title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F09_10025B]


title: SMY19_MET4_t15

status: Public on Jan 03 2020

type: RNA

city: South San Francisco

first: Scott

last: McIsaac

state: CA

address: 1170 Veterans Blvd.

country: USA

institute: Calico Life Sciences LLC

hyb_protocol: 8x15k Microarray hybridization: Set up 60°C heat block; Prepare 10x Blocking Agent: Add 1250 µL of nuclease-free water to vial containing 10x lyophilized Gene Expression Blocking Agent (part #5188-5281); Vortex and spin down; Prepare hybridization samples; For 8x15k (8-pack) microarrays, mix the following components: 450 ng Cy3-amplified cRNA, 450 ng Cy5-amplified cRNA, 7.5 µL 10X Gene Expression Blocking Agent, bring volume to 36 µL with water, and then add 1.5 µL 25x fragmentation buffer; Incubate at 60°C for 30 minutes to fragment the RNA; Add 37.5 µL of 2x Hi-RPM Hybridization Buffer to strip tube and leave on ice; Add fragmented RNA directly to Hi-RPM Buffer to stop the reaction; Mix well by pipetting up and down (avoid bubbles and do not vortex); Put sample on ice and load onto array as soon as possible; Put clean gasket onto metal hybridization chamber; Add 45 µL of hybridization onto gasket; Place array (Agilent facing down) onto gasket and close the hybridization chamber; Incubate on rotisserie at 65°C for 17 hr

scan_protocol: Labeled RNA was hybridized to Agilent 8x15k microarrays, which were then washed, scanned, and processed using the Agilent Feature Extraction software with default settings and loess dye bias correction.

data_processing: Each microarray has some number of spots (usually 2) for each gene. All microarrays for the GEV experiments had identical probes, likewise for the ZEV experiments. For each spot, we computed ratio = max(red, C) / max(green, C), where C=2 in arbitrary units. This minimum value application only affects 0.3% of spots. Typical genes have red and green channel measurements above 200. These (red, green, ratio) values foreach spot serve as the raw data. For each dataset, we aggregated the data across individual spots. Specifically, for each timecourse, time point, and gene, we aggregated the spot values and measured the minimum value, maximum value, median value, and standard deviation of the values. In the usual case of 2 spots, the median value is equivalent to mean and standard deviation is equivalent to (max-min)/sqrt(2). At this stage we corrected the most extreme outlier observations. First, for a given sample, we examined the case where, for a given gene, the ratio of the spot values, was larger than four. Since the spots values do not agree, we interpolated the value with the geometric mean across bracketing time points (or neighboring time point in the case of first or last time point). The second class of outliers is where the median ratio moves by a factor of at least four between two time points, and then by a factor of four in the opposite direction for the next time point.  In these cases we again replaced the central point with the geometric mean of the bracketing points. These corrections apply to less than 0.2% of the data. In processing gene expression microarrays, crosstalk between red and green channels can occur. When the red channel fluorescence is much larger than the green channel fluorescence, there can be leakage of signal, and the green channel measurement is affected. To identify instances of this occurring,  we first computed the green channel ratio relative to the time zero measurement.  We then measured the 30% quantile of this value within each timecourse (for time points after t = 0), as well as the 30% quantile of the log-ratio.  We then flagged timecourses where the green ratio quantile exceeded a factor of eight, and the log-ratio quantile exceeds a two-fold change.  These represent cases where the green channel is increasing a great deal when it should be constant. For these rare cases, we repaired the red to green ratios by duplicating the time zero green channel across the full timecourse.  This affects about two dozen TF-gene timecourses (out of more than a million). The GEV and ZEV systems both have characteristic gene expression signatures, including a mild stress response. Previously, it has been shown that Singular Value Decomposition (SVD) is one way to remove such signals. Here, we used a slightly different approach. First, we computed the median time series for each gene in each class of experiments (GEV and ZEV).  We then subtracted this median time series, leaving a normalized log-ratio.  Because a given gene is not directly or indirectly affected by a transcription factor in most experiments, the median is an accurate reflection of any background time-dependent behavior.  We refer to the dataset where outliers are removed and the GEV/ZEV signal is removed as the cleaned dataset.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: SMY19 inducing MET4 with estradiol at t15 minute timepoint

label_protocol: Crude RNA was purified using either the QIAGEN RNeasy kit or RNAClean Ampure XP beads. 200 ng of cleaned RNA was used as an input to generate dye-labeled cRNA using the Agilent Quick-Amp Labeling Kit. 1) Prepare labeling reaction: Get clean PCR strip tubes ready; Dilute RNA to 57.2 ng/µL; Add 3.5 µl of RNA (200 ng total) to PCR tube; Make T7 Primer Mix (0.8 µL T7, 1 µL water);Add 1.8 µl of T7 Primer Mix to each tube. Each tube now has 5.3 µl; Denature the template and primer by incubating at 65°C for 10 min; Put reactions on ice for 5 min; 2) cDNA synthesis: Heat 5x First Strand Buffer 80°C for 3-4 minutes, vortex, do a quick spin, and keep at room temperature; Make cDNA master mix (2µL 5x First Strand Buffer, 1 µL 0.1M DTT, 0.5 µL 10 mM dNTP mix, 1.2 µL Affinity Script RNase Block Mix); Briefly spin sample and master mix tubes; Add 4.7 µL of cDNA Master Mix to sample tubes and mix by pipetting up and down. Each tube now has 10 µL; Incubate at 40°C for 2 hours; Incubate at 70°C for 15 minutes (inactivates the AffinityScript enzyme); If you don’t continue to next step, freeze samples -80°C; Ice for 5 min. 3) Labeled cRNA synthesis: Keep T7 RNA polymerase (red cap) on ice. Master Mix = 0.75 µL Water, 3.2 µL 5x Transcription Buffer, 0.6 µL 0.1M DTT, 1 µL NTP Mix, .21µL T7 RNA polymerase Blend; 0.24 µL Cy3-CTP or C5-CTP; Add 6 µL of Transcrption Master Mix with Dye to the cDNA. Each tube now contains a total volume of 16 µL; Incubate samples at 40°C for 2 hours. 4) SPRI cleanup of cRNA: Before beginning: Bring RNAClean XP to RT, Make up enough 80% ethanol for >2 200 µL washes per reaction, Set 96 well thermomixer to 37°C; Add 48 µL (3X) of RNAClean XP beads to each reaction and incubate for 10 minutes; Place plate on magnet and allow supernatant to clear (~5 minutes); Remove supernatant carefully, avoiding beads, and discard; Add 200 µL of 80% ethanol to each well and incubate for 30 seconds; Remove ethanol and repeat for a total of two washes; Remove ethanol, cover plate, and spin down for ~1 minute; Place plate back on magnet and use a p20 to remove residual ethanol; Dry beads at 37°C until beads no longer move around when placed on magnet (~4 minutes); Add 42.5 of RNAse-free water and resuspend beads, then incubate for 2-3 minutes; Place plate on magnet and transfer 40 µL to a new well before placing on ice

growth_protocol: All experiments were performed in chemostats (continuous cultures). We chose chemostats, in part, because the steady-state condition of chemostat cultures is a particularly useful feature for mathematical modeling. Under steady-state conditions, the levels of molecules and activities of process are not changing at a culture-wide level. Cells were grown under continuous culturing conditions in 500 mL vessels as previously described with minor adjustments (Saldanha AJ, Brauer MJ, Botstein D. Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. 2004;15: 4089–4104). Cultures were aerated with 6 L/min of humidified air at 30C, maintained at 300 mL, and stirred with a magnetic impeller at 400 RPM. For the majority of experiments, cultures were maintained with minimal medium under phosphate limitation (20 mg/L). Nitrogen-limited cultures were maintained at 40 mg/L ammonium sulfate. Methionine-limited cultures (McIsaac et al, 2012) were maintained at 7.5 mg/L methionine. Growth rates were maintained from 0.15-0.17 vol/hour.  Batch growth in the chemostat vessels was initiated from a 1:60 dilution of a saturated overnight culture prior to turning on the chemostat pumps. Cells were grown to steady state, as determined by culture density, prior to the addition of 1 micromolar beta-estradiol to the culture and subsequent sampling. Chemostat experiments were performed with either the Infors Sixfors or Multifors systems.

extract_protocol: RNA was prepared using a standard acid phenol extraction. Lysis buffer: 600 µL of 0.5M EDTA, 1.5 mL of 10% SDS, 300 µL 1M Tris, 27.6 mL Rnase-free water.

treatment_protocol: The t = 0 was taken (between 3 and 5 mL of culture) and vacuum filtered. Estradiol was then added the continuous culture and sampled at various timepoints.

tag: strain

tag: background


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G02_100322]

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

hyb_protocol: Standard Affymetrix GeneAtlas® Hybridization, Wash, and Stain Kit.

scan_protocol: Standard GeneTitan® multi channel instrument.

data_processing: Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 2.15.1; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Affy package version 1.36.1. Array data were background corrected by Robust Multi-array Average, quantiles-normalized and summarized by medianpolish using the expresso function. The resultant 49,386 probe intensities were filtered by means of a 0.5 variance cutoff using the genefilter method to recover 24,646 expressed probes. The occurrence of non-experimental chip effects was evaluated by means of the Surrogate Variable Analysis (R package version 3.4.0) and corrected by the empirical Bayes method ComBat.

label: biotin

organism: Homo sapiens

source_name: blood

label_protocol: 100ng total RNA was labeled using standard GeneChip® 3' IVT Express Kit (Affymetrix)

growth_protocol: PAXgene blood

extract_protocol: Total RNA was isolated by means of the QIAcube machine (Qiagen, Venlo, the Netherlands) in combination with the PAXgene Blood mRNA kit (Qiagen) according to manufacturer’s instructions.

