title: Cirrhosis-NASH 3

status: Public on Jul 09 2021

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to hg19 whole genome using, for RNA-Seq reads, tophat2 with default settings and using additional transcript annotation data for the hg19 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against hg19 with the --local and --very-sensitive options.
Reads overlapping the Ensembl build 75 human 3' UTRs +/- a 500bp window were counted and the final gene counts table was calculated based on the 3' UTR counts. The counts table was normalized using DESeq normalization and analyzed for differential expression using the PANDORA method from the metaseqR Bioconductor package (Moulos and Hatzis, 2015, PMID: 25452340). The final list of differentially expressed genes was derived by the genes demonstrating a PANDORA p-value less than 0.05 and an absolute fold change of 0.58 in log2 scale (or 1.5 times up/down in natural scale).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized 3'UTR counts for each Ensembl gene for RNA data.

source_name: Liver

growth_protocol: Liver specimens (1-2 cm3) were washed once with DMEM (Sigma) supplemented with 1% FCS and with 1% Penicillin Streptomycin (PS, Sigma), minced and incubated at 37°C with the digestion solution (collagenase 2,5 mg/ml in HBSS). Incubation was performed for 30 minutes, further mincing and mixing the tissue every 10 minutes. To recover the cells, digestion solution was passed through a 70M strainer in a 50 ml tube (GreinerBio) and washed with 45 ml Advanced DMEM (Gibco) supplemented with 1% PS, 10 mM HEPES (Gibco) and 1% GlutaMax (Gibco), henceforth Ad+++. Partially digested tissue was recovered from the strainer and further incubated with TrypLE Express (Thermoscientific) for 15 minutes at 37°C. Cells obtained from the first and second digestion were pooled together and washed twice with Ad+++. After the second centrifugation (200g, 5 minutes) cells were counted, mixed with an appropriate amount of BME solution (2/3 Basement Membrane Extract, Type 2 (Pathclear) diluted with 1/3 Ad+++) and seeded in 25ul drops containing 10000-15000 cells in 48 well suspension plates (GreinerBio). After BME solution had solidified, wells were filled with 250 l of human liver organoid isolation medium consisting Ad+++ supplemented of 1X B27 supplement without retinoic acid (Gibco), 1X N2 supplement (Gibco), 1.25-mM N-acetyl-L-cysteine (Sigma), 10% (vol/vol) Rspo-1 conditioned medium (Huch et al, Nat Methods), 10% (vol/vol) Wnt3a-conditioned medium (Huch et al, Nat Methods), 10-mM nicotinamide (Sigma), 10-nM recombinant human (Leu15)-gastrin I (Sigma), 50 ng/ml recombinant human EGF (Peprotech), 100 ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human HGF (Peprotech), 10 μM Forskolin (Sigma), 5 μM A8301 (Tocris), 25 ng/ml Noggin (Peprotech) and 10-μM Y27632 (Sigma). After 1 week, isolation media was changed to human liver expansion media (EM; Ad+++ supplemented of 1X B27 supplement without retinoic acid (Gibco), 1X N2 supplement (Gibco), 1.25-mM N-acetyl-L-cysteine (Sigma), 10% (vol/vol) Rspo-1 conditioned medium, 10-mM nicotinamide (Sigma), 10-nM recombinant human (Leu15)-gastrin I (Sigma), 50 ng/ml recombinant human EGF (Peprotech), 100 ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human HGF (Peprotech), 10 μM Forskolin (Sigma) and 5 μM A8301 (Tocris)).   EM was changed twice a week, and cultures were split every 7-10 days according to organoid density.

extract_protocol:
For each RNA preparation, 2 wells of organoids in expansion phase were collected in Trizol reagent (Sigma) 4-5 days after splitting. RNA was extracted according to manufacturer’s instruction and resuspended in 30ul of nuclease free water. Total RNA was quantitated (ND1000 Spectrophotometer – PEQLAB). Samples were diluted accordingly to a mean concentration of approximately 100-150ng/μl and their quality assessed on a Bioanalyzer (Agilent Technologies) using the Agilent RNA 6000 Nano Kit reagents and protocol (Agilent Technologies).
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI™ Hi-Q™ OT2 200 Kit (ThermoFisher Scientific) on Ion OneTouch 2 System. Sequencing was performed using the Ion PI™ Hi-Q™ Sequencing 200 Kit and Ion PI™ Chip Kit v3 (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.

treatment_protocol: Organoids were seeded as described above from biopsy liver (healthy donor or infected patient) tissue. During growth EM was changed twice a week, and cultures were split every 7-10 days according to organoid density and were harvested at passages 2-5.

value: cirrhotic liver due to NASH-HCC

value: cirrhotic liver, NASH

value: liver


title: 01-Epithelium

status: Public on Oct 25 2021

type: SRA

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

country: Netherlands

institute: MERLN Institute

library_source: transcriptomic

data_processing:
BCL files resulting from sequencing were transformed to FASTQ files with 10x Genomics Cell Ranger mkfastq.
FASTQ files were mapped with Cell Ranger count. During sequencing, 28 bp read 1 were used for identification of the Illumina library barcode, cell barcode and UMI. Read 2 was used to map to the reference transcriptome GRCh38. Filtering of empty barcodes was done in Cell Ranger.
The data from all samples were loaded in R (version 3.6.2) and processed using the Seurat package (version 3.2.0). More specifically, cells with at least 1000 UMIs per cell and less than 20% mitochondrial gene content were retained for analysis. The data of all 10x libraries was merged and processed together. The merged dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. The patient effect was corrected using the integration function of Seurat and used for dimensionality reduction and clustering of all cells or cells selected per layer. Cells were clustered using graph-based clustering and the original Louvain algorithm was utilized for modularity optimization.
Genome_build: Human: Hg38
Supplementary_files_format_and_content: filtered_counts.csv; final dataset containing the expression counts for all genes across filtered cells
Supplementary_files_format_and_content: metadata_percell.csv; file containing metadata per single cell
Supplementary_files_format_and_content: matrix.mtx.gz; barcodes.tsv.gz, features.tsv.gz; cell ranger output for each 10X library

molecule: total RNA

organism: Homo sapiens

source_name: Cornea

growth_protocol: Both male and female donor corneas, with ages ranging from 22 to 79 years and preserved either in Optisol-GS (Corneas 01, 02, 03 and 04) at 4°C or in Organ culture media (Corneas 05, 06, 07 and 08) at 31°C were used.  Organ culture media comprised the following: minimum essential medium supplemented with 20 mM HEPES, 26 mM sodium bicarbonate, 2% (v/v) newborn calf serum (Thermo Fisher Scientific), 10 IU/mL penicillin, 0.1 mg/mL streptomycin and 0.25 μg/mL amphotericin.

extract_protocol:
Manual dissection of the corneal tissue: Eight donor corneas were dissected for scRNAseq. First, cells were isolated from six corneas that were manually dissected to separate the epithelial, stromal and the endothelial layers to ensure the gentlest possible enzymatic dissociation of each layer. The corneas were vacuum fixed in a punch base (e.janach) endothelial-cell side up, stained with trypan blue solution (0.4%) for 30 s and washed with BSS ophthalmic irrigation solution. The corneal endothelium was then gently lifted following the Schwalbe line using a DMEK cleavage hook (e.janach) and fully stripped using angled McPherson tying forceps. The remaining tissue was trephined using a 9.5 mm Ø Barron vacuum punch (Katena) in order to separate the epithelium and stroma from the scleral ring. The remaining two corneas were used for limbus isolation. A surgical scalpel was used to cut the limbus into approximately 1 × 2 mm fragments, which were then rinsed with PBS.    Tissue dissociation to single cells: The six manually dissected corneal tissues were enzymatically treated to obtain single cell suspensions. The stripped corneal endothelium was incubated with 2 mg/mL collagenase (Sigma) solution in human endothelial serum free media (SFM) (Thermo Fisher Scientific) for 1–2 h at 37°C followed by a 10 min incubation with Accutase (Thermo Fisher Scientific) at 37°C to obtain a single cell suspension. The cells were centrifuged for 5 min at 800 × g and resuspended in 0.5 mL of human endothelial SFM media.    The corneal epithelium–stroma tissues were treated with 1.5 mg/mL collagenase and 0.2 mg/mL bovine testis hyaluronidase (Sigma) in DMEM/F12 (Thermo Fisher Scientific) for approximately 1 h at 37 °C. The released corneal epithelium was suctioned with a P1000 micropipette and further treated with Accutase for 10 min at 37°C to obtain a single cell suspension of corneal epithelial cells. The cells were centrifuged for 5 min at 800 × g and resuspended in 0.5 mL of DMEM/F12. The remaining corneal stroma was treated with 1.5 mg/mL collagenase and 0.2 mg/mL bovine testis hyaluronidase in DMEM/F12 for 5–7 h to obtain a single cell suspension of corneal keratocytes. After the incubation, the cells were centrifuged for 5 min at 800 × g and resuspended in 0.5 mL of DMEM/F12 media.    The limbus fragments isolated from the two corneas for limbal isolation were digested with four trypsinization cycles. In each cycle, the limbus fragments were incubated in 10 mL of 0.05% trypsin/0.01% EDTA (Thermo Fisher Scientific) at 37°C for 30 min. The trypsin containing dissociated cells were transferred to a 50 mL centrifuge tube containing 10 mL DMEM/F12 media and centrifuged for 5 min at 300 × g, after which the cells were resuspended in 0.5 mL of DMEM/F12 media. The undigested limbal fragments were placed again in 10 mL of 0.05% trypsin/0.01% EDTA for the following trypsinization cycle. The cells isolated from the limbus of the two donor corneas were pooled for the following steps.    Methanol cell fixation  After dissociation, the single cell suspensions were passed through a 100 μm Ø cell strainer, centrifuged for 5 min at 300 × g and resuspended in 1 mL ice-cold PBS to eliminate any medium remnants. Next, the cells were again centrifuged for 5 min at 300 × g and resuspended in ice-cold PBS at a ratio of 200 μL PBS per 1×10^6 cells followed by the dropwise addition of ice-cold methanol, at a ratio of 800 μL per 1×10^6 cells. The cells were stored at -80°C until sequencing.
Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3’ V3.1 chemistry protocol. Prior to loading the cells on the 10x Chromium controller, cells were rehydrated in rehydration buffer. Cells were then counted to assess cell integrity and concentration. Approximately 9,000 cells (comprising 3,000 cells from each of the three layers) from corneas 01, 02, 03 and 04 were separately loaded by layer and cornea. Furthermore, 3,000 cells (1,000 cells from each of the three layers) from corneas 05 and 06, and 3,000 cells from corneas 07 and 08 (from the limbal samples) were separately loaded by cornea. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol.

treatment_protocol: Not applicable to this study.

