title: Single U2OS cell P14_355


title: Single U2OS cell P13_357

status: Public on Dec 11 2020

type: SRA

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

country: Sweden

institute: KTH Royal Institute of Technology

library_source: transcriptomic

data_processing:
Alignment and quantification were performed with RSEM (version 1.3.2-0) using STAR (version 2.7.0f-0.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: Comma-delimited files with TPM or counts for all samples or for all ERCC spike-in sequences.
Supplementary_files_format_and_content: fucci_coords.csv: Comma-delimited file includes FACS intensities and postprocessing from those intensities.

molecule: polyA RNA

organism: Homo sapiens

source_name: Single U2OS human cell

growth_protocol: U-2 OS FUCCI cells were kindly provided by Dr. Miyawaki. These cells are endogenously tagged with two fluorescent proteins fused to cell cycle regulators to allow cell cycle monitoring; CDT1 (mKO2-hCdt1+) accumulates in G1 phase, while Geminin (mAG-hGem+) accumulates in S and G2 phases. Cells expressing FUCCI probes are divided into red mKO2(+)mAG(-), yellow mKO2(+)mAG(+), and green mKO2(-)mAG(+) emitting populations. The cells were cultivated in Petri dishes at 37 °C in a 5.0 % CO2 humidified environment in McCoy’s 5A (modified) medium GlutaMAX supplement, (ThermoFisher, 36600021, MA, USA) supplemented with 10% fetal bovine serum (FBS, VWR, Radnor, PA, USA) without antibiotics. The cells were maintained sub-confluent and harvested by trypsinization at log-phase growth (60% confluency) for subsequent analysis.

extract_protocol:
We used the polyA-RNA extraction method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013.
We used the cDNA library preparation method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013, along with ERCC spike-in sequences.