tag: age

tag: gender

value: male

tag: hospital

value: amc

tag: subject

tag: timepoint pre(-)/post(+) lps

value: +2 hours

tag: stem cell dose

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G01_100302]

value: umc

value: medium


title: 6C3-N711-S506_S141

type: SRA

city: Stanford

first: Charles

middle: Chan

last: KF

address: 265 Campus Drive

institute: Stanford

library_source: transcriptomic

data_processing:
Raw reads were preprocessed with the sequence-grooming tools FASTQC30 (Treutlein et al., 2014) cutadapt31 (Treutlein et al., 2014) and PRINSEQ32 (Treutlein et al., 2014).
We mapped the processed reads with Olego (Wu et al., 2013) (http://nar.oxfordjournals.org/content/41/10/5149) and used SAMtools (Li et al., 2009) (http://www.ncbi.nlm.nih.gov/pubmed/19505943) for processing of post-map ∗.sam files generated by Olego.
We quantified the transcript levels as fragments per kilobase of transcript per million mapped reads (FPKM) generated by Cuffdiff2 (Trapnell et al., 2013) (http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) using the default geometrical scaling and blind dispersion model options.
We applied stringent filter criteria as described before (Treutlein et al., 2014) to weed out cells with suboptimal data, which may result from unhealthy cells or other technical reasons.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing a FPKM-normalized gene expression table

organism: Mus musculus

source_name: Long Bones

extract_protocol:
We sorted live individual skeletal stem and progenitor populations (mSSC, CSP, Thy+, and 6C3+) by double sorting on FACS ARIA 2. Sorted cells were captured on a small-sized (5–10 μm cell diameter) microfluidic RNA-seq chip (Fluidigm, South San Francisco, CA, USA) using the Fluidigm C1 system. We loaded 10 μl of 500–1000 cells/μl onto the chip and imaged each capture site after the capture run to assess the number and viability of cells by phase-contrast and fluorescence microscopy. We included only single, live cells in the analysis.
We prepared amplified cDNAs on chip using C1 mRNA-RT+Amp program that uses reagents from the SMARTer Ultra Low RNA kit for Illumina (Clontech, Takara Bio Group, Mountain View, CA, USA) as per protocol provided by Fluidigm. We added the ERCC (External RNA Controls Consortium) RNA spike-in Mix (Ambion, Life Technologies, NY, USA) to the lysis reaction to be processed in parallel to cellular messenger RNA. For each C1 experiment, we processed a bulk RNA control (about 200 cells) and a no-cell negative control in parallel in PCR tubes, using the same reagent mixes as used on chip. We constructed libraries from the diluted cDNAs in 96-well plates using the Nextera XT DNA Sample Preparation kit (Illumina, San Diego, CA, USA) as described previously (Treutlein et al., 2014) using the protocol supplied by Fluidigm (Fluidigm). We quantified the libraries by Agilent Bioanalyzer, using High Sensitivity DNA analysis kit, and also fluorometrically, using Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorome

tag: tissue

value: Bone and Bone marrow

value: Post-natal day 3 (P3)

tag: gating strategy


title: 6C3-N711-S511_S189


title: 6C3-N711-S507_S153


title: SMY19_MET4_t45

source_name: SMY19 inducing MET4 with estradiol at t45 minute timepoint


title: SMY19_MET4_t5

source_name: SMY19 inducing MET4 with estradiol at t5 minute timepoint


title: SMY19_MET4_t0

source_name: SMY19 inducing MET4 with estradiol at t0 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F10_100326]

value: +6 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F03_100194]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F01_1002924]

value: +24 hours

value: high


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F05_1003024]


title: SMY22_CBF1_t45

source_name: SMY22 inducing CBF1 with estradiol at t45 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F11_100196]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F07_100296]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F06_100290]

value: 0 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E12_100282]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F02_100306]


title: 6C3-N711-S505_S129


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F08_100280]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E11_100320]


title: SMY22_CBF1_t30

source_name: SMY22 inducing CBF1 with estradiol at t30 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F04_100324]


title: 6C3-N711-S502_S105


title: 6C3-N711-S503_S117


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E10_100284]


title: 6C3-N710-S511_S188


title: SMY22_CBF1_t15

source_name: SMY22 inducing CBF1 with estradiol at t15 minute timepoint


title: SMY22_CBF1_t90

source_name: SMY22 inducing CBF1 with estradiol at t90 minute timepoint


title: SMY22_CBF1_t5

source_name: SMY22 inducing CBF1 with estradiol at t5 minute timepoint


title: 6C3-N710-S507_S152


title: 6C3-N710-S508_S164


title: SMY22_CBF1_t0

source_name: SMY22 inducing CBF1 with estradiol at t0 minute timepoint


title: 6C3-N710-S506_S140


title: 6C3-N710-S510_S176


title: GB-S1

city: Suwon

first: Jin-A

last: Lee

address: 2066 Seoburo

department: School of medicine

country: South Korea

institute: Sungkyunkwan university

library_source: genomic

data_processing:
Raw reads generated by Illumina sequencing were quality checked using FastQC, version 0.10.1.
Quality checked reads were mapped onto the mm10 genome sequence using Bowtie.
The mapping results in SAM were converted to BAM and sorted by coordinates using same tools, version 0.1.19
The mapping statistics were extracted using Picard, version 1.90
Genome_build: mm10

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: 1X10^5 of mouse ES cells were used to form EBs in the Biotin-SAHA G-containing medium for 2 days.

extract_protocol:
EBs were harvested and the chromatin was isolated using the ChromaFlash Chromatin Extraction Kit (EpiGentek). The isolated chromatin was sheared using the EpiSonic 2000 Sonication System (EpiGentek). A 200-ml volume of chromatin solution was collected, and concentration was measured by fluorescent quantification of chromatin-associated DNA. DNA was purified using 5 μl of sheared chromatin as input and the DNA was eluted with 12 μl of water. One μl of purified DNA was used for fluorescent quantification. For fragment analysis, DNA fragment size distribution was determined to be 100 to 600 bp by Agilent Bioanalyzer analysis. For isolation of the PIP-binding DNA fragments, 8 μg of sheared chromatin were combined with 4 μl of C1 streptavidin assay beads and 500 μl assay buffer in a 1.5-mL tube. The sample was incubated at room temperature for 1 hour with continuous rotation. After incubation, the beads were washed and the precipitated DNA was purified and eluted in 21 μl of water.
For library preparation, DNA end polishing was performed, and adaptors were ligated to both ends of the polished DNA fragments for amplification and sequencing. Library application was used to induce primers and for library purification. Purified library DNA was eluted with 13 μl water. The library was verified on a Bioanalyzer and KAPA qPCR library quantification. 10 nM of sample libraries were subjected to next-generation sequencing on an Illumina Hiseq 4000. The basic analysis of Chem-Seq was performed based on the published protocol utilizing Bowtie2, version 2.2.6 and MACS, version 2.1.1.
Cchp (Chem-seq)

tag: cell type

value: mouse ES cell derived embyonic body with 1 uM Biotin-SAHA-PIP G

tag: passage


title: Old.SD12hr.66975.C5

city: Philadelphia

first: Allan

middle: I

last: Pack

address: 125 South 31st St

institute: University of Pennsylvania

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-v2.5.3a.
Data were quantified using PORT quantification script. The code is available at https://github.com/itmat/Normalization (PORT-v0.8.4-beta)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level contains counts from unique reads that only map to one gene.

source_name: medial prefrontal cortex

growth_protocol: C57BL/6 mice at 2-4 months (young) and 18-20 months (old) housed individually

extract_protocol:
Mice were euthanized, and brains were removed and stored at -80°C. Microdissection of mPFC was performed using micropunch. RNA extraction was performed using an RNAqueous-Micro Kit and genome DNA was removed with RNase-Free DNase.
Total RNA from each sample was prepared for sequencing using the Illumina: TruSeq Stranded mRNA Sample Preparation Kit. 200 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 19-32 million single 100bp reads were generated for each sample.

treatment_protocol: Half of the mice were sleep deprived for various of durations using gentle handling

value: Old

tag: behavior

value: SD

tag: timepoint

value: medial prefrontal cortex


title: Old.SD12hr.66994.F8


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E06_100314]

value: male

value: placebo


title: 6C3-N710-S505_S128


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E05_100322_2]

value: amc

value: +2 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E09_10030B]

value: -24 hours


title: Old.SD12hr.66959.E2


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E01_100250]

value: umc


title: Old.SD12hr.66955.F11


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E03_10027B]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E02_100250_2]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E04_10019B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E07_1002724]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_E08_100286]

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D09_1001924]


title: 6C3-N710-S503_S116

value: Bone and Bone marrow

value: Post-natal day 3 (P3)


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D08_100274]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D12_100272]


title: Old.SD12hr.66937.C8


title: 6C3-N710-S502_S104


title: Old.SD12hr.66920.B5


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D11_1003224]

value: +24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D10_100272]


title: 6C3-N707-S511_S187


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D07_1002824]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D06_100312]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D05_100300]

value: 0 hours


title: Old.SD9hr.66995.B9


title: Old.SD9hr.66979.G5


title: 6C3-N707-S510_S175


title: 6C3-N707-S508_S163


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D04_10032B]


title: Old.SD9hr.66958.D2


title: 6C3-N707-S506_S139


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D03_100270]


title: Old.SD9hr.66953.D11


title: 6C3-N707-S507_S151


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D01_100240]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C11_1002424]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C12_100316]

value: +6 hours


title: 6C3-N707-S503_S115


title: 6C3-N707-S505_S127


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C08_10017B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C07_100164]

value: high


title: Old.SD6hr.66999.F9

value: Old

value: SD


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C09_1002124]

value: male


title: 6C3-N707-S502_S103


title: Old.SD6hr.66978.F5

value: medial prefrontal cortex


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C06_100222]

value: amc


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C05_100176]

value: placebo


title: 6C3-N706-S511_S186


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C03_100242]

value: +2 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C04_100260]


title: Old.SD6hr.66963.C3


title: Old.SD9hr.66936.B8


title: Old.SD6hr.66952.C11


title: Old.SD9hr.66917.E4


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C02_100236]

value: umc


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B11_100246]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C01_1001624]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B10_100186]