tag: sample number

tag: gender

value: Female

tag: age

tag: tissue

value: cornea

tag: dissected tissue

value: Epithelium


title: Cirrhosis-NASH 4

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr Molewaterplein 40

institute: Erasmus Medical Center

tag: strain

tag: genotype


title: Cirrhosis-NASH 2


title: Cirrhosis-NASH 1


title: Healthy donor 22

value: Healthy donor liver

value: Healthy donor


title: Infected patient-BCC5

value: HBV infected liver

value: HBV infected


title: WT25-RA-8hr

status: Public on May 05 2021

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

country: USA

institute: University of Pennsylvania School of Veterinary Medicine

description: WT RA 8h

data_processing:
1172.7 million reads were able to be assigned to genomic coordinates corresponding to mouse genomic assembly (version GRCm38.p4) using STAR (v 2.5.1b)
Reads per gene were summarized using feature counts against mouse genes described in the Gencode database (version M4)
Differentially expressed genes were identified using DESeq method.
A p-adjusted (pAdj) value of ≤ 0.05 and a log2 fold change of ± 1 (-2 ≤ fold change ≥ 2) was used as filtering criteria to identify significantly differentially expressed genes.
An ANOVA was performed and the interaction-term was used to produce significance values to sort genes where the two genotypes (WT and Stra8-KO) differ signficiantly in their response to RA (WT vs RA) - see file ANOVA_interaction_term_data.xlsx
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Excel file containing contrasts and gene expression data

organism: Mus musculus

source_name: Germ cell culture

growth_protocol: Germ cell culture derived from THY1+ testis cells derived from wildtype or Stra8-knockout mice. Cells maintained in mouse serum free media with 20ng/ml GDNF, 150ng/ml GFRA1 and 1ng/ml FGF2 on STO feeder cells. Cells used in this study were between passage P3 and P12.

extract_protocol:
Total RNA from all samples were isolated on the same day using miRNeasy kit from Qiagen (Cat# 217004). Quality of RNA was checked on 2100 Bioanalyzer (Agilent Technologies) and only samples with RNA integrity number (RIN) at or above 9.2 were selected for library preparation.
True Seq Stranded mRNA LT kit (Cat# RS-122-2101) from Illumina Technologies following the manufacturer’s protocol

treatment_protocol: Cells were treated for a length of time indicated by the variable 'time point' with either 0.01% DMSO or 0.01M all trans retinoic acid.

tag: replicate

value: WT

tag: treatment

value: RA

tag: time point


title: Infected Donor 3

value: Donor liver, cleared HBV

value: cleared HBV


title: WT25-RA-4hr

description: WT RA 4h


title: Infected Donor 2


title: Infected Donor 4


title: WT25-NTC-0hr

description: WT non-treated control 0h

value: NTC


title: 06-3 layer pool

value: 3 layer pool


title: WT25-DMSO-8hr

description: WT DMSO 8h

value: DMSO


title: MseI5old: Total population sample E

status: Public on Nov 22 2021

library_source: genomic

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
The FASTQ files were processed to remove gene trap vector primers. To this end, we used R/Bioconductor packages ShortRead and Biostrings to match primer sequences within the sequenced reads, allowing for two mismatches at maximum for each primer sequence. The identified primers were trimmed and reads shorter than 15 bp were discarded. The remaining reads were aligned to the human reference genome version hg19 retrieved from the Illumina iGenomes repository, using bwa mem.
The produced BAM files were subjected to integration site identification. To this end, we re-implemented the HaSAPPy algorithm in R. We added attributes for i) filtering out read artifacts from introns, based on the overall intronic read distribution for each sample, ii) selecting the fraction of neighboring (Independent Insertions, Disrupting Insertions, Bias) triplets for LOF analysis and iii) library normalization across samples. After the quality control steps, our HaSAPPY reimplementation assigns a Local Outlier Factor (LOF) score to each gene in a sample based on a triplet score derived from the number of putative GT integrations in the sample compared to the reference, additionally taking into account the potential bias arising from unbalanced sense and anti-sense read numbers.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing HaSAPPy triplet read counts.

molecule: genomic DNA

source_name: myeloid leukemia

growth_protocol: KBM7 (a kind gift from Thijn Brummelkamp) and Hap-Lat (latently HIV-1-infected KBM7-derived cell line) cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) (ThermoFisher Scientific) supplemented with 10% fetal calf serum (FCS) and 2% penicillin-streptomycin (Pen/Strep). Haploidy of KBM7 cells was maintained by periodically sorting cells for size (5% smallest). Ploidy of cells was determined by propidium iodide staining using Jurkat cells as a diploid control.

extract_protocol:
Genomic DNA was isolated from 5 million cells using the DNeasy kit (Qiagen). Four micrograms of genomic DNA (gDNA) was digested with NlaIII or MseI. After PCR spin column purification (Qiagen), 50 ml of eluted digested DNA was ligated using T4 DNA ligase (Roche) in a volume of 2 ml. The reaction mix was purified using spin columns and used as the template in a PCR with primers annealing to internal sequences in the gene-trap vector (59-CTGCAGCATCGTTCTGTGTT-39 and 59-TCTCCAAATCTCGGTGGAAC-39). The resulting PCR products were used for library preparation.
Sequencing libraries were created using the Ion Plus Fragment Library Kit (ThermoFisher Scientific) according to manufacturer’s instructions, with minor modifications: briefly, 15 ng of the PCR products were diluted with ddH2O to a final volume of 39 μl. The samples were end repaired, adaptor ligated and amplified; this was followed by 2 rounds of purification using Agencourt AMPure XP beads. Library qualities and quantities were assessed by Bioanalyzer, using the DNA High Sensitivity Kit (Agilent Technologies). The quantified libraries were pooled together in 10plex, at a final concentration of 40 pM. Templating, enrichment and chip loading was performed on an Ion Proton Chef system using the Ion PI™ Hi-Q™ Chef Kits (ThermoFisher Scientific); sequencing was performed on an Ion Proton PI™ V3 chip, with the Ion PI™ Hi-Q™ Sequencing 200 Kit, on an Ion Proton instrument (ThermoFisher Scientific), according to manufacturer’s instructions.

treatment_protocol: Minimal HIV-1 (LTR-GFP, HIV-1-658) virus was produced by transfection of 293T cells in 15-cm culture dishes using polyethylenimine (PEI) (Sigma-Aldrich) with a mixture of 6.8 mg p658, 2 mg vesicular stomatitis virus G (VSVG), and 4.5 mg Gag-Pol plasmids. Haploid KBM7 cells were infected with HIV-1-derived virus at low MOI such that approximately 5 to 10% of cells became productively infected as determined by GFP expression. Five days after infection, the GFP-negative cell population harboring uninfected and potentially latently infected cells was sorted by flow cytometry-activated cell sorting (FACS) and stimulated with 350 nM suberoylanilide hydroxamic acid (SAHA) (Selleck Chem), and 5 ng/ml TNF-a (Sigma-Aldrich). Twenty-four hours poststimulation, GFP-positive cells were single cell-sorted by FACS into 96-well plates. Clones were expanded and characterized for their basal GFP expression and their potential for reactivation. From the clonal cell lines generated, Hap-Lat was selected for low background and relative high reactivation upon stimulation (GFP-negative under basal conditions but amenable to induction to express GFP upon activation). Gene-trap virus was produced by transfection of HEK293FT cells in 15-cm culture dishes using 180 ml polyethylenimine (PEI) with a mixture of 8 mg pGT-mCherry, 2.1 mg pAdvantage, 3.1 mg cytomegalovirus (CMV)-VSVG, and 4.8 mg Gag-Pol plasmids in at total volume of 1 ml serum-free RPMI medium. After 12 h the growth medium was changed to fresh FCS and G418-supplemented RPMI. The virus was collected at 12, 24, 36, and 48 h. For the GT mutagenesis, 192 million Hap-Lat cells were preincubated with 100 mM deoxynucleoside triphosphates (dNTPs) (Invitrogen) 1 h before transduction. Cells were resuspended in 192 ml of undiluted GT virus. Spin infection was performed for 90 min at 1,500 rpm in 24-well plates containing 2 million cells per well and 8 ml protamine sulfate per ml. After 24 h cells were subjected to a second round of infection after which virus was removed, and cells were left to recover in supplemented IMDM. We estimate that this sequential infection resulted in 1 to 4 GT integrations per cell, with the majority of cells containing one integration. A first round of sorting was performed 8 days after the second infection. Subsequently, between 500,000 and 1 million GFP-mCherry double-positive cells were sorted each day for 5 consecutive days using two cell sorters (BD FACSAria II SORP and BD FACSAria III). Sorted cells were pooled, left to recover, and expanded for the next round of sorting. A second round of sorting was performed 17 days after the second infection. Between 2.6 and 3 million cells were collected each day for 3 consecutive days using two sorters. These cells were pooled and left to recover and expand for a third round of sorting on day 22 after the second infection, yielding 6.1 million cells from 1-day sorting on two machines. On day 29 after the second infection a fourth round of sorting was performed, yielding 7.2 million cells from 1-day sorting on two machines. After the cells of the fourth round of sorting were left to recover and expand, a subpopulation of highly mCherry and GFP double-positive cells were apparent. In a final fifth round of sorting the total GFP-positive, mCherry-positive population (10.1 million cells) was sorted as soon as enough cells were available (day 33 after the second infection) while the GFP-mCherry-positive stable subpopulation (5.9 million cells) was cultured for several more days and sorted (>>35 days after the second infection). After recovery, genomic DNA was isolated from the sorted cell populations, as well as from a population of mutagenized unsorted cells.

