: CH2756


title: CH2730


title: CH2678


title: CH2690


title: CH2682


title: CH2707


title: CH2718


title: CH2657


title: CH2639


title: CH2698


title: CH2713


title: CH2705


title: CH2675


title: CH2665


title: CH2848


title: CH2685


title: CH2677


title: CH2623


title: CH2598


title: CH2658


title: CH2597


title: CH2560


title: CH2660


title: CH2543


title: CH2608


title: CH2500


title: CH2522


title: CH2582


title: CH2591


title: 85884

status: Public on Mar 22 2019

description: TDP43 with R151A mutation, fused to EGFP

data_processing:
RNA-Seq was performed using Illumina 4000 High-seq platform
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Expression quantitation was performed with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: htseq raw counts

growth_protocol: HEK293T cells were maintained in DMEM (GIBCO), 10% FBS, 100 units/mL Penicillin/Streptomycin at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T cells were transiently transfected with EGFP or TDP43 variants using Lipofectamine 2000 (Invitrogen) 48h prior to isolation of RNA

value: Human embryonic kidney (HEK) 293T cells

tag: passages

tag: transfection


title: CF592_Iso2

value: Germany:University hospital Essen


title: CH2527


title: 85885

description: TDP43 with D247A mutation, fused to EGFP


title: CF609_Iso3


title: 85876

description: Enhanced green fluorescent protein,  (EGFP) as a negative control

source_name: GFP

value: EGFP


title: 85883

description: RNA binding deficient TDP43 with F147L and F149L mutations, fused to EGFP

source_name: FL


title: 85882

description: WT TDP43 fused to EGFP

source_name: WT


title: 85881


title: 85880


title: 85878


title: 85877

description: WT TDP43 fused to EGFP


title: 85874


title: 85875


title: 85873


title: 85872

description: WT TDP43 fused to EGFP


title: 85871


title: CH2502

value: clinical isolate


title: 85879