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B07_100266]


title: Old.SD6hr.66933.D7


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B12_100234]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B09_100224]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B06_100150]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B08_1002224]


title: Old.SD6hr.66916.D4


title: 6C3-N706-S507_S150

value: Bone and Bone marrow


title: 6C3-N706-S510_S174

value: Post-natal day 3 (P3)


title: 6C3-N706-S506_S138


title: Old.SD3hr.66998.E9


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B05_100212]


title: 6C3-N706-S508_S162


title: Old.SD3hr.66983.E6


title: 6C3-N706-S505_S126


title: 6C3-N706-S503_S114


title: 6C3-N706-S502_S102


title: Old.SD3hr.66949.E10


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B03_1003124]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B01_100244]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A12_10026B]

value: -24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A11_10018B]


title: Old.SD3hr.66932.C7


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A10_100210]

value: 0 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A09_100230]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B04_100184]


title: Old.SD3hr.66913.G3


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_B02_100226]

value: +6 hours


title: Old.SS12hr.67003.E10

value: SS


title: 6C3-N705-S507_S149


title: 6C3-N705-S508_S161


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A07_100232]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_D02_100310]


title: 6C3-N705-S511_S185


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A06_100200]

value: high


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A05_10021B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A04_1002324]

value: +24 hours


title: Old.SS12hr.66982.D6

value: Old


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A08_100174]

value: male


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A02_1001524]

value: amc


title: 6C3-N705-S506_S137


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A03_10016B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H12_10022B]


title: Old.SS12hr.66967.G3

value: medial prefrontal cortex


title: 6C3-N705-S510_S173


title: 6C3-N705-S505_S125


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_A01_100310_2]

value: placebo


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H10_100204]


title: Old.SS12hr.66948.D10


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H11_100180]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H07_100170]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H09_100252]

value: +2 hours


title: Old.SS12hr.66929.E6


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H08_100254]


title: Old.SS12hr.66912.F3


title: 6C3-N704-S511_S184


title: Old.SS9hr.67002.D10


title: Old.SD3hr.66962.B3

value: SD


title: 6C3-N704-S510_S172


title: Old.SS9hr.66987.D7


title: 6C3-N705-S503_S113


title: 6C3-N704-S507_S148


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H04_100084]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H05_10015B]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H03_100066]

value: umc


title: Old.SS9hr.66945.F9


title: 6C3-N705-S502_S101

value: Bone and Bone marrow

value: Post-natal day 3 (P3)


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_C10_100156]


title: 6C3-N704-S506_S136


title: Old.SS9hr.66928.D6


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G07_1000124]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H01_1000824]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G12_100096]

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G10_1001124]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H06_100162]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G06_100126]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_H02_1000924]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G08_100016]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G05_1001324]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G03_10006B]

value: -24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G04_10014B]


title: 6C3-N704-S508_S160


title: Old.SS9hr.66909.C3


title: 6C3-N704-S503_S112


title: 6C3-N704-S505_S124


title: Old.SS9hr.66966.F3


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G02_10012B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G09_100050]

value: 0 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F12_100032]


title: Old.SS6hr.66986.C7

value: SS


title: 6C3-N704-S502_S100


title: Old.SS6hr.67007.D11


title: Old.SS6hr.66971.E4


title: 6C3-N703-S511_S183


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_G01_100140]

value: high


title: Old.SS6hr.66925.G5


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F11_1000724]

value: +24 hours


title: 6C3-N703-S510_S171


title: 6C3-N703-S507_S147


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F10_100094]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F09_100126]

value: male

value: +6 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F08_100142]

value: amc


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F07_100102]


title: Old.SS6hr.66908.B3

value: Old

value: medial prefrontal cortex


title: 6C3-N703-S506_S135


title: 6C3-N703-S505_S123


title: Old.SS3hr.67006.C11


title: Old.SS6hr.66944.E9


title: Old.SS3hr.66991.C8


title: 6C3-N703-S503_S111


title: 6C3-N703-S508_S159


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F02_100100]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F04_10005B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E12_100132]

value: +2 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F06_100024]

value: placebo


title: Old.SS3hr.66970.D4


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F01_100082]

value: umc


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E11_100054]


title: Old.SS3hr.66941.B9


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E09_100034]


title: 6C3-N703-S502_S99

value: Bone and Bone marrow


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E10_1000424]


title: 6C3-N702-S511_S182

value: Post-natal day 3 (P3)


title: 6C3-N702-S510_S170


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E07_10011B]


title: Old.SS3hr.66924.F5


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F05_100064]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E05_100070]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E08_10007B]

value: -24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_F03_100120]

value: 0 hours


title: Old.SS3hr.66905.E2

value: SS


title: 6C3-N702-S508_S158


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E04_10004B]

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E02_100090]


title: Old.Z0.67009.F11

value: baseline


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E06_10008B]

value: high


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D11_100166]

value: male


title: Old.Z0.66990.B8


title: 6C3-N702-S507_S146


title: Old.Z0.66974.B5


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E01_10013B]


title: Old.Z0.66940.F8


title: 6C3-N702-S505_S122


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D10_100012]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_E03_100110]


title: 6C3-N702-S503_S110


title: Old.Z0.66921.C5


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D09_1000324]

value: +24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D08_100036]

value: amc

value: +6 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D06_100214]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D12_100152]

value: +2 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D07_100216]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D03_100026]

value: placebo


title: Old.Z0.66904.D2

value: Old

value: medial prefrontal cortex


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D02_1001824]

value: umc


title: 6C3-N701-S508_S157

value: Bone and Bone marrow

value: Post-natal day 3 (P3)


title: 6C3-N702-S506_S134


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D04_100014]

value: medium


title: 6C3-N701-S510_S169


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D01_100130]

value: 0 hours


title: Young.SD12hr.66993.E8

value: Young

value: SD


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_D05_10002B]

value: -24 hours


title: Young.SD12hr.66973.G4


title: Young.SD12hr.66957.C2


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C11_100136]

value: male

value: low


title: Young.SD12hr.66954.E11


title: 6C3-N701-S506_S133


title: 6C3-N701-S505_S121


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C12_100172]

value: amc


title: Young.SD12hr.66935.F7


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C10_100182]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C08_100206]

value: +6 hours

value: high


title: Young.SD12hr.66918.F4


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C06_100110_2]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C04_100264]

value: +4 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C09_100160]


title: 6C3-N701-S507_S145


title: Young.SD9hr.66992.D8


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C07_100232_2]

value: +2 hours

value: placebo


title: Young.SD9hr.66977.E5

value: medial prefrontal cortex


title: 6C3-N701-S511_S181


title: SAHA_PIP_G_EB3d_H3K4me3

data_processing:
Illumia sequencing libraries were quantified and sequenced on NestSeq 500.
Sequences were aligned to the mouse genome (mm10) and the Drosophila genome (dm3) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p-value = 1e-7. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
The spike-in normalization was performed by equalizing the Drosophila tag counts across all samples so that the final tag counts were based off of the sample containing the lowest number of Drosophila tags. Then the mouse tag counts for all samples were proportionally scaled based on the ratios used to adjust the drosophila tag counts. Scaling to the target tag number was performed by randomly removing excess tags.
Genome_build: mm10
Supplementary_files_format_and_content: The resulting histograms (genomic “signal maps”) were stored in bigWig files.

source_name: Mouse embryonic stem cells

growth_protocol: 2 X 10^6 mouse ES cells were used to form EBs with/without SAHA-PIP G for 3 days in ultra-low culture 24-well plates (Corning).

extract_protocol:
Embryonic  bodies were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300–500 bp with Active Motif’s EpiShear probe sonicator (Active Motif) and cooled sonication platform (Active Morif).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation using Active Motif’s custom liquid handling robotics pipeline. After the final 15-cycle PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500. Sequences (75 bp, single end) were aligned to the mouse genome (mm10) and the Drosophila genome (dm3) using the BWA algorithm (default settings) (30). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome.

value: mouse ES cell derived embyonic body with 1 uM SAHA-PIP G

tag: chip antibody


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C05_1001724]

value: umc

value: +24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C03_100142]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C02_100144]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B12_10010B]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_C01_100154]


title: Control_EB3d_H3K4me3

value: mouse ES cell derived embyonic body


title: Young.SD9hr.66956.B2

value: Young


title: 6C3-N701-S503_S109

value: Bone and Bone marrow

value: Post-natal day 3 (P3)


title: ATAC-seq-BM-Sca-neg-#3

city: Lund

first: Johan

last: Flygare

address: Sölvegatan 19

country: Sweden

institute: Lund University

description:
BM-idr-ATAC-peaks-annotated-mm10.txt
Bone marrows (BM) and spleens were homogenized and filtered to single cell suspensions. Prior to FACS, enrichment for progenitors was carried out by lineage depletion using unconjugated antibodies produced in rat against murine B220, CD4, CD8, Gr-1 and Ter-119 (all from BioLegend, San Diego, CA, USA). Lineage-positive cells were removed with a magnetic particle concentrator (MPC-6; ThermoFisher Scientific, Göteborg, Sweden) and sheep anti-rat Fc-conjugated immunomagnetic beads (ThermoFisher Scientific).
For FACS, the following antibodies against murine epitopes were used: CD71 (FITC; BioLegend or biotin; BD Biosciences), CD9 (PE or FITC, clone MZ3; BioLegend), CD24a (PE-Cy7, clone M1/69; BioLegend), CD150 (APC, clone TC15-12F12.2; BioLegend), CD133 (PE, clone 315-2C11; BioLegend), c-Kit (APC780; eBioscience/ThermoFisher Scientific), Sca1 (BV421; BioLegend), B220 (Biotin or PE-Cy5; BioLegend), CD3 (Biotin or PE-Cy5; BD Biosciences), Gr-1 (Biotin or PE-Cy5; BioLegend) and Ter-119 (Biotin or PE-Cy5; BioLegend). All biotinylated antibodies were detected with Streptavidin-conjugated Qdot605 (ThermoFisher Scientific), except for the sorting of steady-state progenitors, where Qdot655 (Life Technologies/ThermoFisher Scientific, Göteborg, Sweden) was used instead. Fc receptor block (BD Biosciences) was used for sorting samples, and dead cells were excluded using 7-aminoactinomycin D (7-AAD; Sigma-Aldrich Sweden, Stockholm, Sweden) or 4',6-diamidino-2-phenylindole (DAPI; ThermoFisher Scientific). Fluorescence activated cell sorting (FACS) was performed on BD FACS Aria IIu or Aria III (Becton Dickinson).

data_processing:
RNA-Sequencing and data analysis: Biological samples were processed and sequenced in triplicate.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings on the Galaxy platform (https://usegalaxy.org/). Further  analyses were performed using the HOMER platform (v4.8, v4.10)(Heinz et al. 2010). Expression matrixes were created using analyzeRepeats.pl with settings mm10 rna and options -count exons, -condeseGenes and -rpkm for normalized expression or -noadj for files for downstream statistical analyses. Statistically different expressed genes were identified using the created raw expression matrix with genes, with less than a mean of 50 raw tags in at least one sample filtered out, and the command getDiffExpression.pl using DESeq2 (REF) as statistical tool.
ATAC-seq: Biological samples were processed and sequenced in triplicate.  For analysis of ATAC-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using Bowtie2  (2.3.4.2) (Langmead, B. etal. 2009 and 2012). Peak calling was performed using the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) (-species mm10, -enable_idr, -no_xcor). Optimal IDR peaks were used for downstream analyses. Further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include txt files of RNA-seq expressionmatrix and annotated-ATAC-peaks. All genomic coordinates are relative to mm10 mouse assembly.