tag: cell cycle phase

tag: cell line


title: Single U2OS cell P14_356


title: Single U2OS cell P12_357


title: Single U2OS cell P13_356


title: Single U2OS cell P12_356


title: Single U2OS cell P12_355


title: Single U2OS cell P13_355


title: Single U2OS cell P11_355


title: Single U2OS cell P11_356


title: Single U2OS cell P11_357


title: Single U2OS cell P10_355


title: Single U2OS cell P14_357


title: Single U2OS cell P17_356


title: Single U2OS cell P10_356


title: Single U2OS cell O9_356

value: S-ph


title: Single U2OS cell O8_357


title: Single U2OS cell O9_357


title: Single U2OS cell O8_356


title: Single U2OS cell O8_355


title: Single U2OS cell P15_356


title: Single U2OS cell O7_357


title: Single U2OS cell O7_356


title: Single U2OS cell P15_355


title: Single U2OS cell O6_356


title: Single U2OS cell O6_357


title: Single U2OS cell O6_355


title: Single U2OS cell O7_355


title: Single U2OS cell O5_356


title: Single U2OS cell O5_355


title: Single U2OS cell O4_357


title: Single U2OS cell O3_356


title: Single U2OS cell O3_357


title: Single U2OS cell O4_356


title: Single U2OS cell O2_357


title: Single U2OS cell O3_355


title: Single U2OS cell O24_357


title: Single U2OS cell O9_355


title: Single U2OS cell P10_357


title: Single U2OS cell O24_356


title: Single U2OS cell O2_355


title: Single U2OS cell O24_355


title: Single U2OS cell O23_355


title: Single U2OS cell O22_355


title: Single U2OS cell O23_356


title: Single U2OS cell O21_357


title: Single U2OS cell O23_357


title: Single U2OS cell O22_356


title: Single U2OS cell O5_357


title: Single U2OS cell O21_355


title: Single U2OS cell O21_356


title: Single U2OS cell O20_357


title: Single U2OS cell O20_355


title: Single U2OS cell O1_357


title: Single U2OS cell O4_355


title: Single U2OS cell O1_356


title: Single U2OS cell O1_355


title: Single U2OS cell O2_356


title: Single U2OS cell O20_356


title: Single U2OS cell O18_356


title: Single U2OS cell O19_356


title: Single U2OS cell O19_355


title: Single U2OS cell O18_357


title: Single U2OS cell O17_356


title: Single U2OS cell O17_357


title: Single U2OS cell O22_357


title: Single U2OS cell O18_355


title: Single U2OS cell O16_357


title: Single U2OS cell O16_356


title: Single U2OS cell O15_357


title: Single U2OS cell O17_355


title: Single U2OS cell O15_356


title: Single U2OS cell O15_355


title: Single U2OS cell O14_356


title: Single U2OS cell O14_355


title: Single U2OS cell O13_356


title: Single U2OS cell O12_357


title: Single U2OS cell O13_355


title: Single U2OS cell O12_356


title: Single U2OS cell O12_355


title: Single U2OS cell O13_357


title: Single U2OS cell O11_357


title: Single U2OS cell O19_357


title: Single U2OS cell O10_357


title: Single U2OS cell O11_355


title: Single U2OS cell O10_356


title: Single U2OS cell O10_355


title: Single U2OS cell N9_356


title: Single U2OS cell O16_355


title: Single U2OS cell N8_356


title: Single U2OS cell N8_355


title: Single U2OS cell N7_356


title: Single U2OS cell N7_357


title: Single U2OS cell N9_355


title: Single U2OS cell N9_357


title: Single U2OS cell N8_357


title: Single U2OS cell O14_357


title: Single U2OS cell N5_356


title: Single U2OS cell N6_357


title: Single U2OS cell N6_355


title: Single U2OS cell N5_357


title: Single U2OS cell N5_355


title: Single U2OS cell N4_357


title: Single U2OS cell N6_356


title: Single U2OS cell O11_356


title: Single U2OS cell N4_356


title: Single U2OS cell N3_355


title: Single U2OS cell N3_356


title: Single U2OS cell N4_355


title: Single U2OS cell N2_357


title: Single U2OS cell N3_357


title: Single U2OS cell N2_356


title: Single U2OS cell N2_355


title: Single U2OS cell N24_356


title: Single U2OS cell N24_357


title: Single U2OS cell N24_355


title: Single U2OS cell N23_357


title: Single U2OS cell N7_355


title: Single U2OS cell N23_356


title: Single U2OS cell N22_355


title: Single U2OS cell N22_356


title: Single U2OS cell N21_357


title: Single U2OS cell N21_355


title: Single U2OS cell N23_355


title: Single U2OS cell N1_357


title: Single U2OS cell N1_356


