title: RJ423EV_rep2

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

data_processing:
Reads were trimmed from the 3' end to have a phred score of at least 30 and adapters were removed using Trimmomatic. Remaining reads were required to have a length of at least 32bp and were aligned to the mouse genome using STAR. Raw counts were generated using HTSeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts

growth_protocol: Cells were cultured in DMEM containing 10%FBS, 1mM sodium pyruvate, 10mM HEPES, 2mM glutamine, 2mM hydrocortisone, 5ug/ml estrogen, 5ug/ml prolactin, 10ug/ml EGF, 1-ug/ml insulin and 1% antibiotic-antimycotic and maintained at 37 C and 5% CO2. For selection of transfected cells, 2mg/ml Geneticin was also supplemented to the culture medium.

extract_protocol:
Total RNA was isolated using the miRVana miRNA isolation kit with Phenol (ThermoFisher).
mRNASeq (stranded) using Illumina TrueSeq adapters

tag: strain background

value: FVB

tag: cell line

value: mouse mammary tumor cell lines derived from the MTB-IGFIR mouse model

tag: genotype/variation

value: pCMV-MIR (empty vector)

tag: mir200a/b/429 expression level

value: miR200a/b/429 low


title: RJ423_miR200a/b/429_rep1

status: Public on Oct 31 2018

type: SRA

country: Canada

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

value: miR200a/b/429 high


title: RJ423_miR200a/b/429_rep2


title: RJ423EV_rep3


title: RJ423EV_rep1


title: RJ423_miR200a/b/429_rep3


title: RRBS_CAID_1_p8

city: Montréal

first: Gregor

middle: Ulrich

last: Andelfinger

state: QC

address: 3175, Chemin de la Côte-Sainte-Catherine

department: Cardiology

institute: CHU Sainte-Justine

library_source: genomic

data_processing:
Bsmap was used for initial data processing, methylation calls ans reads alignment.
Methylkit was used to do analysis and statistic of differentially methylated regions, specific parameters: 100 bp step-wise tiling windows, 1 CpG minimum per tile and a minimum 20x CpG coverage of each tile per sample.
Significant DNA methylation changes ≥ 30%.
HOMER was used for sequences annotations.
HOMER was used to analyze DNA binding motifs
Genome_build: hg19
Supplementary_files_format_and_content: .map : file containing raw methylation calls. There is one file per sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human dermal fibroblasts

growth_protocol: Cells were cultured in DMEM, 10% FBS, 1% pen/strep

extract_protocol:
DNA from human fibroblast was extracted using QIAamp DNA mini kit according to the manufacturer's instructions
500ng/sample of extracted DNA was digested with Msp1 enzyme (NEB #R0106M) Methylated adaptors (NEB #E7535L) were ligated with T4 ligase (NEB #M0202M) following by qPCR amplification with Illumina indexing primers. Libraries clean up and size selection was done using Agencourt® AMPure® XP magnetic beads (Beckman Coulter # A63881).

value: Dermal fibroblasts

tag: genotype

tag: passage


title: BR.Dam.m_DamIDSeq

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads from each sample were first adapter clipped and aligned to the reference genome (BDGP R5/dm3) using “bowtie2” (Langmead and Salzberg, Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4),357-9, 2012). For biological samples which were generated using multiple technical replicates (uninduced Dam only controls from larval central brain), the read counts were summed over the technical replicates. Next, reads that did not align or aligned more than once were discarded, as well as the chromosomes “U”, “M” and “Uextra” were excluded from the subsequent analysis. Then, reads were counted by “HTSeq-count” software (Anders et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2), 166-9, 2015) in the 1-kb genomic bins and read counts were merged between biological replicates of the same combination of protein / tissue or cell type (Dam only, Dam-Pc, Dam-Lam and Dam-HP1 / larval central brain, Repo+ glial cells of larval central brain, Elav+ neurons of larval central brain and larval fat bodies), as they were highly correlated. After that, the obtained counts were converted to reads per million mapped reads (RPM). Finally, the normalized DamID scores were calculated as the log2 of the ratio of the Dam-Pc/Dam only, Dam-Lam/Dam only and Dam-HP1a/Dam only.
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph format; log2(Dam-POI/Dam)

organism: Drosophila melanogaster

source_name: brain without ventral nerve cord

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium.

extract_protocol:
Two μl of Proteinase K (20 mg/ml) [Roche, 03115887001] were added to dissected central brains and the sample was incubated at 65°C for 6 hours. Next, 1 μl of RNase A (100 mg/ml) [QIAGEN, 1007885] was added and the sample was incubate at 37°C for 30 minutes. The lysate was transferred to a pre-spun (1 minute at 14,000 rpm just prior to use) phase lock gel light 1.5ml tube [5prime, 2302800] and 100 μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added. The sample was mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase (~90 μl) was transferred into a new tube. To precipitate DNA, 1 µl of glycogen (20 mg/ml) [Fermentas, R0561], 10 µl of 3M NaAc (pH 5.2) and 300 µl of ethanol were added, mixed well by inversion and the solution was kept overnight at -20°C. The tube was spun for 30 minutes at 14,000 rpm at 4°C. The supernatant was removed and the pellet was washed with 500 µl of ice cold 70% ethanol. The tube was spun for 5 minutes at 14,000 rpm at 4°C. The supernatant was carefully removed and the pellet was air dried for 15 minutes and dissolved in 12 µl of double distilled water. DNA concentration was measured using a NanoDrop spectrophotometer. Dam-methylated fragments were amplified as described previously (Vogel, M.J. et al. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2(6), 1467-78, 2007) using 500 ng of DNA as an input.
The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (QIAGEN, 28104) according to the manufacturer’s instructions. DNA was eluted in nuclease-free water (Ambion, AM9938). From 200 ng to 3 µg of the purified PCR products were diluted in 100 μl of nuclease-free water and transferred into a snap-cap microTUBE (6 × 16 mm) with AFA fiber (Covaris, 520045). DNA was sheared using the Covaris S2 instrument at the following settings: duty cycle = 10%, intensity = 5, cycles/burst = 200, time = 45 sec (as consequence, power = ~23W and bath temperature = ~4°C). The size of the DNA fragments before shearing was usually a smear in the range of 250–2000 bp with a peak at 600 bp, after shearing this was reduced to become a range of 100–500 bp with a peak around 300 bp. After shearing, the DNA was purified and concentrated using Agencourt magnetic beads (Beckman Coulter, A63881; 160 µl of beads were added to 100 µl of sheared DNA solution). DNA was eluted in 50 µl of nuclease-free water. DNA concentration was measured using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506). One μg of sheared material was used to prepare Illumina sequencing library with TruSeq DNA HT Sample Prep Kit (Illumina, FC-121-2003) according to the manufacturer’s instructions. Seven cycles of PCR were performed. This step included sample indexing. The library was quantified on an Agilent BioAnalyzer 2100 DNA 7500 chip that lists the product size distribution and quantifies the concentration in µg/µl and in nM.

treatment_protocol: Central brains were dissected from 20 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in 100 μl TENS solution [100 mM Tris-HCl (pH 8.0); 5 mM EDTA (pH 8.0); 200 mM NaCl; 0.2% SDS] at room temperature.

value: larval central brain

tag: gender

value: male

tag: developmental stage

value: wandering third instar larvae

tag: tissue

value: brain without ventral nerve cord

tag: dam-fusion protein

value: Dam only

tag: damid system used

value: Dam4-HT-intein@L127C, uninduced


title: FB.Lam.m_DamIDSeq

source_name: fat bodies

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium supplemented with 4-hydroxytamoxifen (Sigma-Aldrich, H7904) at a final concentration of 25 µM.

extract_protocol:
Four hundred μl of Lysis Buffer [5% sucrose; 100 mM Tris-HCl (pH 9.1); 50 mM EDTA (pH 8.0); 5% SDS] and 5 μl of Proteinase K (20 mg/ml) [Roche, 03115887001] were added to dissected fat bodies, the tissue was disrupted by passing through 21G needle 15-20 times and the sample was incubated at 55°C with 600 rpm shaking for 4 hours. Next, 2 μl of RNase A (100 mg/ml) [QIAGEN, 1007885] were added and the sample was incubate at 37°C for 30 minutes. The lysate was transferred to a pre-spun (1 minute at 14,000 rpm just prior to use) phase lock gel heavy 1.5ml tube [5prime, 2302810] and 500 μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added. The sample was mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase was transferred to another pre-spun phase lock gel heavy 1.5ml tube. Five hundred μl of phenol:chloroform:isoamylalcohol (25:24:1) [Sigma-Aldrich, P2069] were added, mixed well by shaking and the tube was spun for 5 minutes at 14,000 rpm at room temperature. The upper phase (~400 μl) was transferred into a new tube. To precipitate DNA, 1 µl of glycogen (20 mg/ml) [Fermentas, R0561], 40 µl of 5M NaCl and 1 ml of ethanol were added, mixed well by inversion and the solution was kept overnight at -20°C. The tube was spun for 1 hour at 14,000 rpm at 4°C. The supernatant was removed and the pellet was washed with 500 µl of ice cold 70% ethanol. The tube was spun for 15 minutes at 14,000 rpm at 4°C. The supernatant was carefully removed and the pellet was air dried for 15 minutes and dissolved in 500 µl of double distilled water. The solution was applied to a microcon YM-30 centrifugal filter (Millipore, 42410) and spun for 12 minutes at 14,000×g at room temperature. This reduced the sample volume to ~10 µl. DNA was collected by inverting the microcon YM-30 centrifugal filter in a fresh tube and spinning for 3 minutes at 1,000×g at room temperature. The sample volume was adjusted to 12 µl with double distilled water. DNA concentration was measured using a NanoDrop spectrophotometer. Dam-methylated fragments were amplified as described previously (Vogel, M.J. et al. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2(6), 1467-78, 2007) using 500 ng of DNA as an input.
The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (QIAGEN, 28104) according to the manufacturer’s instructions. DNA was eluted in nuclease-free water (Ambion, AM9938). From 200 ng to 3 µg of the purified PCR products were diluted in 100 μl of nuclease-free water and transferred into a snap-cap microTUBE (6 × 16 mm) with AFA fiber (Covaris, 520045). DNA was sheared using the Covaris S2 instrument at the following settings: duty cycle = 10%, intensity = 5, cycles/burst = 200, time = 45 sec (as consequence, power = ~23W and bath temperature = ~4°C). The size of the DNA fragments before shearing was usually a smear in the range of 250–2000 bp with a peak at 600 bp, after shearing this was reduced to become a range of 100–500 bp with a peak around 300 bp. After shearing, the DNA was purified and concentrated using Agencourt magnetic beads (Beckman Coulter, A63881; 160 µl of beads were added to 100 µl of sheared DNA solution). DNA was eluted in 50 µl of nuclease-free water. DNA concentration was measured using an Agilent BioAnalyzer 2100 DNA 7500 chip (Agilent, 5067-1506). One μg of sheared material was used to prepare Illumina sequencing library with TruSeq DNA HT Sample Prep Kit (Illumina, FC-121-2003) according to the manufacturer’s instructions. Seven cycles of PCR were performed. This step included sample indexing. The library was quantified on an Agilent BioAnalyzer 2100 DNA 7500 chip that lists the product size distribution and quantifies the concentration in µg/µl and in nM.