source_name: Steady-state bone marrow

extract_protocol: For ATAC-seq: sorted cells were washed in ice cold PBS  prior to Assay for Transposase Accessible Chromatin (ATAC-seq) library preparation was performed essentially as described by Buenrostro et al. 2013, using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers. Sequencing was performed on a NextSeq500 (Illumina, San Diego, CA, USA). RNA-seq libraries were constructed using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian; Takara Bio USA, Mountain View, CA, USA) followed by sequencing on a HiSeq3000 (Illumina, San Diego, CA, USA)

tag: strain background

value: Steady-state BFU-E


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B11_100024]

value: male


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B09_100020]

value: amc

value: 0 hours


title: Input DNA


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B10_100092]

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B06_10001B]

value: -24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B07_100010]


title: Young.SD9hr.66951.B11

value: SD


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B08_10003B]

value: high


title: Young.SD9hr.66934.E7

value: medial prefrontal cortex


title: ATAC-seq-BM-Sca-neg-#2


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B05_100072]

value: +2 hours

value: placebo


title: Young.SD9hr.66915.C4


title: ATAC-seq-BM-Sca-neg-#1


title: ATAC-seq-Spleen-Sca-neg-#3

description:
Spleen-idr-ATAC-peaks-annotated-mm10.txt
Bone marrows (BM) and spleens were homogenized and filtered to single cell suspensions. Prior to FACS, enrichment for progenitors was carried out by lineage depletion using unconjugated antibodies produced in rat against murine B220, CD4, CD8, Gr-1 and Ter-119 (all from BioLegend, San Diego, CA, USA). Lineage-positive cells were removed with a magnetic particle concentrator (MPC-6; ThermoFisher Scientific, Göteborg, Sweden) and sheep anti-rat Fc-conjugated immunomagnetic beads (ThermoFisher Scientific).
For FACS, the following antibodies against murine epitopes were used: CD71 (FITC; BioLegend or biotin; BD Biosciences), CD9 (PE or FITC, clone MZ3; BioLegend), CD24a (PE-Cy7, clone M1/69; BioLegend), CD150 (APC, clone TC15-12F12.2; BioLegend), CD133 (PE, clone 315-2C11; BioLegend), c-Kit (APC780; eBioscience/ThermoFisher Scientific), Sca1 (BV421; BioLegend), B220 (Biotin or PE-Cy5; BioLegend), CD3 (Biotin or PE-Cy5; BD Biosciences), Gr-1 (Biotin or PE-Cy5; BioLegend) and Ter-119 (Biotin or PE-Cy5; BioLegend). All biotinylated antibodies were detected with Streptavidin-conjugated Qdot605 (ThermoFisher Scientific), except for the sorting of steady-state progenitors, where Qdot655 (Life Technologies/ThermoFisher Scientific, Göteborg, Sweden) was used instead. Fc receptor block (BD Biosciences) was used for sorting samples, and dead cells were excluded using 7-aminoactinomycin D (7-AAD; Sigma-Aldrich Sweden, Stockholm, Sweden) or 4',6-diamidino-2-phenylindole (DAPI; ThermoFisher Scientific). Fluorescence activated cell sorting (FACS) was performed on BD FACS Aria IIu or Aria III (Becton Dickinson).

source_name: Spleen day 8 after lethal irradiation and transplantation of unfractionated bone marrow cells

value: Splenic stress-BFU-E


title: ATAC-seq-Spleen-Sca-neg-#2


title: Young.SD6hr.66976.D5


title: Young.SD6hr.66997.D9


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B01_100076]

value: +6 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B02_100106]

value: umc

value: medium


title: ATAC-seq-Spleen-Sca-neg-#1


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B03_10009B]


title: Young.SD6hr.66961.G2

value: Young


title: Young.SD6hr.66950.F10


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A08_100040]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A11_100122]


title: mei-p26-2

city: Taipei

first: Hweijan

last: Hsu

address: no 128, Sec 2,  Academia Rd. Nankang

department: Institute of Cellular Biology

country: Taiwan

institute: Academia Research

data_processing:
Sequencing data was processed using the Illumina software BCL2FASTQ v2.20.
The sequences generated went through a filtering process to obtain qualified reads. Trimmomatic (1) was implemented to clip the 3′ adaptor sequence, trim or remove the reads according to the quality score and discard trimmed reads shorter than 18 nucleotides.
Qualified reads after filtering low-quality data were analyzed using miRDeep2 (2) for aligning reads to the reference genome downloaded from UCSC.
Only reads that mapped perfectly to the genome five or less times were used for miRNA detection, since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs, and also identifies novel miRNAs.
Genome_build: BDGP5 (GCA_000001215.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Drosophila melanogaster

growth_protocol: Flies with the genotype: w1118 (control) and wh7, mei-p26 (experiments) cultured at 25 degree.

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen, USA) according to the instructions. RNA was quantified at by absorbance at 260 nm using a ND-1000 spectrophotometer (Nanodrop Techonology, USA) and quality was assessed using a Bioanalyzer 2100 (Agilent Technology, USA) with a RNA 6000 labchip kit (Agilent Technologies, USA)
Sample libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer's protocols. Adaptors are ligated sequentially to the 3' and 5' ends of miRNAs. Subsequently, universal cDNA synthesis with UMI assignment, cDNA cleanup, library amplification and library cleanup are performed. Libraries were sequenced on an Illumina instrument (75-cycle single-end read, 75SE). Sequencing data was processed using the Illumina software BCL2FASTQ v2.20.

tag: genotype/variation

value: ovary


title: mei-p26-1


title: Young.SD6hr.66914.B4

tag: strain


title: w1118-2

source_name: wild type_ovary

value: wild type


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A06_100080]

source_name: blood

value: male


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A10_1000524]

value: amc

value: +24 hours


title: WT biorep2 techrep2

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
The sequencing library templates were prepared for sequencing using the Illumina HiSeq SR Cluster V4 Kit.
Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling
RNA sequences were aligned to mouse genome assembly mm9 using TopHat v2
Ensemble gene expression levels were calculated using HTseq-count
Bioconductor package edgeR was used to normalize the data and calculate P value and log2 fold change among groups.
Genome_build: UCSC: Mouse genome assembly mm9
Supplementary_files_format_and_content: Both processed data files are txt files that contain the raw reads aligned to the mm9 reference genome for one technical replicate of the four samples used for sequencing.

source_name: GFP Positive Prostate Cells

extract_protocol:
RNA samples were extracted from GFP positive cells, sorted from fresh mouse prostate tissue, using TRIZOL (500 μL, Zymo Research)
The library was prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v4 (TaKaRa Clontech) and KAPA Hyper Prep Kiet (KAPA Biosystems) according to manufacturer protocols. The resulting double stranded cDNA was sheared using a Covaris LE220 Plus (Covaris) with a 200 bp peak in the 50μl volume setting. The fragmented cDNA underwent end repair, 3′ end adenylation and ligation with barcoded adapters.The libraries were validated using the Agilent Bioanalzyer DNA High Sensitivity kit (Agilent), and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific)

tag: organ

value: Prostate

value: WT

tag: tamoxifen dose

value: Two 1mg doses at postnatal day 14 & 17

value: postnatal day 28


title: ARKO biorep1 techrep2

value: ARKO

tag: age


title: Young.SD3hr.66996.C9

value: SD

value: medial prefrontal cortex


title: ARKO biorep2 techrep2


title: ARKO biorep2 techrep1


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A09_1000624]

tag: gender

tag: hospital


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_B04_100030]

tag: subject

tag: timepoint pre(-)/post(+) lps

value: 0 hours

value: high


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A05_100072_2]

value: +2 hours

tag: stem cell dose

value: placebo


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A07_100116]

value: +6 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A12_1001224]


title: Young.SD3hr.66981.C6

value: Young

tag: tissue


title: Wh7-Exp2

description: e2 c587>tkvRNAi

data_processing:
Illumina BCL2FASTQ v2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: BDGP6 (GCA_000001215.4)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: Flies with the genotype: w1118 (control) and wh7 (experiment) cultured at 25 degree.

extract_protocol:
Total RNA were extracted by Trizol reagent (Invitrogen, USA) according to the instructions. RNA was quantified at by absorbance at 260 nm using a ND-1000 spectrophotometer (Nanodrop Techonology, USA) and quality was assessed using a Bioanalyzer 2100 (Agilent Technology, USA) with a RNA 6000 labchip kit (Agilent Technologies, USA)
Library construction for all samples was accomplished with Agilent's SureSelect Strand Specific RNA library Preparation Kit for 75bp single-end sequencing on the Illumina platform

value: ovary


title: w1118-1

value: wild type


title: wh7-mutant

description: e1 c587>tkvRNAi


title: w118-ctrl

description: c1 UAS-tkvRNAi/+


title: W118-ctrl2

description: c2 UAS-tkvRNAi/+


title: Young.SD6hr.66931.B7


title: ARKO biorep1 techrep1


title: wh7-1


title: WT biorep1 techrep2


title: wh7-2


title: Young.SD3hr.66960.F2


title: WT biorep2 techrep1


title: Young.SD3hr.66947.C10


title: CG7009_2

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq v2.19
The data was mapped against ensembl release 90 using STAR version 2.5.2b
Reads per gene were retrieved using featureCounts ( v.1.5.1)
Genome_build: BDGP6
Supplementary_files_format_and_content: tab separated value file with counts per gene

molecule: polyA RNA

source_name: S2R+ cells

growth_protocol: S2R+ cells were grown at room temperature in Schneider's medium (Gibco) supplemented with 10% FBS (Sigma) and 1% penicilin-streptomycin (sigma)

extract_protocol:
RNA were harvested using Trizol reagent
Libraries were prepared using the Illumina TruSeq Sequencing Kit (Illumina) by following the manufacturer's protocol and were sequenced on a NextSeq500 with an 42 bp paired endlength, directional, paired-end.

treatment_protocol: Knock downs were performed in a serum-free medium using 7.5 µg of dsRNA per 106 cells and stopped 2 h after cell starvation with the addition of the serum-supplemented medium. dsRNA treatment was repeated after 48 h and cells were collected 96 h after the first treatment.

tag: cell line

value: S2R+ cells

tag: cell type

value: Embryonic derived

tag: treatment

value: CG7009 KD using dsRNA


title: CG7009_1


title: WT biorep1 techrep1

value: Prostate

value: WT


title: Ctrl_2

value: LacZ KD using dsRNA


title: Young.SD3hr.66930.F6

tag: behavior

tag: timepoint


title: Ctrl_1


title: Young.SD3hr.66911.E3


title: Young.SS12hr.66980.B6

value: SS


title: RNASeq.HK2_ENL_T3_mut_C

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1

growth_protocol: HEK293 cells were maintained in alpha-MEM supplemented with 10% FBS, HK-2 cells were maintained in keratinocyte serum free medium. All cells were culture at 37C with 5% CO2.