tag: cell line

tag: cell type

value: myeloid leukemia

value: genetrap


title: WT25-DMSO-24hr

description: WT DMSO 24h


title: WT25-RA-24hr

description: WT RA 24h


title: WT25-DMSO-4hr

description: WT DMSO 4h


title: WT23-RA-24hr

description: WT RA 24h


title: WT23-RA-8hr

description: WT RA 8h


title: WT23-RA-4hr

description: WT RA 4h


title: WT23-NTC-0hr

description: WT non-treated control 0h


title: WT23-DMSO-24hr

description: WT DMSO 24h


title: WT17-RA-24hr 2

description: WT RA 24h


title: WT23-DMSO-8hr

description: WT DMSO 8h


title: WT23-DMSO-4hr

description: WT DMSO 4h


title: BMP4-treated micropatterned hPSCs (700um diameter) after 42h

status: Public on Aug 14 2021

city: Ann Arbor

first: Idse

last: Heemskerk

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
Reads were aligned using cellranger-4.0.0 and produced filtered_feature_bc_matrix.h5 with default settings
filtered_feature_bc_matrix.h5 was processed in python using primarily scprep, library size was filtered to allow 20k and 50k, mitochondrial expression between 150 and 950 (as measured in scprep), gene expressed in fewer than 50 cells were excluded
data was sqrt transformed
clustering was performed using Louvain and visualization using PHATE, both on a subset of genes (see biorxiv link above)
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data is a feature-barcode (gene-cell) matrix in h5 format

source_name: hESCs

extract_protocol:
Cells were collected using accutase and resuspended in ice cold PBS
Cells were barcoded using the 10x Genomics Chromium system (part numbers 1000268, 1000120, 1000215). For quality control cDNA was quantified by Qubit High Sensitivity DNA assay and Agilent TapeStation

value: BMP4 50ng/ml


title: WT17-RA-8hr

description: WT RA 8h


title: WT17-RA-4hr

description: WT RA 4h


title: WT17-NTC-0hr

description: WT non-treated control 0h


title: WT17-DMSO-24hr

description: WT DMSO 24h


title: KO21-RA-24hr

description: Stra8-KO RA 24h


title: KO21-RA-4hr

description: Stra8-KO RA 4h


title: WT17-DMSO-4hr

description: WT DMSO 4h


title: KO21-RA-8hr

description: Stra8-KO RA 8h


title: KO21-NTC-0hr

description: Stra8-KO non-treated control 0h


title: KO21-DMSO-8hr

description: Stra8-KO DMSO 8h


title: KO21-DMSO-4hr

description: Stra8-KO DMSO 4h


title: KO20-RA-24hr

description: Stra8-KO RA 24h


title: KO21-DMSO-24hr

description: Stra8-KO DMSO 24h


title: KO20-RA-4hr

description: Stra8-KO RA 4h


title: KO20-RA-8hr

description: Stra8-KO RA 8h


title: KO20-DMSO-24hr

description: Stra8-KO DMSO 24h


title: KO20-DMSO-8hr

description: Stra8-KO DMSO 8h


title: KO20-DMSO-4hr

description: Stra8-KO DMSO 4h


title: KO12-RA-24hr

description: Stra8-KO RA 24h


title: KO12-RA-4hr

description: Stra8-KO RA 4h


title: KO12-NTC-0hr

description: Stra8-KO non-treated control 0h


title: KO12-DMSO-24h

description: Stra8-KO DMSO 24h


title: WT17-RA-24hr 1

description: WT RA 24h


title: KO12-DMSO-8h

description: Stra8-KO DMSO 8h


title: KO12-DMSO-4h

description: Stra8-KO DMSO 4h


title: 1357: COMET_1357_CD45_Day7

status: Public on Mar 03 2021

city: San Francisco

first: Beth

middle: Shoshana

last: Zha

state: CA

address: 400 Parnassus Ave

department: Medicine

institute: University of California San Francisco

description:
single cell RNA sequencing
*** Raw data is not included in this GEO submission due to patient privacy concerns ***

data_processing:
alignment using STAR aligner to a custom genome containing GRCh38 and SARS2 isolate Wuhan-Hu-1
Genome_build: mm9
Supplementary_files_format_and_content: Readcount matrices generated through 10X genomics cellranger pipeline v3.0

source_name: Tracheal Aspirate

extract_protocol:
Single cell suspension was counted and loaded onto a 10X Genomics Chip A aiming to caputre 10,000 cells (10X Genomics).
10X Genomics

treatment_protocol: TA was freshly processed in a BSL-3, dissociated in collagenase type 4 and DnaseI, filtered, and cells washed and purified for CD45 using MojoSort (Biolegend)

tag: patient id

tag: disease state

value: COVID-19 ARDS

value: M

tag: race

value: Other

tag: hispanic ethnicity

value: Y

tag: 30 day mortality

value: N

tag: development of vap

tag: lrti pathogen

value: Citrobacter koserii

tag: reason for intubation

tag: sample obtained days before vap

tag: sample obtained days since intubation

value: Tracheal Aspirate


title: 1320: COMET_1320_CD45_Day13

tag: age

tag: gender

value: White

tag: tissue


title: 1357: COMET_1357_CD45_Day2


title: 1290: COMET_1290_CD45_Day7

value: F


title: WT17-DMSO-8hr

description: WT DMSO 8h

tag: replicate

tag: genotype

value: WT

tag: treatment


title: 1271: COMET_1271_CD45_Day16

value: Black


title: 1271: COMET_1271_CD45_Day12


title: 1233: COMET_1233_CD45_Day0

value: Serratia marcescens


title: 1264: COMET_1264_CD45_Day14

value: Pseudomonas aeruginosa


title: 1161: COMET_1161_CD45_Day3


title: 1154: COMET_1154_CD45_Day13

value: Klebsiella aerogenes


title: 1172: COMET_1172_CD45_Day5


title: 1154: COMET_1154_CD45_Day6


title: 1115: COMET_1115_CD45_Day6


title: KO20-NTC-0hr

description: Stra8-KO non-treated control 0h

value: NTC

tag: time point


title: 1072: COMET_1072_CD45_Day10

tag: patient id


title: 1072: COMET_1072_CD45_Day4

tag: disease state


title: 1002: COMET_1002_CD45_D0

tag: race


title: 1047: COMET_1047_CD45_Day2

tag: hispanic ethnicity

value: Methicillin susceptible Staphylococcus aureus


title: KO12-RA-8hr

description: Stra8-KO RA 8h

value: RA


title: MBAL473: MBAL473

description:
bulk RNA sequencing
*** Raw data is not included in this GEO submission due to patient privacy concerns ***

data_processing:
Pseudoalignment with kallisto 0.46.1
Genome_build: ENSEMBL v.99
Supplementary_files_format_and_content: Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport30, with the scaledTPM method.

extract_protocol:
RNA was extracted with Zymo Pathogen Magbead Kit, treated with DNAse, and ribodeplted with FastSelect
NEBNext Ultra II RNAseq Kit

treatment_protocol: TA was collected and mixed 1:1 with DNA/RNA shield

value: ARDS not due to COVID

tag: study group

value: control


title: MBAL563: MBAL563

value: Mechanically ventilated control:neurosurgical procedure

tag: development of vap


title: MBAL555: MBAL555


title: MBAL477: MBAL477

value: Mechanically ventilated control:retroperitoneal bleed

value: M


title: MBAL413: MBAL413

value: N


title: MBAL414: MBAL414

value: Tracheal Aspirate


title: MBAL227: MBAL227

value: White


title: 1254: RR100e_00582

value: COVID-19 ARDS

value: Other

value: Y

value: VAP - longitudinal


title: MBAL462: MBAL462

value: Mechanically ventilated control:subdural hematoma

value: Asian


title: 1158: COMET_1158_CD45_Day4

tag: 30 day mortality

tag: lrti pathogen


title: 1233: RR100e_00519

tag: sample obtained days before vap


title: 1254: RR100e_00537

value: VAP - early

tag: sample obtained days since intubation


title: 1244: RR100e_00581

tag: age

value: F

value: No VAP - late


title: 1254: RR100e_00556

tag: gender


title: 1233: RR100e_00495

value: VAP - late

tag: tissue


title: 1233: RR100e_00505


title: 1196: RR100e_00563


title: 1223: RR100e_00489

value: White, American Indian/Alaska Native

value: No VAP - early


title: 1196: RR100e_00558


title: 1196: RR100e_00515


title: 1001: COMET_1001_CD45_D0

tag: reason for intubation


title: 1196: RR100e_00498


title: 1196: RR100e_00508


title: 1196: RR100e_00460


title: 1196: RR100e_00481


title: 1223: RR100e_00504

value: No VAP - longitudinal


title: 1196: RR100e_00523


title: 1185: RR100e_00470


title: 1185: RR100e_00433


title: 1172: RR100e_00438

value: M


title: 1158: RR100e_00436

value: N


title: 1172: RR100e_00428

value: Tracheal Aspirate


title: 1158: RR100e_00579

value: White


title: 1196: RR100e_00454

value: COVID-19 ARDS


title: 1158: RR100e_00344


title: 1158: RR100e_00329


title: 1154: RR100e_00578

value: Other


title: 1158: RR100e_00323

value: Y


title: 1154: RR100e_00337

value: VAP - longitudinal


title: 1154: RR100e_00332


title: 1154: RR100e_00304


title: 1154: RR100e_00324


title: 1154: RR100e_00314


title: 1115: RR100e_00268


title: 1154: RR100e_00301


title: 1115: RR100e_00264


title: 1115: RR100e_00263


title: 1136: RR100e_00294


title: 1115: RR100e_00265


title: 1072: RR100e_00206


title: 1115: RR100e_00262


title: 1115: RR100e_00260


title: 1115: RR100e_00231


title: 1072: RR100e_00204


title: 1072: RR100e_00156


title: 1154: RR100e_00421


title: 1115: RR100e_00230


title: 1115: RR100e_00219


title: 1072: RR100e_00151


title: 1158: RR100e_00422


title: 1072: RR100e_00157


title: 1072: RR100e_00149


title: 1072: RR100e_00146


title: 1072: RR100e_00148


title: 1072: RR100e_00153


title: 1072: RR100e_00152


title: 1072: RR100e_00155


title: 1072: RR100e_00154


title: 1059: RR100e_00198


title: 1059: RR100e_00195


title: 1059: RR100e_00196


title: 1072: RR100e_00150


title: 1072: RR100e_00205


title: 1059: RR100e_00199


title: 1072: RR100e_00159


title: 1059: RR100e_00197


title: 1072: RR100e_00158


title: 1059: RR100e_00193


title: 1059: RR100e_00192


title: 1059: RR100e_00190


title: 1047: RR100e_00091


title: 1047: RR100e_00090


title: 1059: RR100e_00189


title: 1047: RR100e_00089


title: 1047: RR100e_00081


title: 1047: RR100e_00078


title: 1047: RR100e_00088


title: 1047: RR100e_00087


title: 1047: RR100e_00086


title: 1002: RR100e_00010


title: 1038: RR100e_00074


title: 1047: RR100e_00079


title: 1002: RR100e_00009


title: 1002: RR100e_00011


title: 1001: RR100e_00006


title: 1059: RR100e_00194


title: 1002: RR100e_00008


title: 1059: RR100e_00191


title: 1001: RR100e_00003


title: 1001: RR100e_00005


title: 1002: RR100e_00007


title: 1001: RR100e_00002


title: 1001: RR100e_00001


title: Donor 2- RK-33 treated- 18 hours

status: Public on Feb 26 2021

data_processing:
Reads were mapped against the UCSC genome browser  GRCh38 reference genome with HiSat2 (version 2.1.0).
Gene expression was quantified using htseq-count (version 0.11.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene expression values for each Sample.

source_name: primary CD4+ T cells

growth_protocol: Primary CD4+ T cells were isolated from buffy coats from healthy donors by Ficoll gradient (GE Healthcare) followed by negative selection with RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCells Technologies). Primary CD4+ T cells were cultured in RPMI-1640 media supplemented with 7% FBS and 100 µg/ml penicillin-streptomycin at 37 oC in a humidified 95%-air-5%CO2 incubator.

extract_protocol:
Three million primary CD4+ T cells for Donor 1 and Five million primary CD4+ T cells from Donor 2 were collected 4 hours and 18 hours post treatement with DDX3 inhibitors RK-33 and FH-1321 in TRI reagent and RNA was extracted according to manufacturer's protocols.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina HiSeq2500 sequencer.

treatment_protocol: Primary CD4+ T cells from two healthy blood donors were left untreated or treated with DDX3 inhibitors RK-33 (2uM) and FH-1321 (1uM) for 4 hours and 18 hours.