treatment_protocol: Fat bodies were dissected from 10 larvae in 1×PBS [140 mM NaCl, 10 mM PO4 Buffer, 3 mM KCl; Invitrogen cat. no. 18912-014] using forceps and dissection needles and collected in 1×PBS solution on ice.

value: larval fat bodies

value: fat bodies

value: Dam-Lamin Dm0

value: Dam4-HT-intein@L127C, induced by 25 µM 4-hydroxytamoxifen


title: Sd RNA-seq rep 1

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

country: USA

institute: University of Michigan

data_processing:
Basecalls performed using Illumina CASAVA bcl2fastq v2.17.1.14
Reads were mapped to mm9 (GENCODE vM1 comprehensive gene annotation) using STAR (v. 2.5.2b) with --outSAMunmapped Within KeepPairs
Mapped reads were filtered to autosomal reads using samtools view (v. 1.3.1) with options -f 3 -F 4 -F 8 -F 256 -F 2048 -q 255
Read counts per gene were gathered using QoRTs (v. 1.0.7;option --stranded)
Genome_build: mm9
Supplementary_files_format_and_content: fwd.bw files contain the normalized RNA-seq signal for the forward strand for each sample; rev.bw files contain the normalized RNA-seq signal for the reverse strand for each sample. These files were generated by first creating strand wiggle files using QoRTs bamToWiggle on the filtered bam files from STAR with flags (--omitTrackDefLine --negativeReverseStrand --stranded --sizefactor XXX), where the size factor for each sample was determined using the get.size.factors function in the QoRTs R package. wigToBigWig (v. 4) was then used to convert the wig files for each strand to bigwig files. geneCount files contain the read counts per gene (formatted for DESeq2), as output by QoRTs.

molecule: polyA RNA

source_name: Sd tailbuds RNA-seq

growth_protocol: All animals were housed in environmentally controlled conditions with 14 hour light and 10 hour dark cycles with food and water provided ad libitum. Sd/+ animals were maintained on an outbred CD-1 background (Charles River Laboratories, Wilmington, MA)

extract_protocol:
Matings for timed embryo isolation were set up using standard animal husbandry techniques. Noon on the day of vaginal plug observation was considered embryonic day (E) 0.5.  Embryos were isolated at E8.5- E10.5.  Embryo tailbuds were dissected just prior to the terminal somite, snap frozen in liquid nitrogen and stored at -80 C.
RNA was collected from the tailbuds using a dounce homogenizer and RNeasy mini extraction kit (Qiagen). First, samples were placed into a dounce homogenizer with 350 uL of RLT buffer and homogenizing with 5 strokes. The extraction procedure was followed as specified by the kit, including the optional DNAse treatment. Samples were eluted in 35 uL of RNAse free water. Libraries were prepared at the University of Michigan DNA Sequencing Core using the Illumina TrueSeq stranded mRNA-seq kit.

value: Sd/Sd

tag: age

value: Tailbuds


title: BR.repo.glia.Dam_DamIDSeq

value: Repo+ glial cells of larval central brain

value: pooled male and female

value: FLP-inducible STOP#1-Dam


title: WT RNA-seq rep 2

source_name: WT tailbuds RNA-seq

value: WT/WT


title: Sd RNA-seq rep 2


title: Sd ATAC-seq rep 4

data_processing:
Basecalls performed using Illumina CASAVA bcl2fastq v2.17.1.14
Adapters were trimmed using cta (v. 0.1.2) with default settings
Reads were aligned to mm9 using bwa mem (v. 0.7.15-r1140; using the -M flag)
Duplicates were marked using picard MarkDuplicates (v. 2.8.1) with VALIDATION_STRINGENCY=LENIENT
Reads were filtered to autosomal reads using samtools view (v. 1.3.1) with options -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30
Peak calling was performed using MACS2 (v. 2.1.1.20160309; options: --nomodel --broad --shift -100 --extsize 200 --keep-dup all)
Peaks were filtered against the mm9 blacklist (downloaded from  http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz)
Genome_build: mm9
Supplementary_files_format_and_content: broadPeak files contain the peak calls for each sample (as output by MACS2). bigwig files contain the normalized ATAC-seq signal for each sample. These files were created by dividing each line in the treat_pileup bedgraph files generated during peak calling with MACS2 by the number of tags in the treatment ('total tags in treatment' line in STDERR stream when MACS2 is run) and multiplying by 10 million. The bedgraph files were then converted to bigwig format using bedGraphToBigWig (v. 4). 'count' files contain the read counts per peak. These numbers were obtained by first merging all 5% FDR broadPeaks across all samples (after removing peaks that overlapped blacklisted regions), retaining those merged peaks that overlapped with 5% FDR peak calls from at least two of the eight ATAC-seq libraries, and then using bedtool's coverageBed (v. 2.26.0; with -counts flag) on each sample's filtered bam file to collect the number of reads falling in these retained merged peaks.

source_name: Sd tailbuds ATAC-seq

extract_protocol:
Matings for timed embryo isolation were set up using standard animal husbandry techniques. Noon on the day of vaginal plug observation was considered embryonic day (E) 0.5.  Embryos were isolated at E8.5- E10.5.  Embryo tailbuds were dissected just prior to the terminal somite, snap frozen in liquid nitrogen and stored at -80 C.
All procedures were done at 4C to minimized degradation of nuclei, and following the previously published protocol (Buenrostro et al) except as noted here. Each tailbud was disrupted in 200 uL of NIB with 0.5% Triton-X buffer by pipetting up and down. Then the samples were spun, supernatant removed and was followed by a second wash with RSB buffer. Each pellet of nuclei was then transported using a home-made Tn5 enzyme (Scott et al 2016; +GR ref). After 30 minutes of incubation at 37C, each sample was cleaned up with MinElute PCR purification kit (Qiagen)


title: WT ATAC-seq rep 3

source_name: WT tailbuds ATAC-seq


title: WT RNA-seq rep 1


title: WT RNA-seq rep 3


title: Sd ATAC-seq rep 3


title: Sd ATAC-seq rep 2


title: WT ATAC-seq rep 1


title: WT ATAC-seq rep 4


title: rat caput sperm

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description: 18 - 45 nt small RNAs

data_processing:
FASTX-Toolkit were used for sequence files preprocessing.
Processed sequence reads were mapped to the mouse mm9 or rat rn5 genome using bowtie (version 0.12.7) with settings -k 1 -v 2.
Genome_build: mm9 for mouse; rn5 for rat

organism: Rattus norvegicus

source_name: spermatozoa

growth_protocol: Normal growth

extract_protocol:
Total RNAs were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols, and 18 - 45 nt fraction of small RNAs were subjected to library construction.

tag: strain

value: Sprague Dawley

value: Caput epididymal sperm (purified)

value: 450g young adult


title: Sd RNA-seq rep 3


title: WT ATAC-seq rep 2


title: Control_mOSE_3

status: Public on Oct 30 2018

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

data_processing:
Pseudoalignment and transcript quantification performed with Kallisto (0.44.0) with -b 50
Differential expression analysis performed with Sleuth (0.30.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing TPM values for each gene across all samples

source_name: Ovarian surface epithelial cells

growth_protocol: mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 4% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems).