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit (Invitrogen). Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. For RNA-seq, RNA was isolated using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer's protocol. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform. RNA-seq samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. Two biological replicates were prepared for each condition. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 3000 platform.

treatment_protocol: For generating Flag-tagged stable cell lines, 10 ug/ml blasticidin was used for stable cells selection. RNA-seq samples were collected 4 days after virus infection. ChIP-seq samples were crosslinked with 1% formaldehyde 9 days after virus infection. T1, T2 and T3 are three recurrent somatic ENL mutations originally identified in Wilms tumors (Ref: Perlman EJ, Nature communication 2015, DOI: 10.1038/ncomms10013). T1 is ENL117_118insNHL, T2 is ENL112_114PPV>L, and T3 is ENL111_113NPP>K.

value: Expressing Flag-tagged human ENL T3 mutant, repeat C


title: RNASeq.HK2_ENL_T2_mut_A

value: Expressing Flag-tagged human ENL T2 mutant, repeat A


title: RNASeq.HK2_ENL_T2_mut_B

value: Expressing Flag-tagged human ENL T2 mutant, repeat B


title: RNASeq.HK2_ENL_T1_mut_A

value: Expressing Flag-tagged human ENL T1 mutant, repeat A


title: RNASeq.HK2_ENL_T1_mut_B

value: Expressing Flag-tagged human ENL T1 mutant, repeat B


title: C0

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

description: barcodes for this sample are appended with "-1"

data_processing:
The 10X scRNA-seq library were sequenced on Illumina HiSeq2500 platform using dual indexed sequencing protocol. The generated reads were de-multiplexed and mapped to mouse genome (mm10) using the 10X CellRanger pipeline (v2.1.0).
The expressional datasets were further processed using R “Seurat” package (V2.3.4), The distribution of nGenes, nUMI, and mitochondrial reads ratio were plotted. The cells used in the study were extracted using cutoff for nGene<5000, nUMI<25000, percent.mito <0.1. The UMI count is normalized to 10,000 in each cell and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: normalized UMI count

source_name: alveolar type II (AT2)

extract_protocol:
Control mice (Sftpc-CreER; Cdc42flox/+; Rosa26-mTmG) and Cdc42 AT2 null mice (Sftpc-CreER; Cdc42flox/-; Rosa26-mTmG) were injected with 4 doses of tamoxifen. Then lungs were inflated with enzyme cocktail solution containing neutral protease (5U/ml, LS02111, Worthington) and DNase I (0.33 U/ml, 10104159001, Roche), and incubated with the enzyme cocktail solution  for 45 minutes at room temperature. Lungs were then cut into small pieces and filtered through 40μm cell strainers (BD Falcon). Cells were futher incubated with red blood lysis buffer. After spinning down, cells were resuspended in DPBS+5% FBS (Gibco, 1767839). DAPI was used to label dead cells. GFP+ cells were sorted on BD Aria II.
RNA libraries were prepared for sequencing using 10X genomics single cell 3' standard protocols

tag: cell marker

value: GFP+ cells from tamoxifen treated Sftpc-CreER; Cdc42flox/+; Rosa26-mTmG mice

value: alveolar type II (AT2)

tag: genotype

value: control

value: Sham treated

value: postnatal day 80


title: N0

description: barcodes for this sample are appended with "-3"

value: GFP+cells from tamoxifen treated Sftpc-CreER; Cdc42flox/-; Rosa26-mTmG mice

value: Cdc42 AT2 null

tag: strain


title: C21

description: barcodes for this sample are appended with "-2"

value: GFP+cells from tamoxifen treated Sftpc-CreER; Cdc42flox/+; Rosa26-mTmG mice

value: post-PNX day 21


title: Young.SS12hr.66965.E3

value: Young

value: medial prefrontal cortex


title: N21

description: barcodes for this sample are appended with "-4"

value: post PNX day 21

value: Sftpc-CreER; Cdc42flox/-; Rosa26-mTmG mice


title: RNASeq.HK2_WT_ENL_B

value: Expressing Flag-tagged wild type human ENL, repeat B


title: RNA-seq-Spleen-Sca-pos-#3

description:
AnalyzeRepeats-Spleen-samples-Sca-neg_Sca-pos_CD9-neg_count-exons_condeseGenes_noadj.txt
AnalyzeRepeats-BM-and-Spleen-samples-Sca-neg_Sca-pos_CD9-neg_count-exons_condeseGenes_rpkm.txt
Bone marrows (BM) and spleens were homogenized and filtered to single cell suspensions. Prior to FACS, enrichment for progenitors was carried out by lineage depletion using unconjugated antibodies produced in rat against murine B220, CD4, CD8, Gr-1 and Ter-119 (all from BioLegend, San Diego, CA, USA). Lineage-positive cells were removed with a magnetic particle concentrator (MPC-6; ThermoFisher Scientific, Göteborg, Sweden) and sheep anti-rat Fc-conjugated immunomagnetic beads (ThermoFisher Scientific).
For FACS, the following antibodies against murine epitopes were used: CD71 (FITC; BioLegend or biotin; BD Biosciences), CD9 (PE or FITC, clone MZ3; BioLegend), CD24a (PE-Cy7, clone M1/69; BioLegend), CD150 (APC, clone TC15-12F12.2; BioLegend), CD133 (PE, clone 315-2C11; BioLegend), c-Kit (APC780; eBioscience/ThermoFisher Scientific), Sca1 (BV421; BioLegend), B220 (Biotin or PE-Cy5; BioLegend), CD3 (Biotin or PE-Cy5; BD Biosciences), Gr-1 (Biotin or PE-Cy5; BioLegend) and Ter-119 (Biotin or PE-Cy5; BioLegend). All biotinylated antibodies were detected with Streptavidin-conjugated Qdot605 (ThermoFisher Scientific), except for the sorting of steady-state progenitors, where Qdot655 (Life Technologies/ThermoFisher Scientific, Göteborg, Sweden) was used instead. Fc receptor block (BD Biosciences) was used for sorting samples, and dead cells were excluded using 7-aminoactinomycin D (7-AAD; Sigma-Aldrich Sweden, Stockholm, Sweden) or 4',6-diamidino-2-phenylindole (DAPI; ThermoFisher Scientific). Fluorescence activated cell sorting (FACS) was performed on BD FACS Aria IIu or Aria III (Becton Dickinson).

tag: strain background

value: Splenic stress-MPP


title: GBM29

city: New York

first: Viviane

last: Tabar

state: New York

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Centre

data_processing:
Demultiplexing and alignment of FASTQ files were performed using SEQC pipeline (The code can be found here: https://github.com/dpeerlab/seqc)
Data pre-processing was performed using typical QC metrics such as the total UMIS per cell, number of cells a gene is expressed in etc. The computational details are explained in the Methods section.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw data files are provided as fastq, processed count data is provided as csv

source_name: human brain tumor

growth_protocol: cells were sorted from dissociated specimen without any in vitro culture or treatment

extract_protocol:
Sorted tumor cells from human GBM specimens were washed once and resuspended in PBS containing 0.05% BSA. 21ul of a cellular suspension at 500 cells/ul with 95% viability, were loaded onto the 10X Genomics Chromium platform to generate barcoded single-cell Gel Bead In-Emulsions (GEMs).
Single-cell RNA sequencing (scRNA-seq) libraries were prepared according to 10X Genomics specifications (Single Cell 3′ V2 Reagent Kits User Guide PN120233, 10x Genomics, Pleasanton, CA, USA).

value: brain tumor

value: freshly sorted glioblastoma cells

tag: cell subpopulation/marker


title: CG7009_3

value: S2R+ cells

value: Embryonic derived

value: CG7009 KD using dsRNA


title: RNASeq.HEK293_ENL_T3_mut_B

value: Expressing Flag-tagged human ENL T3 mutant, repeat B


title: GBM28


title: RNASeq.HK2_WT_ENL_A

value: Expressing Flag-tagged wild type human ENL, repeat A


title: Young.SS12hr.66946.B10

tag: age

value: SS


title: GBM27


title: RNASeq.HK2_ENL_T3_mut_A

value: Expressing Flag-tagged human ENL T3 mutant, repeat A


title: Young.SS12hr.66910.D3


title: Young.SS12hr.67001.C10


title: RNASeq.HEK293_ENL_T3_mut_A


title: RNA-seq-Spleen-Sca-pos-#2


title: V025

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description: serum circulating miRNAs

data_processing:
data processing miRge pipeline v1
mapptin to miRBase release 21
data were normalised using DEseq2 package
processed data files format and content: data were normalised using DEseq2 package

source_name: plasma

extract_protocol:
50 ul serum using Qiagen miRNeasy plasma/serum kit
Illumina Truseq small RNA prep kit

tag: gender

value: Female

tag: time after overdose (hours)


title: RNA-seq-Spleen-Sca-neg-#3

description:
AnalyzeRepeats-mm10-count-exons-condenseGenes-rpkm-BM-Sca-neg-Spleen-Sca-neg.txt
AnalyzeRepeats-Spleen-samples-Sca-neg_Sca-pos_CD9-neg_count-exons_condeseGenes_noadj.txt
AnalyzeRepeats-mm10-count-exons-condenseGenes-noadj-BM-Sca-neg-Spleen-Sca-neg-filtered-on-mean50tags.txt
Bone marrows (BM) and spleens were homogenized and filtered to single cell suspensions. Prior to FACS, enrichment for progenitors was carried out by lineage depletion using unconjugated antibodies produced in rat against murine B220, CD4, CD8, Gr-1 and Ter-119 (all from BioLegend, San Diego, CA, USA). Lineage-positive cells were removed with a magnetic particle concentrator (MPC-6; ThermoFisher Scientific, Göteborg, Sweden) and sheep anti-rat Fc-conjugated immunomagnetic beads (ThermoFisher Scientific).
For FACS, the following antibodies against murine epitopes were used: CD71 (FITC; BioLegend or biotin; BD Biosciences), CD9 (PE or FITC, clone MZ3; BioLegend), CD24a (PE-Cy7, clone M1/69; BioLegend), CD150 (APC, clone TC15-12F12.2; BioLegend), CD133 (PE, clone 315-2C11; BioLegend), c-Kit (APC780; eBioscience/ThermoFisher Scientific), Sca1 (BV421; BioLegend), B220 (Biotin or PE-Cy5; BioLegend), CD3 (Biotin or PE-Cy5; BD Biosciences), Gr-1 (Biotin or PE-Cy5; BioLegend) and Ter-119 (Biotin or PE-Cy5; BioLegend). All biotinylated antibodies were detected with Streptavidin-conjugated Qdot605 (ThermoFisher Scientific), except for the sorting of steady-state progenitors, where Qdot655 (Life Technologies/ThermoFisher Scientific, Göteborg, Sweden) was used instead. Fc receptor block (BD Biosciences) was used for sorting samples, and dead cells were excluded using 7-aminoactinomycin D (7-AAD; Sigma-Aldrich Sweden, Stockholm, Sweden) or 4',6-diamidino-2-phenylindole (DAPI; ThermoFisher Scientific). Fluorescence activated cell sorting (FACS) was performed on BD FACS Aria IIu or Aria III (Becton Dickinson).

