title: AI_CH3 [WAM528A13_S21]


title: mTeSR1_H9 [WAM464A20_S20]

status: Public on Jan 03 2020

type: SRA

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma

description: hESC cultured in mTeSR1 medium

library_source: transcriptomic

data_processing:
Read quality control was performed using FastQC v0.11.6 and results integrated with multiqc v0.9. Quality and adapter trimming with Trim Galore! v0.5.0 were applied to samples that did not pass the quality controls (mainly due to adapter contamination).
Mapping was performed against the human reference transcriptome GRCh38 using salmon v0.11.3 to generate *_quant.sf files.
Transcript IDs were mapped to gene IDs and official gene symbols using biomaRt v2.36.1.
Gene-level summarisation of counts was carried out with tximport v1.8.0.
Genome_build: Human reference transcriptome GRCh38
Supplementary_files_format_and_content: Quantification files produced by salmon v0.11.3 (*.sf) and gene-level summarisation of counts from tximport v1.8.0 in R's list format.

molecule: polyA RNA

organism: Homo sapiens

source_name: Human embryonic stem cell

growth_protocol: For culture in mTeSR1 medium (StemCell Technologies), cells were generally maintained on Matrigel-coated (BD Biosciences) tissue culture plates. Matrigel coating was performed for one hour at room temperature (RT) per the manufacturer’s instructions. Cells were passaged as clumps using ReLeSR (Stemcell Technologies). ReLeSR was added to wells for 30 seconds at RT then aspirated, then plates were incubated for 5 minutes at 37°C, quenched with mTeSR1 and lightly tapped to dislodge clumps of the desired size. Cells were also adapted to plates coated with 0.5 g/cm2 Laminin 511 (Biolamina LN-511, Takara iMatrix-511 T303). Laminin coating was performed either overnight at 4°C or for one hour at 37°C per manufacturer’s instructions. Cells on Laminin-511 were also passaged with ReLeSR with a 7-minute incubation at 37°C, or dissociated to single cell level with Accumax (Fisher Scientific), with a 10 minute incubation at 37°C. For culture in AI medium, cells were maintained on plates coated with 0.5 g/cm2 Laminin 511. Early passage newly-derived hESCs in AI medium were passaged by manual picking. Established cells in AI medium were also split using various dissociation reagents. For ReLeSR, cells were passaged similar to cells in mTeSR1 on Laminin. For Accutase (StemCell Technologies) or AccuMax, dissociation reagent was added to wells for 5 – 10 minutes, the well contents were collected and pelleted, and the dissociation reagent removed. Cells were resuspended in AI medium with or without 10 M ROCK inhibitor (Y27632, Tocris) for plating. For Gentle Cell Dissociation Reagent (StemCell Technologies), reagent was added to wells for 6 minutes, then aspirated and AI medium added. Well contents were collected and disaggregated with a 5 ml stripette. For 0.5 mM EDTA (Sigma), reagent was added for 5 minutes then aspirated, AI medium added and cells disaggregated. For salt-free PBS (Gibco, Life Technologies), reagent was added for 6 minutes, aspirated, then AI medium added and cells disaggregated.

extract_protocol:
cDNA was generated from single cells using the SMART-Seq V4 Ultra Low Input Kit (Clontech 634898) as previously described (Blakely et al. 2015). cDNA was amplified by adding 25 μl 2X SeqAmp PCR buffer, 1 μl PCR Primer II A (12 μM), 1 μl SeqAmp DNA polymerase, 3 μl nuclease-free water, and incubated on a PCR machine at 95°C for 1 min, 23 cycles of 98°C for 10 s, 65°C for 30 s and 68°C for 3 min, before a final extension for 10 min at 72°C. Amplified cDNA was purified using 50 μl AMPure XP beads (Beckman Coulter) per manufacturer’s instructions. Sample tubes were mixed well and incubated at RT for 8 min to bind the DNA to the beads. Tubes were put on a magnet until the supernatant ran clear so that it could be removed and discarded. The beads were washed twice with 200 μl 80% ethanol. Any remaining ethanol was removed and beads allowed to dry, then resuspended in 12 μl of elution buffer. Tubes were returned to the magnet and the clear supernatant containing the cDNA was collected in a new tube and stored at −80°C until library preparation. cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser, with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using Qubit dsDNA HS kit (Life Technologies).
In preparation for library generation, 10 μl of cDNA sample and 32 μl purification buffer were added to a Covaris microTUBE AFA Fiber Pre-Slit Snap Cap. cDNA was sheared to a 200-500 bp range using an E220 focused-ultrasonicator (Covaris) for 2 mins at Peak Incident power 175 W, Duty Factor 10%, 200 cycles per burst, water level 5. Libraries were prepared using a Low Input Library Prep Kit HT (Clontech, 634900) per manufacturer’s instructions. Library quality and DNA concentration was assessed by Bioanalyser and Qubit. For library purification, 75 μl of AMPure XP beads was added to each collection tube containing the genomic DNA and treated as described above.

tag: cell type

value: pluripotent stem cell

tag: cell line

tag: growth condition


title: AI_CH2 [WAM464A16_S16]

description: hESC cultured in Activin and IGF1 (AI) medium

value: AI


title: mTeSR1_H9 [WAM464A18_S18]

description: hESC cultured in mTeSR1 medium


title: mTeSR1_H9 [WAM464A17_S17]

description: hESC cultured in mTeSR1 medium


title: SMY2067_GAL4_t0

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: SMY2067 including GAL4 at the t0 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: AI_CH3 [WAM528A12_S20]

description:
AI_CH3
hESC cultured in Activin and IGF1 (AI) medium

growth_protocol: For culture in mTeSR1 medium (StemCell Technologies), cells were generally maintained on Matrigel-coated (BD Biosciences) tissue culture plates. Matrigel coating was performed for one hour at room temperature (RT) per the manufacturer’s instructions. Cells were passaged as clumps using ReLeSR (Stemcell Technologies). ReLeSR was added to wells for 30 seconds at RT then aspirated, then plates were incubated for 5 minutes at 37°C, quenched with mTeSR1 and lightly tapped to dislodge clumps of the desired size. Cells were also adapted to plates coated with 0.5 μg/cm2 Laminin 511 (Biolamina LN-511, Takara iMatrix-511 T303). Laminin coating was performed either overnight at 4°C or for one hour at 37°C per manufacturer’s instructions. Cells on Laminin-511 were also passaged with ReLeSR with a 7-minute incubation at 37°C, or dissociated to single cell level with Accumax (Fisher Scientific), with a 10 minute incubation at 37°C. For culture in AI medium, cells were maintained on plates coated with 0.5 μg/cm2 Laminin 511. Early passage newly-derived hESCs in AI medium were passaged by manual picking. Established cells in AI medium were also split using various dissociation reagents. For ReLeSR, cells were passaged similar to cells in mTeSR1 on Laminin. For Accutase (StemCell Technologies) or AccuMax, dissociation reagent was added to wells for 5 – 10 minutes, the well contents were collected and pelleted, and the dissociation reagent removed. Cells were resuspended in AI medium with or without 10 μM ROCK inhibitor (Y27632, Tocris) for plating. For Gentle Cell Dissociation Reagent (StemCell Technologies), reagent was added to wells for 6 minutes, then aspirated and AI medium added. Well contents were collected and disaggregated with a 5 ml stripette. For 0.5 mM EDTA (Sigma), reagent was added for 5 minutes then aspirated, AI medium added and cells disaggregated. For salt-free PBS (Gibco, Life Technologies), reagent was added for 6 minutes, aspirated, then AI medium added and cells disaggregated.

extract_protocol:
cDNA was generated from single cells using the SMART-Seq V4 Ultra Low Input Kit (Clontech 634898) as previously described (Blakeley et al. 2015). cDNA was amplified by adding 25 μl 2X SeqAmp PCR buffer, 1 μl PCR Primer II A (12 μM), 1 μl SeqAmp DNA polymerase, 3 μl nuclease-free water, and incubated on a PCR machine at 95°C for 1 min, 23 cycles of 98°C for 10 s, 65°C for 30 s and 68°C for 3 min, before a final extension for 10 min at 72°C. Amplified cDNA was purified using 50 μl AMPure XP beads (Beckman Coulter) per manufacturer’s instructions. Sample tubes were mixed well and incubated at RT for 8 min to bind the DNA to the beads. Tubes were put on a magnet until the supernatant ran clear so that it could be removed and discarded. The beads were washed twice with 200 μl 80% ethanol. Any remaining ethanol was removed and beads allowed to dry, then resuspended in 12 μl of elution buffer. Tubes were returned to the magnet and the clear supernatant containing the cDNA was collected in a new tube and stored at −80°C until library preparation. cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser, with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using Qubit dsDNA HS kit (Life Technologies).
In preparation for library generation, 10 μl of cDNA sample and 32 μl purification buffer were added to a Covaris microTUBE AFA Fiber Pre-Slit Snap Cap. cDNA was sheared to a 200-500 bp range using an E220 focused-ultrasonicator (Covaris) for 2 mins at Peak Incident power 175 W, Duty Factor 10%, 200 cycles per burst, water level 5. Libraries were prepared using a Low Input Library Prep Kit HT (Clontech, 634900) per manufacturer’s instructions. Library quality and DNA concentration was assessed by Bioanalyser and Qubit. For library purification, 75 μl of AMPure XP beads was added to each collection tube containing the genomic DNA and treated as described above.


title: AI_CH2 [WAM464A15_S15]


title: SMY2066_FZF1_t30

source_name: SMY2066 including FZF1 at the t30 minute timepoint


title: SMY2066_FZF1_t15

source_name: SMY2066 including FZF1 at the t15 minute timepoint


title: SMY2066_FZF1_t90

source_name: SMY2066 including FZF1 at the t90 minute timepoint


title: SMY2066_FZF1_t5

source_name: SMY2066 including FZF1 at the t5 minute timepoint


title: SMY2067_GAL4_t10

source_name: SMY2067 including GAL4 at the t10 minute timepoint


title: SMY2066_FZF1_t0

source_name: SMY2066 including FZF1 at the t0 minute timepoint


title: AI_CH2 [WAM464A13_S13]


title: SMY2066_FZF1_t10

source_name: SMY2066 including FZF1 at the t10 minute timepoint


title: AI_CH2 [WAM464A14_S14]


title: AI_CH1 [WAM464A11_S11]


title: SMY2113_SIP4_t45

source_name: SMY2113 including SIP4 at the t45 minute timepoint


title: AI_CH1 [WAM464A12_S12]


title: SMY2113_SIP4_t90

source_name: SMY2113 including SIP4 at the t90 minute timepoint


title: AI_CH3 [WAM528A11_S19]


title: mTeSR1_H9 [WAM464A19_S19]

description: hESC cultured in mTeSR1 medium


title: AI_CH1 [WAM464A10_S10]


title: SMY2113_SIP4_t30

source_name: SMY2113 including SIP4 at the t30 minute timepoint


title: SMY2113_SIP4_t15

source_name: SMY2113 including SIP4 at the t15 minute timepoint


title: SMY2113_SIP4_t20

source_name: SMY2113 including SIP4 at the t20 minute timepoint


title: SMY2113_SIP4_t5

source_name: SMY2113 including SIP4 at the t5 minute timepoint


title: SMY2113_SIP4_t10

source_name: SMY2113 including SIP4 at the t10 minute timepoint


title: AI_H9 [WAM464A8_S8]


title: AI_H9 [WAM464A7_S7]


title: AI_H9 [WAM464A6_S6]


title: SMY2113_SIP4_t0

source_name: SMY2113 including SIP4 at the t0 minute timepoint


title: SMY2063_CST6_t90

source_name: SMY2063 including CST6 at the t90 minute timepoint


title: AI_CH1 [WAM464A9_S9]

source_name: Human embryonic stem cell


title: AI_H9 [WAM464A5_S5]