extract_protocol:
Total RNA was collected using the RNeasy Kit (Qiagen)
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: TGFB1-treated cells were treated with 10ng/mL TGFB1 (R&D Systems) for 4 days prior to RNA extraction

value: Ovarian surface epithelial cells

tag: treatment

value: Untreated


title: TGFB1_mOSE_3

value: 10ng/mL TGFB1


title: Control_mOSE_1


title: TGFB1_mOSE_2


title: TGFB1_mOSE_1


title: Cultured, patient-derived glioblastoma cells [GBMUT_H11_S191]

status: Public on Oct 26 2018

city: Cambridge

first: Sanjay

last: Prakadan

address: 77 Massachusetts Ave, E25-356

institute: Massachusetts Institute of Technology

description:
GBMUT_H11_S191
gbmut_rsem.txt

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Genome_build: human: hg19, mouse: mm10
Supplementary_files_format_and_content: cd8_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmt_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmut_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: l1201_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: fl5_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

source_name: Transcriptome of single glioblastoma cell following measurement with sSMR device

extract_protocol:
Smart-seq 2
Illumina Nextera XT


title: Sd ATAC-seq rep 1


title: Cultured, patient-derived glioblastoma cells [GBMUT_H08_S188]

description:
GBMUT_H08_S188
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H06_S186]

description:
GBMUT_H06_S186
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H03_S183]

description:
GBMUT_H03_S183
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H01_S181]

description:
GBMUT_H01_S181
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H10_S190]

description:
GBMUT_H10_S190
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H04_S184]

description:
GBMUT_H04_S184
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H02_S182]

description:
GBMUT_H02_S182
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H07_S187]

description:
GBMUT_H07_S187
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G12_S180]

description:
GBMUT_G12_S180
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H05_S185]

description:
GBMUT_H05_S185
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G10_S178]

description:
GBMUT_G10_S178
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G08_S176]

description:
GBMUT_G08_S176
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G07_S175]

description:
GBMUT_G07_S175
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G05_S173]

description:
GBMUT_G05_S173
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G06_S174]

description:
GBMUT_G06_S174
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G04_S172]

description:
GBMUT_G04_S172
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H09_S189]

description:
GBMUT_H09_S189
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_H12_S192]

description:
GBMUT_H12_S192
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G03_S171]

description:
GBMUT_G03_S171
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G02_S170]

description:
GBMUT_G02_S170
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G01_S169]

description:
GBMUT_G01_S169
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F11_S167]

description:
GBMUT_F11_S167
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F12_S168]

description:
GBMUT_F12_S168
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G11_S179]

description:
GBMUT_G11_S179
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F08_S164]

description:
GBMUT_F08_S164
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F09_S165]

description:
GBMUT_F09_S165
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F02_S158]

description:
GBMUT_F02_S158
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F01_S157]

description:
GBMUT_F01_S157
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E12_S156]

description:
GBMUT_E12_S156
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F07_S163]

description:
GBMUT_F07_S163
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E10_S154]

description:
GBMUT_E10_S154
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E11_S155]

description:
GBMUT_E11_S155
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F03_S159]

description:
GBMUT_F03_S159
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F06_S162]

description:
GBMUT_F06_S162
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_G09_S177]

description:
GBMUT_G09_S177
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F05_S161]

description:
GBMUT_F05_S161
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E09_S153]

description:
GBMUT_E09_S153
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E05_S149]

description:
GBMUT_E05_S149
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E07_S151]

description:
GBMUT_E07_S151
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E06_S150]

description:
GBMUT_E06_S150
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E04_S148]

description:
GBMUT_E04_S148
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E02_S146]

description:
GBMUT_E02_S146
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E01_S145]

description:
GBMUT_E01_S145
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E03_S147]

description:
GBMUT_E03_S147
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D12_S144]

description:
GBMUT_D12_S144
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F10_S166]

description:
GBMUT_F10_S166
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D11_S143]

description:
GBMUT_D11_S143
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_F04_S160]

description:
GBMUT_F04_S160
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D09_S141]

description:
GBMUT_D09_S141
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D08_S140]

description:
GBMUT_D08_S140
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D10_S142]

description:
GBMUT_D10_S142
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D07_S139]

description:
GBMUT_D07_S139
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D01_S133]

description:
GBMUT_D01_S133
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C11_S131]

description:
GBMUT_C11_S131
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D04_S136]

description:
GBMUT_D04_S136
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D03_S135]

description:
GBMUT_D03_S135
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C12_S132]

description:
GBMUT_C12_S132
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D05_S137]

description:
GBMUT_D05_S137
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D06_S138]

description:
GBMUT_D06_S138
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_D02_S134]

description:
GBMUT_D02_S134
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_E08_S152]

description:
GBMUT_E08_S152
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C10_S130]

description:
GBMUT_C10_S130
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C06_S126]

description:
GBMUT_C06_S126
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C08_S128]

description:
GBMUT_C08_S128
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C04_S124]

description:
GBMUT_C04_S124
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C09_S129]

description:
GBMUT_C09_S129
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C05_S125]

description:
GBMUT_C05_S125
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C03_S123]

description:
GBMUT_C03_S123
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B12_S120]

description:
GBMUT_B12_S120
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C02_S122]

description:
GBMUT_C02_S122
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C01_S121]

description:
GBMUT_C01_S121
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B11_S119]

description:
GBMUT_B11_S119
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B07_S115]

description:
GBMUT_B07_S115
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B10_S118]

description:
GBMUT_B10_S118
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B08_S116]

description:
GBMUT_B08_S116
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B06_S114]

description:
GBMUT_B06_S114
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B09_S117]

description:
GBMUT_B09_S117
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B05_S113]

description:
GBMUT_B05_S113
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B04_S112]

description:
GBMUT_B04_S112
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_C07_S127]

description:
GBMUT_C07_S127
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A12_S108]

description:
GBMUT_A12_S108
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B01_S109]

description:
GBMUT_B01_S109
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A11_S107]

description:
GBMUT_A11_S107
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B03_S111]

description:
GBMUT_B03_S111
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A08_S104]

description:
GBMUT_A08_S104
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_B02_S110]

description:
GBMUT_B02_S110
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A07_S103]

description:
GBMUT_A07_S103
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A09_S105]

description:
GBMUT_A09_S105
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A03_S99]

description:
GBMUT_A03_S99
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A02_S98]

description:
GBMUT_A02_S98
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A06_S102]

description:
GBMUT_A06_S102
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A05_S101]

description:
GBMUT_A05_S101
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A10_S106]

description:
GBMUT_A10_S106
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H07_S283]

description:
GBMT_H07_S283
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H09_S285]

description:
GBMT_H09_S285
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H10_S286]

description:
GBMT_H10_S286
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H12_S288]

description:
GBMT_H12_S288
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H08_S284]

description:
GBMT_H08_S284
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A04_S100]

description:
GBMUT_A04_S100
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H03_S279]

description:
GBMT_H03_S279
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H06_S282]

description:
GBMT_H06_S282
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G12_S276]

description:
GBMT_G12_S276
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H04_S280]

description:
GBMT_H04_S280
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H02_S278]

description:
GBMT_H02_S278
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H01_S277]

description:
GBMT_H01_S277
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H05_S281]

description:
GBMT_H05_S281
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells [GBMUT_A01_S97]

description:
GBMUT_A01_S97
gbmut_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G11_S275]

description:
GBMT_G11_S275
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G10_S274]

description:
GBMT_G10_S274
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G07_S271]

description:
GBMT_G07_S271
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G09_S273]

description:
GBMT_G09_S273
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G08_S272]

description:
GBMT_G08_S272
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_H11_S287]

description:
GBMT_H11_S287
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G04_S268]

description:
GBMT_G04_S268
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G05_S269]

description:
GBMT_G05_S269
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G06_S270]

description:
GBMT_G06_S270
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G03_S267]

description:
GBMT_G03_S267
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G02_S266]

description:
GBMT_G02_S266
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F09_S261]

description:
GBMT_F09_S261
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F08_S260]

description:
GBMT_F08_S260
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F11_S263]

description:
GBMT_F11_S263
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_G01_S265]

description:
GBMT_G01_S265
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F06_S258]

description:
GBMT_F06_S258
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F12_S264]

description:
GBMT_F12_S264
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F05_S257]

description:
GBMT_F05_S257
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F07_S259]

description:
GBMT_F07_S259
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F04_S256]

description:
GBMT_F04_S256
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F01_S253]

description:
GBMT_F01_S253
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E12_S252]

description:
GBMT_E12_S252
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E11_S251]

description:
GBMT_E11_S251
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F03_S255]

description:
GBMT_F03_S255
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E09_S249]

description:
GBMT_E09_S249
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E10_S250]

description:
GBMT_E10_S250
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E08_S248]

description:
GBMT_E08_S248
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F02_S254]

description:
GBMT_F02_S254
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E04_S244]

description:
GBMT_E04_S244
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E02_S242]

description:
GBMT_E02_S242
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D12_S240]

description:
GBMT_D12_S240
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E07_S247]

description:
GBMT_E07_S247
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D11_S239]

description:
GBMT_D11_S239
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_F10_S262]

description:
GBMT_F10_S262
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E06_S246]

description:
GBMT_E06_S246
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E05_S245]

description:
GBMT_E05_S245
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E03_S243]

description:
GBMT_E03_S243
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_E01_S241]

description:
GBMT_E01_S241
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D10_S238]

description:
GBMT_D10_S238
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D09_S237]

description:
GBMT_D09_S237
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D08_S236]

description:
GBMT_D08_S236
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D07_S235]

description:
GBMT_D07_S235
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D04_S232]

description:
GBMT_D04_S232
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D06_S234]

description:
GBMT_D06_S234
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D03_S231]

description:
GBMT_D03_S231
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D01_S229]

description:
GBMT_D01_S229
gbmt_rsem.txt


title: BR.Pc.m_DamIDSeq

value: larval central brain

value: male

value: wandering third instar larvae

value: brain without ventral nerve cord

value: Dam-Polycomb

value: Dam4-HT-intein@L127C, uninduced


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C12_S228]

description:
GBMT_C12_S228
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D02_S230]

description:
GBMT_D02_S230
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C07_S223]

description:
GBMT_C07_S223
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C10_S226]

description:
GBMT_C10_S226
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C08_S224]

description:
GBMT_C08_S224
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C06_S222]

description:
GBMT_C06_S222
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C09_S225]

description:
GBMT_C09_S225
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C05_S221]