tag: cell type

value: primary CD4+ T cells

tag: time

value: 18 hours

tag: individual

value: Donor 2


title: Donor 2- FH-1321 treated- 18 hours

tag: treatment


title: Donor 2- Mock treated- 18 hours

value: Mock


title: Donor 1- FH-1321 treated- 18 hours

value: Donor 1


title: Donor 2- RK-33 treated- 4 hours

value: 4 hours


title: Donor 2- Mock treated- 4 hours


title: 1047: RR100e_00077

tag: patient id

tag: disease state

value: F


title: Donor 2- FH-1321 treated- 4 hours


title: Donor 1- RK-33 treated- 18 hours


title: Donor 1- Mock treated- 18 hours


title: Donor 1- Mock treated- 4 hours


title: Donor 1- FH-1321 treated- 4 hours


title: Donor 1- RK-33 treated- 4 hours


title: Tibialis anterior WT ASO Control 7w rep 4

status: Public on Dec 15 2020

city: ILLKIRCH

first: Jocelyn

last: Laporte

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description:
WT ASO Control 4
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx

data_processing:
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_gene_counts_matrix_Cohort_DNM2.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.

source_name: Tibialis anterior

extract_protocol:
RNA was extracted from Tibialis anterior muscles using TRI Reagent (Molecular Research Center, Cincinnati, USA).
RNA sequencing library have been prepared using the TruSeq Stranded mRNA Sample Preparation Kit.

tag: strain

tag: genotype

value: WT

tag: Sex

value: Male

value: Tibialis anterior muscles

value: ASO Control


title: Tibialis anterior WT ASO Control 7w rep 3

description:
WT ASO Control 3
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO1 7w rep 3

description:
Dnm2SL/+ ASO1 3
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO1 7w rep 2

description:
Dnm2SL/+ ASO1 2
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 6

description:
Dnm2SL/+ ASO Control 6
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior WT ASO1 7w rep 2

description:
WT ASO1 2
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 3

description:
Dnm2SL/+ ASO Control 3
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO1 7w rep 1

description:
Dnm2SL/+ ASO1 1
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 4

description:
Dnm2SL/+ ASO Control 4
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 5

description:
Dnm2SL/+ ASO Control 5
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior WT ASO Control 7w rep 1

description:
WT ASO Control 1
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 2

description:
Dnm2SL/+ ASO Control 2
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: T-Short Frozen 4c

status: Public on Mar 15 2022

data_processing:
Fastq files generated with BaseSpace (Illumina)
Count matricies generated with indrops.py (github.com/indrops) using the rat and mouse genome builds listed below using Bowtie v1.2.3. These are the processed files listed above (i.e. tsv files)
QC, filtering and UMAP generated with Seurat v.3.1
Pseudotime generated with Monocle v3
Pathway analysis using Ingenuity Pathway Analysis (Qiagen)
Genome_build: Rattus norvegicus 6.0 DNA primary assembly (Rattus_norvegicus.Rnor_6.0.dna_sm.primary_assembly.fa.gz) along with the corresponding GTF file (Rattus_norvegicus.Rnor_6.0.85.gtf.gz) from Ensembl along with the Mus_musculus.GRCm38.dna_sm.primary_assembly.fa and Mus_musculus.GRCm38.85.gtf.gz GTF files for mouse.
Supplementary_files_format_and_content: csv file containing contrasts between each treatment and the 0ng FGF control

molecule: polyA RNA

organism: Rattus rattus

source_name: testis

growth_protocol: Fresh tissue from rat testes were used as appropriate. Cells were digested in collagenase, trypsin and Miltenyi Dead Cell Removal Kit before encapsulation. For transplantation experiments, EpCAM+ cells were used to transplant into J:Nu nude mice and allowed to grow for 2+ months before being harvested in the same manner.

extract_protocol:
Cells were encapulated in a salinized chip and RT reaction was performed at 70°C instead of 65°C but otherwise followed the inDrops protocol.
Library generated per inDrops protocol. Sequenced on NextSeq500 (Illumina) 75 cycle-cycle high output to depth of approximately 30k reads per cell

treatment_protocol: Cells for transplantation or encapsulation were either used fresh, frozen for 1-4 months or frozen for 23+ years. Cells were used unselected or following EpCAM MACS antibody selection.

tag: replicate

value: Transplanted Short Frozen

tag: selection

value: EpCAM+


title: Tibialis anterior WT ASO Control 7w rep 2

description:
WT ASO Control 2
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: Tibialis anterior Dnm2SL/+ ASO Control 7w rep 1

description:
Dnm2SL/+ ASO Control 1
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: s9_1ngFGF2

status: Public on Oct 26 2020

description: 1ng/ml FGF2

data_processing:
Salmon using GRCm38.primary_assembly.genome.fa
Genomic alignments using STAR
Differential gene expression lists were created via DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing contrasts between each treatment and the 0ng FGF control

source_name: Cultured germ cells p9-12

growth_protocol: Germ cell culture with mouse serum-free media + 20ng/ml GDNF + 150ng/ml GFRA1 + 1ng/ml FGF2 between passages 9 and 12.

extract_protocol:
RNA was extracted using miRNAeasy Mini Kit (QIAGEN, Germany)
mRNA libraries were created using TruSeq Stranded mRNA kit (Illumina, USA)

treatment_protocol: Germ cell culture with mouse serum-free media + 20ng/ml GDNF + 150ng/ml GFRA1 + treatment

value: Cultured germ cells

value: 1ng/ml FGF2

tag: passages


title: s9_20ngFGF9

description: 20ng/ml FGF9

value: 20ng/ml FGF9


title: s9_1ngFGF9

description: 1ng/ml FGF9

value: 1ng/ml FGF9


title: s8_20ngFGF9

description: 20ng/ml FGF9


title: s9_0ngFGF

description: Control (no FGF)

value: 0ng FGF


title: s8_1ngFGF2

description: 1ng/ml FGF2


title: Tibialis anterior Dnm2SL/+ ASO1 7w rep 4

description:
Dnm2SL/+ ASO1 4
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: s8_0ngFGF

description: Control (no FGF)


title: s6_1ngFGF2

description: 1ng/ml FGF2


title: s8_1ngFGF9

description: 1ng/ml FGF9


title: Tibialis anterior WT ASO1 7w rep 1

description:
WT ASO1 1
Raw_gene_counts_matrix_Cohort_DNM2_Updated-07-01-2024.xlsx


title: s7_20ngFGF9

description: 20ng/ml FGF9


title: s7_1ngFGF2

description: 1ng/ml FGF2


title: s7_1ngFGF9

description: 1ng/ml FGF9


title: s7_0ngFGF

description: Control (no FGF)


title: s6_0ngFGF

description: Control (no FGF)


title: s6_1ngFGF9

description: 1ng/ml FGF9


title: Control

description: Control (no FGF)

data_processing:
Fastq files generated with CellRanger
Count matricies generated with CellRanger and loom files created using velocyto
QC, filtering and UMAP generated with Seurat v.3.1
Pseudotime generated with Monocle v3
Genome_build: Mouse reference mm10 (GENCODE vM23/Ensembl 98)
Supplementary_files_format_and_content: csv file containing contrasts between each treatment and the 0ng FGF control

extract_protocol:
Cells were treated with BioLegend anti-KIT antibody and encapsulated with 10X Chromium Next GEM Single Cells 3' Kit v3.1 with Feature Barcoding according to respective manufacturers' protocols.
Library generated per 10X Next GEM 3.1 protocol. Sequenced on NextSeq500 (Illumina) 75 cycle-cycle high output to depth of 30k reads per cell

treatment_protocol: Germ cell culture with mouse serum-free media + treatment (see characteristics)

value: cultured germ cells


title: isFISH Positive Sample

status: Public on Aug 11 2020

city: San Diego

first: Sheng

last: Zhong

email: szhong@ucsd.edu, szhong.ucsd@gmail.com

address: 5556 Caminito Mundano

institute: UCSD

data_processing:
Single-cell clustering and visualization were done using Seurat 3
Classification of cells were done using the singleCellNet R package
The training set for singleCellNet analysis was generated using a published single-cell transcriptome dataset from 68k PBMCs
Genome_build: hg38
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

source_name: PBMC

growth_protocol: 10 mL of the LRS-WBC samples obtained from the San Diego Blood Bank were transferred to CPT vacutainer tubes (BD cat. #362753). Blood samples were mixed by inverting the tube 8-10 times immediately before centrifugation. Blood samples were centrifuged at room temperature for 25 minutes at 1800 x g. In the tissue culture hood, open a spun CPT tube and carefully discard the serum. Gently pipet up and down around the top and sides of the gel plug to dislodge and PBMCs that are stuck to it without touching the plug. Transfer to a new labeled 15 mL falcon tube and centrifuge at 400 x g for 5 minutes. Wash PBMCs twice with PBS or cell media and culture cells for 30 min in suspension flasks before labeling.

extract_protocol: We used Chromium Single Cell 3′ Reagent kit v3.1 (10x genomics) to generate single-cell RNA-seq libraries, which were sequenced using the Illumina HiSeq4000 (IGM Genomics Center, UCSD).

value: Blood

tag: group

value: isFISH Positive


title: isFISH Negative Sample

value: isFISH Negative


title: FP_2_575

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequence data with the Trimmomatic package [2]. A minimum of 50 bp read length filter was applied.
Sequence alignment to the human genome (hg38) was performed using STAR (v2.7.0)
The resulting bam file was sorted and uniquely mapped reads were counted using HTSeq and Genecode human primary genome assembly (GRCh38, v33).
Read counts were generated with featureCounts
Read counts were imported into the R software for differential analysis to identify maxRNA. A threshold of summed normalized counts > 5 was used to filter genes detected. Pre-processed data were analyzed with R/Bioconductor package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: gene counts from featureCounts