title: Single U2OS cell N1_355


title: Single U2OS cell N19_357


title: Single U2OS cell N19_356


title: Single U2OS cell N20_356


title: Single U2OS cell N18_356


title: Single U2OS cell N17_355


title: Single U2OS cell N19_355


title: Single U2OS cell N16_357


title: Single U2OS cell N17_357


title: Single U2OS cell N18_355


title: Single U2OS cell N20_357


title: Single U2OS cell N16_356


title: Single U2OS cell N16_355


title: Single U2OS cell N15_355


title: Single U2OS cell N21_356


title: Single U2OS cell N14_357


title: Single U2OS cell N14_356


title: Single U2OS cell N15_356


title: Single U2OS cell N14_355


title: Single U2OS cell N13_355


title: Single U2OS cell N13_357


title: Single U2OS cell N13_356


title: Single U2OS cell N12_357


title: Single U2OS cell N12_356


title: Single U2OS cell N11_357


title: Single U2OS cell N11_356


title: Single U2OS cell N11_355


title: Single U2OS cell N10_357


title: Single U2OS cell N10_356


title: Single U2OS cell N10_355


title: Single U2OS cell N15_357


title: Single U2OS cell M9_357


title: Single U2OS cell M8_357


title: Single U2OS cell M9_356


title: Single U2OS cell M9_355


title: Single U2OS cell M7_357


title: Single U2OS cell M8_356


title: Single U2OS cell M7_356


title: Single U2OS cell M7_355


title: Single U2OS cell M6_357

value: NotAssigned


title: Single U2OS cell M6_355


title: Single U2OS cell M8_355


title: Single U2OS cell M6_356


title: Single U2OS cell M5_357


title: Single U2OS cell M5_355


title: Single U2OS cell M5_356


title: Single U2OS cell M4_357


title: Single U2OS cell M4_356


title: Single U2OS cell N12_355


title: Single U2OS cell M4_355


title: Single U2OS cell M3_357


title: Single U2OS cell M3_356


title: Single U2OS cell M3_355


title: Single U2OS cell M2_356


title: Single U2OS cell M2_355


title: Single U2OS cell M24_357


title: Single U2OS cell M24_356


title: Single U2OS cell M22_357


title: Single U2OS cell M22_356


title: Single U2OS cell M24_355


title: Single U2OS cell M23_357


title: Single U2OS cell M23_355


title: Single U2OS cell M23_356


title: Single U2OS cell M20_355


title: Single U2OS cell M21_357


title: Single U2OS cell M1_357


title: Single U2OS cell M22_355


title: Single U2OS cell M21_355


title: Single U2OS cell M20_357


title: Single U2OS cell M2_357


title: Single U2OS cell M19_357


title: Single U2OS cell M19_356


title: Single U2OS cell M18_357


title: Single U2OS cell M18_356


title: Single U2OS cell M17_356


title: Single U2OS cell M18_355


title: Single U2OS cell M21_356


title: Single U2OS cell M20_356


title: Single U2OS cell M1_356


title: Single U2OS cell M16_357


title: Single U2OS cell M17_355


title: Single U2OS cell M15_355


title: Single U2OS cell M15_356


title: Single U2OS cell M15_357


title: Single U2OS cell M1_355


title: Single U2OS cell M16_355


title: Single U2OS cell M14_357


title: Single U2OS cell M14_355


title: Single U2OS cell M14_356


title: Single U2OS cell M13_356


title: Single U2OS cell M13_357


title: Single U2OS cell M17_357


title: Single U2OS cell M19_355


title: Single U2OS cell N22_357


title: Single U2OS cell M13_355


title: Single U2OS cell M12_356


title: Single U2OS cell M12_357


title: Single U2OS cell M12_355


title: Single U2OS cell M11_355


title: Single U2OS cell M16_356


title: Single U2OS cell M10_357


title: Single U2OS cell M10_356


title: Single U2OS cell M11_357


title: Single U2OS cell L8_357


title: Single U2OS cell L9_356


title: Single U2OS cell L7_356


title: Single U2OS cell L7_357


title: Single U2OS cell L9_355


title: Single U2OS cell L8_355


title: Single U2OS cell M10_355


title: Single U2OS cell L7_355


title: Single U2OS cell L6_357


title: Single U2OS cell L6_356


title: Single U2OS cell L6_355


title: Single U2OS cell L9_357


title: Single U2OS cell L5_357


title: Single U2OS cell L5_356


title: Single U2OS cell L5_355


title: Single U2OS cell L4_357


title: Single U2OS cell L3_356


title: Single U2OS cell L4_356


title: Single U2OS cell L3_357


title: Single U2OS cell M11_356


title: Single U2OS cell L4_355