title: AI_H1 [WAM464A3_S3]


title: AI_H1 [WAM464A2_S2]


title: AI_H1 [WAM464A4_S4]


title: AI_H1 [WAM464A1_S1]


title: SMY2063_CST6_t15

source_name: SMY2063 including CST6 at the t15 minute timepoint


title: SMY2063_CST6_t10

source_name: SMY2063 including CST6 at the t10 minute timepoint


title: SMY2063_CST6_t20

source_name: SMY2063 including CST6 at the t20 minute timepoint


title: SMY2057_AZF1_t45

source_name: SMY2057 including AZF1 at the t45 minute timepoint


title: SMY2057_AZF1_t90

source_name: SMY2057 including AZF1 at the t90 minute timepoint


title: SMY2063_CST6_t0

source_name: SMY2063 including CST6 at the t0 minute timepoint


title: SMY2063_CST6_t30

source_name: SMY2063 including CST6 at the t30 minute timepoint


title: SMY2063_CST6_t45

source_name: SMY2063 including CST6 at the t45 minute timepoint


title: SMY2057_AZF1_t30

source_name: SMY2057 including AZF1 at the t30 minute timepoint


title: SMY2076_HAP5_t45

source_name: SMY2076 including HAP5 at the t45 minute timepoint


title: SMY2063_CST6_t5

source_name: SMY2063 including CST6 at the t5 minute timepoint


title: SMY44_MET4_M_t45

source_name: SMY44 inducing MET4 with estradiol at t45 minute timepoint


title: SMY44_MET4_M_t30

source_name: SMY44 inducing MET4 with estradiol at t30 minute timepoint


title: SMY44_MET4_M_t60

source_name: SMY44 inducing MET4 with estradiol at t60 minute timepoint


title: SMY44_MET4_M_t15

source_name: SMY44 inducing MET4 with estradiol at t15 minute timepoint


title: SMY44_MET4_M_t90

source_name: SMY44 inducing MET4 with estradiol at t90 minute timepoint


title: SMY2057_AZF1_t15

source_name: SMY2057 including AZF1 at the t15 minute timepoint


title: SMY2057_AZF1_t10

source_name: SMY2057 including AZF1 at the t10 minute timepoint


title: SMY2057_AZF1_t5

source_name: SMY2057 including AZF1 at the t5 minute timepoint


title: SMY2056_ASH1_t90

source_name: SMY2056 including ASH1 at the t90 minute timepoint


title: SMY2057_AZF1_t0

source_name: SMY2057 including AZF1 at the t0 minute timepoint


title: SMY2056_ASH1_t45

source_name: SMY2056 including ASH1 at the t45 minute timepoint


title: SMY44_MET4_M_t5

source_name: SMY44 inducing MET4 with estradiol at t5 minute timepoint


title: SMY44_MET4_M_t0

source_name: SMY44 inducing MET4 with estradiol at t0 minute timepoint


title: SMY39_CBF1_M_t90

source_name: SMY39 inducing CBF1 with estradiol at t90 minute timepoint


title: SMY44_MET4_M_t2.5

source_name: SMY44 inducing MET4 with estradiol at t2.5 minute timepoint


title: SMY39_CBF1_M_t45

source_name: SMY39 inducing CBF1 with estradiol at t45 minute timepoint


title: SMY39_CBF1_M_t60

source_name: SMY39 inducing CBF1 with estradiol at t60 minute timepoint


title: SMY2056_ASH1_t20

source_name: SMY2056 including ASH1 at the t20 minute timepoint


title: SMY2056_ASH1_t10

source_name: SMY2056 including ASH1 at the t10 minute timepoint


title: SMY2056_ASH1_t15

source_name: SMY2056 including ASH1 at the t15 minute timepoint


title: SMY2057_AZF1_t20

source_name: SMY2057 including AZF1 at the t20 minute timepoint


title: SMY2056_ASH1_t30

source_name: SMY2056 including ASH1 at the t30 minute timepoint


title: SMY39_CBF1_M_t30

source_name: SMY39 inducing CBF1 with estradiol at t30 minute timepoint


title: SMY39_CBF1_M_t2.5

source_name: SMY39 inducing CBF1 with estradiol at t2.5 minute timepoint


title: SMY39_CBF1_M_t15

source_name: SMY39 inducing CBF1 with estradiol at t15 minute timepoint


title: SMY39_CBF1_M_t5

source_name: SMY39 inducing CBF1 with estradiol at t5 minute timepoint


title: SMY39_CBF1_M_t0

source_name: SMY39 inducing CBF1 with estradiol at t0 minute timepoint


title: SMY2056_ASH1_t0

source_name: SMY2056 including ASH1 at the t0 minute timepoint


title: SMY2056_ASH1_t5

source_name: SMY2056 including ASH1 at the t5 minute timepoint


title: SMY155_GIS1_t90

source_name: SMY155 inducing GIS1 with estradiol at t90 minute timepoint


title: SMY155_GIS1_t60

source_name: SMY155 inducing GIS1 with estradiol at t60 minute timepoint


title: SMY2114_SKN7_t45

source_name: SMY2114 including SKN7 at the t45 minute timepoint


title: SMY2114_SKN7_t90

source_name: SMY2114 including SKN7 at the t90 minute timepoint


title: hLO-230day

city: Gwangju

first: Seongmin

last: Cheon

state: N/A = Not Applicable

address: Yongbong street 77

department: School of Biological Sciences and Technology

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY.

data_processing:
Basecalling were performed cellranger mkfastq v3.0.2
mapping were performed cellranger count v3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature-barcode matrix

source_name: H9 human PSCs cell line

growth_protocol: Human ES cell (H9 passage 58) cultured using definitive endoderm differentiation kit (STEMCELL Technology, Vencouver, CA) during 4 days. Next, differentiated cells were re-plating on top of new Matrigel-coated plates using DMEM/F12 containing N2, B27, Penicillin-Streptomycin (P/S), 10 μM SB431542, 100 ng/ml Noggin, and Matrigel. After 24 hours, the medium was changed to DMEM/F12 containing N2, B27, P/S, 1 μM IWP4, and 10 μM SB431542. On day 7, anterior foregut endoderm medium (DMEM/F12 containing N2, B27, P/S, 3μM CHIR99021, 10 ng/ml BMP4, 10 ng/ml FGF7, 10 ng/ml FGF10, 50 nM all-trans retinoic acid, and Matrigel) were changed every two days until day 20. On day 13-20, cells were harvested by pipetting and then prepared for suspension culture on ultra-low attachment plates (Corning, New York, US). That medium was changed half and half every other day until day 230.

extract_protocol:
organoids were dissociated with 0.25% trypsin-EDTA for 5 min at 37C. after washing, RNA were extracted by 10X Genomics Chrominum Single Cell RNA sequencing protocol.
The alveolar type hLO on day 230 were incubated with 0.25% trypsin-EDTA for 5 min at 37°C. Dissociated cells were neutralized with 5% FBS in DMEM/F12 medium, and filtered through a 30μm filter. After washing step with DPBS, a target capture of 1x 104 cells was performed using the 10X Genomics Chromium Single Cell RNA sequencing. Briefly, single cell gel bead-in-emulsions(GEMs) are generated by passing cells with enzyme mix, partitioning oil, and barcoded gel beads by 10X Chromium chip. After GEM formation, the gel bead is dissolved and co-partitioned cell is lysed. Subsequently, reverse transcription (RT) occurs inside GEMs and barcoded full-length cDNA is generated. After RT, amplified cDNAs with barcode sequences (cell index and UMI) are pooled and single cell library is constructed using the Single Cell 3` Reagent Kit (v3 chemistry). The resulting library was sequenced on illumina HiseqX platform with 150bp paired end
10X Genomics Chromium Single Cell 3` Reagent RNA sequencing Kit

value: human lung organoid

tag: age

value: 230 days

tag: derived from

value: H9 human PSCs cell line


title: SMY2073_HAP2_t15

source_name: SMY2073 including HAP2 at the t15 minute timepoint


title: SMY155_GIS1_t15

source_name: SMY155 inducing GIS1 with estradiol at t15 minute timepoint


title: SMY2114_SKN7_t30

source_name: SMY2114 including SKN7 at the t30 minute timepoint


title: SMY155_GIS1_t30

source_name: SMY155 inducing GIS1 with estradiol at t30 minute timepoint


title: SMY2062_CIN5_t90

source_name: SMY2062 including CIN5 at the t90 minute timepoint


title: SMY155_GIS1_t10

source_name: SMY155 inducing GIS1 with estradiol at t10 minute timepoint


title: SMY2062_CIN5_t45

source_name: SMY2062 including CIN5 at the t45 minute timepoint


title: sample 3, non-cancerous tissue

city: Nanjing

first: Keith

last: Ma

address: No.44 Baiziting Road

country: China

institute: Nanjing Medical University

hyb_protocol: The labeled cRNA targets were then hybridized in the slides

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner.

data_processing: Data were extracted with Agilent Feature Extraction software . Raw data were normalized by GeneSpring GX v12.1 (Agilent Technologies), limma package the R program.

source_name: corresponding non-cancerous tissue 3

label_protocol: the enriched circular RNAs were amplified and transcribed into fluorescent cRNA. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar)

growth_protocol: The tissues were obtained from surgical resections of CRC patients without preoperative treatment

extract_protocol: Total RNAs were isolated from the paired tissues samples of five CRC patients by TRIzol reagent (Invitrogen), digested with RNase R and purified by RNeasy Mini Kit (Qiagen).

treatment_protocol: The tissues were confirmed by two experienced pathologists independently and stored in RNAlater Stabilization Solution (Invitrogen)