extract_protocol:
PBMC Isolation:  10 mL of the LRS-WBC samples obtained from the San Diego Blood Bank were transferred to CPT vacutainer tubes (BD cat. #362753). Blood samples were mixed by inverting the tube 8-10 times immediately before centrifugation. Blood samples were centrifuged at room temperature for 25 minutes at 1800 x g. In the tissue culture hood, open a spun CPT tube and carefully discard the serum. Gently pipet up and down around the top and sides of the gel plug to dislodge and PBMCs that are stuck to it without touching the plug. Transfer to a new labeled 15 mL falcon tube and centrifuge at 400 x g for 5 minutes. Wash PBMCs twice with PBS or cell media and culture cells for 30 min in suspension flasks before labeling.  Antisense Probe Hybridization  Oligo probe libraries were denatured at 70 °C, 5 minutes and kept at 37 °C before hybridization. Cells or PBMCs were suspended in culture media at 1 million cells/ ml and were incubated with an oligonucleotide library (final concentration 10 nM) for 1 hour at  37 °C. Cells were washed three times in 1x PBS and pelleted by centrifuging at 500 x g for 5min.  Psoralen Cross-linking:  The cell pellet was resuspended (~250 million cells) in 5 mL of ice-cold 4′-Aminomethyltrioxsalen hydrochloride (AMT) solution (0.5 mg/mL in PBS; Sigma, cat. #A4330), and incubated on ice for 15 minutes. The cell suspension was transferred to a pre-chilled 10-cm tissue culture dish, which was then placed on ice under a long-wave UV bulb (350 nm) in a UV Stratalinker 2400 (Stratagene). Cells should be approximately 3-4 cm away from the light source. Crosslinking of probe-maxRNA chimeras was performed under UV light at maximum power (6500 μW/cm2) for 10 minutes, with gentle mixing every 2.5 minutes. Cells were then transferred to cold tubes and pelleted at 330 × g for 4 minutes.  Membrane Isolation:  Cells were resuspended in 1mL hypotonic lysis buffer (10 mM Tris-HCl pH=7.5, 10 mM KCl, 2 mM MgCl2, 33 μL protease inhibitor cocktail (Sigma) and 10μL RNasin per 10 mL of solution), and incubated on ice for 15 min. Cell membranes were disrupted using a 2 mL Dounce homogenizer with a tight-fitting pestle (Size B) for 20 passes. The homogenates were transferred into an ultracentrifuge tube and centrifuged at 20,000g for 20min to remove membrane-bounded organelles. In a fresh ultracentrifuge tube, the supernatant was centrifuged again at 100,000 x g for 35min, to pellet the membrane and remove ribosomes, RNAs and other cytosolic molecules. The pellet was resuspended in storage buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, and 10 μL RNasin per 10 mL of solution). Centrifuge at 100,000 x g for 35 min. Membrane-associated RNA concentration was quantified by Qubit.  maxRNA Streptavidin Bead Pulldown:  Streptavidin C1 (Invitrogen) beads were subjected to RNase removal treatment, blocked in BSA/PBST at 4 °C until ready. The beads were washed in B&W buffer (10 mM Tris-HCl [pH 7.5], 1 mM EDTA, 2 M NaCl) and incubated membrane extracts per at 4 degrees for 1 hour and RT for 30 mins. Beads were washed three times in urea low salt wash buffer (8 M Urea, 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.10 % NP-40, 150 mM NaCl, 0.50 % SDS), three times in high salt wash buffer (10 mM Tris-HCl pH 7.5, 4 M NaCl, 1 mM EDTA, 0.2% Tween 20), and once with PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2). Reverse cross-linking were performed in the plate under a short-wave UV bulb (265 nm) in a UV Stratalinker 2400 (Stratagene).
Libraries were generated using the NEB Low Input/Single Cell library prep kit (NEB cat. #E6420S). Paired-end sequencing of the library was performed using Illumina Miniseq Platform, using the High Output reagent kit (150-cycles).


title: s6_20ngFGF9

description: 20ng/ml FGF9


title: FGF9

description: 20ng/ml FGF9

source_name: Cultured germ cells p9-13


title: FN_2_561


title: FP_1_575


title: A2_MC_MNCP

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequence data with the Trimmomatic (v0.36).
Sequence alignment to the mouse genome (GRCm38/mm10) was performed using STAR (v2.7.3a)
The gene read counts were summarized using featureCounts (v1.6.4) with GENCODE mouse gene annotation (GRCm38, release M24).
genome build: GRCm38/mm10
processed data files format and content: tsv files of gene read counts summarized by featureCounts

source_name: lymphoma cell line

growth_protocol: Cell lines were obtained through ATCC and cultured with their recommending culturing protocol and media. Murine lymphoma EL4 and human leukemia Jurkat T cells were cultured at 37 °C, 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) and RPMI 1640 medium (Corning), respectively. Both cell culture media were supplemented with 10% (vol/vol) heat-inactivated FBS, 2 mM glutamine, 1 mM sodium pyruvate, 1 mM MEM nonessential amino acids and 100 U/mL each of penicillin G and streptomycin (ThermoFisher).

extract_protocol:
Preparation of membrane-coated nanoparticle  EL4 cell membranes were utilized to generate membrane nanoparticles, following the previously described protocol [1]. EL4 mouse lymphoma cells were cultured in T175 flasks, collected (~1.2-1.5 billion total cells), and washed three times with PBS by centrifugation at 500 x g for 5 minutes. Cells were then resuspended in hypotonic lysis buffer (10mM Tris-HCl pH 7.5, 10 mM KCl, 2 mM MgCl2, 33 μL protease inhibitor cocktail  (Sigma, #S8830) and 10 μL RNAsin per 10mL of solution) and homogenized with a tight-fitting pestle for 20 passes. The homogenate is transferred into an ultracentrifuge tube and centrifuged at 20,000 x g for 20 minutes. This centrifugation removes intact cells and membrane-bounded organelles, such as mitochondria, nucleus, lysosomes, Golgi, apparatus, endoplasmic reticulum, etc. The obtained supernatant is then transferred into another ultracentrifuge tube and centrifuged at 100,000 x g for 35 mins. The supernatant containing enzymes, ribosomes and metabolites are discarded, and the pellet was resuspended with storage buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, and RNasin [Promega, cat. #N2111] at 1:1000 dilution). This step is repeated one more time and membrane protein was quantified by BCA assay.  PLGA nanoparticles were prepared by the nanoprecipitation method by adding 1 mL of PLGA (PLGA-COOH, 0.67 dL/g, 10mg/mL in acetone) into 4mL water and the organic solvent was evaporated for 2h. The membrane was diluted in storage buffer to a final protein concentration of 1mg/mL. The PLGA nanoparticles were diluted to a final concentration of 2 mg/mL in water. Mix 1 mL of the membrane and 1 mL PLGA nanoparticle and extrude through a 400 nm polycarbonate membrane for 11 passes. The membrane-coated nanoparticles (MCNPs) are centrifuged at 21,000 x g for 10 minutes. The supernatant was collected, and the pellet was resuspended in 1 mL of 10 mM Tris-HCl (pH 8.0, supplemented with RNasin at 1:1000 dilution).  RNA isolation from MNCPs  RNA was isolated by adding 500 μL of phenol (acid phenol: CHCl3 5:1 solution (pH 4.5; Ambion cat. #AM9720) to 500 μL of nanoparticle samples (membrane concentration of 2mg/mL and PLGA nanoparticles of 4 mg/mL) and mixed with gentle vortex for 5 seconds. The sample mix was incubated at 37 °C with a gentle vortex (~1100 rpm) for 15 minutes and transferred to 2 mL Phase Lock Gel Heavy tubes (Quantabio, cat.# 2302830) and centrifuged at 16,000 x g for 5 minutes. The upper layer or aqueous phase was transferred to and new 2 mL Eppendorf tube and 3 M Sodium acetate (pH 5.5,1:10; Ambion) was added for RNA precipitation followed by 1.5 volume of isopropanol. Samples were incubated at -20 °C overnight and the next day washed twice with 80% ethanol at 7500g for 5 minutes at 4 °C. RNA quantification and quality were assessed using Qubit and Bioanalyzer.  End repair of small RNA fragments  We carried out end repair of 5' and 3' ends of fragmented RNAs for library preparation. End repair was carried out using T4 Polynucleotide Kinase (NEB, cat. #MO201S) that catalyzes the transfer and exchange of Pi from the gamma position of ATP to the 5'-hydroxyl termini of the RNA fragment. It also catalyzes the removal of 3'- phosphoryl groups from 3' phosphoryl ends. End repair was carried out by adding all the following components in a 1.5 mL Eppendorf tube: 0.5 μL of Murine RNAase inhibitor; 2 μL of 10X T4 PNK Buffer; 1 μL of T4 PNK Enzyme; 2.5 μL of Nuclease free water and 12 μL of purified small RNAs (100 ng) in a total volume of 18 ul. The components were incubated at 37 °C for 30 min in a thermoblock followed by adding 2 μL of 10mM ATP. Incubation continued for another 30 min. Nuclease free water was added to complete the volume to 100 μL for further purification using RNeasy MinElute Cleanup Kit (Qiagen cat. #74204).  The yield and size distribution of the fragmented RNA was analyzed in the Bioanalyzer RNA Pico Chip.
RNA Library Preparation  After end repair, we continue the ligation of the 3’ and 5’ adaptors. Ligation of the 3’ SR adaptor was carried out as follows: 6 μL of input RNA (100 ng) and 1 μL of 3’SR Adaptor for Illumina in a total volume of 7 ul. The mix was incubated in a pre-heated thermal cycler for 2 min at 70 °C and a transfer tube on ice. After, the following components were added: 10 μL of 2X 3’ Ligation Reaction Buffer and 3 μL of 3’ ligation mix to a final volume of 20 μL and incubated for 1 hour at 25 °C in a thermal cycler. To prevent adaptor-dimer formation, hybridization of the reverse transcription primer was carried out to remove excess 3' SR adaptors that remain free after 3' ligation reaction by transforming single-stranded DNA adaptor into double-stranded DNA molecule, which is not substrates for ligation-mediated by T4 RNA ligase and therefore does not ligate to the 5' SR adaptor. To hybridize the reverse transcription primer, 1 μL of the SR RT primer for Illumina was added to the 20 μL sample and bring the volume to 25.5 μL with 4.5 μL nuclease-free water. Samples were incubated in the thermal cycler as follows: 75 °C /5’, 37 °C /15’, 25 °C /15'. Ligation of the 5' SR adaptor was carried out as follows: 1 μL of denatured 5' SR adaptor for Illumina, 1 μL of 10X 5’ ligation reaction buffer and 2.5 μL of 5’ ligation mix in a final volume of 30 ul. The new mix was incubated for 1 hour at 25oC in a thermal cycler.  Direct 3’ adaptor ligation on MCNPs  Membrane-coated NPs generated from ~250 million suspension cells were centrifuged at 20,000xg for 20 minutes. The MCNP pellet was resuspended in 120 ul of the 3’ ligation reaction mix (6 ul of 3’ SR Adaptor, 60 ul of 3’ Ligation Reaction Buffer, 18ul of 3’ Ligation Enzyme mix, 1ul RNase inhibitor and 35 ul 1x PBS) and incubated at 25 °C during 1h using PCR machine. Once incubation was completed, RNA was isolated using silane magnetic beads and resuspended in 120 ul RNAse free water. RNA quality was assessed using Bioanalyzer. The isolated RNA was aliquoted in 6 PCR tubes, each with 20 ul volume. Excess of 3’ adaptor was removed by adding 1 ul of the reverse transcription primer and 4.5 ul of RNA-free water to each PCR tube containing 20 ul of RNA and incubated using the following program: 75 °C /5’, 37 °C /15’ 25 °C /15’. The RT primer will hybridize to an unligated 3’ adaptor and will prevent the formation of adaptor-dimer formation. The following steps: 5’ adaptor ligation, reverse transcription and library amplification were performed using standard library preparation procedures (NEB cat. # E7300L). DNA enrichment was optimized by increasing the RNA input and the number of PCR cycles. Library size distribution was determined using Bioanalyzer and library size selection with Pippin HT.