title: Single U2OS cell L3_355


title: Single U2OS cell L2_357


title: Single U2OS cell L2_356


title: Single U2OS cell L24_357


title: Single U2OS cell L2_355


title: Single U2OS cell L8_356


title: Single U2OS cell L24_355


title: Single U2OS cell L22_357


title: Single U2OS cell L22_355


title: Single U2OS cell L23_356


title: Single U2OS cell L24_356


title: Single U2OS cell L23_357


title: Single U2OS cell L21_357


title: Single U2OS cell L23_355


title: Single U2OS cell L22_356


title: Single U2OS cell L20_356


title: Single U2OS cell L20_357


title: Single U2OS cell L21_356


title: Single U2OS cell L1_357


title: Single U2OS cell L20_355


title: Single U2OS cell L21_355


title: Single U2OS cell L1_356


title: Single U2OS cell L1_355


title: Single U2OS cell N18_357


title: Single U2OS cell L18_355


title: Single U2OS cell L17_357


title: Single U2OS cell L19_357


title: Single U2OS cell L18_356


title: Single U2OS cell L18_357


title: Single U2OS cell L17_356


title: Single U2OS cell L19_355


title: Single U2OS cell L17_355


title: Single U2OS cell L19_356


title: Single U2OS cell L16_357


title: Single U2OS cell L16_356


title: Single U2OS cell L16_355


title: Single U2OS cell N17_356


title: Single U2OS cell L15_356


title: Single U2OS cell L14_355


title: Single U2OS cell L13_356


title: Single U2OS cell L14_356


title: Single U2OS cell L13_357


title: Single U2OS cell L13_355


title: Single U2OS cell L12_355


title: Single U2OS cell L11_357


title: Single U2OS cell L12_356


title: Single U2OS cell L11_356


title: Single U2OS cell N20_355


title: Single U2OS cell L12_357


title: Single U2OS cell L10_356


title: Single U2OS cell K8_356


title: Single U2OS cell L10_355


title: Single U2OS cell K9_355


title: Single U2OS cell K8_355


title: Single U2OS cell L10_357


title: Single U2OS cell K9_356


title: Single U2OS cell K9_357


title: Single U2OS cell L15_355


title: Single U2OS cell L15_357


title: Single U2OS cell K7_356


title: Single U2OS cell K6_357


title: Single U2OS cell K6_355


title: Single U2OS cell K6_356


title: Single U2OS cell K7_355


title: Single U2OS cell K7_357


title: Single U2OS cell L14_357


title: Single U2OS cell K5_357


title: Single U2OS cell K5_356


title: Single U2OS cell K4_355


title: Single U2OS cell K4_357


title: Single U2OS cell K3_356


title: Single U2OS cell K4_356


title: Single U2OS cell K3_357


title: Single U2OS cell K3_355


title: Single U2OS cell K2_356


title: Single U2OS cell K8_357


title: Single U2OS cell L11_355


title: Single U2OS cell K2_355


title: Single U2OS cell K22_357


title: Single U2OS cell K24_355


title: Single U2OS cell K23_355


title: Single U2OS cell K24_357


title: Single U2OS cell K23_356


title: Single U2OS cell K22_356


title: Single U2OS cell K22_355


title: Single U2OS cell K21_356


title: Single U2OS cell K20_357


title: Single U2OS cell K20_356


title: Single U2OS cell K21_355


title: Single U2OS cell K23_357


title: Single U2OS cell K21_357


title: Single U2OS cell K5_355


title: Single U2OS cell K20_355


title: Single U2OS cell K1_357


title: Single U2OS cell K19_356


title: Single U2OS cell K19_355


title: Single U2OS cell K1_356


title: Single U2OS cell K1_355


title: Single U2OS cell K19_357


title: Single U2OS cell K2_357


title: Single U2OS cell K18_357


title: Single U2OS cell K17_357


title: Single U2OS cell K17_355


title: Single U2OS cell K24_356


title: Single U2OS cell K16_357


title: Single U2OS cell K17_356


title: Single U2OS cell K15_357


title: Single U2OS cell K18_355


title: Single U2OS cell K16_356


title: Single U2OS cell K14_357


title: Single U2OS cell K16_355


title: Single U2OS cell K13_357


title: Single U2OS cell K13_356


title: Single U2OS cell K15_355


title: Single U2OS cell K12_357


title: Single U2OS cell K12_356


title: Single U2OS cell K12_355


title: Single U2OS cell K11_357


title: Single U2OS cell K13_355


title: Single U2OS cell K14_356


title: Single U2OS cell K11_356


title: Single U2OS cell K10_357


title: Single U2OS cell K11_355


title: Single U2OS cell J9_357


title: Single U2OS cell K10_355