tag: gender

value: Male

tag: tissue

value: non-cancerous colorectal tissue


title: sample 4, non-cancerous tissue

source_name: corresponding non-cancerous tissue 4


title: SMY2114_SKN7_t0

source_name: SMY2114 including SKN7 at the t0 minute timepoint


title: SMY155_GIS1_t0

source_name: SMY155 inducing GIS1 with estradiol at t0 minute timepoint


title: SMY170_MAC1_t90

source_name: SMY170 inducing MAC1 with estradiol at t90 minute timepoint


title: SMY2114_SKN7_t20

source_name: SMY2114 including SKN7 at the t20 minute timepoint


title: SMY2062_CIN5_t30

source_name: SMY2062 including CIN5 at the t30 minute timepoint


title: SMY2114_SKN7_t5

source_name: SMY2114 including SKN7 at the t5 minute timepoint


title: sample 5, non-cancerous tissue

source_name: corresponding non-cancerous tissue 5

value: Female


title: SMY155_GIS1_t45

source_name: SMY155 inducing GIS1 with estradiol at t45 minute timepoint


title: sample 2, non-cancerous tissue

source_name: corresponding non-cancerous tissue 2


title: SMY2062_CIN5_t20

source_name: SMY2062 including CIN5 at the t20 minute timepoint


title: SMY170_MAC1_t45

source_name: SMY170 inducing MAC1 with estradiol at t45 minute timepoint


title: SMY2062_CIN5_t15

source_name: SMY2062 including CIN5 at the t15 minute timepoint


title: SMY170_MAC1_t30

source_name: SMY170 inducing MAC1 with estradiol at t30 minute timepoint


title: SMY2114_SKN7_t10

source_name: SMY2114 including SKN7 at the t10 minute timepoint


title: SMY2062_CIN5_t10

source_name: SMY2062 including CIN5 at the t10 minute timepoint


title: SMY2062_CIN5_t5

source_name: SMY2062 including CIN5 at the t5 minute timepoint


title: SMY2062_CIN5_t0

source_name: SMY2062 including CIN5 at the t0 minute timepoint


title: Sample 5, cancer tissue

source_name: human colorectal cancer tissue 5

value: colorectal cancer tissue


title: SMY2120_STP2_t90

source_name: SMY2120 including STP2 at the t90 minute timepoint


title: sample 1, non-cancerous tissue

source_name: corresponding non-cancerous tissue 1


title: Sample 4, cancer tissue

source_name: human colorectal cancer tissue 4


title: SMY170_MAC1_t5

source_name: SMY170 inducing MAC1 with estradiol at t5 minute timepoint


title: SMY2120_STP2_t45

source_name: SMY2120 including STP2 at the t45 minute timepoint


title: Sample 3, cancer tissue

source_name: human colorectal cancer tissue 3


title: SMY2120_STP2_t15

source_name: SMY2120 including STP2 at the t15 minute timepoint


title: SMY2120_STP2_t10

source_name: SMY2120 including STP2 at the t10 minute timepoint


title: SMY143_HAC1_t90

source_name: SMY143 inducing HAC1 with estradiol at t90 minute timepoint


title: SMY2120_STP2_t30

source_name: SMY2120 including STP2 at the t30 minute timepoint


title: SMY2120_STP2_t5

source_name: SMY2120 including STP2 at the t5 minute timepoint


title: SMY2120_STP2_t20

source_name: SMY2120 including STP2 at the t20 minute timepoint


title: SMY170_MAC1_t0

source_name: SMY170 inducing MAC1 with estradiol at t0 minute timepoint


title: SMY170_MAC1_t15

source_name: SMY170 inducing MAC1 with estradiol at t15 minute timepoint


title: SMY2120_STP2_t0

source_name: SMY2120 including STP2 at the t0 minute timepoint


title: SMY2114_SKN7_t15

source_name: SMY2114 including SKN7 at the t15 minute timepoint


title: SMY143_HAC1_t60

source_name: SMY143 inducing HAC1 with estradiol at t60 minute timepoint


title: SMY2119_STP1_t90

source_name: SMY2119 including STP1 at the t90 minute timepoint


title: SMY143_HAC1_t15

source_name: SMY143 inducing HAC1 with estradiol at t15 minute timepoint


title: SMY143_HAC1_t30

source_name: SMY143 inducing HAC1 with estradiol at t30 minute timepoint


title: Sample 1, cancer tissue

source_name: human colorectal cancer tissue 1


title: SMY143_HAC1_t45

source_name: SMY143 inducing HAC1 with estradiol at t45 minute timepoint


title: Mutant_sample_6_mRNA-Seq

city: Belvaux

first: Jens

middle: Christian

last: Schwamborn

state: Luxembourg

address: Avenue du Swing, 6

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine (University of Luxembourg)

data_processing:
Illumina Hi-Seq single-end reads were filtered by using BBDuk (trimq=10 qtrim=r ktrim=r k=23 mink=11 hdist=1 tpetbominlen=40; http://jgi.doe.gov/data-and-tools/bb-tools/) to remove illumina adapters, PhiX library adapters, and to quality trim the reads.
FastQC was used to check the quality of the reads in order to assure that only high-quality reads are retained for subsequent analysis. Resulting reads were mapped to human GRCh37 genome by using tophat (version 2.1.1) (library-type=fr-secondstrand) and Bowtie2 (version 2.3.2.0).
Obtained alignment files were sorted by using samtools (version 1.6-5) and the statistics of the alignment rate were obtained by using samtoolsflagstat.
Cufflinks (version 2.2.1) was used to quantify the transcripts and resulting expression values per gene were obtained in FPKM (fragments per kb per million reads).
Differential expression analysis between the Control and CLN3Q352X mutant samples was conducted by using the cuffdiff program from the cufflinks tool.
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM values from tophat

source_name: Cerebral organoids

growth_protocol: Cerebral organoids grown following the Lancaster and Knoblich protocol from 2014. Organoids were differentiated for 55 days.

extract_protocol:
Total RNA was isolated from cerebral organoids using the RNeasy Mini Kit (Qiagen, cat no. 74106). Six replicates per condition, constituted by a pool of three organoids per replicate, were extracted. RNA quality was assessed in a Bioanalyzer 2100 (Agilent).
Library preparation for sequencing was done with 1 μg of total RNA using the TruSeq mRNA Stranded Library Prep Kit (Illumina) according to manufacturer’s protocol. Pooled libraries were sequenced on NextSeq500 using manufacturer’s instructions.

value: hiPSC-derived cerebral organoids

tag: differentiation days

value: 55 days

tag: genotype

value: CLN3 Q352X mutant


title: SMY2119_STP1_t45

source_name: SMY2119 including STP1 at the t45 minute timepoint


title: Sample 2, cancer tissue

source_name: human colorectal cancer tissue 2


title: Mutant_sample_5_mRNA-Seq


title: SMY2119_STP1_t30

source_name: SMY2119 including STP1 at the t30 minute timepoint


title: SMY2119_STP1_t15

source_name: SMY2119 including STP1 at the t15 minute timepoint


title: SMY2119_STP1_t20

source_name: SMY2119 including STP1 at the t20 minute timepoint


title: Mutant_sample_4_mRNA-Seq


title: Mutant_sample_3_mRNA-Seq


title: SMY2119_STP1_t10

source_name: SMY2119 including STP1 at the t10 minute timepoint


title: SMY143_HAC1_t5

source_name: SMY143 inducing HAC1 with estradiol at t5 minute timepoint


title: SMY2119_STP1_t5

source_name: SMY2119 including STP1 at the t5 minute timepoint


title: SMY2119_STP1_t0

source_name: SMY2119 including STP1 at the t0 minute timepoint


title: Mutant_sample_2_mRNA-Seq


title: SMY143_HAC1_t0

source_name: SMY143 inducing HAC1 with estradiol at t0 minute timepoint


title: SMY58_UPC2_t60

source_name: SMY58 inducing UPC2 with estradiol at t60 minute timepoint


title: Mutant_sample_1_mRNA-Seq


title: Control_sample_6_mRNA-Seq

value: Control


title: SMY58_UPC2_t90

source_name: SMY58 inducing UPC2 with estradiol at t90 minute timepoint


title: SMY2059_CAD1_t20

source_name: SMY2059 including CAD1 at the t20 minute timepoint


title: SMY2059_CAD1_t30

source_name: SMY2059 including CAD1 at the t30 minute timepoint


title: SMY58_UPC2_t45

source_name: SMY58 inducing UPC2 with estradiol at t45 minute timepoint


title: SMY2055_ARR1_t90

source_name: SMY2055 including ARR1 at the t90 minute timepoint


title: SMY2059_CAD1_t15

source_name: SMY2059 including CAD1 at the t15 minute timepoint


title: SMY2055_ARR1_t45

source_name: SMY2055 including ARR1 at the t45 minute timepoint


title: SMY2059_CAD1_t45

source_name: SMY2059 including CAD1 at the t45 minute timepoint


title: SMY2059_CAD1_t0

source_name: SMY2059 including CAD1 at the t0 minute timepoint


title: SMY2059_CAD1_t90

source_name: SMY2059 including CAD1 at the t90 minute timepoint


title: Control_sample_5_mRNA-Seq

source_name: Cerebral organoids


title: SMY2059_CAD1_t10

source_name: SMY2059 including CAD1 at the t10 minute timepoint


title: SMY2055_ARR1_t20

source_name: SMY2055 including ARR1 at the t20 minute timepoint


title: Control_sample_4_mRNA-Seq


title: SMY58_UPC2_t30

source_name: SMY58 inducing UPC2 with estradiol at t30 minute timepoint


title: SMY2055_ARR1_t15

source_name: SMY2055 including ARR1 at the t15 minute timepoint


title: SMY58_UPC2_t15

source_name: SMY58 inducing UPC2 with estradiol at t15 minute timepoint


title: Control_sample_3_mRNA-Seq


title: SMY2055_ARR1_t10

source_name: SMY2055 including ARR1 at the t10 minute timepoint


title: SMY2055_ARR1_t5

source_name: SMY2055 including ARR1 at the t5 minute timepoint


title: Control_sample_2_mRNA-Seq


title: SMY58_UPC2_t5

source_name: SMY58 inducing UPC2 with estradiol at t5 minute timepoint


title: SMY2059_CAD1_t5

source_name: SMY2059 including CAD1 at the t5 minute timepoint


title: SMY2055_ARR1_t30

source_name: SMY2055 including ARR1 at the t30 minute timepoint


title: SMY58_UPC2_t0

source_name: SMY58 inducing UPC2 with estradiol at t0 minute timepoint


title: SMY2049_ACA1_t45

source_name: SMY2049 including ACA1 at the t45 minute timepoint


title: SMY59_ECM22_t90

source_name: SMY59 inducing ECM22 with estradiol at t90 minute timepoint


title: Control_sample_1_mRNA-Seq


title: SMY2049_ACA1_t90

source_name: SMY2049 including ACA1 at the t90 minute timepoint


title: SMY2055_ARR1_t0

source_name: SMY2055 including ARR1 at the t0 minute timepoint


title: ChIPSeq.CDK9_T3_mut

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

library_source: genomic

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

molecule: genomic DNA

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:
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.

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.

tag: treatment

value: Expressing Flag-tagged human ENL T3 mutant

tag: antibody


title: ChIPSeq.CDK9_WT_ENL

value: Expressing Flag-tagged wild type human ENL


title: ChIPSeq.CDK9_T2_mut

value: Expressing Flag-tagged human ENL T2 mutant


title: SMY59_ECM22_t60

source_name: SMY59 inducing ECM22 with estradiol at t60 minute timepoint


title: SMY59_ECM22_t45

source_name: SMY59 inducing ECM22 with estradiol at t45 minute timepoint


title: SMY2049_ACA1_t30

source_name: SMY2049 including ACA1 at the t30 minute timepoint


title: SMY2049_ACA1_t20

source_name: SMY2049 including ACA1 at the t20 minute timepoint


title: SMY2049_ACA1_t15

source_name: SMY2049 including ACA1 at the t15 minute timepoint


title: SMY2049_ACA1_t10

source_name: SMY2049 including ACA1 at the t10 minute timepoint


title: SMY59_ECM22_t30

source_name: SMY59 inducing ECM22 with estradiol at t30 minute timepoint


title: SMY2049_ACA1_t5

source_name: SMY2049 including ACA1 at the t5 minute timepoint


title: SMY2108_RPH1_t90

source_name: SMY2108 including RPH1 at the t90 minute timepoint


title: SMY2108_RPH1_t45

source_name: SMY2108 including RPH1 at the t45 minute timepoint


title: SMY2108_RPH1_t30

source_name: SMY2108 including RPH1 at the t30 minute timepoint


title: SMY59_ECM22_t15

source_name: SMY59 inducing ECM22 with estradiol at t15 minute timepoint


title: SMY2049_ACA1_t0

source_name: SMY2049 including ACA1 at the t0 minute timepoint


title: SMY59_ECM22_t5

source_name: SMY59 inducing ECM22 with estradiol at t5 minute timepoint


title: SMY2108_RPH1_t20

source_name: SMY2108 including RPH1 at the t20 minute timepoint


title: ChIPSeq.PolII_S2P_WT_ENL

value: Pol II S2P, Abcam ab5095


title: SMY59_ECM22_t0

source_name: SMY59 inducing ECM22 with estradiol at t0 minute timepoint


title: SMY2108_RPH1_t15

source_name: SMY2108 including RPH1 at the t15 minute timepoint


title: ChIPSeq.PolII_S2P_T3_mut


title: SMY2108_RPH1_t5

source_name: SMY2108 including RPH1 at the t5 minute timepoint


title: SMY2108_RPH1_t10

source_name: SMY2108 including RPH1 at the t10 minute timepoint


title: ChIPSeq.PolII_S2P_T1_mut

value: Expressing Flag-tagged human ENL T1 mutant


title: ChIPSeq.PolII_S2P_T2_mut


title: SMY104_CRZ1_t90

source_name: SMY104 inducing CRZ1 with estradiol at t90 minute timepoint


title: SMY104_CRZ1_t60

source_name: SMY104 inducing CRZ1 with estradiol at t60 minute timepoint


title: SMY2077_HCM1_t90

source_name: SMY2077 including HCM1 at the t90 minute timepoint


title: SMY2108_RPH1_t0

source_name: SMY2108 including RPH1 at the t0 minute timepoint


title: ChIPSeq.CDK9_T1_mut


title: SMY104_CRZ1_t45

source_name: SMY104 inducing CRZ1 with estradiol at t45 minute timepoint


title: SMY104_CRZ1_t30

source_name: SMY104 inducing CRZ1 with estradiol at t30 minute timepoint


title: SMY2107_ROX1_t45

source_name: SMY2107 including ROX1 at the t45 minute timepoint


title: SMY2107_ROX1_t90

source_name: SMY2107 including ROX1 at the t90 minute timepoint


title: SMY104_CRZ1_t15

source_name: SMY104 inducing CRZ1 with estradiol at t15 minute timepoint


title: THY-N729-S508_S72

city: Stanford

first: Charles

middle: Chan

last: KF

address: 265 Campus Drive

institute: Stanford

description: THY+

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

value: Bone and Bone marrow

value: Post-natal day 3 (P3)