treatment_protocol: EL4 lymphoma suspension cells were cultured in DMEM media supplemented with 10% fetal bovine serum, penicillin, and streptomycin in T25 flasks. EU was added to the cell culture media to 1mM final concentration and incubated with the cells for 1h. After EU labeling, cells were collected and washed twice with 1x PBS to remove the excess of media and fixed with 4% paraformaldehyde (PFA) for 10 minutes. The fixative was removed by washing cells twice with 1x PBS and Click-IT was performed. Click reaction was carried out by mixing non-permeabilized fixed cells with 500 ul of the Click reaction cocktail (1.8 ul of Alexa Fluor Azide 488, 20 ul Copper II Sulfate (CuSO4), 428 ul of reaction buffer and 50 ul of reaction buffer additive). (See Invitrogen CAT# C10329 for detailed protocol) and incubated for 2 h at room temperature with rotation and protected from light. Wash cells twice with 1x PBS and imaged by fluorescence microscopy and differential interference contrast (DIC).

tag: cell line


title: A3_S2_MNCP


title: MP_1_561


title: MP_2_575


title: MP_3_730


title: FN_1_561


title: B2_AL_MNCP


title: MT_1_561


title: PN_1_9799


title: MT_2_575


title: PN_C1_9799


title: PP_1_9799


title: MT_3_730


title: PN_C2_9799


title: No40_ES_P63

status: Public on Jun 12 2020

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Embryonic stem cells

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

value: Embryonic stem cells


title: B1_AL_MNCP


title: A1_S3_MNCP


title: IRI12h1_1

status: Public on Jun 08 2020

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

description: single nucleus RNA-seq

data_processing: We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single nucleus sequencing data from mouse and human kidneys. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to reference genome (mm10 and hg19) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis. Subsequently, we applied SoupX to remove ambient RNA

source_name: Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 5-µm cell strainer (pluriSelect 43-50020-50) and counted. We used the inDrops protocol developed by Klein et al to generate single nucleus transcriptome.
We followed the guideline provided by the manufacturer (10x Genomics) to generate single nucleus transcriptomes
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure

tag: replicates


title: IRI12h2

description: single nucleus RNA-seq


title: IRI12h3

description: single nucleus RNA-seq


title: IRIsham2

description: single nucleus RNA-seq

value: Sham


title: Infected patient-BFA2

status: Public on Feb 20 2020

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to hg19 whole genome using, for RNA-Seq reads, tophat2 with default settings and using additional transcript annotation data for the hg19 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against hg19 with the --local and --very-sensitive options.
Reads overlapping the Ensembl build 75 human 3' UTRs +/- a 500bp window were counted and the final gene counts table was calculated based on the 3' UTR counts. The counts table was normalized using DESeq normalization and analyzed for differential expression using the PANDORA method from the metaseqR Bioconductor package (Moulos and Hatzis, 2015, PMID: 25452340). The final list of differentially expressed genes was derived by the genes demonstrating a PANDORA p-value less than 0.05 and an absolute fold change of 0.58 in log2 scale (or 1.5 times up/down in natural scale).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized 3'UTR counts for each Ensembl gene for RNA data.

growth_protocol: Liver specimens (1-2 cm3) were washed once with DMEM (Sigma) supplemented with 1% FCS and with 1% Penicillin Streptomycin (PS, Sigma), minced and incubated at 37°C with the digestion solution (collagenase 2,5 mg/ml in HBSS). Incubation was performed for 30 minutes, further mincing and mixing the tissue every 10 minutes. To recover the cells, digestion solution was passed through a 70uM strainer in a 50 ml tube (GreinerBio) and washed with 45 ml Advanced DMEM (Gibco) supplemented with 1% PS, 10 mM HEPES (Gibco) and 1% GlutaMax (Gibco), henceforth Ad+++. Partially digested tissue was recovered from the strainer and further incubated with TrypLE Express (Thermoscientific) for 15 minutes at 37°C. Cells obtained from the first and second digestion were pooled together and washed twice with Ad+++. After the second centrifugation (200g, 5 minutes) cells were counted, mixed with an appropriate amount of BME solution (2/3 Basement Membrane Extract, Type 2 (Pathclear) diluted with 1/3 Ad+++) and seeded in 25ul drops containing 10000-15000 cells in 48 well suspension plates (GreinerBio). After BME solution had solidified, wells were filled with 250 ul of human liver organoid isolation medium consisting Ad+++ supplemented of 1X B27 supplement without retinoic acid (Gibco), 1X N2 supplement (Gibco), 1.25-mM N-acetyl-L-cysteine (Sigma), 10% (vol/vol) Rspo-1 conditioned medium (Huch et al, Nat Methods), 10% (vol/vol) Wnt3a-conditioned medium (Huch et al, Nat Methods), 10-mM nicotinamide (Sigma), 10-nM recombinant human (Leu15)-gastrin I (Sigma), 50 ng/ml recombinant human EGF (Peprotech), 100 ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human HGF (Peprotech), 10 μM Forskolin (Sigma), 5 μM A8301 (Tocris), 25 ng/ml Noggin (Peprotech) and 10-μM Y27632 (Sigma). After 1 week, isolation media was changed to human liver expansion media (EM; Ad+++ supplemented of 1X B27 supplement without retinoic acid (Gibco), 1X N2 supplement (Gibco), 1.25-mM N-acetyl-L-cysteine (Sigma), 10% (vol/vol) Rspo-1 conditioned medium, 10-mM nicotinamide (Sigma), 10-nM recombinant human (Leu15)-gastrin I (Sigma), 50 ng/ml recombinant human EGF (Peprotech), 100 ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human HGF (Peprotech), 10 μM Forskolin (Sigma) and 5 μM A8301 (Tocris)).   EM was changed twice a week, and cultures were split every 7-10 days according to organoid density.

extract_protocol:
For each RNA preparation, 2 wells of organoids in expansion phase were collected in Trizol reagent (Sigma) 4-5 days after splitting. RNA was extracted according to manufacturer’s instruction and resuspended in 30ul of nuclease free water. Total RNA was quantitated (ND1000 Spectrophotometer – PEQLAB). Samples were diluted accordingly to a mean concentration of approximately 100-150ng/μl and their quality assessed on a Bioanalyzer (Agilent Technologies) using the Agilent RNA 6000 Nano Kit reagents and protocol (Agilent Technologies).
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI™ Hi-Q™ OT2 200 Kit (ThermoFisher Scientific) on Ion OneTouch 2 System. Sequencing was performed using the Ion PI™ Hi-Q™ Sequencing 200 Kit and Ion PI™ Chip Kit v3 (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.

tag: age

value: HBV infected

tag: tissue

value: liver organoids


title: Infected patient-BFA

description: iP-BFA


title: IRIsham1_2

description: single nucleus RNA-seq


title: Infected patient-BDFA

description: iP-BDFA

value: HBV HDV infected


title: Infected patient-BDFA2


title: Infected patient-BDCC

description: iP-BDCC


title: IRIsham3

description: single nucleus RNA-seq


title: Infected patient-BCC2


title: IRIsham1_1

description: single nucleus RNA-seq


title: Infected Donor 1


title: Infected patient-BCC3


title: Infected patient-BC

description: iP-BC


title: Healthy donor 9

value: Healthy donor


title: Infected patient-BCC4


title: Healthy donor 10


title: Infected patient-BCC1


title: IRI12h1_2

description: single nucleus RNA-seq


title: Healthy donor 7


title: Healthy donor 8


title: KI384_Input_GM07492

status: Public on Feb 15 2020

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: KI384_Input_GM07492_Ste08413_hg19_BT2q20x200n.bw

data_processing:
ChIP-seq reads were mapped to the hg19 human reference genome using Bowtie2 with the default “--sensitive” parameter. Reads with MAPQ score greater than 20 were used in downstream analyses.
Reads from biological replicates of ChIP and corresponding input samples were used as input files for MACS2. In MACS2, duplicate reads were removed first, and then significantly enriched peak regions were called, and input-normalized perbase coverage of 200 nt-extended reads was computed (“fold enrichment bedgraph”).
Genome_build: hg19

source_name: GM07492 normal fibroblast

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS) and penicillin-streptomycin. Progeria-patient primary skin fibroblasts AG11498 (Coriell Cell Repository) and primary skin fibroblasts from a healthy donor GM07492 (Coriell Cell Repository) were grown in MEM Alpha (Life Technologies, 12561-056) with 9% FBS and penicillin-streptomycin.

extract_protocol:
Cells in culture dishes were crosslinked in 1% formaldehyde for 15 min and the reaction was quenched by 125 mM glycine. Cross-linked cells were washed with LB1 (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and then with LB2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 10 mM Tris-HCl pH 8.0). Chromatin was extracted by sonication in LB3-Triton (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton). LB1, LB2, and LB3-Triton used during extraction were supplmented with 1x protease inhibitor cocktail (Calbiochem 539131) and 100 nM phosphatase inhibitor Nodularin (Enzo ALX-350-061).  One million cells were used in a single 200-µL ChIP reaction. Antibodies used in ChIP are: rabbit monoclonal anti-phospho-Ser22-LMNA antibody D2B2E (Cell Signaling 13448S, Lot # 1; 5 µL per IP); mouse monoclonal anti-unphospho-Ser22-LMNA antibody E1 (Santa Cruz Biotechnology sc-376248, Lot # H2812; 10 µL per IP); mouse monoclonal anti-acetyl-Lys27 histone H3 antibody (Wako MABI0309, Lot # 14007; 2 µL per IP); mouse monoclonal anti-trimethyl-Lys4 histone H3 antibody (Wako MABI14004, Lot # 14004; 2 µL per IP); mouse monoclonal anti-Ty1 antibody (Diagenode C15200054, Lot # 005; 1 µL per IP).
Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

tag: lmna genotype

value: Wild type

tag: transgene

value: No

tag: cell sorting

value: No sorting

tag: antibody


title: KI351_K27ac_GM07492

description: K27ac_GM07492_macs2hg19_t351t422c384_fe_k1sort.bw


title: N2 Input rep2

status: Public on Aug 22 2018

city: Cambridge

first: Susan

middle: E.