description:
GBMT_C05_S221
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C04_S220]

description:
GBMT_C04_S220
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C03_S219]

description:
GBMT_C03_S219
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C02_S218]

description:
GBMT_C02_S218
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C01_S217]

description:
GBMT_C01_S217
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B12_S216]

description:
GBMT_B12_S216
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B11_S215]

description:
GBMT_B11_S215
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B09_S213]

description:
GBMT_B09_S213
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B08_S212]

description:
GBMT_B08_S212
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B07_S211]

description:
GBMT_B07_S211
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B04_S208]

description:
GBMT_B04_S208
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B05_S209]

description:
GBMT_B05_S209
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B06_S210]

description:
GBMT_B06_S210
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B10_S214]

description:
GBMT_B10_S214
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_D05_S233]

description:
GBMT_D05_S233
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B03_S207]

description:
GBMT_B03_S207
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B01_S205]

description:
GBMT_B01_S205
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A11_S203]

description:
GBMT_A11_S203
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_B02_S206]

description:
GBMT_B02_S206
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A12_S204]

description:
GBMT_A12_S204
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A09_S201]

description:
GBMT_A09_S201
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A10_S202]

description:
GBMT_A10_S202
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_C11_S227]

description:
GBMT_C11_S227
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A06_S198]

description:
GBMT_A06_S198
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A07_S199]

description:
GBMT_A07_S199
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A04_S196]

description:
GBMT_A04_S196
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A05_S197]

description:
GBMT_A05_S197
gbmt_rsem.txt


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A08_S200]

description:
GBMT_A08_S200
gbmt_rsem.txt


title: WT-2

status: Public on Oct 01 2018

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Base-calling: cellranger mkfastq (version 2.0.1).
Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.0.1).
Dim. reduction, clustering, html hdf matrix exports: cellranger reanalyse (version 2.0.1).
Normalization, grouped dim reduction, clustering: cellranger aggr (version 2.0.1).
csv exports: cellranger mat2csv (version 2.0.1).
Differential gene expression: cellranger reanalyse (version 2.0.1) loupe cell browser (version 2.0.0).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: XXX_summary.html: summary HTML file containing summary metrics and automated secondary analysis results.
Supplementary_files_format_and_content: XXX_expression.csv : gene-barcode matrix in dense CSV format (where every row-column entry is explicitly stored, even if it's a zero).

source_name: Cortical organoids

growth_protocol: Free-floating iPSC aggregates were kept under agitation for 6 months and the media was replaced in order to promote neuronal induction (Dual SMAD inhibition), proliferation (FGF2 and EGF), differentiation (growth factors such as BDNF, GDNF) and maturation.

extract_protocol: 10X chromium chemistry V2.

treatment_protocol: Cortical organoids were dissociated using ACCUMAX and mechanical dissociation for 30min.

value: CVB - iPSC (Coriell GM25430)

tag: age of organoid

value: 6 months

tag: reprogramming strategy

value: Retroviral


title: WT-1


title: IFN_enriched_cells

status: Public on Oct 05 2018

city: Seattle

first: Jesse

middle: D

last: Bloom

state: WA

address: 1100 Fairview Ave N, room B3-123

institute: Fred Hutch Cancer Research Center

description:
A549 cells infected with influenza, enriched for IFN+, then with canine cells spiked in for multiplet control.
Human (A549) cells with some canine (MDCK) cells spiked in as control.
mRNA
Fastq files: R1 file contains the cell barcode (first 16 nt) and UMI (next 10 nt); R2 file contains the biological reads spanning the 3' end of the transcripts; I1 file contains the sample indices for de-multiplexing.

data_processing:
All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/IFNsorted_flu_single_cell
The Illumina sequencing for the transcriptomics was processed using the 10X cellranger program (version 2.2.0) to generate the cell-gene matrices after mapping against a multi-species (human+flu and canine) transcriptome.
The cellranger alignments were then analyzed by a custom Python script (at https://github.com/jbloomlab/IFNsorted_flu_single_cell) to assign viral transcripts to one of the two viral barcode variants, and this information was annotated on the cells for the cell-gene matrices.
The PacBio circular consensus sequencing data were processed using the PacBio's ccs program (version 3.1.0, https://github.com/PacificBiosciences/unanimity) to build the circular consensus sequences (CCSs).
Custom Python code (at https://github.com/jbloomlab/IFNsorted_flu_single_cell) was used to analyze the PacBio CCS data to call viral mutations, and add these to the PacBio annotated cells for the humanplusflu cell-gene matrix.
Genome_build: Human genome GRCh38 with protein-coding genes defined in GRCh38.87; canine genome CanFam3.1 with protein-coding genes defined in CanFam3.1.87; Influenza A virus (A/WSN/1933(H1N1)) variant (influenza_virus_reference.fasta).
Supplementary_files_format_and_content: The processed data consist of the cell-gene matrices for the human and canine cells, with *.tsv files indicating the cells and genes, and the *.mtx files indicating the counts in the matrices.
Supplementary_files_format_and_content: merged_humanplusflu_cells.tsv: humanplusflu cell barcodes annotated by viral barcode.
Supplementary_files_format_and_content: merged_humanplusflu_genes.tsv: humanplusflu genes.
Supplementary_files_format_and_content: merged_humanplusflu_matrix.mtx: cell-gene matrix for humanplusflu cells.
Supplementary_files_format_and_content: merged_canine_cells.tsv: canine cell barcodes.
Supplementary_files_format_and_content: merged_canine_genes.tsv: canine genes.
Supplementary_files_format_and_content: merged_canine_matrix.mtx: cell-gene matrix for canine cells.
Supplementary_files_format_and_content: PacBio_annotated_merged_humanplusflu_cells.tsv: humanplusflu cell barcodes annotated by mutations called from PacBio sequencing of viral genes.

organism:
Homo sapiens
Canis lupus familiaris
Influenza A virus (A/WSN/1933(H1N1))

source_name: A549 cells with an IFN reporter

extract_protocol:
Cells were processed on the 10X Chromium.
Transcriptomics was performed by Illumina sequencing per 10X guidelines.

tag: human cell line

value: infection with influenza virus

tag: time

value: 13 hours post-infection

value: IFN-enriched cells

tag: canine cell line

value: MDCK


title: 23dpa -scRNAseq samples 4 to 6 and 3dpa -scRNAseq samples 1 to 3

status: Public on Oct 25 2018

city: Lund

first: Nicholas

last: Leigh

state: Skåne

address: BMC A12, Sölvegatan 17

department: Laboratory Medicine

country: Sweden

institute: Lund University

data_processing:
16 single-cell libraries were sequenced using an Illumina NextSeq 500 as 3 different pools. All three pools used inDrops v3 design (indices included above as a sample characteristic). To process these libraries we used the inDrops pipeline with modifications (https://github.com/brianjohnhaas/indrops). Included with the paper are example .yaml files for processing these data and a full description of the pipeline used to process these data can be found on the referenced github page.
Base-calling and FASTQ file generation: Raw BCL files were converted to FASTQ files using bcl2fastq command "bcl2fastq --use-bases-mask y*,y*,y*,y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0". If desired one can make a sample sheet and demultiplex the libraries here using the the library indices included above (see sample characteristic section) however, this is not necessary as demultiplexing will occur within the inDrops pipeline. Read 1 = 61 bp gene read, read 2 = 14bp part 2 cell barcode (8bp)/ UMI (6bp) / poly T, index read 1 (i7)= 8bp part 1 single cell barcode, index read 2 (i5) = 8bp library index (this is the index sequence found in the sample characteristcs section)
Build axolotl transcriptome bowtie index: The axolotl transcriptome was downloaded from https://portals.broadinstitute.org/axolotlomics/. Using bowtie v1.2.2 a bowtie index was made using the command "bowtie-build Axolotl.Trinity.CellReports2017 Axolotl.Trinity.CellReports2017"
Filtering: inDrops.py (found on https://github.com/brianjohnhaas/indrops) was they run as such "python indrops.py project.yaml filter" to find reads with two cell barcode sequences, a unique molecular identifier (UMI), and illumina library index (which will allow for demultiplexing, this is required with these samples). Read 1 (gene read) is then tripped using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:16).
Identify abundant barcodes: Run as "python indrops.py project.yaml identify_abundant_barcodes" compares the cell barcodes to a list of possible barcodes. Read 1 (gene read) is split into barcode-specific files for mapping and UMI filtering.
Sorting: barcodes are sorting using "python extract_barcoded_reads.py project.yaml sort" which sorts the reads according to their barcode while also fitlering out barcodes with less than 250 reads.
Quantification: Reads, sample identity, cell barcodes, and UMIs were extracted from the Illumina data and encoded into a single fastq file like so "python extract_barcoded_reads.py project.yaml quantify --no-bam > barcoded_reads.fastq". Next read names were made unique: encode_read_number_in_fastq.pl barcoded_reads.fastq > barcoded_reads.adj.fq and then reads were aligned to the bowtie index: bowtie target.fasta.bowtie -q -p 20 -a --best --strata --chunkmbs 1000 --sam -m 200 -n 1 -l 15 -e 100 barcoded_reads.adj.fq  >  target.bowtie.adj.sam. Aligned reads were counted according to targeted transcripts (using script 'bam_to_count_matrix.pl --bam target.bowtie.adj.sam > sc.counts.matrix', this script can be modified depending on library size to allow a determined max number of cells through the filter, We assume 3000 cells per library and modify max_top_cells according to the number of libraries in the pool (e.g. 5 x 3000 = 15000)), with reads fractionally assigned across multi-mapped targets, restricted to unique UMIs at target transcripts. Finally, read counts were aggregated across transcript isoforms to yield a gene count matrix, in which a single representative isoform was chosen to represent each respective gene. This was performed using trinity_trans_matrix_to_rep_trans_gene_matrix.pl (found on the linked github)
Matrix annotation: Count matrices were then annotated using the following 'perl ./rename_matrix_feature_identifiers.pl sc.counts.matrix Axo.Mar2014.Trinotate.xls.annot_mapping > sc.counts.annotated.matrix'. With scripts and annotation files available at https://github.com/brianjohnhaas/indrops.
Genome_build: N/A
Supplementary_files_format_and_content: Three cell by gene matrices are provided. These are tsv files that are the result of the above data processing steps. These include intact_contralateral_cell_by_gene.repGene, which has five total samples S_1 and S_2 are intact limbs, while S_3, S_4, and S_5 are contralateral limbs. The second matrix, early_and_medium_bud.repGene, has 5 samples labeled S_1 through S_5, with S_1, S_2, and S_4 being medium-bud blastema samples and S_3 and S_5 being early-bud blastema samples. The third matrix, wound_healing_and_medium_bud.repGene, has 6 samples labeled N_1 through N_6, with N_1, N_2, and N_3 being medium-bud blastema samples and N_4, N_5, N_6 being wound healing samples.