tag: gating strategy


title: THY-N729-S506_S48

description: THY+


title: SMY2077_HCM1_t20

source_name: SMY2077 including HCM1 at the t20 minute timepoint


title: SMY2077_HCM1_t30

source_name: SMY2077 including HCM1 at the t30 minute timepoint


title: THY-N729-S505_S36

description: THY+


title: SMY2077_HCM1_t0

source_name: SMY2077 including HCM1 at the t0 minute timepoint


title: SMY2107_ROX1_t30

source_name: SMY2107 including ROX1 at the t30 minute timepoint


title: SMY2107_ROX1_t20

source_name: SMY2107 including ROX1 at the t20 minute timepoint


title: SMY2077_HCM1_t45

source_name: SMY2077 including HCM1 at the t45 minute timepoint


title: THY-N729-S503_S24

description: THY+


title: THY-N729-S507_S60

description: THY+


title: SMY2107_ROX1_t15

source_name: SMY2107 including ROX1 at the t15 minute timepoint


title: SMY104_CRZ1_t2.5

source_name: SMY104 inducing CRZ1 with estradiol at t2.5 minute timepoint


title: SMY2077_HCM1_t10

source_name: SMY2077 including HCM1 at the t10 minute timepoint


title: SMY2077_HCM1_t15

source_name: SMY2077 including HCM1 at the t15 minute timepoint


title: SMY2107_ROX1_t10

source_name: SMY2107 including ROX1 at the t10 minute timepoint


title: SMY104_CRZ1_t0

source_name: SMY104 inducing CRZ1 with estradiol at t0 minute timepoint


title: THY-N729-S502_S12

description: THY+


title: SMY104_CRZ1_t5

source_name: SMY104 inducing CRZ1 with estradiol at t5 minute timepoint


title: SMY27_MSN4_t90

source_name: SMY27 inducing MSN4 with estradiol at t90 minute timepoint


title: SMY27_MSN4_t60

source_name: SMY27 inducing MSN4 with estradiol at t60 minute timepoint


title: THY-N728-S507_S59

description: THY+


title: THY-N728-S506_S47

description: THY+


title: THY-N728-S508_S71

description: THY+


title: SMY2106_RME1_t30

source_name: SMY2106 including RME1 at the t30 minute timepoint


title: SMY2106_RME1_t20

source_name: SMY2106 including RME1 at the t20 minute timepoint


title: SMY2106_RME1_t10

source_name: SMY2106 including RME1 at the t10 minute timepoint


title: SMY2106_RME1_t90

source_name: SMY2106 including RME1 at the t90 minute timepoint


title: SMY2106_RME1_t15

source_name: SMY2106 including RME1 at the t15 minute timepoint


title: SMY27_MSN4_t45

source_name: SMY27 inducing MSN4 with estradiol at t45 minute timepoint


title: SMY2106_RME1_t5

source_name: SMY2106 including RME1 at the t5 minute timepoint


title: SMY27_MSN4_t30

source_name: SMY27 inducing MSN4 with estradiol at t30 minute timepoint


title: SMY27_MSN4_t20

source_name: SMY27 inducing MSN4 with estradiol at t20 minute timepoint


title: SMY2106_RME1_t0

source_name: SMY2106 including RME1 at the t0 minute timepoint


title: SMY2077_HCM1_t5

source_name: SMY2077 including HCM1 at the t5 minute timepoint


title: SMY27_MSN4_t15

source_name: SMY27 inducing MSN4 with estradiol at t15 minute timepoint


title: SMY2107_ROX1_t0

source_name: SMY2107 including ROX1 at the t0 minute timepoint


title: THY-N728-S503_S23

description: THY+

source_name: Long Bones


title: SMY2107_ROX1_t5

source_name: SMY2107 including ROX1 at the t5 minute timepoint


title: THY-N728-S502_S11

description: THY+


title: SMY2106_RME1_t45

source_name: SMY2106 including RME1 at the t45 minute timepoint


title: THY-N728-S505_S35

description: THY+


title: THY-N727-S508_S70

description: THY+


title: SMY27_MSN4_t12.5

source_name: SMY27 inducing MSN4 with estradiol at t12.5 minute timepoint


title: THY-N727-S507_S58

description: THY+


title: SMY2099_PHO4_t10

source_name: SMY2099 including PHO4 at the t10 minute timepoint


title: SMY2099_PHO4_t15

source_name: SMY2099 including PHO4 at the t15 minute timepoint


title: SMY2099_PHO4_t20

source_name: SMY2099 including PHO4 at the t20 minute timepoint


title: SMY2099_PHO4_t45

source_name: SMY2099 including PHO4 at the t45 minute timepoint


title: SMY2099_PHO4_t30

source_name: SMY2099 including PHO4 at the t30 minute timepoint


title: SMY27_MSN4_t10

source_name: SMY27 inducing MSN4 with estradiol at t10 minute timepoint


title: SMY2099_PHO4_t5

source_name: SMY2099 including PHO4 at the t5 minute timepoint


title: SMY2099_PHO4_t0

source_name: SMY2099 including PHO4 at the t0 minute timepoint


title: SMY2099_PHO4_t90

source_name: SMY2099 including PHO4 at the t90 minute timepoint


title: THY-N727-S506_S46

description: THY+


title: SMY2081_KAR4_t45

source_name: SMY2081 including KAR4 at the t45 minute timepoint


title: SMY27_MSN4_t7.5

source_name: SMY27 inducing MSN4 with estradiol at t7.5 minute timepoint


title: THY-N727-S505_S34

description: THY+


title: SMY27_MSN4_rep_t0

source_name: SMY27 inducing MSN4 with estradiol at t0_2 minute timepoint


title: THY-N727-S503_S22

description: THY+


title: SMY2081_KAR4_t30

source_name: SMY2081 including KAR4 at the t30 minute timepoint


title: SMY2081_KAR4_t5

source_name: SMY2081 including KAR4 at the t5 minute timepoint


title: SMY2081_KAR4_t10

source_name: SMY2081 including KAR4 at the t10 minute timepoint


title: THY-N727-S502_S10

description: THY+

source_name: Long Bones


title: SMY2081_KAR4_t0

source_name: SMY2081 including KAR4 at the t0 minute timepoint


title: SMY27_MSN4_t0

source_name: SMY27 inducing MSN4 with estradiol at t0 minute timepoint


title: SMY26_MSN2_t60

source_name: SMY26 inducing MSN2 with estradiol at t60 minute timepoint


title: SMY2082_LEU3_t90

source_name: SMY2082 including LEU3 at the t90 minute timepoint


title: SMY26_MSN2_t90

source_name: SMY26 inducing MSN2 with estradiol at t90 minute timepoint


title: SMY2081_KAR4_t20

source_name: SMY2081 including KAR4 at the t20 minute timepoint


title: SMY2082_LEU3_t30

source_name: SMY2082 including LEU3 at the t30 minute timepoint


title: SMY2081_KAR4_t90

source_name: SMY2081 including KAR4 at the t90 minute timepoint


title: SMY2081_KAR4_t15

source_name: SMY2081 including KAR4 at the t15 minute timepoint


title: THY-N726-S507_S57

description: THY+


title: THY-N726-S508_S69

description: THY+


title: SMY2082_LEU3_t45

source_name: SMY2082 including LEU3 at the t45 minute timepoint


title: SMY26_MSN2_t30

source_name: SMY26 inducing MSN2 with estradiol at t30 minute timepoint


title: SMY2082_LEU3_t15

source_name: SMY2082 including LEU3 at the t15 minute timepoint


title: SMY2082_LEU3_t20

source_name: SMY2082 including LEU3 at the t20 minute timepoint


title: SMY2082_LEU3_t10

source_name: SMY2082 including LEU3 at the t10 minute timepoint


title: SMY2082_LEU3_t0

source_name: SMY2082 including LEU3 at the t0 minute timepoint


title: SMY64_ACE2_t90

source_name: SMY64 including ACE2 at the t90 minute timepoint


title: SMY26_MSN2_t20

source_name: SMY26 inducing MSN2 with estradiol at t20 minute timepoint


title: SMY27_MSN4_t5

source_name: SMY27 inducing MSN4 with estradiol at t5 minute timepoint


title: SMY64_ACE2_t45

source_name: SMY64 including ACE2 at the t45 minute timepoint


title: THY-N726-S503_S21

description: THY+

source_name: Long Bones


title: SMY2082_LEU3_t5

source_name: SMY2082 including LEU3 at the t5 minute timepoint


title: THY-N726-S502_S9

description: THY+


title: THY-N726-S506_S45

description: THY+


title: SMY26_MSN2_t45

source_name: SMY26 inducing MSN2 with estradiol at t45 minute timepoint


title: SMY64_ACE2_t30

source_name: SMY64 including ACE2 at the t30 minute timepoint


title: SMY26_MSN2_t15

source_name: SMY26 inducing MSN2 with estradiol at t15 minute timepoint


title: SMY64_ACE2_t20

source_name: SMY64 including ACE2 at the t20 minute timepoint


title: SMY26_MSN2_t12.5

source_name: SMY26 inducing MSN2 with estradiol at t12.5 minute timepoint


title: THY-N726-S505_S33

description: THY+


title: SMY64_ACE2_t15

source_name: SMY64 including ACE2 at the t15 minute timepoint


title: THY-N724-S506_S44

description: THY+


title: SMY26_MSN2_t7.5

source_name: SMY26 inducing MSN2 with estradiol at t7.5 minute timepoint


title: SMY26_MSN2_t5

source_name: SMY26 inducing MSN2 with estradiol at t5 minute timepoint


title: SMY26_MSN2_t10

source_name: SMY26 inducing MSN2 with estradiol at t10 minute timepoint


title: SMY64_ACE2_t10

source_name: SMY64 including ACE2 at the t10 minute timepoint


title: SMY26_MSN2__rep_t0

source_name: SMY26 inducing MSN2 with estradiol at t0_2 minute timepoint


title: SMY64_ACE2_t5

source_name: SMY64 including ACE2 at the t5 minute timepoint


title: SMY64_ACE2_t0

source_name: SMY64 including ACE2 at the t0 minute timepoint


title: THY-N724-S503_S20

description: THY+


title: SMY62_ACE1_t30

source_name: SMY62 including ACE1 at the t30 minute timepoint


title: THY-N724-S505_S32

description: THY+


title: SMY62_ACE1_t45

source_name: SMY62 including ACE1 at the t45 minute timepoint


title: SMY62_ACE1_t15

source_name: SMY62 including ACE1 at the t15 minute timepoint


title: THY-N724-S507_S56

description: THY+

source_name: Long Bones


title: SMY62_ACE1_t10

source_name: SMY62 including ACE1 at the t10 minute timepoint


title: SMY62_ACE1_t20

source_name: SMY62 including ACE1 at the t20 minute timepoint


title: SMY26_MSN2_t0

source_name: SMY26 inducing MSN2 with estradiol at t0 minute timepoint


title: SMY62_ACE1_t5

source_name: SMY62 including ACE1 at the t5 minute timepoint


title: THY-N723-S508_S67

description: THY+


title: SMY62_ACE1_t90

source_name: SMY62 including ACE1 at the t90 minute timepoint


title: SMY62_ACE1_t0

source_name: SMY62 including ACE1 at the t0 minute timepoint


title: THY-N723-S507_S55

description: THY+


title: SMY257_GCN4_4ZEV_t180

source_name: SMY257 inducing GCN4 with estradiol at t180 minute timepoint


title: SMY196_YAP1_t90

source_name: SMY196 including YAP1 at the t90 minute timepoint


title: THY-N723-S506_S43

description: THY+


title: SMY196_YAP1_t30

source_name: SMY196 including YAP1 at the t30 minute timepoint


title: SMY196_YAP1_t15

source_name: SMY196 including YAP1 at the t15 minute timepoint


title: THY-N724-S502_S8

description: THY+


title: SMY257_GCN4_4ZEV_t90

source_name: SMY257 inducing GCN4 with estradiol at t90 minute timepoint