last: Mango

state: MA

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Reads were aligned to the C. elegans reference genome (ce10) with Bowtie2 (version 2.3.1), using default parameters and '--very-sensitive'.
Log-likelihood-ratio tracks were created using MACS2 (version 2.1.1.20160309).  For each sample: $ macs2 callpeak -t ${sample}_ChIP.bam -c ${sample}_Input.bam -f BAMPE -g ce --keep-dup all --bdg --SPMR; macs2 bdgcmp -t ${sample}_treat_pileup.bdg -c ${sample}_control_lambda.bdg -o ${sample}_logLR.bdg -m logLR -p 0.00001
LogLR tracks were converted to BigWig using linux sort and the UCSC tool bedGraphToBigWig.  For each sample: $ sort -k1,1 -k2,2n ${sample}_logLR.bdg > ${sample}_logLR_sort.bdg; bedGraphToBigWig ${sample}_logLR_sort.bdg ce10genome.txt ${sample}_logLR.bw
Correlations of the logLR-bigWig files were calculated using the UCSC tool wigCorrelate.
Genome_build: ce10
Supplementary_files_format_and_content: bigWigs of log-likelihood-ratio tracks produced by 'macs2 bdgcmp'

organism: Caenorhabditis elegans

source_name: embryonic lysate

growth_protocol: Mix-staged embryos were collected from adult worms by bleaching. Embryos were shaken at 200rpm at 20oC in CSM medium (100mM NaCl, 5.6mM K2HPO4, 4.4mM KH2PO4, 10μg/ml cholesterol, 10mM potassium citrate, 2mM CaCl2, 2mM MgSO4, 1X trace metals.) without food. Once the embryos hatched and became L1s, concentrated NA22 bacteria were added to the culture. Synchronized embryos were harvested by bleaching after 62-66 hours when most worms carried 1-8 embryos, frozen in liquid nitrogen and stored at -80oC.

extract_protocol:
H3K9me2 ChIP was done as described previously (Hsu et. al, Science 2015) with the following changes: Embryos frozen in liquid nitrogen were thawed on ice and fixed in 1.5% Formaldehyde (Electron Microscopy Sciences, #15686) for 15 minutes at room temperature. Using the QSonica Q800 Sonicator, samples were sonicated at 30% amplitude, 30 seconds ON, 30 seconds OFF for a total of 15 minutes at 4oC, yielding 100-300 base pair fragments. 6μl of MABI0307 H3K9me2 antibody was coupled to 25μl beads (Pierce Protein A/G magnetic beads, #88802) for 8 hours at 4oC prior to ChIP. 40 μg of chromatin was used per ChIP reaction and chromatin was pre-cleared for 2 hours at 4°C using uncoupled magnetic beads (Pierce #88802). To elute the bound immunocomplexes, 150 μL of elution buffer (50mM NaHCO3, 140mM NaCl, 1% SDS) was added to each tube and heated at 65°C for 15 minutes.
The ChIP-Seq libraries were generated by using the Apollo 324 System and PrepX ILM DNA Library Kit from IntergenX. After adaptor ligation, the input and ChIP DNA were enriched by PCR amplification using NEBNext High-Fidelity 2X PCR master Mix with Q5 polymerase and PrepX PCR primer with the following PCR conditions: 30 seconds at 98°C, [10 seconds at 98°C, 30 seconds at 60°C, 30 seconds at 72°C] for 8 cycles for Input libraries and 11 cycles for ChIP libraries, followed by 5 minutes at 72°C (~15 uL adaptor ligated DNA, 25 uL NEBNext High-Fidelity 2X PCR master Mix, 2uL Universal PCR primer, brought to to 50ul with Nuclease-Free water). The enriched DNA was then purified using 50 uL (1:1 ratio of DNA volume and beads) of PCR Clean DX Beads (Aline) and size selected by Pippin Prep, 180-600bp. 1 uL of each library was applied to measure the concentration using a Qubit dsDNA assay kit (Invitrogen). 1 ng of DNA from each library was checked by a TapeStation (Agilent Technologies). Input and ChIP libraries were pooled such that they had the same expected number of sequence reads.

value: N2 wild-type Bristol


title: N2 ChIP rep1

value: anti-H3K9me2  (MABI0307)


title: N2 ChIP rep2


title: KI422_K27ac_GM07492


title: FOL_3dcast_rep4

city: Madison

first: Chad

middle: Michael

last: Vezina

state: WI

address: 1656 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq, v2.17.1.14
Reads were filtered and trimmed for adapters and quality.
Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with a table of Expected Counts expression estimates from the RSEM application

source_name: ventral prostates

extract_protocol:
RNA was isolated from the ventral prostates of four mice per group from each of six groups: Control diet-Intact, FA diet-Intact, Control diet-3d post-castration, FA diet-3d post-castration, Control diet-10d post-castration and FA diet-10d post-castration using the Illustra RNAspin Mini kit (#25-0500-72, GE Healthcare, Chicago, Illinois, USA).
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

treatment_protocol: Mice were exposed to a control (4mg/kg folic acid) or folic acid enriched diet (24mg/kg folic acid) from in utero and throughout lifetime. At 7weeks of age,intact mice were sacrificed to collected ventral prostates or castrated and the ventral prostate collected after 3 or 10 days.

tag: tissue type

value: ventral prostates

tag: experimental groups

value: Folate diet-3d post castration


title: FOL_10dcast_rep4

tag: strain

value: Folate diet-10d post castration


title: FOL_10dcast_rep2


title: FOL_3dcast_rep2


title: FOL_Intact_rep4

value: Folate diet-Intact


title: CNTRL_10dcast_rep2

value: Control diet-10d post castration


title: CNTRL_3dcast_rep1

value: Control diet-3d post castration


title: FOL_3dcast_rep1


title: FOL_10dcast_rep3


title: CNTRL_10dcast_rep3


title: N2 Input rep1

tag: genotype


title: FOL_Intact_rep2


title: CNTRL_3dcast_rep4


title: CNTRL_10dcast_rep4


title: Healthy donor 1

source_name: Liver

tag: disease state


title: FOL_3dcast_rep3


title: CNTRL_10dcast_rep1


title: CNTRL_Intact_rep4

value: Control diet-Intact


title: CNTRL_Intact_rep2


title: FOL_10dcast_rep1


title: CNTRL_Intact_rep1


title: CNTRL_3dcast_rep3


title: FOL_Intact_rep3


title: Tdp_1_Hpl2-2_ChIP

status: Public on May 17 2018

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
genomic DNA (Hpl-2 IP)
Supplementary_files_format_and_content: Processed data file "tdp1-2_Hpl2_ChIP.bw" is an RPKM normalized bigwig and "tdp1-2_HPL2Chip_subtractedControl.bw" has been normalized by RPKM and by the OK803 genomic control via subtraction using DeepTools compare function.
HPL2_ChIP_consensusPeaks.xlsx
tdp1ChIP-1_subtractedControl.bw
tdp1ChIP-2_subtractedControl.bw
HPL2_SigDiffPeaks_overlapWith_TDP1ChIP.xlsx
TDP-1_Chip_control.bw
TDP-1_Chip_rep1.bw
TDP-1_Chip_rep2.bw

data_processing:
Basecalls performed using CASAVA software from Illumina
Analysis of library complexity and per-base sequence quality (i.e. q > 30) was assessed using FastQC (v0.11.2) software. Low quality bases (q < 10) were trimmed from the 3’ end of reads.
Reads were aligned to the C. elegans WS220 genome using TopHat2 (v2.0.14) --b2-very-sensitive -i 30 -I 5000 --read-edit-dist 3 -N 3 - -read-realign-edit-dist 0 -p 10 --segment-length 25 --segment-mismatches 2 --no- coverage-search --min-coverage-intron 30 --max-coverage-intron 5000 --min-segment-intron 30 --max-segment-intron 5000
(RNAseq) For poly-A selected RNA-Seq reads, uniquely mapped reads were used as input to obtain gene counts using the WS220 annotation with Rsubread (v 1.18.0). Differential expression of genes was determined using DESeq2 (v1.14.1)
(ChIPseq) Reads were uniquely mapped to the WS220 genome with Bowtie1 allowing 2 mismatches in a 45bp seed. Total genomic DNA control libraries were processed and mapped in an identical manner. MACS version 1.4.2 (47) was used to identify significant peaks (p<0.05, FDR<10%) and total genomic sequencing of DNA from wild type and tdp-1(ok803) worms respectively were used as the control datasets to normalize HPL-2 ChIP-seq peaks. Diffbind (version 1.10.2) was used to call differentially represented peaks between wild type and tdp-1(ok803). HPL-2 ChIP-seq and respective total genomic sequencing for each sample was used for normalization. A p-value cut off of P<0.05 and FDR<10% was used.
Genome_build: ws220
Supplementary_files_format_and_content: (RNA-Seq) abundance measurements and differential expression of genes
(ChIPseq) bigwig files

source_name: whole worm

growth_protocol: Worms were grown at on agarose plates and harvested as young adults

extract_protocol:
(RNAseq) Worms were broken by bead beating (Minibead Beater; Biospec Products) in homogenization buffer [10 mM KCl/1.5/1 mM DTT/10 mM Tris·HCl (pH 8.0)/50 mM Sucrose/0.05% Nonidet P-40/1 mM complete protease inhibitors (Sigma #P2714) at a 1:1 ratio of 0.1mm glass beads to packed worm volume for 3 cycles of 30 secs at 5,000 rpm. Extracts were used immediately for immunoprecipitations and equal concentration of extract as determined by protein quantification was added to each IP
(ChIPseq) All worms were maintained and grown on op50 seeded NGM plates and harvested in water. The worms were washed three times in water, and the bacteria were cleared by sucrose flotation. The worms were then frozen in liquid nitrogen and ground to a powder with a mortar and pestle. The resulting worm powder was transferred into cross-linking buffer (1 mM phenylmethylsulfonyl fluoride [PMSF], 1 mM EDTA, 1 mM EGTA, 1% formaldehyde, phosphate-buffered saline [PBS]) for 10 min at room temperature. The reaction was quenched for 5 min at room temperature by the addition of glycine to the mixture to a final concentration of 125 mM and sedimented at 4,000 × g. Pellets were washed three times with FA buffer plus 0.1% SDS (50 mM HEPES [pH 7.5], 1 mM EDTA, 1% Triton, 0.1% deoxycholic acid, 150 mM NaCl, 0.1% SDS) containing protease inhibitors. Each wash mixture was incubated for 5 min at 4°C and then sedimented at 4,000 × g. The pellets were then divided into 500-μl aliquots and stored at −80°C. Each aliquot was resuspended in 1.5 ml of FA buffer plus 0.3% SDS containing protease (Complete cocktail tablets, catalog number 11697498001; Roche) and phosphatase inhibitors (catalog number 786-450; GBiosciences). The samples were sonicated with a Virsonic digital 600 sonicator using a microtip (20 pulses of 11 s each at 30% amplitude with bursts of 0.9 s on and 0.5 s off) to generate DNA fragments of approximately 500 bp, as determined experimentally. Samples were sedimented at 13,000 × g for 15 min at 4°C, and the supernatant was transferred into a new tube, which was then diluted to 4.5 ml with FA buffer containing protein and phosphatase inhibitors.
Total RNA sequencing libraries was extracted from whole animals by TRIzol extraction. Genomic DNA was removed using TURBO DNase (Invitrogen). Poly-A selected, single-ended, 125 bp strand-specific libraries were prepared by the UCCC Genomics Core (Aurora, CO) using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For the J2-IP analyses, RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) was converted into strand‐specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080‐044) using incrementally increasing temperatures from 42 to 59°C to allow for transcription though structured RNAs. rRNA was not removed from J2‐IP RNA samples. Immunoprecipitated DNA from ChIP samples were converted into sequencing libraries using ChIP‐Seq DNA Sample Prep Kit (IP‐102– 1001). Cluster generation and sequencing were performed on the Illumina HiSeq 2500 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina.