value: Splenic stress-BFU-E


title: RNASeq.HEK293_ENL_T2_mut_A

value: Expressing Flag-tagged human ENL T2 mutant, repeat A


title: RNASeq.HEK293_ENL_T1_mut_B

value: Expressing Flag-tagged human ENL T1 mutant, repeat B


title: Young.SS9hr.67000.B10

value: Young

value: medial prefrontal cortex


title: V024

description: serum circulating miRNAs


title: Young.SS9hr.66984.F6


title: RNA-seq-Spleen-CD9-neg-#3

value: Splenic stress-CFU-E


title: RNA-seq-Spleen-Sca-neg-#2


title: V023

description: serum circulating miRNAs


title: RNA-seq-Spleen-Sca-neg-#1


title: Young.SS9hr.66964.D3


title: V022

description: serum circulating miRNAs


title: RNASeq.HEK293_ENL_T2_mut_B

value: Expressing Flag-tagged human ENL T2 mutant, repeat B


title: Young.SS9hr.66943.D9


title: Young.SS12hr.66927.C6


title: V021

description: serum circulating miRNAs


title: RNASeq.HEK293_WT_ENL_A


title: RNASeq.HEK293_WT_ENL_B

value: Expressing Flag-tagged wild type human ENL, repeat B


title: RNASeq.HEK293_ENL_T1_mut_A

value: Expressing Flag-tagged human ENL T1 mutant, repeat A


title: Young.SS9hr.66926.B6


title: RNA-seq-Spleen-CD9-neg-#2


title: RNA-seq-Spleen-Sca-pos-#1

value: Splenic stress-MPP


title: V020

description: serum circulating miRNAs


title: RNA-seq-Spleen-CD9-neg-#1


title: ChIPSeq.HK2_input_S31

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. For RNA-seq, RNA was isolated using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer's protocol. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform. RNA-seq samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. Two biological replicates were prepared for each condition. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 3000 platform.

value: input genomic DNA

tag: antibody

value: none (input)


title: Young.SS9hr.66907.G2


title: V019

description: serum circulating miRNAs


title: Young.SS6hr.67004.F10


title: RNA-seq-BM-Sca-neg-#3

description:
AnalyzeRepeats-mm10-count-exons-condenseGenes-rpkm-BM-Sca-neg-Spleen-Sca-neg.txt
AnalyzeRepeats-mm10-count-exons-condenseGenes-noadj-BM-Sca-neg-Spleen-Sca-neg-filtered-on-mean50tags.txt
AnalyzeRepeats-BM-and-Spleen-samples-Sca-neg_Sca-pos_CD9-neg_count-exons_condeseGenes_rpkm.txt
Bone marrows (BM) and spleens were homogenized and filtered to single cell suspensions. Prior to FACS, enrichment for progenitors was carried out by lineage depletion using unconjugated antibodies produced in rat against murine B220, CD4, CD8, Gr-1 and Ter-119 (all from BioLegend, San Diego, CA, USA). Lineage-positive cells were removed with a magnetic particle concentrator (MPC-6; ThermoFisher Scientific, Göteborg, Sweden) and sheep anti-rat Fc-conjugated immunomagnetic beads (ThermoFisher Scientific).
For FACS, the following antibodies against murine epitopes were used: CD71 (FITC; BioLegend or biotin; BD Biosciences), CD9 (PE or FITC, clone MZ3; BioLegend), CD24a (PE-Cy7, clone M1/69; BioLegend), CD150 (APC, clone TC15-12F12.2; BioLegend), CD133 (PE, clone 315-2C11; BioLegend), c-Kit (APC780; eBioscience/ThermoFisher Scientific), Sca1 (BV421; BioLegend), B220 (Biotin or PE-Cy5; BioLegend), CD3 (Biotin or PE-Cy5; BD Biosciences), Gr-1 (Biotin or PE-Cy5; BioLegend) and Ter-119 (Biotin or PE-Cy5; BioLegend). All biotinylated antibodies were detected with Streptavidin-conjugated Qdot605 (ThermoFisher Scientific), except for the sorting of steady-state progenitors, where Qdot655 (Life Technologies/ThermoFisher Scientific, Göteborg, Sweden) was used instead. Fc receptor block (BD Biosciences) was used for sorting samples, and dead cells were excluded using 7-aminoactinomycin D (7-AAD; Sigma-Aldrich Sweden, Stockholm, Sweden) or 4',6-diamidino-2-phenylindole (DAPI; ThermoFisher Scientific). Fluorescence activated cell sorting (FACS) was performed on BD FACS Aria IIu or Aria III (Becton Dickinson).

value: Steady-state BFU-E


title: Young.SS6hr.66985.B7


title: RNA-seq-BM-Sca-neg-#2


title: V018

description: serum circulating miRNAs


title: Young.SS6hr.66969.C4


title: ChIPSeq.HK2_F_T2_mut

value: Expressing Flag-tagged human ENL T2 mutant

value: Flag M2, Sigma F1804


title: V016

description: serum circulating miRNAs


title: ChIPSeq.HK2_F_T1_mut

value: Expressing Flag-tagged human ENL T1 mutant


title: V017

description: serum circulating miRNAs

value: Female


title: ChIPSeq.HEK293_input


title: V015

description: serum circulating miRNAs


title: Young.SS6hr.66923.E5

value: SS


title: V014

description: serum circulating miRNAs


title: ChIPSeq.HEK293_F_T3_mut

value: Expressing Flag-tagged human ENL T3 mutant


title: Young.SS6hr.66942.C9


title: Young.SS3hr.67005.B11


title: V013

description: serum circulating miRNAs


title: ChIPSeq.HK2_F_ENL

value: Expressing Flag-tagged wild type human ENL


title: ChIPSeq.HEK293_F_T2_mut


title: V012

description: serum circulating miRNAs


title: V011

description: serum circulating miRNAs


title: RNA-seq-BM-Sca-neg-#1


title: ChIPSeq.HK2_F_T3_mut


title: ChIPSeq.HEK293_F_T1_mut


title: Young.SS3hr.66989.F7

value: Young


title: Young.SS3hr.66968.B4

value: medial prefrontal cortex


title: ChIPSeq.HEK293_F_ENL


title: V010

description: serum circulating miRNAs


title: ChIPSeq.HEK293_Y78A_B_mut

value: Expressing Flag-tagged human ENL Y78A mutant


title: Young.SS6hr.66906.F2


title: Young.SS3hr.66939.E8


title: V008

description: serum circulating miRNAs


title: ChIPSeq.HEK293_vec

value: Expressing empty vector


title: Young.SS3hr.66922.D5


title: V007

description: serum circulating miRNAs


title: ChIPSeq.HEK293_T3_Y78A_mut

value: Expressing Flag-tagged human ENL T3-Y78A double mutant


title: Young.SS3hr.66903.C2


title: Young.Z0.67008.E11

value: baseline


title: Microtia_plus BMP7_F1

city: Akron

first: Robin

last: DiFeo Childs

state: Ohio

address: 215 W. Bowery St., Suite3300

department: Plastic & Reconstructive Surgery

institute: Childrens Hospital Medical Center of Akron

hyb_protocol: Sample labeling and hybridization was performed according to the manufacturer’s protocols. Samples were hybridized to the SurePrint G3 Human GE 8x60K Microarray (AMADID 039494).

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. This high resolution scanner represents the very latest technology from Agilent for Arrays and features an industry-leading extended dynamic range of 10 million (20-bits) for high sensitivity scanning without saturation, low-level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk that enables detection of weak features.

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house specifically for this analysis.

source_name: chondrocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug 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). The concentration of the samples provided was determined using the NanoDrop® ND-1000 UV-Vis Spectrophotometer. RNA samples were analyzed by the BGC using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples. The RNA was of high quality and all samples, with the exception of Microtia Cartilage 3 passed our QC cutoff.

growth_protocol: Respective donor cells from human normal and microtia auricular cartilage isolated from digested specimens were expanded in culture for approximately one week.  The complete medium of DMEM/F12 (50:50), 10% fetal bovine serum, gentamycin, penicillin/streptomycin and primocin was exchanged every other day and supplemented with 10 ng/ml FGF-2.  After reaching confluency, cells were trypsinized from the flasks, combined and concentrated to 100 x 106 cells/ml.  Nano-polyglycolic acid dry and sterile sheets (1 cm x 1 cm x 80 µm in length, width and thickness, respectively) were seeded with 5 x 106 cells.

extract_protocol: Samples were harvested after 10 weeks in vivo and stored in RNALater. Specimens stored at -80°C for microarray analysis were separately ground to powders under liquid nitrogen in a Spex 6870 freezer/grinder mill.  Each powder was transferred to a sterile tube containing 2-3 ml of TRI Reagent® and total RNA was isolated according to the protocol of the manufacturer.  Purification of total RNA was accomplished with a PicoPure kit.  Purified RNA for microarray analysis was shipped on dry ice to the Biomedical Genomics Core of The Research Institute at Nationwide Children’s Hospital, Columbus, OH, an Agilent-certified service provider.

treatment_protocol: Four experimental groups of samples were examined in this study.  They were normal isolated auricular chondrocytes cultured without (Group 1) and with BMP7 supplementation (Group 2) and chondrocytes derived from microtia remnants cultured without (Group 3) and with BMP7 addition (Group 4). Five µg of BMP7 were added to a gelatin-based hydrogel that allows for the slow release of the bioactive growth factor over 2-3 weeks.  One hour before surgery, culture medium was removed from appropriate cell-seeded nanoPGA scaffolds and 10 µl of BMP7-prepared gelatin were applied by pipet to the cell-seeded scaffold constructs.  Pairs of cell-seeded constructs treated with BMP7 were separately implanted in mice from animals implanted with constructs without BMP7.