organism: Ambystoma mexicanum

source_name: Medium-bud limb blastema and Wound healing-stage limb

extract_protocol:
Animals were narcotized in 0.1% Tricaine. Following this, iridectomy scissors were used to remove the blastema at its interface with the stump. The removed blastema was placed in 400uL papain (Worthington LK003178, resuspended in 2.5mL 0.7X PBS) in an Eppendorf tube. The tube was placed on a nutating rocker for 30 minutes, with gentle pipetting performed every 5 minutes after an initial 10 minute incubation. After 30 minutes, the cells were carefully passed through a 70um cell strainer to a well of a 6 well plate on ice and 0.7X HBSS ice cold was used to collect any cells that remained in the tube and subsequently this was passed through the cell strainer into the 6-well plate. With 2mL 0.7X HBSS ice cold wash the cell strainer, making sure that 0.7X HBSS passing through the strainer enters the 6-well plate. This plate was allowed to sit for 10 minutes on ice to allow cells to settle. Following, a 3mL syringe was used to slowly layer 3mL of 5% Optiprep (diluted in 0.7X HBSS) down the side of the well. Cells were then let to sit for 2 minutes, before carefully removing 3mL of the 0.7X HBSS with a p1000 pipette. These steps were then repeated with 10% and 15% Optiprep, removing the more dilute sample after each step. At the end, around 200uL of 15% Optiprep should be left with the cells. A trypan blue count was taken to ensure viability greater than 90%, and 0.5% BSA by volume was added to the remaining cells. A detailed protocol can be found on protocols.io (dx.doi.org/10.17504/protocols.io.qmmdu46)
TruSeq HT

tag: days post amputation

value: 3 and 23


title: 23dpa -scRNAseq samples 1 to 3 and 14dpa -scRNAseq samples to 14dpa -scRNAseq samples1 to 2

source_name: Early and Medium-bud limb blastema


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A01_S193]

description:
GBMT_A01_S193
gbmt_rsem.txt

tag: cell type


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A03_S195]

description:
GBMT_A03_S195
gbmt_rsem.txt


title: Influenza A virus (A/WSN/1933(H1N1))

description: PacBio circular consensus sequencing for viral genotypes.

organism: Influenza A virus (A/WSN/1933(H1N1))

source_name: Influenza virus infection

extract_protocol:
Cells were processed on the 10X Chromium.
PacBio was performed using circular-consensus sequencing of PCR amplified viral transcripts.


title: Cultured, patient-derived glioblastoma cells, treated with MDM2-inhibitor [GBMT_A02_S194]

description:
GBMT_A02_S194
gbmt_rsem.txt


title: 1447

city: Philadelphia

first: Caroline

middle: R

last: Bartman

state: PA

address: 34th st.

department: Department of Bioengineering

institute: University of Pennsylvania

data_processing:
used bcl2fastq to convert and demultiplex the reads
we used Bowtie to map reads to mm9 genome
used MACS to get wig files
used wigToBigWig to convert wig to bigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: G1E-ER4 erythroid cells

growth_protocol: cells grown in suspension in IMDM supplemented with erythropoietin

extract_protocol:
Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody.
use Illumina TruSeq ChIP sample preparation kit
size selection using SPRI beads, confirmed ~340bp using Bioanalyzer

treatment_protocol: treated with either 60 min 250nM JQ1, 300nM triptolide, or 100nM flavopiridol

value: immortalized erythroid cell overexpressing GATA1-ER fusion

tag: differentiation

value: differentiated 24 hours with 100nM estradiol

tag: chip antibody

value: RBP-1 (santa cruz sc899)


title: 1181


title: 1446


title: 1177


title: 1180


title: 1450


title: 1448


title: 1442


title: 1444


title: 1176


title: 1443


title: 1449


title: 1178


title: 1445


title: 1179


title: mOSN_RNAseq_rep5

status: Public on Sep 27 2018

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol:
Crosslinked-ChIP: Chromatin from formaldehyde cross-linked cells was sheared on a Covaris S220 Focused-ultrasonicator to a size range of 200-500bp. Approximately 1-2ug of sheared chromatin was used for immunoprecipitation with antibodies, and precipitated DNA was column purified. RNA: Cells were lysed in Trizol-LS (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
Crosslinked-ChIP: ChIP-seq Libraries were prepared using a Nugen Ultralow V2 kit. RNA: RNA-seq libraries were prepared using a TruSeq Stranded Total RNA with Ribo-Zero Gold Set B kit (Illumina RS-1222302).

treatment_protocol: = Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting. For Krt5Cre knockout cells, at 6-weeks of age, deletion of the conditional allele in horizontal basal cells was induced by two intraperitoneal injections of tamoxifen twenty-four hours apart. One week later, differentiation of horizontal basal cells into olfactory cell types was induced by intraperitoneal injection with methimazole, which triggers ablation of olfactory epithelium and regeneration of the tissue from horizontal basal cells. The olfactory epithelium was allowed to regenerate for 8-weeks, and then  TdTomato+ cell were purified by FACS. TdTomato bright and dim populations were collected separately, followed by RNA-seq.

tag: genotype/variation

value: OMP-IRES-GFP

tag: tissue/cell type

value: mature olfactory sensory neurons


title: mOSN_RNAseq_rep4


title: Intact- scRNAseq samples 1 to 2 and Contralateral- scRNAseq samples 1 to 3

description: intact_contralateral_cell_by_gene.repGene

source_name: Homeostatic limb and Intact limb and contralateral to early-bud blastema

extract_protocol:
Animals were narcotized in 0.1% Tricaine. Intact limbs were amputated and placed into 420ul of 0.7X PBS with 5mM EDTA, 25mM cysteine, and 40ul papain (Sigma P3125) within a 1.5mL eppendorf tube. Tissue was minced with scissors in this solution for 3-5 min until tissue was completely broken down. 0.6mL of ice cold 0.7XHBSS was added to the cells and cells were dumped (not pipetted) onto a 70um filter held above a 6 well plate on ice. The filter was washed with 2mL ice cold 0.7X HBSS.  This plate was allowed to sit for 10 minutes on ice. Following, a 3mL syringe was used to slowly layer 3mL of 5% Optiprep (diluted in 0.7X HBSS) down the side of the well. Cells were then let to sit for 2 minutes, before carefully removing 3mL of the 0.7X HBSS with a p1000 pipette. These steps were then repeated with 10% and 15% Optiprep, removing the more dilute solution (top layer) after each step. At the end, around 200uL of 15% Optiprep should be left with the cells. A trypan blue count was taken to ensure viability greater than 90%, and 0.5% BSA by volume was added to the remaining cells.
Animals were narcotized in 0.1% Tricaine. Following this, iridectomy scissors were used to remove the blastema at its interface with the stump. The removed blastema was placed in 400uL papain (Worthington LK003178, resuspended in 2.5mL 0.7X PBS) in an Eppendorf tube. The tube was placed on a nutating rocker for 30 minutes, with gentle pipetting performed every 5 minutes after an initial 10 minute incubation. After 30 minutes, the cells were carefully passed through a 70um cell strainer to a well of a 6 well plate on ice and 0.7X HBSS ice cold was used to collect any cells that remained in the tube and subsequently this was passed through the cell strainer into the 6-well plate. With 2mL 0.7X HBSS ice cold wash the cell strainer, making sure that 0.7X HBSS passing through the strainer enters the 6-well plate. This plate was allowed to sit for 10 minutes on ice to allow cells to settle. Following, a 3mL syringe was used to slowly layer 3mL of 5% Optiprep (diluted in 0.7X HBSS) down the side of the well. Cells were then let to sit for 2 minutes, before carefully removing 3mL of the 0.7X HBSS with a p1000 pipette. These steps were then repeated with 10% and 15% Optiprep, removing the more dilute sample after each step. At the end, around 200uL of 15% Optiprep should be left with the cells. A trypan blue count was taken to ensure viability greater than 90%, and 0.5% BSA by volume was added to the remaining cells. A detailed protocol can be found on protocols.io (dx.doi.org/10.17504/protocols.io.qmmdu46)
TruSeq HT

value: N/A and 14


title: mOSN_Lhx2KO_Input_ChIPseq

tag: molecule subtype

value: Crosslinked-ChIP


title: mOSN_Lhx2KO_Ldb1_ChIPseq_rep2

value: anti-Ldb1 (Santa Cruz Biotechnology, sc-11198)


title: Olfr1507_Ldb1_ChIPseq_rep2

value: Olfr1507+ cells


title: Olfr1507_Ldb1_ChIPseq_rep1


title: Olfr1507_Input_ChIPseq_rep2


title: Olfr1507_Input_ChIPseq_rep1


title: DEX_Day1

status: Public on Sep 26 2018

city: Nagoya

first: Takumi

last: Kagawa

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Drug Safety Sciences

country: Japan

institute: Nagoya university

data_processing:
FASTQ files obtained from the MiSeq were analyzed with CLC Genomics Workbench (Qiagen) as follows. Adaptor sequences were trimmed and sequences with the length below 15 or more than 55 bp were discarded before counting. Trimmed data were mapped to the rattus mature miRNA sequences in the miRbase 21 database, wherein 765 rattus mature miRNAs are listed, allowing 2 mismatches, then mature sequences were counted and grouped.
MiRNA with the read counts less than 10 at all time points were filtered out. Furthermore, miRNAs whose read counts were zero in the control samples were excluded to avoid dividing by zero when fold change is calculated. Normalization of count data was performed with DESeq package (ver. 1.28.0) of R software (ver. 3.40).
Genome_build: miRBase21 Rattus mature
Supplementary_files_format_and_content: xlsx file containing raw and normalized read counts in individual sheets.