title: Single U2OS cell K10_356


title: Single U2OS cell J9_356


title: Single U2OS cell J8_357


title: Single U2OS cell J9_355


title: Single U2OS cell K18_356


title: Single U2OS cell J8_356


title: Single U2OS cell K15_356


title: Single U2OS cell J8_355


title: Single U2OS cell J7_357


title: Single U2OS cell J7_356


title: Single U2OS cell J6_357


title: Single U2OS cell J7_355


title: Single U2OS cell J6_355


title: Single U2OS cell K14_355


title: Single U2OS cell J5_357


title: Single U2OS cell J5_356


title: Single U2OS cell J4_357


title: Single U2OS cell J4_356


title: Single U2OS cell J4_355


title: Single U2OS cell J2_357


title: Single U2OS cell J3_356


title: Single U2OS cell J3_355


title: Single U2OS cell J2_355


title: Single U2OS cell J3_357


title: Single U2OS cell J24_356


title: Single U2OS cell J2_356


title: Single U2OS cell J24_357


title: Single U2OS cell J23_356


title: Single U2OS cell J22_355


title: Single U2OS cell J21_357


title: Single U2OS cell J21_356


title: Single U2OS cell J6_356


title: Single U2OS cell J22_356


title: Single U2OS cell J24_355


title: Single U2OS cell J21_355


title: Single U2OS cell J22_357


title: Single U2OS cell J20_356


title: Single U2OS cell J20_355


title: Single U2OS cell J1_357


title: Single U2OS cell J1_355


title: Single U2OS cell J20_357


title: Single U2OS cell J5_355


title: Single U2OS cell J1_356


title: Single U2OS cell J19_357


title: Single U2OS cell J19_356


title: Single U2OS cell J19_355


title: Single U2OS cell J18_357


title: Single U2OS cell J17_357


title: Single U2OS cell J18_355


title: Single U2OS cell J23_355


title: Single U2OS cell J16_357


title: Single U2OS cell J23_357


title: Single U2OS cell J17_355


title: Single U2OS cell J17_356


title: Single U2OS cell J18_356


title: Single U2OS cell J16_355


title: Single U2OS cell J16_356


title: Single U2OS cell J15_357


title: Single U2OS cell J15_356


title: Single U2OS cell J14_357


title: Single U2OS cell J14_355


title: Single U2OS cell J14_356


title: Single U2OS cell J13_356


title: Single U2OS cell J15_355


title: Single U2OS cell J13_355


title: Single U2OS cell J12_357


title: Single U2OS cell J12_355


title: Single U2OS cell J11_355


title: Single U2OS cell J11_357


title: Single U2OS cell J11_356


title: Single U2OS cell J10_356


title: Single U2OS cell J10_357


title: Single U2OS cell I9_356


title: Single U2OS cell I9_357


title: Single U2OS cell I9_355


title: Single U2OS cell I8_357


title: Single U2OS cell I8_356


title: Single U2OS cell I7_357


title: Single U2OS cell I7_355


title: Single U2OS cell I7_356


title: Single U2OS cell I8_355


title: Single U2OS cell I6_356


title: Single U2OS cell I6_357


title: Single U2OS cell I6_355


title: Single U2OS cell I5_357


title: Single U2OS cell I4_357


title: Single U2OS cell I5_355


title: Single U2OS cell I4_356


title: Single U2OS cell I5_356


title: Single U2OS cell J13_357


title: Single U2OS cell I4_355


title: Single U2OS cell I3_356


title: Single U2OS cell J12_356


title: Single U2OS cell I3_357


title: Single U2OS cell I2_356


title: Single U2OS cell J10_355


title: Single U2OS cell I24_357


title: Single U2OS cell I24_356


title: Single U2OS cell I2_357


title: Single U2OS cell I24_355


title: Single U2OS cell I23_356


title: Single U2OS cell I23_355


title: Single U2OS cell I23_357


title: Single U2OS cell I22_357


title: Single U2OS cell I22_356


title: Single U2OS cell I22_355


title: Single U2OS cell I21_355


title: Single U2OS cell I21_357


title: Single U2OS cell I20_357


title: Single U2OS cell I21_356


title: Single U2OS cell I20_355


title: Single U2OS cell I20_356


title: Single U2OS cell I3_355


title: Single U2OS cell I1_355


title: Single U2OS cell I1_357


title: Single U2OS cell I19_357


title: Single U2OS cell I18_355


title: Single U2OS cell I1_356


title: Single U2OS cell I18_357


title: Single U2OS cell I19_356


title: Single U2OS cell I2_355


title: Single U2OS cell I17_357


title: Single U2OS cell I19_355


title: Single U2OS cell I17_356


title: Single U2OS cell I17_355


title: Single U2OS cell I18_356