title: THY-N723-S505_S31

description: THY+


title: SMY196_YAP1_t10

source_name: SMY196 including YAP1 at the t10 minute timepoint


title: SMY257_GCN4_4ZEV_t120

source_name: SMY257 inducing GCN4 with estradiol at t120 minute timepoint


title: THY-N723-S502_S7

description: THY+


title: THY-N722-S508_S66

description: THY+


title: SMY196_YAP1_t20

source_name: SMY196 including YAP1 at the t20 minute timepoint


title: SMY257_GCN4_4ZEV_t60

source_name: SMY257 inducing GCN4 with estradiol at t60 minute timepoint


title: SMY257_GCN4_4ZEV_t30

source_name: SMY257 inducing GCN4 with estradiol at t30 minute timepoint


title: SMY179_YAP3_t90

source_name: SMY179 including YAP3 at the t90 minute timepoint


title: THY-N722-S507_S54

description: THY+

source_name: Long Bones


title: SMY196_YAP1_t45

source_name: SMY196 including YAP1 at the t45 minute timepoint


title: SMY179_YAP3_t45

source_name: SMY179 including YAP3 at the t45 minute timepoint


title: SMY179_YAP3_t10

source_name: SMY179 including YAP3 at the t10 minute timepoint


title: SMY257_GCN4_4ZEV_t45

source_name: SMY257 inducing GCN4 with estradiol at t45 minute timepoint


title: SMY179_YAP3_t5

source_name: SMY179 including YAP3 at the t5 minute timepoint


title: SMY196_YAP1_t5

source_name: SMY196 including YAP1 at the t5 minute timepoint


title: SMY179_YAP3_t20

source_name: SMY179 including YAP3 at the t20 minute timepoint


title: THY-N722-S506_S42

description: THY+


title: THY-N723-S503_S19

description: THY+


title: SMY159_PDR8_t90

source_name: SMY159 including PDR8 at the t90 minute timepoint


title: SMY159_PDR8_t45

source_name: SMY159 including PDR8 at the t45 minute timepoint


title: SMY128_FKH2_t90

source_name: SMY128 inducing FKH2 with estradiol at t90 minute timepoint


title: SMY179_YAP3_t30

source_name: SMY179 including YAP3 at the t30 minute timepoint


title: SMY128_FKH2_t60

source_name: SMY128 inducing FKH2 with estradiol at t60 minute timepoint


title: SMY257_GCN4_4ZEV_t15

source_name: SMY257 inducing GCN4 with estradiol at t15 minute timepoint


title: SMY159_PDR8_t30

source_name: SMY159 including PDR8 at the t30 minute timepoint


title: THY-N722-S505_S30

description: THY+


title: SMY128_FKH2_t45

source_name: SMY128 inducing FKH2 with estradiol at t45 minute timepoint


title: SMY257_GCN4_4ZEV_t0

source_name: SMY257 inducing GCN4 with estradiol at t0 minute timepoint


title: SMY179_YAP3_t15

source_name: SMY179 including YAP3 at the t15 minute timepoint


title: SMY159_PDR8_t20

source_name: SMY159 including PDR8 at the t20 minute timepoint


title: THY-N722-S502_S6

description: THY+

source_name: Long Bones


title: SMY159_PDR8_t15

source_name: SMY159 including PDR8 at the t15 minute timepoint


title: THY-N721-S508_S65

description: THY+


title: SMY128_FKH2_t30

source_name: SMY128 inducing FKH2 with estradiol at t30 minute timepoint


title: THY-N721-S507_S53

description: THY+


title: SMY179_YAP3_t0

source_name: SMY179 including YAP3 at the t0 minute timepoint


title: SMY128_FKH2_t8

source_name: SMY128 inducing FKH2 with estradiol at t8 minute timepoint


title: SMY159_PDR8_t0

source_name: SMY159 including PDR8 at the t0 minute timepoint


title: SMY159_PDR8_t10

source_name: SMY159 including PDR8 at the t10 minute timepoint


title: SMY153_MOT3_t90

source_name: SMY153 including MOT3 at the t90 minute timepoint


title: SMY153_MOT3_t45

source_name: SMY153 including MOT3 at the t45 minute timepoint


title: SMY128_FKH2_t15

source_name: SMY128 inducing FKH2 with estradiol at t15 minute timepoint


title: SMY153_MOT3_t20

source_name: SMY153 including MOT3 at the t20 minute timepoint


title: SMY153_MOT3_t15

source_name: SMY153 including MOT3 at the t15 minute timepoint


title: SMY159_PDR8_t5

source_name: SMY159 including PDR8 at the t5 minute timepoint


title: THY-N721-S505_S29

description: THY+


title: SMY153_MOT3_t10

source_name: SMY153 including MOT3 at the t10 minute timepoint


title: SMY128_FKH2_t5

source_name: SMY128 inducing FKH2 with estradiol at t5 minute timepoint


title: SMY128_FKH2_t0

source_name: SMY128 inducing FKH2 with estradiol at t0 minute timepoint


title: SMY146_FKH1_t90

source_name: SMY146 inducing FKH1 with estradiol at t90 minute timepoint


title: THY-N722-S503_S18

description: THY+

source_name: Long Bones


title: SMY146_FKH1_t60

source_name: SMY146 inducing FKH1 with estradiol at t60 minute timepoint


title: SMY153_MOT3_t5

source_name: SMY153 including MOT3 at the t5 minute timepoint


title: SMY153_MOT3_t0

source_name: SMY153 including MOT3 at the t0 minute timepoint


title: THY-N721-S503_S17

description: THY+


title: THY-N721-S506_S41

description: THY+


title: THY-N720-S508_S64

description: THY+


title: THY-N721-S502_S5

description: THY+


title: THY-N720-S507_S52

description: THY+


title: SMY146_FKH1_t45

source_name: SMY146 inducing FKH1 with estradiol at t45 minute timepoint


title: SMY146_FKH1_t30

source_name: SMY146 inducing FKH1 with estradiol at t30 minute timepoint


title: SMY2126_UGA3_t90

source_name: SMY2126 including UGA3 at the t90 minute timepoint


title: SMY2126_UGA3_t20

source_name: SMY2126 including UGA3 at the t20 minute timepoint


title: SMY2126_UGA3_t45

source_name: SMY2126 including UGA3 at the t45 minute timepoint


title: SMY2126_UGA3_t30

source_name: SMY2126 including UGA3 at the t30 minute timepoint


title: SMY2126_UGA3_t10

source_name: SMY2126 including UGA3 at the t10 minute timepoint


title: SMY2126_UGA3_t15

source_name: SMY2126 including UGA3 at the t15 minute timepoint


title: SMY146_FKH1_t15

source_name: SMY146 inducing FKH1 with estradiol at t15 minute timepoint


title: SMY2126_UGA3_t5

source_name: SMY2126 including UGA3 at the t5 minute timepoint


title: THY-N720-S506_S40

description: THY+


title: THY-N720-S505_S28

description: THY+


title: THY-N720-S503_S16

description: THY+


title: SMY2121_SUM1_t45

source_name: SMY2121 including SUM1 at the t45 minute timepoint


title: SMY2126_UGA3_t0

source_name: SMY2126 including UGA3 at the t0 minute timepoint


title: SMY2121_SUM1_t90

source_name: SMY2121 including SUM1 at the t90 minute timepoint


title: SMY146_FKH1_t5

source_name: SMY146 inducing FKH1 with estradiol at t5 minute timepoint


title: SMY146_FKH1_t8

source_name: SMY146 inducing FKH1 with estradiol at t8 minute timepoint


title: SMY2121_SUM1_t20

source_name: SMY2121 including SUM1 at the t20 minute timepoint


title: SMY146_FKH1_t0

source_name: SMY146 inducing FKH1 with estradiol at t0 minute timepoint


title: THY-N720-S502_S4

description: THY+

source_name: Long Bones


title: THY-N719-S508_S63

description: THY+


title: THY-N719-S507_S51

description: THY+


title: SMY54_AFT1_t60

source_name: SMY54 inducing AFT1 with estradiol at t60 minute timepoint


title: SMY54_AFT1_t90

source_name: SMY54 inducing AFT1 with estradiol at t90 minute timepoint


title: SMY2105_RLM1_t30

source_name: SMY2105 including RLM1 at the t30 minute timepoint


title: SMY2121_SUM1_t5

source_name: SMY2121 including SUM1 at the t5 minute timepoint


title: THY-N719-S506_S39

description: THY+


title: SMY2105_RLM1_t90

source_name: SMY2105 including RLM1 at the t90 minute timepoint


title: SMY2105_RLM1_t20

source_name: SMY2105 including RLM1 at the t20 minute timepoint


title: SMY2121_SUM1_t15

source_name: SMY2121 including SUM1 at the t15 minute timepoint


title: SMY2121_SUM1_t0

source_name: SMY2121 including SUM1 at the t0 minute timepoint


title: SMY2105_RLM1_t45

source_name: SMY2105 including RLM1 at the t45 minute timepoint


title: SMY54_AFT1_t30

source_name: SMY54 inducing AFT1 with estradiol at t30 minute timepoint


title: SMY54_AFT1_t45

source_name: SMY54 inducing AFT1 with estradiol at t45 minute timepoint


title: SMY2121_SUM1_t10

source_name: SMY2121 including SUM1 at the t10 minute timepoint


title: THY-N719-S505_S27

description: THY+


title: SMY2105_RLM1_t15

source_name: SMY2105 including RLM1 at the t15 minute timepoint


title: THY-N719-S503_S15

description: THY+


title: SMY2105_RLM1_t5

source_name: SMY2105 including RLM1 at the t5 minute timepoint


title: SMY153_MOT3_t30

source_name: SMY153 including MOT3 at the t30 minute timepoint


title: SMY2105_RLM1_t0

source_name: SMY2105 including RLM1 at the t0 minute timepoint


title: SMY2103_RFX1_t90

source_name: SMY2103 including RFX1 at the t90 minute timepoint


title: SMY2103_RFX1_t45

source_name: SMY2103 including RFX1 at the t45 minute timepoint


title: SMY54_AFT1_t15

source_name: SMY54 inducing AFT1 with estradiol at t15 minute timepoint


title: SMY2103_RFX1_t30

source_name: SMY2103 including RFX1 at the t30 minute timepoint


title: THY-N719-S502_S3

description: THY+

source_name: Long Bones


title: SMY54_AFT1_t5

source_name: SMY54 inducing AFT1 with estradiol at t5 minute timepoint


title: THY-N718-S508_S62

description: THY+


title: THY-N718-S507_S50

description: THY+


title: THY-N718-S510_S74

description: THY+


title: SMY124_DAL82_t30

source_name: SMY124 inducing DAL82 with estradiol at t30 minute timepoint


title: SMY2087_MIG2_t90

source_name: SMY2087 including MIG2 at the t90 minute timepoint


title: THY-N718-S506_S38

description: THY+


title: SMY54_AFT1_t0

source_name: SMY54 inducing AFT1 with estradiol at t0 minute timepoint


title: SMY2103_RFX1_t0

source_name: SMY2103 including RFX1 at the t0 minute timepoint


title: SMY2103_RFX1_t20

source_name: SMY2103 including RFX1 at the t20 minute timepoint


title: THY-N718-S505_S26

description: THY+


title: SMY124_DAL82_t90

source_name: SMY124 inducing DAL82 with estradiol at t90 minute timepoint


title: SMY124_DAL82_t45

source_name: SMY124 inducing DAL82 with estradiol at t45 minute timepoint


title: SMY124_DAL82_t15

source_name: SMY124 inducing DAL82 with estradiol at t15 minute timepoint


title: SMY2103_RFX1_t5

source_name: SMY2103 including RFX1 at the t5 minute timepoint


title: SMY2103_RFX1_t10

source_name: SMY2103 including RFX1 at the t10 minute timepoint


title: SMY2087_MIG2_t30