value: female

value: microtia auricular cartilage

tag: agent


title: Microtia_plus BMP7_M2

value: male


title: V005

description: serum circulating miRNAs


title: Microtia_plus BMP7_M3


title: ChIPSeq.HEK293_T2_Y78A_mut

value: Expressing Flag-tagged human ENL T2-Y78A double mutant


title: ChIPSeq.HEK293_T3_B_mut


title: V006

description: serum circulating miRNAs


title: Young.Z0.66988.E7


title: V004

description: serum circulating miRNAs


title: Normal_plus BMP7_F2

value: normal auricular chondrocytes


title: Normal_plus BMP7_F3


title: Normal_plus BMP7_M1


title: Microtia_plus BMP7_M1


title: Normal_plus BMP7_F1


title: V003

description: serum circulating miRNAs


title: ChIPSeq.HEK293_T2_B_mut

value: Expressing Flag-tagged human ENL T2 mutant

value: Flag M2, Sigma F1804


title: Young.Z0.66972.F4


title: Microtia_minus BMP7_F1


title: V002

description: serum circulating miRNAs

value: Female


title: Young.Z0.66938.D8


title: Young.Z0.66919.G4


title: ChIPSeq.HEK293_T1_mut_C

value: Expressing Flag-tagged human ENL T1 mutant


title: V001

description: serum circulating miRNAs


title: Microtia_minus BMP7_M3


title: ChIPSeq.HEK293_WT_ENL_B


title: Microtia_minus BMP7_M1


title: Normal_minus BMP7_F2


title: Normal_minus BMP7_F3


title: ChIPSeq.HEK293_T1_Y78A_mut

value: Expressing Flag-tagged human ENL T1-Y78A double mutant


title: Normal_minus BMP7_M1


title: Young.Z0.66902.B2


title: Liver-CARKO_male-Rep6

status: Public on Jan 02 2020

city: Toulouse

first: Céline

last: Lukowicz

address: 180 chemin de tournefeuille

department: ToxAlim

country: France

institute: INRA UMR1331

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34012 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31343 rows each corresponding to a unique ProbeName (provided as data Matrix).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: The experimental work on animals was conducted in the Toxalim Unit, INRA, Toulouse (France), followed the European Union guidelines for laboratory animal use and care, and was approved by an independent ethics committee. Eight weeks-old female and male C57 BL/6J mice were purchased from Janvier Laboratories, France. Mean body weights were 18.9 and 23.1g for females and males respectively. The animals were allowed to acclimatise to laboratory conditions for 2 weeks before starting the experiment

extract_protocol: Total RNA was extracted with TRIzol® reagent (Sigma-Aldrich). For real-time quantitative polymerase chain reaction (qPCR), total RNA samples (2 ug) were reverse-transcribed using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Courtaboeuf, France).

treatment_protocol: Thirty-six WT or CAR-/- males and 36 WT or CAR-/- females were housed in the laboratory animal room (23 ± 2 ºC) and segregated in 2 groupes each including 18 mice. One groupe of WT and CAR-/- males and females was sacrified at the age of 16 weeks. Transcriptomic analyzes were performed in 16-week-old mice.

value: C57 BL/6J

tag: genotype/variation

value: CARKO

tag: Sex

value: 16 weeks

value: Liver


title: Liver-CARWT_male-Rep6

value: CARWT

tag: tissue


title: Liver-CARKO_male-Rep1


title: Liver-CARWT_female-Rep5


title: Liver-CARKO_female-Rep5


title: Liver-CARKO_female-Rep1


title: Liver-CARWT_female-Rep6


title: Liver-CARWT_male-Rep5


title: Liver-CARWT_male-Rep3


title: Liver-CARWT_female-Rep3


title: Liver-CARKO_female-Rep3


title: Liver-CARKO_male-Rep4


title: Liver-CARKO_male-Rep2


title: Normal_minus BMP7_F1

tag: cell type


title: Liver-CARWT_male-Rep4


title: Liver-CARKO_female-Rep2


title: Liver-CARWT_female-Rep4


title: Liver-CARKO_male-Rep3


title: Liver-CARKO_female-Rep4


title: Liver-CARKO_male-Rep5


title: RFC2596_TAGCTT

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description:
Isolation of poly A+ RNA from total RNA
2 months treatment with rapamycin diet. Fasting overnight, refeeding for 3 hours and sacrifice.

data_processing:
RNA-seq processing:
Single-end sequenced reads were analyzed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing two mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1, using the mouse NCBI37/mm9 gene annotation from https://ccb.jhu.edu/software/tophat/igenomes.shtml. Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: liver

growth_protocol: All mice were generated and maintained at the Animal Facility of the Spanish National Cancer Research Centre (CNIO) under specific pathogen-free conditions in accordance with the recommendation of the Federation of European Laboratory Animal Science Associations (FELASA)

extract_protocol:
Supplementary file
Total RNA samples (1µg) were used and the obtained Integrity Number was 8.3 (range 7.9-8.8) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) as recommended by the manufacturer.  [This kit generates directional libraries stranded in the antisense orientation (the read1 (the only read in single read format) has the antisense orientation (--library-type fr-firststrand in TopHat, --stranded=reverse in HTSeq).]  Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

treatment_protocol: 2 months treatment with rapamycin or control diet

value: hepatocytes

tag: treatment

value: rapamycin diet

value: Terc+/+


title: Liver-CARWT_female-Rep1

value: female


title: Liver-CARKO_female-Rep6


title: RFC2607_GATCAG

description:
Isolation of poly A+ RNA from total RNA
2 months treatment with control diet. Fasting overnight, refeeding for 3 hours and sacrifice.

value: male

value: control diet


title: RFC2593_GCCAAT


title: Liver-CARWT_male-Rep1


title: RFD913_GGCTAC

value: G2 Terc-/-


title: RFC2599_CGATGT


title: RFD901_CAGATC


title: RFD903_CTTGTA


title: RFC2600_ATCACG


title: RFD914_ACTTGA


title: Liver-CARWT_female-Rep2


title: mouse SLAMf6+ Vg4 T cells, biological rep 3 [DV4-SF6]

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

description: Gene expression data from lung Vg4 T cells positive for SLAMf6 and negative for SLAMf1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: requested

source_name: SLAMf6+ SLAMf1- Vgamma4 T cells from mouse lungs

label_protocol: standard Affymetrix protocol

growth_protocol: Naïve 8 to 11 weeks old female C57BL/6J were used. All animals were maintained on 12 hour light/dark cycle and provided chow and water ad libitum in an AALAC-accredited facility. Mice were housed in the specific-pathogen-free facility at the University of Vermont. All experiments were approved by the University of Vermont Institutional Animal Care and Use Committee.

extract_protocol: RNA purification was performed using the RNeasy microkit (Qiagen) following the manufacturer's instructions. RNA quality was assessed with a Eukaryote Total RNA Pico Series II chip (Agilent).

treatment_protocol: Mice were euthanized using carbon dioxide inhalation. Lungs were extracted and finely minced with scissors in enzymatic digestion buffer (Dubecco's modified Eagle's medium [DMEM], 1 mg/ml collagenase type IV [Invitrogen], 0.2 mg/ml DNase [Sigma]). Lung tissue was resuspended in additional enzymatic digestion buffer and shaken at 200 rpm at 37°C for 20 min. The samples were triturated with a 16-gauge needle and allowed to digest for an additional 20 min while shaking, after which they were triturated one more time. After red blood cell lysis using Gey's solution single cell suspensions were passed through a 70-μm-pore-size filter and washed in PBS–2% FCS. Cells were resuspended in MACS-buffer, counted, and positively selected with anti-mouse CD45 microbeads (Miltenyi Biotec) following the manufacturer's instructions. Cells were stained with fluorophore-labeled antibodies for TCRdelta, CD45, SLAMf1, CD11b, CD19, TCRbeta, SLAMf6, NK1.1, TCR-Vgamma4*, TCR-Vgamma1*, amine-reactive Live/Dead (eBioscience). After 30 minute incubation on ice, cells were washed 2x, filtered through a 35 mm-pore filter and sorted on a BD FACS-ARIA III flow cytometer. All isolated cells were negative for: CD11b, CD19, TCRbeta, Live/Dead and positive for: CD45, TCRdelta, TCR-Vgamma4. The resulting Vgamma4+ population was flow sorted into either SLAMf1positive/SLAMf6-negative cells or SLAMf1negative/SLAMf6positive cells. Cells were sorted into Click's media with 20% FCS, spun down postsort, and washed with PBS.      *Heilig-Tonegawa nomenclature used throughout

value: 8 to 11 weeks

value: lung

value: gamma delta T cell subset expressing Vgamma4 chain


title: mouse SLAMf6+ Vg4 T cells, biological rep 2 [CV4-SF6]


title: mouse SLAMf6+ Vg4 T cells, biological rep 1 [BV4-SF6]


title: mouse SLAMf1+ Vg4 T cells, biological rep 1 [BV4-SF1]

description: Gene expression data from lung Vg4 T cells positive for SLAMf1 and negative for SLAMf6

source_name: SLAMf1+ SLAMf6- Vgamma4 T cells from mouse lungs


title: Liver-CARWT_male-Rep2


title: mouse SLAMf1+ Vg4 T cells, biological rep 3 [DV4-SF1]


title: mouse SLAMf1+ Vg4 T cells, biological rep 2 [CV4-SF1]


title: RFD892_TGACCA


title: RFD900_TTAGGC


title: RFC2601_ACAGTG


title: BJ1 Vascular smooth muscle

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: Affymetrix protocol

scan_protocol: An Affymetrix Gene Chip Scanner 3000 7G was used to scan the probe arrays.

data_processing: The data were analyzed using the R oligo package to generate RMA expression values

source_name: BJ1 Vascular smooth muscle

label_protocol: 300ng of total RNA was labeled and hybridized to GeneChip Human Gene 2.0 ST arrays (Affymetrix) according to the manufacturer’s protocol and scanned on a GeneChip Scanner 3000 7G (Affymetrix).

growth_protocol: Fibroblasts were cultured in DMEM media supplemented with 15% fetal bovine serum and 2mM L-glutamine. H9 hESCs and iPSCs were maintained on Matrigel in E8 medium (DMEM/F12 supplemented with L-ascorbic acid, sodium selenite, bFGF, TGF-β1, sodium bicarbonate, holo-transferrin, and gentamycin).

extract_protocol: Total RNA was isolated from cell pellets using the Nucleospin® RNA kit (Machery-Nagel) according to the manufacturer’s instructions.  Integrity and quantity of the isolated RNA was measured using the Bioanalyzer RNA 6000 nanochip (Agilent).