source_name: Plasma

growth_protocol: Male Sprague-Dawley rats (6-week-old) were obtained from Japan SLC (Hamamatsu, Japan). The animals were housed under 12 h light/dark cycle (9:00 to 21:00) in a controlled environment (temperature 23 ± 2℃ and humidity 55 ± 10%) in the institutional animal facility with ad libitum access to food and water. The rats were acclimated for one week before treatment. All animal experiments were approved by the Animal Care Committee of Nagoya University Graduate School of Medicine and were carried out in accordance with the guidelines established by the Institute for Laboratory Animal Research of the Medical School of Nagoya University, Japan.

extract_protocol:
Total RNA including small RNA was extracted from 200 µL of plasma samples thawed on ice, using a miRNeasy Serum/Plasma Kit with a modification. One milliliter of QIAzol (Qiagen) Lysis Reagent was added to plasma samples. After vigorous vortexing, 200 µL of chloroform were added to each tube, mixed for 15 s and incubated at room temperature for 2 min, followed by centrifugation for 15 min (12,000 × g, 4℃). In the next step, the aqueous phase was pooled in a tube, and mixed with 1.5 volumes of 100% ethanol. The rest of the procedures were performed according to the protocol of the miRNeasy Serum/Plasma Kit. The quantity and quality of RNA samples were checked with Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using the RNA6000 NanoChip (Agilent Technologies). RNA samples were stored at -80℃ until further analyses.
cDNA libraries were prepared with a NEBNext Multiplex Small RNA Library Prep Set for Illumina according to the manufacturer’s protocols. Briefly, extracted RNA (10-100 ng) was used for 3’ and 5’ adapter ligation and primer hybridization, followed by cDNA synthesis and PCR amplification (15 cycles). The amplified cDNA libraries were purified with a QIAquick PCR Purification Kit. The purified products were then loaded on a 6% Novex TBE PAGE gel (Invitrogen, Carlsbad, CA) and separated for size selection. The cDNA fragment of 130~160 bp was isolated and extracted from the gel in accordance with the instruction of the NEBNext Multiplex Small RNA Library Prep Set for Illumina. The purified cDNA libraries were quantified with Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) using a Qubit dsDNA HS Assay Kit (Life Technologies).

treatment_protocol: In the time-course experiments, five rats were used per group. To make the hepatocellular injury models, rats were intragastrically administered 1500 mg/kg Acetaminophen (APAP) suspended in 0.5% carboxymethylcellulose (CMC), 10 mL/kg after fasting for 12 h. Rats were intragastrically administered 100 mg/kg thioacetamide (TAA) in 0.5% CMC, 10 mL/kg. Plasma and liver samples were collected 3, 6, 12, 24 h after administration. To make cholestasis models, rats were intragastrically administered 250 mg/kg 4,4'-methylenedianiline (MDA) in 0.5% CMC, 10 mL/kg, or 150 mg/kg α-naphthylisothiocyanate (ANIT) in corn oil, 5 mL/kg. Plasma and liver samples were collected 3, 6, 12, 24, 48 h after administration. To make the steatosis models, rats were intragastrically administered 300 mg/kg (carbon tetrachloride) CCl4, 5 ml/kg in corn oil once a day for up to 5 days. Plasma and liver samples were collected 1, 3, 5 days after the first administration. Rats were intragastrically administered 15 mg/kg dexamethasone (DEX) in corn oil, 5 mL/kg once a day for up to 3 days. Plasma and liver samples were collected 1, 2, 3 days after the first administration. Vehicle groups were treated with the solvent used to make each DILI model. Blood and liver samples were collected under isoflurane anesthesia. Blood was collected from descending aorta, and EDTA was used as an anticoagulant. After centrifugation, plasma was collected and kept at -80℃ until the experiment.

value: Sprague-Dawley

tag: gender

value: Male

tag: drug

value: DEX

tag: time after administration

value: Day 1


title: DEX_Day3

tag: strain

tag: age

value: Day 3


title: MDA_48h

value: MDA


title: CCl4_Day1


title: DEX_Day2

value: Day 2


title: MDA_12h


title: MDA_24h


title: MDA_3h

value: 3 h


title: ANIT_12h_1

value: ANIT


title: ANIT_24h_1


title: ANIT_48h_2


title: MDA_vehicle

value: CMC

value: 0 h


title: CCl4/DEX_vehicle

description: CCl4_counts.xlsx and DEX_counts.xlsx

value: corn oil

value: Day 0


title: ANIT_vehicle_2


title: MDA_6h

value: 6 h


title: ANIT_24h_2


title: ANIT_3h


title: ANIT_vehicle_1


title: TAA_24h

value: TAA


title: TAA_6h


title: CCl4_Day3


title: CCl4_Day5

value: Day 5


title: ANIT_48h_1


title: TAA_vehicle


title: ANIT_12h_2


title: APAP_24h

value: APAP


title: TAA_3h

value: Sprague-Dawley


title: APAP_12h

value: Male


title: ANIT_6h


title: APAP_vehicle


title: APAP_6h


title: APAP_3h


title: TAA_12h


title: AGN24HR3

status: Public on Sep 15 2018

city: CASTANET TOLOSAN

first: Thomas

last: Rey

address: 24 chemin de borde rouge, BP42617

country: France

institute: DE SANGOSSE

description: AGN24H - AGN24HR3_TTAGGC_L008_R1 (paired) (GE) - RPKM

data_processing:
Quality check with FastQC
RNAseq reads were aligned to the Arabidopsis thaliana TAIR10 genome using CLC Genomics Workbench version 8.5.1
Genome_build: TAIR10
Supplementary_files_format_and_content: AGN23_RPKM_TAIR10.xlsx

organism: Arabidopsis thaliana

source_name: Two seedlings_AGN23_24hr

growth_protocol: Seeds of Arabidopsis thaliana Col-0 were soaked in water for 40 min, and then treated for 30 min in 2.4% sodium hypochlorite solution, followed by four washings in sterile water. The surface-sterilized seeds were transferred into wells of 24-well microtiter plates (2 seeds per well), containing 300 μl of Murashige and Skoog medium (MS; Sigma-Aldrich) supplemented with 1% sucrose. The plates were incubated under 16 h illumination period (270 μmol m−2 s−1) and 8 h night period at 23°C on a rotary shaker at 90 rpm for 3 days and then on a static tray for 12 days. For SA analysis and pathogenicity tests, plants were grown on pots (Jiffy, Lyon, France) in a growth chamber under 12 h light (270 μmol m−2 s−1), at 23°C and 12 h dark at 20°C during 3 weeks.

extract_protocol:
Total RNAs were extracted using the SV Total RNA Isolation System kit (Promega®, Charbonnières, France) according to manufacturers recommandations.
Librairy prepared with Kit Illumina TruSeq Stranded mRNA, Sequencing with HiSeq SBS v3 (2x100 pb),

treatment_protocol: Surface sterilized seeds of Arabidopsis thaliana Col-0 wild-type plants were grown for 12 days in 24-well microtiter plates (2 seeds per well) containing 300μl of Murashige and Skoog medium (MS; Sigma-Aldrich) supplemented with 1% sucrose. The plates were incubated under 16 h illumination period (270 μmol m−2 s−1) and 8h night period at 23°C on a rotary shaker at 90rpm for 3 days and then on a static tray for 12 days. For the treatment, Streptomyces AGN23 culture supernatant obtained after 5 days of growth in liquid medium was added to fresh MS medium (without sucrose) containing  Actilandes (1 µl/l) at a final dilution of 100X,

tag: ecotype

tag: tissue

value: seedlings

tag: treatment

value: Streptomyces AGN23 culture supernatant

tag: time point

value: 24 hours post treatment

tag: replicate

value: Biological replicate 2


title: ACT1HR3

description: ACT1H - ACT1HR3_ATCACG_L005_R1 (paired) (GE) - RPKM

source_name: Two seedlings_mock_1hr

value: Actilande (Mock)