source_name: SMY2087 including MIG2 at the t30 minute timepoint


title: SMY196_YAP1_t0

source_name: SMY196 including YAP1 at the t0 minute timepoint


title: SMY2087_MIG2_t15

source_name: SMY2087 including MIG2 at the t15 minute timepoint


title: SMY2087_MIG2_t5

source_name: SMY2087 including MIG2 at the t5 minute timepoint


title: SMY124_DAL82_t5

source_name: SMY124 inducing DAL82 with estradiol at t5 minute timepoint


title: SMY2087_MIG2_t10

source_name: SMY2087 including MIG2 at the t10 minute timepoint


title: SMY124_DAL82_t0

source_name: SMY124 inducing DAL82 with estradiol at t0 minute timepoint


title: SMY2087_MIG2_t20

source_name: SMY2087 including MIG2 at the t20 minute timepoint


title: SMY2121_SUM1_t30

source_name: SMY2121 including SUM1 at the t30 minute timepoint


title: SMY2087_MIG2_t0

source_name: SMY2087 including MIG2 at the t0 minute timepoint


title: SMY2087_MIG2_t45

source_name: SMY2087 including MIG2 at the t45 minute timepoint


title: THY-N718-S503_S14

description: THY+

source_name: Long Bones


title: SMY2086_MIG1_t45

source_name: SMY2086 including MIG1 at the t45 minute timepoint


title: SMY2086_MIG1_t90

source_name: SMY2086 including MIG1 at the t90 minute timepoint


title: THY-N716-S508_S61

description: THY+


title: THY-N716-S510_S73

description: THY+


title: SMY2105_RLM1_t10

source_name: SMY2105 including RLM1 at the t10 minute timepoint


title: SMY2086_MIG1_t30

source_name: SMY2086 including MIG1 at the t30 minute timepoint


title: SMY2103_RFX1_t15

source_name: SMY2103 including RFX1 at the t15 minute timepoint


title: SMY110_DAL81_t90

source_name: SMY110 inducing DAL81 with estradiol at t90 minute timepoint


title: THY-N716-S507_S49

description: THY+


title: SMY2086_MIG1_t20

source_name: SMY2086 including MIG1 at the t20 minute timepoint


title: SMY2086_MIG1_t15

source_name: SMY2086 including MIG1 at the t15 minute timepoint


title: SMY110_DAL81_t45

source_name: SMY110 inducing DAL81 with estradiol at t45 minute timepoint


title: SMY2086_MIG1_t5

source_name: SMY2086 including MIG1 at the t5 minute timepoint


title: THY-N716-S506_S37

description: THY+


title: SMY2086_MIG1_t0

source_name: SMY2086 including MIG1 at the t0 minute timepoint


title: SMY110_DAL81_t30

source_name: SMY110 inducing DAL81 with estradiol at t30 minute timepoint


title: THY-N716-S503_S13

description: THY+


title: SMY2085_MBP1_t90

source_name: SMY2085 including MBP1 at the t90 minute timepoint


title: THY-N716-S505_S25

description: THY+


title: SMY110_DAL81_t15

source_name: SMY110 inducing DAL81 with estradiol at t15 minute timepoint


title: SSC-N729-S517_S240

description: mSSC


title: SSC-N729-S522_S288

description: mSSC


title: SSC-N728-S521_S275

description: mSSC


title: SMY2085_MBP1_t30

source_name: SMY2085 including MBP1 at the t30 minute timepoint


title: SMY2085_MBP1_t5

source_name: SMY2085 including MBP1 at the t5 minute timepoint


title: SMY2085_MBP1_t0

source_name: SMY2085 including MBP1 at the t0 minute timepoint


title: SMY2086_MIG1_t10

source_name: SMY2086 including MIG1 at the t10 minute timepoint


title: SMY55_ADR1_t90

source_name: SMY55 inducing ADR1 with estradiol at t90 minute timepoint


title: SMY110_DAL81_t0

source_name: SMY110 inducing DAL81 with estradiol at t0 minute timepoint


title: SMY2083_LYS14_t15

source_name: SMY2083 including LYS14 at the t15 minute timepoint


title: SMY2083_LYS14_t30

source_name: SMY2083 including LYS14 at the t30 minute timepoint


title: SMY110_DAL81_t5

source_name: SMY110 inducing DAL81 with estradiol at t5 minute timepoint


title: SMY2085_MBP1_t45

source_name: SMY2085 including MBP1 at the t45 minute timepoint


title: SMY2083_LYS14_t90

source_name: SMY2083 including LYS14 at the t90 minute timepoint


title: SMY55_ADR1_t45

source_name: SMY55 inducing ADR1 with estradiol at t45 minute timepoint


title: SMY55_ADR1_t30

source_name: SMY55 inducing ADR1 with estradiol at t30 minute timepoint


title: SSC-N728-S518_S251

description: mSSC

source_name: Long Bones


title: SMY2083_LYS14_t0

source_name: SMY2083 including LYS14 at the t0 minute timepoint


title: SMY2083_LYS14_t10

source_name: SMY2083 including LYS14 at the t10 minute timepoint


title: yRSM209_OAF1_t45

source_name: yRSM209 including OAF1 at the t45 minute timepoint


title: SMY2083_LYS14_t45

source_name: SMY2083 including LYS14 at the t45 minute timepoint


title: SSC-N728-S516_S227

description: mSSC


title: SMY55_ADR1_t15

source_name: SMY55 inducing ADR1 with estradiol at t15 minute timepoint


title: SMY55_ADR1_t5

source_name: SMY55 inducing ADR1 with estradiol at t5 minute timepoint


title: SSC-N728-S515_S215

description: mSSC


title: yRSM209_OAF1_t30

source_name: yRSM209 including OAF1 at the t30 minute timepoint


title: SSC-N728-S520_S263

description: mSSC


title: yRSM209_OAF1_t15

source_name: yRSM209 including OAF1 at the t15 minute timepoint


title: yRSM209_OAF1_t20

source_name: yRSM209 including OAF1 at the t20 minute timepoint


title: SMY2083_LYS14_t5

source_name: SMY2083 including LYS14 at the t5 minute timepoint


title: SMY117n_GLN3_N_t90

source_name: SMY117n inducing GLN3 with estradiol at t90 minute timepoint


title: yRSM209_OAF1_t10

source_name: yRSM209 including OAF1 at the t10 minute timepoint


title: SSC-N727-S522_S286

description: mSSC


title: yRSM209_OAF1_t90

source_name: yRSM209 including OAF1 at the t90 minute timepoint


title: SSC-N727-S518_S250

description: mSSC


title: SSC-N726-S522_S285

description: mSSC


title: yRSM209_OAF1_t5

source_name: yRSM209 including OAF1 at the t5 minute timepoint


title: SSC-N726-S520_S261

description: mSSC


title: SMY55_ADR1_t0

source_name: SMY55 inducing ADR1 with estradiol at t0 minute timepoint


title: yRSM92_ARG80_t90

source_name: yRSM92 including ARG80 at the t90 minute timepoint


title: yRSM209_OAF1_t0

source_name: yRSM209 including OAF1 at the t0 minute timepoint


title: SMY117n_GLN3_N_t45

source_name: SMY117n inducing GLN3 with estradiol at t45 minute timepoint


title: SMY117n_GLN3_N_t15

source_name: SMY117n inducing GLN3 with estradiol at t15 minute timepoint


title: yRSM92_ARG80_t20

source_name: yRSM92 including ARG80 at the t20 minute timepoint


title: yRSM92_ARG80_t45

source_name: yRSM92 including ARG80 at the t45 minute timepoint


title: yRSM92_ARG80_t30

source_name: yRSM92 including ARG80 at the t30 minute timepoint


title: SSC-N726-S516_S225

description: mSSC

source_name: Long Bones


title: SMY117n_GLN3_N_t0

source_name: SMY117n inducing GLN3 with estradiol at t0 minute timepoint


title: SSC-N726-S513_S201

description: mSSC


title: SMY117n_GLN3_N_t5

source_name: SMY117n inducing GLN3 with estradiol at t5 minute timepoint


title: SMY117n_GLN3_N_t30

source_name: SMY117n inducing GLN3 with estradiol at t30 minute timepoint


title: SSC-N724-S522_S284

description: mSSC


title: yRSM92_ARG80_t15

source_name: yRSM92 including ARG80 at the t15 minute timepoint


title: yRSM92_ARG80_t5

source_name: yRSM92 including ARG80 at the t5 minute timepoint


title: SMY117_GLN3_P_t90

source_name: SMY117 inducing GLN3 with estradiol at t90 minute timepoint


title: yRSM92_ARG80_t0

source_name: yRSM92 including ARG80 at the t0 minute timepoint


title: SMY117_GLN3_P_t45

source_name: SMY117 inducing GLN3 with estradiol at t45 minute timepoint


title: yRSM92_ARG80_t10

source_name: yRSM92 including ARG80 at the t10 minute timepoint


title: SSC-N724-S518_S248

description: mSSC


title: yRSM86_ARR1_t30

source_name: yRSM86 including ARR1 at the t30 minute timepoint


title: SSC-N724-S521_S272

description: mSSC


title: yRSM86_ARR1_t90

source_name: yRSM86 including ARR1 at the t90 minute timepoint


title: SMY117_GLN3_P_t30

source_name: SMY117 inducing GLN3 with estradiol at t30 minute timepoint


title: yRSM86_ARR1_t0

source_name: yRSM86 including ARR1 at the t0 minute timepoint


title: yRSM86_ARR1_t10

source_name: yRSM86 including ARR1 at the t10 minute timepoint


title: yRSM86_ARR1_t5

source_name: yRSM86 including ARR1 at the t5 minute timepoint


title: yRSM84_ARG81_t45

source_name: yRSM84 including ARG81 at the t45 minute timepoint


title: yRSM86_ARR1_t15

source_name: yRSM86 including ARR1 at the t15 minute timepoint


title: yRSM86_ARR1_t45

source_name: yRSM86 including ARR1 at the t45 minute timepoint


title: yRSM86_ARR1_t20

source_name: yRSM86 including ARR1 at the t20 minute timepoint


title: SMY117_GLN3_P_t15

source_name: SMY117 inducing GLN3 with estradiol at t15 minute timepoint


title: SSC-N723-S522_S283

description: mSSC

source_name: Long Bones


title: SMY117_GLN3_P_t5

source_name: SMY117 inducing GLN3 with estradiol at t5 minute timepoint


title: yRSM84_ARG81_t90

source_name: yRSM84 including ARG81 at the t90 minute timepoint


title: yRSM84_ARG81_t20

source_name: yRSM84 including ARG81 at the t20 minute timepoint


title: yRSM84_ARG81_t30

source_name: yRSM84 including ARG81 at the t30 minute timepoint


title: SSC-N723-S520_S259

description: mSSC


title: SSC-N723-S517_S235

description: mSSC


title: yRSM84_ARG81_t15

source_name: yRSM84 including ARG81 at the t15 minute timepoint


title: SMY117_GLN3_P_t0

source_name: SMY117 inducing GLN3 with estradiol at t0 minute timepoint


title: yRSM84_ARG81_t0

source_name: yRSM84 including ARG81 at the t0 minute timepoint


title: SSC-N724-S516_S224

description: mSSC


title: SSC-N723-S516_S223

description: mSSC


title: yRSM84_ARG81_t5

source_name: yRSM84 including ARG81 at the t5 minute timepoint


title: SMY108n_DAL80_N_t30

source_name: SMY108n inducing DAL80 with estradiol at t30 minute timepoint


title: SSC-N722-S521_S270

description: mSSC


title: yRSM84_ARG81_t10

source_name: yRSM84 including ARG81 at the t10 minute timepoint


title: SMY108n_DAL80_N_t45

source_name: SMY108n inducing DAL80 with estradiol at t45 minute timepoint


title: yRSM206_STB5_t90

source_name: yRSM206 including STB5 at the t90 minute timepoint


title: SSC-N723-S515_S211

description: mSSC


title: yRSM206_STB5_t20