title: Single U2OS cell I16_355


title: Single U2OS cell I16_357


title: Single U2OS cell I15_357


title: Single U2OS cell I14_357


title: Single U2OS cell I14_355


title: Single U2OS cell I13_357


title: Single U2OS cell I12_356


title: Single U2OS cell I12_355


title: Single U2OS cell I11_357


title: Single U2OS cell I11_356


title: Single U2OS cell H9_357


title: Single U2OS cell I16_356


title: Single U2OS cell I10_357


title: Single U2OS cell I10_355


title: Single U2OS cell I15_355


title: Single U2OS cell I10_356


title: Single U2OS cell I11_355


title: Single U2OS cell I15_356


title: Single U2OS cell H7_356


title: Single U2OS cell H9_355


title: Single U2OS cell H8_356


title: Single U2OS cell H7_357


title: Single U2OS cell H8_355


title: Single U2OS cell H6_357


title: Single U2OS cell H6_356


title: Single U2OS cell H8_357


title: Single U2OS cell H6_355


title: Single U2OS cell I14_356


title: Single U2OS cell I12_357


title: Single U2OS cell H5_357


title: Single U2OS cell I13_356


title: Single U2OS cell I13_355


title: Single U2OS cell H5_356


title: Single U2OS cell H4_357


title: Single U2OS cell H4_356


title: Single U2OS cell H9_356


title: Single U2OS cell H5_355


title: Single U2OS cell H7_355


title: Single U2OS cell H3_357


title: Single U2OS cell H4_355


title: Single U2OS cell H3_356


title: Single U2OS cell H2_357


title: Single U2OS cell H2_356


title: Single U2OS cell H2_355


title: Single U2OS cell H23_357


title: Single U2OS cell H20_357


title: Single U2OS cell H22_357


title: Single U2OS cell H24_357


title: Single U2OS cell H24_356


title: Single U2OS cell H23_355


title: Single U2OS cell H24_355


title: Single U2OS cell H23_356


title: Single U2OS cell H21_355


title: Single U2OS cell H22_356


title: Single U2OS cell H21_356


title: Single U2OS cell H21_357


title: Single U2OS cell H20_356


title: Single U2OS cell H1_357


title: Single U2OS cell H1_355


title: Single U2OS cell H1_356


title: Single U2OS cell H19_357


title: Single U2OS cell H18_356


title: Single U2OS cell H18_357


title: Single U2OS cell H18_355


title: Single U2OS cell H19_355


title: Single U2OS cell H3_355


title: Single U2OS cell H17_357


title: Single U2OS cell H19_356


title: Single U2OS cell H17_355


title: Single U2OS cell H16_356


title: Single U2OS cell H22_355


title: Single U2OS cell H15_355


title: Single U2OS cell H17_356


title: Single U2OS cell H16_355


title: Single U2OS cell H12_357


title: Single U2OS cell H15_356


title: Single U2OS cell H15_357


title: Single U2OS cell H12_355


title: Single U2OS cell H14_356


title: Single U2OS cell H14_355


title: Single U2OS cell H13_356


title: Single U2OS cell H13_357


title: Single U2OS cell H12_356


title: Single U2OS cell H13_355


title: Single U2OS cell H11_356


title: Single U2OS cell H11_355


title: Single U2OS cell H11_357


title: Single U2OS cell H10_357


title: Single U2OS cell H16_357


title: Single U2OS cell G9_357


title: Single U2OS cell G8_357


title: Single U2OS cell G9_355


title: Single U2OS cell H10_356


title: Single U2OS cell H10_355


title: Single U2OS cell G9_356


title: Single U2OS cell G7_357


title: Single U2OS cell G8_356


title: Single U2OS cell H14_357


title: Single U2OS cell H20_355


title: Single U2OS cell G7_356


title: Single U2OS cell G7_355


title: Single U2OS cell G6_355


title: Single U2OS cell G6_356


title: Single U2OS cell G5_355


title: Single U2OS cell G5_357


title: Single U2OS cell G6_357


title: Single U2OS cell G5_356


title: Single U2OS cell G4_357


title: Single U2OS cell G4_356


title: Single U2OS cell G2_357


title: Single U2OS cell G3_357


title: Single U2OS cell G2_356


title: Single U2OS cell G3_356


title: Single U2OS cell G2_355


title: Single U2OS cell G8_355


title: Single U2OS cell G24_356


title: Single U2OS cell G24_357


title: Single U2OS cell G24_355


title: Single U2OS cell G4_355


title: Single U2OS cell G22_355


title: Single U2OS cell G23_356


title: Single U2OS cell G22_357


title: Single U2OS cell G22_356


title: Single U2OS cell G23_355


title: Single U2OS cell G21_356