treatment_protocol: hpl-2(tm1489)  and tdp-1(ok803) mutants strains were compared to WT (N2 Bristol) worms.

tag: Stage

value: young adult

tag: temperature

tag: ip antibody

value: HPL-2 antibody, Research antibody provided by the Palladino lab


title: phyB-9.D100h.rep2

status: Public on Dec 31 2017

city: Riverside

first: Meng

last: Chen

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

description: Null mutant of Arabidopsis PHYB, Col-0 background

data_processing:
Illumina Casava1.7 software used for basecalling??
Sequenced reads were de-multicomplexed according to the barcodes.
Paired-end reads were mapped to the Arabidopsis TAIR10 genome and transcriptome using Tophat/v2.0.14 (Kim et al., 2013).
Gene expression was estimated using Cufflinks/v2.2.1 (Trapnell, Williams et al. 2010), and then differential gene expression between BCY and phyB-9 was determined by Cuffdiff/v2.2.1 (Trapnell, Hendrickson et al. 2013) using a q-value cutoff of 0.05 and a fold-change equal to or greater than 1.5. Since the RNA-seq libraries were constructed using the NEBNext Ultra Directional RNA library prep kit for Illumina and preserved information about the RNA strand orientation, the tophat and cufflinks parameter “--library-type fr-firststrand” was used to distinguish sense reads and anti-sense reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited gene_exp.diff txt file generated by cuffdiff software. The file contains differential gene expression FPKM values between BCY and phyB-9.

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Arabidopsis thaliana seeds were stratified for 5 days at 4 degree celcius in the dark, followed by a 3h far-red light (10 µmol m-2 s-1) treatment and then wrapped in the dark for another 97h in a growth chamber maintained at 21 degree celcius.

extract_protocol:
100 mg 100h dark-grown seedlings were collected under dim green light, flash frozen in liquid nitrogen, and total RNA was extracted using Zymo Quick-RNA™ MiniPrep (R1055).
RNA libraries were prepared for sequencing using the standard protocol of NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (#E7420S)

treatment_protocol: Seedlings were grown for 100h in the dark, and harvested under dim green light using liquid nitrogen.

tag: transgenic-line

tag: replicate


title: N2_genomic_control

description: Supplementary_files_format_and_content: Processed data file "N2_genomic_control.bw" is an RPKM normalized bigwig

value: N2 (Bristol)


title: phyB-9.D100h.rep1


title: BCY.D100h.rep3

description: Transgenic line overexpressing PHYB C-terminal module fused to YFP in phyB-9 null mutant background

value: BCY


title: BCY.D100h.rep2


title: FOL_Intact_rep1


title: Tdp_1_Hpl2-1_ChIP

description:
genomic DNA (Hpl-2 IP)
Supplementary_files_format_and_content: Processed data file "tdp1-1_Hpl2_ChIP.bw" is an RPKM normalized bigwig and "tdp1-1_HPL2Chip_subtractedControl.bw" has been normalized by RPKM and by the OK803 genomic control via subtraction using DeepTools compare function.
HPL2_ChIP_consensusPeaks.xlsx
tdp1ChIP-1_subtractedControl.bw
tdp1ChIP-2_subtractedControl.bw
HPL2_SigDiffPeaks_overlapWith_TDP1ChIP.xlsx
TDP-1_Chip_control.bw
TDP-1_Chip_rep1.bw
TDP-1_Chip_rep2.bw


title: BCY.D100h.rep1


title: PDX cells +Crenolanib + AZA  after co-culture replicate 2

status: Public on Apr 03 2017

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015).
Reads were aligned to the mouse genome mm10 and human genome hg19 using STAR 2.4.0 (Dobin et al., 2013).
Unique gene-wise counts were generated using the Drop-seq pipeline.
For data deposition, samples were demultiplexed using bamtools filter command.
Genome_build: hg19;mm10
Supplementary_files_format_and_content: sample- and gene-wise expression tables

source_name: patient derived AML cell line

extract_protocol:
Total RNA was isolated from murine EL08 and human PDX cells using the RNeasy Mini Kit (Qiagen).
cDNA was synthesized, barcoded, pooled and pre-amplified according to the UMI-seq protocol in Parekh et al. 2016. 800 pg of the cDNA pool was used for library preparation using the Nextera XT Kit (Illumina)

tag: treatment

value: Crenolanib + AZA


title: PDX cells +Crenolanib after co-culture replicate 4

value: Crenolanib


title: PDX cells +Crenolanib + AZA  after co-culture replicate 4


title: PDX cells +Crenolanib + AZA  after co-culture replicate 3


title: EL08 cells +Crenolanib after co-culture replicate 4

source_name: stromal cell line


title: PDX cells +Crenolanib after co-culture replicate 3


title: EL08 cells +Crenolanib + AZA  after co-culture replicate 1


title: CNTRL_Intact_rep3


title: EL08 cells +Crenolanib + AZA  after co-culture replicate 4


title: EL08 cells +Crenolanib + AZA  after co-culture replicate 2


title: EL08 cells +Crenolanib + AZA  after co-culture replicate 3


title: PDX cells +Crenolanib after co-culture replicate 2


title: EL08 cells +Crenolanib after co-culture replicate 2


title: PDX cells +Crenolanib after co-culture replicate 1


title: PDX cells +AZA after co-culture replicate 4

value: AZA


title: EL08 cells +Crenolanib after co-culture replicate 3


title: phyB-9.D100h.rep3


title: PDX cells +AZA after co-culture replicate 3


title: EL08 cells +Crenolanib after co-culture replicate 1


title: EL08 cells +AZA after co-culture replicate 4


title: PDX cells +AZA after co-culture replicate 2


title: PDX cells +Crenolanib + AZA  after co-culture replicate 1


title: PDX cells +AZA after co-culture replicate 1


title: EL08 cells +AZA after co-culture replicate 3


title: EL08 cells +DMSO after co-culture replicate 4

value: DMSO


title: EL08 cells +AZA after co-culture replicate 2


title: PDX cells before FACS

value: before FACS


title: PDX cells +DMSO after co-culture replicate 2


title: PDX cells +DMSO after co-culture replicate 1


title: EL08 cells +AZA after co-culture replicate 1


title: PDX cells +DMSO after co-culture replicate 3


title: EL08 cells +DMSO after co-culture replicate 2


title: EL08 cells 4 days after mono culure replicate 2

value: 5 day mono culture


title: EL08 cells +DMSO after co-culture replicate 3


title: EL08 cells 4 days after mono culure replicate 3

value: 6 day mono culture


title: EL08 cells +DMSO after co-culture replicate 1


title: EL08 cells 4 days after mono culure replicate 4

value: 7 day mono culture


title: EL08 before co-culture replicate 4

value: before co-culure


title: EL08 before co-culture replicate 3


title: EL08 cells 4 days after mono culure replicate 1

value: 4 day mono culture


title: EL08 before co-culture replicate 1


title: EL08 before co-culture replicate 2


title: MT2 HAT mutant BRD4 MNase-seq

status: Public on May 08 2016

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

data_processing:
Sequenced reads were mapped to the human genome (hg19) reference genomes using BWA-MEM and all duplicated reads were removed using PICARD
Nucleosome profiles were obtained using DANPOS (Chen et al. 2013).  DNA fragment size was determined by the distance between the paired-end reads and read length was adjusted to be half of the nucleosome size (74 bp).
Reads were aligned the human genome (hg19) reference genomes using Tophat
RPKM values were calculated using SeqGene package (Deng 2011)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM and WIG

source_name: U2OS cells

growth_protocol: U2OS cells were routinely generated as adherent cultures (typically 2 × 106 cells in a 10 cm tissue culture plate) in DMSO medium.

extract_protocol:
For Mnase-seq Lysates were clarified from sonicated chromatin to obtain mononucleosomes, followed by DNA purification. For RNA-seq, total RNA was extracted using Trizol reagent (Invitrogen), mRNA purified using the Dynabeads direct mRNA purification kit (Life technologies, Cat no. 61011), converted into cDNA using standard protocols and used for library construction
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired, an 'A' overhang added, ligated to Illumina's adapters.  After adapter ligation DNA was PCR amplified with Illumina primers and library fragments were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were transfected with pCDNA vector or plasimd constructs with wild type or HAT mutant BRD4 using lipofectamine using standard methods for 18 hours before being harvested.

tag: transfected with

value: HAT mutant BRD4

tag: exp. replicate

value: Replicate 2

tag: cell line


title: MT1 HAT mutant BRD4 MNase-seq

value: Replicate 1


title: WT1 Wild type BRD4 MNase-seq

value: Wild type BRD4


title: NT2 pCDNA vector MNase-seq

value: pCDNA vector


title: PDX cells +DMSO after co-culture replicate 4


title: NT1 pCDNA vector MNase-seq


title: MT1 HAT mutant BRD4 RNA-seq


title: MT2 HAT mutant BRD4 RNA-seq


title: hCD45+PDX cells after FACS

value: after FACS


title: WT1 Wild type BRD4 RNA-seq


title: WT2 Wild type BRD4 RNA-seq


title: NT2 pCDNA vector RNA-seq


title: WT2 Wild type BRD4 MNase-seq


title: Sample_Nt_2

status: Public on Mar 20 2016

city: Blacksburg

first: Allison

middle: N

last: Tegge

address: 250 Drillfield Drive

institute: Virginia Tech

data_processing:
Reads were aligned to mm9 using TopHat
Transcript levels were quantified using Cufflinks
Both analyses used default settings
Genome_build: mm9
Supplementary_files_format_and_content: fpkm data

source_name: Neural stem cells

extract_protocol:
RNA was extracted, Trizol (Life Technologies) extracted and further purified with RNAeasy (Qiagen).
Samples for RNASeq were prepared according to Illumina instructions

tag: cell type

value: neural stem cells

tag: timepoint

tag: antagomir

value: control


title: Sample_Nt_3


title: Sample_4d_C_3


title: Sample_Nt_1


title: Sample_2d_C_2


title: Sample_4d_a137_2


title: Sample_2d_C_1


title: Sample_4d_C_2


title: Sample_4d_C_1


title: Sample_4d_a137_3


title: Sample_2d_a137_3


title: Sample_2d_a137_2


title: Sample_2d_a137_1


title: Sample_4d_a128_2


title: Sample_2d_a128_3


title: Sample_4d_a128_1


title: Sample_4d_a124_3


title: Sample_2d_a128_1


title: Sample_2d_a128_2


title: Sample_4d_a124_1


title: Sample_2d_a124_1


title: Sample_2d_a124_2


title: Sample_4d_a124_2


title: NT1 pCDNA vector RNA-seq


title: Sample_2d_a124_3


title: Sample_2d_C_3


title: Sample_4d_a137_1


title: Sample_4d_a128_3