value: Male

tag: cell line

tag: condition

value: Normal

value: Vascular Smooth Muscle


title: BJ1 Fibroblast early passage replicate 1

value: Fibroblast


title: AG01972 iPSC Fibroblast early passage replicate 1

value: Female

value: HGPS


title: BJ1 Fibroblast late passage replicate 1

source_name: BJ1 Fibroblast late passage replicate 1


title: BJ1 iPSC replicate 2

source_name: BJ1 iPSC replicate 2

value: iPSC


title: BJ1 iPSC replicate 4

source_name: BJ1 iPSC replicate 4


title: AG01972 iPSC Fibroblast late passage replicate 2


title: AG01972 iPSC Fibroblast late passage replicate 1


title: H9 ESC replicate 2

source_name: H9 ESC replicate 2

value: Embryonic Stem Cell


title: H9 ESC replicate 1

source_name: H9 ESC replicate 1


title: AG01972 iPSC Fibroblast early passage replicate 2


title: AG01972 iPSC replicate 1

source_name: AG01972 iPSC replicate 1


title: HGFDFN168 Fibroblast late passage replicate 2


title: HGFDFN168 iPSC replicate 1

source_name: HGFDFN168 iPSC replicate 1


title: HGFDFN168 Fibroblast early passage replicate 2


title: HGFDFN168 Fibroblast early passage replicate 1


title: AG01972 iPSC replicate 2

source_name: AG01972 iPSC replicate 2


title: HGFDFN168 Fibroblast late passage replicate 1


title: HGFDFN168 iPSC replicate 4

source_name: HGFDFN168 iPSC replicate 4


title: AG01972 iPSC replicate 3

source_name: AG01972 iPSC replicate 3


title: HGFDFN168 iPSC replicate 2

source_name: HGFDFN168 iPSC replicate 2


title: AG01972 iPSC replicate 4

source_name: AG01972 iPSC replicate 4


title: HGFDFN168 iPSC replicate 3

source_name: HGFDFN168 iPSC replicate 3


title: BJ1 Fibroblast late passage replicate 2

source_name: BJ1 Fibroblast late passage replicate 2


title: HGADFN167 Fibroblast late passage replicate 2


title: BJ1 iPSC replicate 1

source_name: BJ1 iPSC replicate 1


title: HGADFN167 Fibroblast late passage replicate 1


title: HGADFN167 iPSC replicate 4

source_name: HGADFN167 iPSC replicate 4


title: BJ1 Fibroblast early passage replicate 2


title: HGADFN167 iPSC replicate 3

source_name: HGADFN167 iPSC replicate 3


title: HGMDFN090 Fibroblast early passage replicate 1


title: HGMDFN090 Fibroblast late passage replicate 2


title: HGADFN167 iPSC replicate 2

source_name: HGADFN167 iPSC replicate 2


title: HGADFN167 iPSC replicate 1

source_name: HGADFN167 iPSC replicate 1


title: HGMDFN090 iPSC Vascular smooth muscle

source_name: HGMDFN090 iPSC Vascular smooth muscle


title: HGMDFN090 Fibroblast early passage replicate 2


title: HGMDFN090 iPSC replicate 2

source_name: HGMDFN090 iPSC replicate 2


title: HGMDFN090 iPSC replicate 4

source_name: HGMDFN090 iPSC replicate 4


title: HGMDFN090 iPSC replicate 3

source_name: HGMDFN090 iPSC replicate 3


title: HGADFN003 Fibroblast early passage replicate 1


title: HGADFN003 Fibroblast late passage replicate 2


title: HGADFN167 Fibroblast early passage replicate 1


title: HGADFN167 Vascular smooth muscle

source_name: HGADFN167 Vascular smooth muscle


title: PACS2 OD3 replicate1

city: Aglantzia

first: Vasilis

middle: J

last: Promponas

state: Nicosia

address: 1 Panepistimiou Avenue

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

description:
PACS2
YAbR34r_OD3_PACS2_.bam

data_processing:
Initial analysis, sample/barcode assignment, and genome mapping was performed on the Ion Proton server. Initial attempts to map reads on the genomes of origin gave poor results with respect to the number of unassigned RNAseq reads (not shown). Instead, we mapped all reads to the annotated P. aeruginosa PA14 genome as a reference (GCF_000014625.1_ASM1462v1_genomic.gff). Reads per gene were counted using featureCounts (Liao et al, 2014) and those corresponding to rRNA genes were in silico depleted to avoid skewing the statistics of independent samples prior to processing with DESeq2 (Love et al, 2014) for the detection of differentially expressed genes.
Pathway enrichment analysis: Relevant gene lists were uploaded to BioCyc SmartTables. Pathway enrichment was performed using the respective BioCyc functionality using the Fischer exact test and the Parent-Child Intersection method that has been shown to be robust against false positives (Grossmann et al., 2007). Multiple testing correction was performed with the Benjamini-Hochberg procedure. Reported adjusted p-values were considered significant when padj<0.05.
Cluster analysis of patterns of differential gene expression: Cluster analysis and visualization of patterns of up-/down-regulation for 78 select metabolic genes of P. aeruginosa PA14 was performed with ClustViz (Metsalu and Vilo, 2015) on a matrix where up-/down-regulation of each gene was represented with +1/-1, respectively.  Zero values were used to denote the absence of significant differential expression.
Genome_build: P. aeruginosa PA14 genome as a reference (GCF_000014625.1_ASM1462v1_genomic.gff)
Aligned RNAseq reads are provided in bam format and contain aligned reads against the P. aeruginosa PA14 genome (GCF_000014625.1_ASM1462v1_genomic.gff).
Supplementary_files_format_and_content: Differential gene expression analysis results were produced using deseq2 and are are provided in tab separated files.

organism: Pseudomonas aeruginosa

source_name: Bacterial cell pellet

growth_protocol: Bacterial RNA was isolated from LB cultures grown at OD600nm 1 and 3

extract_protocol:
For bacteria RNA extraction we used the QIAzol lysis reagent and protocol (Qiagen).
The quantity of the bacterial RNA samples was measured on a NanoDrop ND1000 system and their quality analyzed on the Agilent 2100 Bioanalyzer system with the Agilent RNA 6000 Nano kit protocol (Agilent Technologies), according to manufacturer’s instructions. Bacterial RNA samples with RNA Integrity Number (RIN) > 7 were chosen for mRNA enrichment. The MICROBExpress™ Bacterial mRNA Enrichment Kit protocol (ThermoFisher Scientific) was performed on 5 – 10μg of bacterial RNA, according to the manufacturer’s instructions. The quality and quantity of enriched mRNA were measured using the NanoDrop and the Bioanalyzer systems. After the assessment of the enriched bacterial mRNAs, libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol and reagents (ThermoFisher Scientific) according to the manufacturer’s instructions. The enriched mRNAs were fragmented, reverse transcribed and amplified after the addition of a specific (~10bp) barcode to each sample. The quantity and quality of the prepared libraries were assessed on a Bioanalyzer using the DNA High Sensitivity Kit, according to the manufacturer’s instructions. All libraries were diluted to 1nM and subsequently pooled together in pools of eight. 40pM of pooled libraries were further processed for templating and enrichment, and loaded onto the Ion Proton PI™ V2 chips (ThermoFisher Scientific). The procedure was performed on the Ion Chef™ System using the Ion PI™ IC200 Chef kit, protocol and reagents (ThermoFisher Scientific), according to the manufacturer's instructions.

tag: lb grown stage

value: Optical Density (OD) at 600nm = 3

tag: replicate number

value: OD3 replicate1


title: PACS2 OD3 replicate2

description:
PACS2
YAbR36_OD3_PACS2_3.bam

tag: strain

value: OD3 replicate2


title: PACS2 OD1 replicate1

description:
PACS2
YAbR17_OD1_PACS2_2.bam

value: Optical Density (OD) at 600nm = 1

value: OD1 replicate1


title: HGADFN003 Fibroblast early passage replicate 2


title: HGMDFN090 iPSC replicate 1

source_name: HGMDFN090 iPSC replicate 1


title: HGADFN003 Vascular smooth muscle

source_name: HGADFN003 Vascular smooth muscle


title: HGMDFN090 Fibroblast late passage replicate 1


title: C3719 OD1 replicate2

description:
C3719
YAbR5r_OD1_C3719_.bam

value: OD1 replicate2


title: HGADFN003 iPSC replicate 2

source_name: HGADFN003 iPSC replicate 2


title: C3719 OD3 replicate2

description:
C3719
YAbR24_OD3_C3719_3.bam


title: HGADFN003 iPSC replicate 4

source_name: HGADFN003 iPSC replicate 4


title: PACS2 OD1 replicate2

description:
PACS2
YAbR18_OD1_PACS2_3.bam


title: C3719 OD1 replicate1

description:
C3719
YAbR4_OD1_C3719_1.bam


title: HGADFN003 Fibroblast late passage replicate 1


title: RNA KO1

city: Berkeley

first: Jose

middle: A

last: Viscarra

state: Ca

address: 220 Morgan Hall

department: NST

institute: UC Berkeley

data_processing:
Base-calling was performed by CASAVA bcl2fastq2 v2.2.
Adapters were trimmed using cutadapt-1.2.1.
For ChIP and ATAC-seq, reads were aligned to mm10 genome assembly using BWA - 0.7.17, peak-calling was performed by MACS2-2.1.1
For RNA-seq, reads were aligned to mm10 genome assembly using HISAT2 - 2.1.0, transcript counts were generated using Quantify to annotation model (Partek E/M), differential expression was determined by DESeq2-3.5.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated by MACS2 and contain summits.
Supplementary_files_format_and_content: transcript count file contains the normalized abundance measurements, gene list file contains list of differentially expressed genes

source_name: liver

growth_protocol: Wild-type or JMJD1C-LKO mice were maintained on chow diet for 6-8 weeks.

extract_protocol:
Kapa Biosystems library prep kit
Livers were collected after 6 hour refeeding and processed for either total RNA extraction for RNA-seq, or nuclei extraction for ChIP and ATAC-seq.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for either the Kapa Biosystems or Nextera library prep kits.

treatment_protocol: Mice were fasted overnight then refed high carbohydrate diet for 6 hours.

value: liver

tag: chip antibody

tag: genotype

value: JMJD1C liver-specific knockout


title: RNA WT2

value: wildtype


title: HGADFN003 iPSC replicate 3

source_name: HGADFN003 iPSC replicate 3

value: Male


title: RNA KO2


title: RNA WT1