title: Single U2OS cell G21_355


title: Single U2OS cell G20_356


title: Single U2OS cell G20_355


title: Single U2OS cell G1_356


title: Single U2OS cell G1_355


title: Single U2OS cell G1_357


title: Single U2OS cell G19_357


title: Single U2OS cell G19_355


title: Single U2OS cell G18_356


title: Single U2OS cell G17_355


title: Single U2OS cell G18_357


title: Single U2OS cell G17_357


title: Single U2OS cell G19_356


title: Single U2OS cell G16_357


title: Single U2OS cell G23_357


title: Single U2OS cell G21_357


title: Single U2OS cell G15_357


title: Single U2OS cell G16_356


title: Single U2OS cell G14_356


title: Single U2OS cell G15_355


title: Single U2OS cell G14_357


title: Single U2OS cell G15_356


title: Single U2OS cell G13_357


title: Single U2OS cell G13_356


title: Single U2OS cell G14_355


title: Single U2OS cell G13_355


title: Single U2OS cell G12_357


title: Single U2OS cell G20_357


title: Single U2OS cell G3_355


title: Single U2OS cell G12_355


title: Single U2OS cell G11_357


title: Single U2OS cell G12_356


title: Single U2OS cell G18_355


title: Single U2OS cell G11_356


title: Single U2OS cell G17_356


title: Single U2OS cell G10_357


title: Single U2OS cell G10_355


title: Single U2OS cell G11_355


title: Single U2OS cell F9_357


title: Single U2OS cell F9_356


title: Single U2OS cell G16_355


title: Single U2OS cell F8_355


title: Single U2OS cell F7_357


title: Single U2OS cell G10_356


title: Single U2OS cell F7_356


title: Single U2OS cell F9_355


title: Single U2OS cell F6_357


title: Single U2OS cell F8_356


title: Single U2OS cell F7_355


title: Single U2OS cell F6_356


title: Single U2OS cell F4_356


title: Single U2OS cell F5_357


title: Single U2OS cell F6_355


title: Single U2OS cell F3_356


title: Single U2OS cell F4_357


title: Single U2OS cell F3_357


title: Single U2OS cell F5_355


title: Single U2OS cell F4_355


title: Single U2OS cell F3_355


title: Single U2OS cell F8_357


title: Single U2OS cell F2_357


title: Single U2OS cell F24_357


title: Single U2OS cell F2_355


title: Single U2OS cell F2_356


title: Single U2OS cell F22_357


title: Single U2OS cell F23_355


title: Single U2OS cell F22_356


title: Single U2OS cell F23_356


title: Single U2OS cell F21_357


title: Single U2OS cell F5_356


title: Single U2OS cell F24_355


title: Single U2OS cell F21_355


title: Single U2OS cell F21_356


title: Single U2OS cell F22_355


title: Single U2OS cell F20_355


title: Single U2OS cell F20_357


title: Single U2OS cell F20_356


title: Single U2OS cell F1_357


title: Single U2OS cell F1_355


title: Single U2OS cell F18_357


title: Single U2OS cell F23_357


title: Single U2OS cell F19_356


title: Single U2OS cell F24_356


title: Single U2OS cell F18_355


title: Single U2OS cell F18_356


title: Single U2OS cell F17_356


title: Single U2OS cell F16_355


title: Single U2OS cell F16_357


title: Single U2OS cell F15_356


title: Single U2OS cell F17_355


title: Single U2OS cell F16_356


title: Single U2OS cell F15_357


title: Single U2OS cell F15_355


title: Single U2OS cell F14_355


title: Single U2OS cell F13_355


title: Single U2OS cell F13_356


title: Single U2OS cell F14_357


title: Single U2OS cell F12_357


title: Single U2OS cell F19_357


title: Single U2OS cell F12_355


title: Single U2OS cell F11_355


title: Single U2OS cell F11_356


title: Single U2OS cell F13_357


title: Single U2OS cell F11_357


title: Single U2OS cell F1_356


title: Single U2OS cell F17_357


title: Single U2OS cell F10_357


title: Single U2OS cell F10_355


title: Single U2OS cell E9_357


title: Single U2OS cell E9_355


title: Single U2OS cell F10_356


title: Single U2OS cell E8_357


title: Single U2OS cell E8_356


title: Single U2OS cell E7_356


title: Single U2OS cell E6_357


title: Single U2OS cell E7_355


title: Single U2OS cell F14_356


title: Single U2OS cell E8_355


title: Single U2OS cell E6_356


title: Single U2OS cell E6_355


title: Single U2OS cell E9_356


title: Single U2OS cell F12_356


title: Single U2OS cell E4_357


title: Single U2OS cell E5_355


title: Single U2OS cell E4_356