value: 1 hour post treatment

value: Biological replicate 3


title: ACT6HR1

description: ACT6H - ACT6HR1_TTAGGC_L004_R1 (paired) (GE) - RPKM

source_name: Two seedlings_mock_6hr

value: 6 hours post treatment

value: Biological replicate 1


title: AGN1HR3

description: AGN1H - AGN1HR3_ACTGAT_L007_R1 (paired) (GE) - RPKM

source_name: Two seedlings_AGN23_1hr


title: AGN6HR2

description: AGN6H - AGN6HR2_GAGTGG_L007_R1 (paired) (GE) - RPKM

source_name: Two seedlings_AGN23_6hr


title: AGN1HR2

description: AGN1H - AGN1HR2_CAGATC_L007_R1 (paired) (GE) - RPKM


title: ACT24HR3

description: ACT24H - ACT24HR3_TGACCA_L005_R1 (paired) (GE) - RPKM

source_name: Two seedlings_mock_24hr


title: AGN1HR1

description: AGN1H - AGN1HR1_ATCACG_L007_R1 (paired) (GE) - RPKM


title: AGN24HR1

description: AGN24H - AGN24HR1_TGACCA_L007_R1 (paired) (GE) - RPKM


title: AGN6HR3

description: AGN6H - AGN6HR3_ATCACG_L008_R1 (paired) (GE) - RPKM


title: ACT24HR2

description: ACT24H - ACT24HR2_ACTGAT_L004_R1 (paired) (GE) - RPKM


title: AGN6HR1

description: AGN6H - AGN6HR1_TTAGGC_L007_R1 (paired) (GE) - RPKM


title: ACT1HR1

description: ACT1H - ACT1HR1_ATCACG_L004_R1 (paired) (GE) - RPKM


title: ACT6HR2

description: ACT6H - ACT6HR2_GAGTGG_L004_R1 (paired) (GE) - RPKM


title: ACT24HR1

description: ACT24H - ACT24HR1_TGACCA_L004_R1 (paired) (GE) - RPKM


title: ACT1HR2

description: ACT1H - ACT1HR2_CAGATC_L004_R1 (paired) (GE) - RPKM


title: IPCT-LRRMSKCC-PT651-102393-B-TU-F01

status: Public on Sep 14 2018

city: Houston

first: Funda

last: Meric-Bernstam

state: TX

address: 1400 Pressler St.

department: Invest. Cancer Therapeutics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
tophat for reads alignment
htseq-count for reads quantification
Genome_build: hg19
Supplementary_files_format_and_content: raw counts produced by htseq-count with rpkm estimated from gene and library size

source_name: breast cancer tissue

extract_protocol:
After isolation, RNA was quantified by Picogreen (Invitrogen) and quality was assessed using the 2200 Tapestation (Agilent). RNA from each sample (10-100 ng) was converted in double stranded cDNA using Ovation RNA-Seq System V2 kit from Nugen. cDNA was sheared by sonication with the following conditions: Peak Incident Power 175, Duty Cycle 20%, Intensity 5, Cycles per Burst 200, and 120 seconds using Covaris E220 instrument (Covaris).
The sheared DNA proceeded to library prep using KAPA library prep hyper kit (KAPA) following the “with beads” manufacturer protocol. At the end of the library prep, samples were analyzed on TapeStation to verify correct fragment size and to ensure the absence of extra bands. Samples were quantified using KAPA qPCR quantification kit. DNA was pooled for capture (2-6 samples per pool).
We used whole exome biotin labeled probes from Roche Nimblegen (V3) and followed manufacture’s protocol for the capture step. The quality of each captured sample was analyzed on TapeStation using the DNA High Sensitivity kit and the enrichment was accessed by qPCR using specific primers designed by Roche Nimblegen. The cutoff for the enrichment was 50 fold minimum.

tag: sample type

value: Primary

tag: eligible (0=no,1=yes,2=not perfect match)

tag: group

value: LRR

tag: age at diagnosis

tag: t stage

tag: n stage

tag: group stage (i=1; iia=2; iib=3; iiia=4)

tag: histology of invasive disease

value: Invasive ductal carcinoma

tag: grade

tag: estrogen receptor positive

value: No

tag: progesterone receptor positive?

tag: was hormonal therapy given?