source_name: yRSM206 including STB5 at the t20 minute timepoint


title: SMY108n_DAL80_N_t90

source_name: SMY108n inducing DAL80 with estradiol at t90 minute timepoint


title: SSC-N722-S517_S234

description: mSSC


title: yRSM206_STB5_t10

source_name: yRSM206 including STB5 at the t10 minute timepoint


title: yRSM206_STB5_t30

source_name: yRSM206 including STB5 at the t30 minute timepoint


title: SMY108n_DAL80_N_t5

source_name: SMY108n inducing DAL80 with estradiol at t5 minute timepoint


title: yRSM206_STB5_t15

source_name: yRSM206 including STB5 at the t15 minute timepoint


title: SMY108n_DAL80_N_t15

source_name: SMY108n inducing DAL80 with estradiol at t15 minute timepoint


title: yRSM206_STB5_t5

source_name: yRSM206 including STB5 at the t5 minute timepoint


title: SSC-N722-S515_S210

description: mSSC

source_name: Long Bones


title: SMY108n_DAL80_N_t0

source_name: SMY108n inducing DAL80 with estradiol at t0 minute timepoint


title: yRSM204_USV1_t90

source_name: yRSM204 including USV1 at the t90 minute timepoint


title: yRSM206_STB5_t45

source_name: yRSM206 including STB5 at the t45 minute timepoint


title: yRSM204_USV1_t45

source_name: yRSM204 including USV1 at the t45 minute timepoint


title: yRSM204_USV1_t30

source_name: yRSM204 including USV1 at the t30 minute timepoint


title: SSC-N721-S518_S245

description: mSSC


title: SMY108_DAL80_P_t90

source_name: SMY108 inducing DAL80 with estradiol at t90 minute timepoint


title: SSC-N721-S515_S209

description: mSSC


title: SMY108_DAL80_P_t45

source_name: SMY108 inducing DAL80 with estradiol at t45 minute timepoint


title: SSC-N721-S513_S197

description: mSSC


title: yRSM206_STB5_t0

source_name: yRSM206 including STB5 at the t0 minute timepoint


title: SSC-N720-S522_S280

description: mSSC


title: yRSM204_USV1_t15

source_name: yRSM204 including USV1 at the t15 minute timepoint


title: yRSM204_USV1_t20

source_name: yRSM204 including USV1 at the t20 minute timepoint


title: yRSM175_PDR3_t90

source_name: yRSM175 including PDR3 at the t90 minute timepoint


title: SMY108_DAL80_P_t15

source_name: SMY108 inducing DAL80 with estradiol at t15 minute timepoint


title: SMY108_DAL80_P_t5

source_name: SMY108 inducing DAL80 with estradiol at t5 minute timepoint


title: yRSM204_USV1_t5

source_name: yRSM204 including USV1 at the t5 minute timepoint


title: SMY108_DAL80_P_t30

source_name: SMY108 inducing DAL80 with estradiol at t30 minute timepoint


title: SMY108_DAL80_P_t0

source_name: SMY108 inducing DAL80 with estradiol at t0 minute timepoint


title: SSC-N719-S520_S255

description: mSSC

source_name: Long Bones


title: yRSM175_PDR3_t45

source_name: yRSM175 including PDR3 at the t45 minute timepoint


title: yRSM175_PDR3_t15

source_name: yRSM175 including PDR3 at the t15 minute timepoint


title: yRSM204_USV1_t0

source_name: yRSM204 including USV1 at the t0 minute timepoint


title: yRSM175_PDR3_t30

source_name: yRSM175 including PDR3 at the t30 minute timepoint


title: yRSM175_PDR3_t20

source_name: yRSM175 including PDR3 at the t20 minute timepoint


title: yRSM204_USV1_t10

source_name: yRSM204 including USV1 at the t10 minute timepoint


title: SMY69_GEV_M_t45

source_name: SMY69 inducing GEV with estradiol at t45 minute timepoint


title: SMY69_GEV_M_t60

source_name: SMY69 inducing GEV with estradiol at t60 minute timepoint


title: yRSM170_MAC1_t90

source_name: yRSM170 including MAC1 at the t90 minute timepoint


title: yRSM175_PDR3_t0

source_name: yRSM175 including PDR3 at the t0 minute timepoint


title: SSC-N719-S515_S207

description: mSSC


title: SSC-N720-S520_S256

description: mSSC


title: SMY69_GEV_M_t30

source_name: SMY69 inducing GEV with estradiol at t30 minute timepoint


title: yRSM170_MAC1_t30

source_name: yRSM170 including MAC1 at the t30 minute timepoint


title: yRSM170_MAC1_t20

source_name: yRSM170 including MAC1 at the t20 minute timepoint


title: SSC-N718-S522_S278

description: mSSC


title: SSC-N718-S518_S242

description: mSSC


title: SSC-N719-S517_S231

description: mSSC


title: SSC-N716-S522_S277

description: mSSC


title: yRSM175_PDR3_t10

source_name: yRSM175 including PDR3 at the t10 minute timepoint


title: yRSM175_PDR3_t5

source_name: yRSM175 including PDR3 at the t5 minute timepoint


title: CSP-N727-S520_S262

description: CSP


title: yRSM170_MAC1_t45

source_name: yRSM170 including MAC1 at the t45 minute timepoint


title: yRSM170_MAC1_t0

source_name: yRSM170 including MAC1 at the t0 minute timepoint


title: SMY2047_GLN3_t90

source_name: YukoSMY2047 including GLN3 at the t90 minute timepoint


title: yRSM170_MAC1_t5

source_name: yRSM170 including MAC1 at the t5 minute timepoint


title: yRSM170_MAC1_t15

source_name: yRSM170 including MAC1 at the t15 minute timepoint


title: SMY2083_LYS14_t20

source_name: SMY2083 including LYS14 at the t20 minute timepoint


title: yRSM170_MAC1_t10

source_name: yRSM170 including MAC1 at the t10 minute timepoint


title: CSP-N727-S513_S202

description: CSP

source_name: Long Bones


title: SMY69_GEV_M_t2.5

source_name: SMY69 inducing GEV with estradiol at t2.5 minute timepoint


title: SMY69_GEV_M_t5

source_name: SMY69 inducing GEV with estradiol at t5 minute timepoint


title: SMY2047_GLN3_t45

source_name: YukoSMY2047 including GLN3 at the t45 minute timepoint


title: SMY69_GEV_M_t15

source_name: SMY69 inducing GEV with estradiol at t15 minute timepoint


title: SMY69_GEV_M_t0

source_name: SMY69 inducing GEV with estradiol at t0 minute timepoint


title: SMY2047_GLN3_t10

source_name: YukoSMY2047 including GLN3 at the t10 minute timepoint


title: SMY42_MET28_M_t60

source_name: SMY42 inducing MET28 with estradiol at t60 minute timepoint


title: SMY2047_GLN3_t20

source_name: YukoSMY2047 including GLN3 at the t20 minute timepoint


title: SMY2047_GLN3_t5

source_name: YukoSMY2047 including GLN3 at the t5 minute timepoint


title: CSP-N727-S517_S238

description: CSP


title: SMY2047_GLN3_t0

source_name: YukoSMY2047 including GLN3 at the t0 minute timepoint


title: CSP-N726-S521_S273

description: CSP


title: SMY69_GEV_M_t90

source_name: SMY69 inducing GEV with estradiol at t90 minute timepoint


title: SMY42_MET28_M_t45

source_name: SMY42 inducing MET28 with estradiol at t45 minute timepoint


title: CSP-N726-S518_S249

description: CSP


title: SMY2047_GLN3_t30

source_name: YukoSMY2047 including GLN3 at the t30 minute timepoint


title: yRSM164_NDT80_t90

source_name: yRSM164 including NDT80 at the t90 minute timepoint


title: SMY42_MET28_M_t90

source_name: SMY42 inducing MET28 with estradiol at t90 minute timepoint


title: SMY2047_GLN3_t15

source_name: YukoSMY2047 including GLN3 at the t15 minute timepoint


title: yRSM164_NDT80_t30

source_name: yRSM164 including NDT80 at the t30 minute timepoint


title: SMY42_MET28_M_t30

source_name: SMY42 inducing MET28 with estradiol at t30 minute timepoint


title: THY-N724-S508_S68

description: THY+

source_name: Long Bones


title: yRSM164_NDT80_t20

source_name: yRSM164 including NDT80 at the t20 minute timepoint


title: yRSM164_NDT80_t15

source_name: yRSM164 including NDT80 at the t15 minute timepoint


title: yRSM164_NDT80_t45

source_name: yRSM164 including NDT80 at the t45 minute timepoint


title: yRSM164_NDT80_t10

source_name: yRSM164 including NDT80 at the t10 minute timepoint


title: CSP-N724-S520_S260

description: CSP


title: CSP-N724-S517_S236

description: CSP


title: yRSM164_NDT80_t5

source_name: yRSM164 including NDT80 at the t5 minute timepoint


title: SMY42_MET28_M_t15

source_name: SMY42 inducing MET28 with estradiol at t15 minute timepoint


title: SMY42_MET28_M_t2.5

source_name: SMY42 inducing MET28 with estradiol at t2.5 minute timepoint


title: CSP-N723-S518_S247

description: CSP


title: SMY141_INO4_t45

source_name: SMY141 including INO4 at the t45 minute timepoint


title: SMY42_MET28_M_t0

source_name: SMY42 inducing MET28 with estradiol at t0 minute timepoint


title: CSP-N723-S521_S271

description: CSP


title: CSP-N726-S517_S237

description: CSP


title: SMY141_INO4_t30

source_name: SMY141 including INO4 at the t30 minute timepoint


title: SMY141_INO4_t20

source_name: SMY141 including INO4 at the t20 minute timepoint


title: SMY42_MET28_M_t5

source_name: SMY42 inducing MET28 with estradiol at t5 minute timepoint


title: yRSM164_NDT80_t0

source_name: yRSM164 including NDT80 at the t0 minute timepoint


title: CSP-N723-S513_S199

description: CSP


title: SSC-N719-S518_S243

description: mSSC


title: CSP-N722-S516_S222

description: CSP


title: CSP-N722-S522_S282

description: CSP


title: SMY41_MET32_M_t90

source_name: SMY41 inducing MET32 with estradiol at t90 minute timepoint


title: SMY141_INO4_t0

source_name: SMY141 including INO4 at the t0 minute timepoint


title: SMY141_INO4_t15

source_name: SMY141 including INO4 at the t15 minute timepoint


title: SMY2035_SIR2_t290

source_name: SMY2035 including SIR2 at the t290 minute timepoint


title: SMY41_MET32_M_t60

source_name: SMY41 inducing MET32 with estradiol at t60 minute timepoint


title: SMY2035_SIR2_t30

source_name: SMY2035 including SIR2 at the t30 minute timepoint


title: SMY2035_SIR2_t45

source_name: SMY2035 including SIR2 at the t45 minute timepoint


title: SMY41_MET32_M_t45

source_name: SMY41 inducing MET32 with estradiol at t45 minute timepoint


title: SMY41_MET32_M_t30

source_name: SMY41 inducing MET32 with estradiol at t30 minute timepoint


title: SMY141_INO4_t5

source_name: SMY141 including INO4 at the t5 minute timepoint


title: SMY2035_SIR2_t90

source_name: SMY2035 including SIR2 at the t90 minute timepoint


title: CSP-N721-S520_S257

description: CSP

source_name: Long Bones


title: CSP-N720-S513_S196

description: CSP


title: SMY41_MET32_M_t15

source_name: SMY41 inducing MET32 with estradiol at t15 minute timepoint


title: SMY2035_SIR2_t20

source_name: SMY2035 including SIR2 at the t20 minute timepoint


title: SMY141_INO4_t10

source_name: SMY141 including INO4 at the t10 minute timepoint


title: SMY2035_SIR2_t10