tag: primary

value: TRUE


title: ACT6HR3

description: ACT6H - ACT6HR3_TTAGGC_L005_R1 (paired) (GE) - RPKM

tag: ecotype

tag: tissue


title: IPCT-LRRMSKCC-PT669-102402-B-TU-F01

value: CTL

value: Yes


title: IPCT-LRRMSKCC-PT667-102401-B-TU-F01

value: DM


title: IPCT-LRRMSKCC-PT655-102395-B-TU-F01


title: IPCT-LRRMSKCC-PT657-102396-B-TU-F01


title: IPCT-LRRMSKCC-PT661-102398-B-TU-F01


title: IPCT-LRRMSKCC-PT665-102400-B-TU-F01

value: Invasive lobular carcinoma


title: IPCT-LRRMSKCC-PT653-102394-B-TU-F01


title: IPCT-LRRMSKCC-PT659-102397-B-TU-F01


title: IPCT-LRRMSKCC-PT641-102388-B-TU-F01


title: IPCT-LRRMSKCC-PT649-102392-B-TU-F01


title: IPCT-LRRMSKCC-PT647-102391-B-TU-F01


title: IPCT-LRRMSKCC-PT643-102389-B-TU-F01


title: IPCT-LRRMSKCC-PT639-102387-B-TU-F01


title: IPCT-LRRMSKCC-PT615-102375-B-TU-F01


title: IPCT-LRRMSKCC-PT627-102381-B-TU-F01


title: IPCT-LRRMSKCC-PT613-102374-B-TU-F01


title: IPCT-LRRMSKCC-PT601-102368-B-TU-F01


title: IPCT-LRRMSKCC-PT621-102378-B-TU-F01


title: IPCT-LRRMSKCC-PT607-102371-B-TU-F01


title: IPCT-LRRMSKCC-PT599-102367-B-TU-F01


title: IPCT-LRRMSKCC-PT619-102377-B-TU-F01


title: IPCT-LRRMSKCC-PT625-102380-B-TU-F01


title: IPCT-LRRMSKCC-PT617-102376-B-TU-F01


title: IPCT-LRRMSKCC-PT595-102365-B-TU-F01

value: Unknown


title: IPCT-LRRM2016-52345-207713-B-TU-F01

value: N

value: FALSE


title: IPCT-LRRMSKCC-PT631-102383-B-TU-F01


title: IPCT-LRRMSKCC-PT635-102385-B-TU-F01


title: IPCT-LRRMSKCC-PT637-102386-B-TU-F01


title: IPCT-LRRMSKCC-PT603-102369-B-TU-F01


title: IPCT-LRRMSKCC-PT623-102379-B-TU-F01


title: IPCT-LRRM2016-52333-207393-B-TU-F01


title: IPCT-LRRMSKCC-PT605-102370-B-TU-F01


title: IPCT-LRRM2016-52334-207394-B-TU-F01


title: IPCT-LRRM2016-52343-207711-B-TU-F01

value: Recurrent


title: IPCT-LRRM2016-52332-207392-B-TU-F01


title: IPCT-LRRM2016-52331-207391-B-TU-F01


title: IPCT-LRRMSKCC-PT611-102373-B-TU-F01


title: IPCT-LRRM2016-52343-207710-B-TU-F01


title: IPCT-LRRM2016-52330-207390-B-TU-F01


title: IPCT-LRRM2016-52344-207712-B-TU-F01


title: IPCT-LRRMSKCC-PT609-102372-B-TU-F01


title: IPCT-LRRMSKCC-PT629-102382-B-TU-F01


title: IPCT-LRRM2016-52328-207388-B-TU-F01


title: IPCT-LRRM2016-52325-207385-B-TU-F01


title: IPCT-LRRM2016-52326-207386-B-TU-F01


title: IPCT-LRRM2016-52329-207389-B-TU-F01


title: IPCT-LRRM2016-52324-207397-B-TU-F01


title: IPCT-LRRM2016-52327-207387-B-TU-F01


title: IPCT-LRRM2016-52323-207396-B-TU-F01


title: IPCT-LRRM2016-52315-207702-B-TU-F01


title: IPCT-LRRM2016-52318-207705-B-TU-F01


title: IPCT-LRRM2016-52322-207709-B-TU-F01


title: IPCT-LRRM2016-52321-207708-B-TU-F01


title: IPCT-LRRM2016-52316-207703-B-TU-F01


title: IPCT-LRRM2016-52317-207704-B-TU-F01


title: IPCT-LRRM2016-52309-207696-B-TU-F01


title: IPCT-LRRM2016-52311-207698-B-TU-F01


title: IPCT-LRRM2016-52313-207700-B-TU-F01


title: IPCT-LRRM2016-52320-207707-B-TU-F01


title: IPCT-LRRM2016-52312-207699-B-TU-F01


title: IPCT-LRRM2016-52310-207697-B-TU-F01


title: IPCT-LRRM2016-52308-207693-B-TU-F01


title: IPCT-LRRM2016-52309-207695-B-TU-F01


title: IPCT-LRRM2016-52314-207701-B-TU-F01


title: IPCT-LRRM2016-52303-207687-B-TU-F01


title: IPCT-LRRM2016-52305-207689-B-TU-F01


title: IPCT-LRRM2016-52307-207691-B-TU-F01


title: IPCT-LRRM2016-52304-207688-B-TU-F01


title: IPCT-LRRM2016-52306-207690-B-TU-F01

value: Mixed ductal/lobular


title: IPCT-LRRM2016-52319-207706-B-TU-F01


title: IPCT-LRRM2016-52307-207692-B-TU-F01


title: IPCT-LRRM2016-52308-207694-B-TU-F01


title: IPCT-LRRM2016-52302-207686-B-TU-F01


title: IPCT-LRRM2016-52301-207685-B-TU-F01


title: IPCT-LRRM2016-52300-207684-B-TU-F01


title: IPCT-LRRM2016-52298-207682-B-TU-F01


title: IPCT-LRRM2016-52290-207742-B-TU-F01


title: IPCT-LRRM2016-52289-207741-B-TU-F01


title: IPCT-LRRM2016-52296-207395-B-TU-F01


title: IPCT-LRRM2016-52299-207683-B-TU-F01


title: IPCT-LRRM2016-52292-207746-B-TU-F01


title: IPCT-LRRM2016-52289-207740-B-TU-F01


title: IPCT-LRRM2016-52290-207743-B-TU-F01


title: IPCT-LRRM2016-52286-207735-B-TU-F01

value: yes


title: IPCT-LRRM2016-52292-207745-B-TU-F01


title: IPCT-LRRM2016-52287-207737-B-TU-F01


title: IPCT-LRRM2016-52288-207739-B-TU-F01


title: IPCT-LRRM2016-52291-207744-B-TU-F01


title: IPCT-LRRM2016-52288-207738-B-TU-F01


title: IPCT-LRRDF-8405-200354-B-TU-F01


title: IPCT-LRRM2016-52287-207736-B-TU-F01


title: IPCT-LRRM2016-52297-207681-B-TU-F01


title: IPCT-LRRDF-8404-200353-B-TU-F01


title: IPCT-LRRDF-8403-200352-B-TU-F01


title: IPCT-LRRM2016-52286-207734-B-TU-F01


title: IPCT-LRRDF-8399-200348-B-TU-F01


title: IPCT-LRRDF-8397-200346-B-TU-F01


title: IPCT-LRRDF-8401-200350-B-TU-F01


title: IPCT-LRRDF-8402-200351-B-TU-F01


title: IPCT-LRRDF-8396-200345-B-TU-F01


title: IPCT-LRR-PT312-101410-B-TU-F01


title: IPCT-LRR-PT308-101408-B-TU-F01


title: IPCT-LRR-PT304-101405-B-TU-F01


title: IPCT-LRR-PT308-101407-B-TU-F01


title: IPCT-LRR-PT302-101404-B-TU-F01


title: IPCT-LRR-PT298-101403-B-TU-F01


title: IPCT-LRR-PT306-101406-B-TU-F01


title: IPCT-LRR-PT277-101392-B-TU-F01


title: IPCT-LRR-PT282-101394-B-TU-F01


title: IPCT-LRR-PT282-101393-B-TU-F01


title: IPCT-LRR-PT277-101390-B-TU-F01


title: IPCT-LRRDF-8398-200347-B-TU-F01


title: IPCT-LRR-PT287-101397-B-TU-F01


title: IPCT-LRR-PT282-101395-B-TU-F01


title: IPCT-LRR-PT287-101398-B-TU-F01


title: IPCT-LRR-PT296-101401-B-TU-F01


title: IPCT-LRR-PT277-101391-B-TU-F01


title: IPCT-LRR-PT292-101399-B-TU-F01


title: IPCT-LRR-PT287-101396-B-TU-F01


title: IPCT-LRR-PT272-101387-B-TU-F01


title: IPCT-LRR-PT267-101386-B-TU-F01


title: IPCT-LRR-PT262-101383-B-TU-F01


title: IPCT-LRR-PT272-101389-B-TU-F01


title: IPCT-LRR-PT267-101385-B-TU-F01


title: IPCT-LRR-PT262-101382-B-TU-F01

value: Adenocarcinoma NOS


title: IPCT-LRR-PT262-101381-B-TU-F01


title: IPCT-LRR-PT272-101388-B-TU-F01


title: IPCT-LRR-PT267-101384-B-TU-F01


title: IPCT-LRR-PT298-101402-B-TU-F01


title: Pitx2 CKO

status: Public on Aug 26 2018

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
snRNA-seq
Pitx2 CKO snRNA-seq 10X Genomics.
processed data file: Merged_ctrl_Pitx2CKO_raw_data_snRNAseq.txt

data_processing:
Sequencing data were handled using the 10X Genomics Cell Ranger software (www.10xgenomics.com). Fastq files were mapped to the mm10 genome, and gene counts were quantified using a gtf file with merged exons and introns (pre-mRNA). Subsequently, expression matrices from each experiment were merged and then were imported into Seurat (version 2.1.0).
Read1: Barcode (basepairs 1-16)/UMI (basepairs 17-26)
Read2: cDNA
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Merged_ctrl_Pitx2CKO_raw_data_snRNAseq.txt: Tab-delimited text file.

molecule: nuclear RNA

source_name: Cardiac tissue 3wk dpmi

extract_protocol:
Nuclei input into 10X Genomics Chromium device.
10X Genomics

tag: genotype/variation

value: MCK-Cre; Pitx2 fl/fl

value: Cardiac

tag: time point

value: 3wk post myocardial infarction


title: IPCT-LRR-PT312-101409-B-TU-F01

tag: sample type

value: Primary

value: Invasive ductal carcinoma


title: Control

description:
snRNA-seq
Control snRNA-seq 10X Genomics.
processed data file: Merged_ctrl_Pitx2CKO_raw_data_snRNAseq.txt

value: Pitx2 fl/fl


title: Gip-Cre scRNA-seq

status: Public on Aug 01 2018

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

institute: Hubrecht Institute

description: EECs sorted for reporter positivity. Columns 1-6 are BMP4 untreated, columns 7-12 are 24hr BMP4 treated, columns 13-24 are d4 BMP4 treated EECs (see readme text file)

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
mm10
Genome_build: coutt files contain UMI barcode normalised abundance counts
Series supplementary files list barcode information

source_name: Experiment3 C57/BL6 mice

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Live cells positive for the hormone reporter were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

tag: genotype

value: Gip reporter

value: Murine intestinal organoids

tag: strain

tag: treatment

value: see readme.txt (untreated, 24h BMP4 treated, 4d BMP4 treated)


title: Gcg-Venus 1 scRNA-seq

value: Gcg reporter


title: Tac1-Cre 2 scRNA-seq

value: Tac1 reporter


title: Gcg-Venus 2 scRNA-seq


title: unstimulated human pericytes_2

status: Public on May 09 2018

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: human placenta

growth_protocol: HUVECs: ECs, isolated from de-identified umbilical cords following enzymatic digestion by collagenase, were  serially cultured on 0.1% gelatin-coated tissue culture plates in M199 medium (Gibco) containing 20% fetal bovine serum, 2 mM L-glutamine, penicillin (100U/mL), streptomycin (100 µg/mL) supplemented with endothelial cell growth supplement (BD Bioscience) and porcine intestinal heparin (100 µg/mL, Sigma-Aldrich). Cells were used between 1st and 4th passage at which time they uniformly express CD31 and are free of contaminating CD45+ leukocytes assessed by flow cytometry.  Human placental PCs: Samples of de-identified human placenta (approximately 10 cm x 10 cm x 3 cm), taken from the region near the insertion of the umbilical cord, were manually minced and then subjected to collagenase digestion on shaker for 3 hours at 37C°. Microvessel segments were collected by sieving and PCs, obtained by explant outgrowth, were serially cultured in M199 medium (Gibco) containing 20% fetal bovine serum, 2 mM  L-glutamine, penicillin (100U/mL), and streptomycin (100 µg/mL). Cells were used between 2nd and 6th passage at which time they expressed NG2, Thy-1 (CD90) and PDGFR-beta assessed by flow cytometry. Where indicated, ECs and PCs were isolated form the same donor.

extract_protocol:
Total RNA was extracted using the TRIZOL-chloroform extraction method. RNA was cleaned using the QIAGEN Rneasy Cleanup kit.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: IFN-γ for 48 hours (50ng/mL)

tag: passage

tag: cell type

value: pericytes

value: placenta


title: unstimulated human pericytes_1


title: unstimulated human pericytes_3


title: Col-7_root_rep3

status: Public on Aug 13 2018

type: RNA

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

description: WT of SAHY1OE

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Col-7. Seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction.

label_protocol: Standard Affymetrix label protocol

growth_protocol: Arabidopsis seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction.

extract_protocol: QIAGEN RNeasy Plant Mini Kit

value: root

tag: age


title: Col-7_root_rep2

description: WT of SAHY1OE


title: sahy1_root_rep2

source_name: sahy1 T-DNA insertion mutant. Seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction.


title: Col-0_root_rep2

description: WT of sahy1

source_name: Col-0. Seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction.


title: Col-0_root_rep1

description: WT of sahy1


title: STING+cGAS-3

status: Public on Aug 02 2018

city: Hangzhou

first: Hanchu

last: Xiong

address: Jiefang Road NO.88

country: China

institute: Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University

description: Gene expression data from HEK293T cells transfected with STING and cGAS expression vector

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Affymetrix OElncRNA for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: not provided

data_processing: Samples were analyzed with Affymetrix software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin solution.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Empty plasmid or various expression plasmids were transfected using Lipofectamine™ 2000 (Invitrogen) according to the manufacturer’s protocol.

tag: cell line

value: fibroblast


title: Col-0_root_rep3

description: WT of sahy1


title: Col-7_root_rep1

description: WT of SAHY1OE


title: SAHY1OE_root_rep2

source_name: SAHY1 overexpression line 4-1. Seeds were grown on basal medium for five days, transferred to fresh medium and grown vertically for another seven days. After the 12-day culture, the roots were removed and used for RNA extraction.

value: SAHY1 overexpression line 4-1


title: SAHY1OE_root_rep3


title: sahy1_root_rep1


title: STING+cGAS-2

source_name: HEK293T cells transfected with STING and cGAS expression vector


title: SAHY1OE_root_rep1


title: STING+cGAS+7312A-1

description: Gene expression data from HEK293T cells transfected with STING, cGAS and Vpx 7312A expression vector


title: STING+cGAS+7312A-2

source_name: HEK293T cells transfected with STING, cGAS and Vpx 7312A expression vector


title: sahy1_root_rep3


title: STING+cGAS+7312A-3