source_name: SMY2035 including SIR2 at the t10 minute timepoint


title: SMY125_FLO8_t30

source_name: SMY125 including FLO8 at the t30 minute timepoint


title: SMY2035_SIR2_t5

source_name: SMY2035 including SIR2 at the t5 minute timepoint


title: SMY41_MET32_M_t5

source_name: SMY41 inducing MET32 with estradiol at t5 minute timepoint


title: SMY41_MET32_M_t2.5

source_name: SMY41 inducing MET32 with estradiol at t2.5 minute timepoint


title: SMY2035_SIR2_t0

source_name: SMY2035 including SIR2 at the t0 minute timepoint


title: CSP-N719-S521_S267

description: CSP


title: SMY41_MET32_M_t0

source_name: SMY41 inducing MET32 with estradiol at t0 minute timepoint


title: SMY125_FLO8_t20

source_name: SMY125 including FLO8 at the t20 minute timepoint


title: CSP-N719-S516_S219

description: CSP


title: SMY125_FLO8_t15

source_name: SMY125 including FLO8 at the t15 minute timepoint


title: CSP-N721-S516_S221

description: CSP


title: CSP-N718-S521_S266

description: CSP


title: SMY125_FLO8_t10

source_name: SMY125 including FLO8 at the t10 minute timepoint


title: SMY125_FLO8_t5

source_name: SMY125 including FLO8 at the t5 minute timepoint


title: SMY40_MET31_M_t60

source_name: SMY40 inducing MET31 with estradiol at t60 minute timepoint


title: SMY2035_SIR2_t15

source_name: SMY2035 including SIR2 at the t15 minute timepoint


title: SMY40_MET31_M_t90

source_name: SMY40 inducing MET31 with estradiol at t90 minute timepoint


title: CSP-N719-S522_S279

description: CSP

source_name: Long Bones


title: SMY113_WAR1_t30

source_name: SMY113 including WAR1 at the t30 minute timepoint


title: SMY125_FLO8_t45

source_name: SMY125 including FLO8 at the t45 minute timepoint


title: SMY125_FLO8_t0

source_name: SMY125 including FLO8 at the t0 minute timepoint


title: SMY113_WAR1_t90

source_name: SMY113 including WAR1 at the t90 minute timepoint


title: SMY40_MET31_M_t45

source_name: SMY40 inducing MET31 with estradiol at t45 minute timepoint


title: SMY40_MET31_M_t30

source_name: SMY40 inducing MET31 with estradiol at t30 minute timepoint


title: SMY113_WAR1_t20

source_name: SMY113 including WAR1 at the t20 minute timepoint


title: SMY113_WAR1_t15

source_name: SMY113 including WAR1 at the t15 minute timepoint


title: SMY40_MET31_M_t15

source_name: SMY40 inducing MET31 with estradiol at t15 minute timepoint


title: SMY113_WAR1_t10

source_name: SMY113 including WAR1 at the t10 minute timepoint


title: SMY113_WAR1_t5

source_name: SMY113 including WAR1 at the t5 minute timepoint


title: SMY40_MET31_M_t5

source_name: SMY40 inducing MET31 with estradiol at t5 minute timepoint


title: CSP-N718-S513_S194

description: CSP


title: CSP-N716-S521_S265

description: CSP


title: SMY113_WAR1_t0

source_name: SMY113 including WAR1 at the t0 minute timepoint


title: SMY181_ZAP1_t90

source_name: SMY181 including ZAP1 at the t90 minute timepoint


title: SMY181_ZAP1_t30

source_name: SMY181 including ZAP1 at the t30 minute timepoint


title: SMY181_ZAP1_t45

source_name: SMY181 including ZAP1 at the t45 minute timepoint


title: CSP-N716-S518_S241

description: CSP

source_name: Long Bones


title: CSP-N716-S515_S205

description: CSP


title: SMY113_WAR1_t45

source_name: SMY113 including WAR1 at the t45 minute timepoint


title: 6C3-N715-S510_S180


title: CSP-N718-S517_S230

description: CSP


title: SMY257_GCN4_t90

source_name: SMY257 including GCN4 at the t90 minute timepoint


title: SMY181_ZAP1_t10

source_name: SMY181 including ZAP1 at the t10 minute timepoint


title: SMY156n_GZF3_N_t90

source_name: SMY156n inducing GZF3 with estradiol at t90 minute timepoint


title: SMY40_MET31_M_t0

source_name: SMY40 inducing MET31 with estradiol at t0 minute timepoint


title: SMY181_ZAP1_t15

source_name: SMY181 including ZAP1 at the t15 minute timepoint


title: 6C3-N715-S508_S168


title: SMY40_MET31_M_t2.5

source_name: SMY40 inducing MET31 with estradiol at t2.5 minute timepoint


title: SMY181_ZAP1_t20

source_name: SMY181 including ZAP1 at the t20 minute timepoint


title: SMY257_GCN4_t45

source_name: SMY257 including GCN4 at the t45 minute timepoint


title: SMY181_ZAP1_t0

source_name: SMY181 including ZAP1 at the t0 minute timepoint


title: SMY156n_GZF3_N_t30

source_name: SMY156n inducing GZF3 with estradiol at t30 minute timepoint


title: SMY257_GCN4_t30

source_name: SMY257 including GCN4 at the t30 minute timepoint


title: 6C3-N715-S507_S156


title: SMY156n_GZF3_N_t45

source_name: SMY156n inducing GZF3 with estradiol at t45 minute timepoint


title: SMY257_GCN4_t20

source_name: SMY257 including GCN4 at the t20 minute timepoint


title: SMY257_GCN4_t10

source_name: SMY257 including GCN4 at the t10 minute timepoint


title: 6C3-N715-S506_S144


title: SMY257_GCN4_t5

source_name: SMY257 including GCN4 at the t5 minute timepoint


title: 6C3-N715-S505_S132

source_name: Long Bones


title: SMY156n_GZF3_N_t15

source_name: SMY156n inducing GZF3 with estradiol at t15 minute timepoint


title: SMY156n_GZF3_N_t5

source_name: SMY156n inducing GZF3 with estradiol at t5 minute timepoint


title: 6C3-N715-S503_S120


title: SMY57_HAP1_t60

source_name: SMY57 inducing HAP1 at t60 min


title: SMY57_HAP1_t90

source_name: SMY57 inducing HAP1 at t90min


title: SMY156_GZF3_P_t90

source_name: SMY156 inducing GZF3 with estradiol at t90 minute timepoint


title: 6C3-N715-S502_S108


title: SMY156n_GZF3_N_t0

source_name: SMY156n inducing GZF3 with estradiol at t0 minute timepoint


title: 6C3-N714-S508_S167


title: 6C3-N714-S510_S179


title: 6C3-N714-S507_S155


title: SMY57_HAP1_t30

source_name: SMY57 inducing HAP1 at t30 min


title: SMY156_GZF3_P_t30

source_name: SMY156 inducing GZF3 with estradiol at t30 minute timepoint


title: SMY156_GZF3_P_t15

source_name: SMY156 inducing GZF3 with estradiol at t15 minute timepoint


title: SMY156_GZF3_P_t5

source_name: SMY156 inducing GZF3 with estradiol at t5 minute timepoint


title: SMY156_GZF3_P_t45

source_name: SMY156 inducing GZF3 with estradiol at t45 minute timepoint


title: SMY57_HAP1_t15

source_name: SMY57 inducing HAP1 at t15 min


title: SMY257_GCN4_t15

source_name: SMY257 including GCN4 at the t15 minute timepoint


title: 6C3-N714-S506_S143


title: SMY57_HAP1_t0_rep

source_name: SMY57 inducing HAP1 at t0 replicate


title: SMY257_GCN4_t0

source_name: SMY257 including GCN4 at the t0 minute timepoint


title: SMY156_GZF3_P_t0

source_name: SMY156 inducing GZF3 with estradiol at t0 minute timepoint


title: SMY57_HAP1_t0

source_name: SMY57 inducing HAP1 at t0


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A04_100046]

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

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.

value: male

tag: hospital

value: amc

tag: subject

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

value: +6 hours

tag: stem cell dose

value: low


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A02_100086]

value: high


title: 6C3-N714-S505_S131

source_name: Long Bones


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A01_100114]

value: +4 hours

value: placebo


title: SMY10_GEV_t90

source_name: SMY10 inducing GEV with estradiol at t90 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A03_100056]


title: 6C3-N714-S502_S107


title: SMY10_GEV_t60

source_name: SMY10 inducing GEV with estradiol at t60 minute timepoint


title: 6C3-N712-S511_S190


title: SMY10_GEV_t30

source_name: SMY10 inducing GEV with estradiol at t30 minute timepoint


title: 6C3-N712-S510_S178


title: SMY10_GEV_t45

source_name: SMY10 inducing GEV with estradiol at t45 minute timepoint


title: SMY10_GEV_t18

source_name: SMY10 inducing GEV with estradiol at t18 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H08_100042]

value: +2 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H10_100220]

value: 0 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H09_10023B]

value: -24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H12_10020B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H07_100044]


title: 6C3-N714-S503_S119


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H11_100262]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H05_100292]


title: 6C3-N712-S508_S166


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H06_1002824_2]

value: +24 hours


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H03_100112]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H04_100052]


title: SMY10_GEV_t5

source_name: SMY10 inducing GEV with estradiol at t5 minute timepoint


title: SMY10_GEV_t2.5

source_name: SMY10 inducing GEV with estradiol at t2.5 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G10_100294]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H02_100104]

value: medium


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H01_100060]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G11_100202]


title: SMY10_GEV_t0

source_name: SMY10 inducing GEV with estradiol at t0 minute timepoint


title: 6C3-N712-S505_S130


title: 6C3-N712-S506_S142


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G09_100256]


title: 6C3-N712-S507_S154


title: 6C3-N712-S503_S118


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G07_10031B]


title: SMY19_MET4_t90

source_name: SMY19 inducing MET4 with estradiol at t90 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G06_10028B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G05_100134]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G08_10024B]


title: 6C3-N712-S502_S106


title: SMY19_MET4_t30

source_name: SMY19 inducing MET4 with estradiol at t30 minute timepoint


title: SMY19_MET4_t60

source_name: SMY19 inducing MET4 with estradiol at t60 minute timepoint


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G03_100190]

value: umc


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_G04_10029B]


title: human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F12_100192]


title: 6C3-N711-S510_S177


title: CSP-N718-S520_S254

description: CSP


title: 6C3-N711-S508_S165