title: Single U2OS cell E5_356


title: Single U2OS cell E4_355


title: Single U2OS cell E7_357


title: Single U2OS cell E3_357


title: Single U2OS cell E5_357


title: Single U2OS cell E3_356


title: Single U2OS cell F19_355


title: Single U2OS cell E2_357


title: Single U2OS cell E2_356


title: Single U2OS cell E2_355


title: Single U2OS cell E24_356


title: Single U2OS cell E24_355


title: Single U2OS cell E24_357


title: Single U2OS cell E23_357


title: Single U2OS cell E3_355


title: Single U2OS cell E23_355


title: Single U2OS cell E22_357


title: Single U2OS cell E22_355


title: Single U2OS cell E22_356


title: Single U2OS cell E20_357


title: Single U2OS cell E23_356


title: Single U2OS cell E20_356


title: Single U2OS cell E21_356


title: Single U2OS cell E20_355


title: Single U2OS cell E1_357


title: Single U2OS cell E19_357


title: Single U2OS cell E18_357


title: Single U2OS cell E17_357


title: Single U2OS cell E19_355


title: Single U2OS cell E18_356


title: Single U2OS cell E19_356


title: Single U2OS cell E17_356


title: Single U2OS cell E17_355


title: Single U2OS cell E16_357


title: Single U2OS cell E16_355


title: Single U2OS cell E16_356


title: Single U2OS cell E15_355


title: Single U2OS cell E15_356


title: Single U2OS cell E21_355


title: Single U2OS cell E14_357


title: Single U2OS cell E1_355


title: Single U2OS cell E15_357


title: Single U2OS cell E13_357


title: Single U2OS cell E21_357


title: Single U2OS cell E14_355


title: Single U2OS cell E1_356


title: Single U2OS cell E11_357


title: Single U2OS cell E12_357


title: Single U2OS cell E13_355


title: Single U2OS cell E11_356


title: Single U2OS cell E12_356


title: Single U2OS cell E18_355


title: Single U2OS cell E10_357


title: Single U2OS cell E11_355


title: Single U2OS cell E12_355


title: Single U2OS cell D9_357


title: Single U2OS cell D8_357


title: Single U2OS cell D9_355


title: Single U2OS cell E10_356


title: Single U2OS cell E14_356


title: Single U2OS cell D8_356


title: Single U2OS cell D7_357


title: Single U2OS cell D7_356


title: Single U2OS cell D6_357


title: Single U2OS cell D9_356


title: Single U2OS cell D6_356


title: Single U2OS cell D6_355


title: Single U2OS cell E13_356


title: Single U2OS cell D5_357


title: Single U2OS cell D5_356


title: Single U2OS cell D5_355


title: Single U2OS cell D4_356


title: Single U2OS cell D4_355


title: Single U2OS cell D3_357


title: Single U2OS cell D3_356


title: Single U2OS cell D4_357


title: Single U2OS cell D2_357


title: Single U2OS cell D2_356


title: Single U2OS cell D3_355


title: Single U2OS cell E10_355


title: Single U2OS cell D24_356


title: Single U2OS cell D23_357


title: Single U2OS cell D23_356


title: Single U2OS cell D8_355


title: Single U2OS cell D7_355


title: Single U2OS cell D22_356


title: Single U2OS cell D22_357


title: Single U2OS cell D24_357


title: Single U2OS cell D21_356


title: Single U2OS cell D22_355


title: Single U2OS cell D1_356


title: Single U2OS cell D1_357


title: Single U2OS cell D1_355


title: Single U2OS cell D19_357


title: Single U2OS cell D19_355


title: Single U2OS cell D20_355


title: Single U2OS cell D19_356


title: Single U2OS cell D2_355


title: Single U2OS cell D18_355


title: Single U2OS cell D18_356


title: Single U2OS cell D24_355


title: Single U2OS cell D23_355


title: Single U2OS cell D17_356


title: Single U2OS cell D18_357


title: Single U2OS cell D17_355


title: Single U2OS cell D17_357


title: Single U2OS cell D16_357


title: Single U2OS cell D16_355


title: Single U2OS cell D16_356


title: Single U2OS cell D21_357


title: Single U2OS cell D15_356


title: Single U2OS cell D15_357


title: Single U2OS cell D15_355


title: Single U2OS cell D14_356


title: Single U2OS cell D21_355


title: Single U2OS cell D14_355


title: Single U2OS cell D14_357


title: Single U2OS cell D20_357


title: Single U2OS cell D20_356


title: Single U2OS cell D13_356


title: Single U2OS cell D13_355


title: Single U2OS cell D12_357


title: Single U2OS cell D13_357


title: Single U2OS cell D12_355


title: Single U2OS cell D11_356


title: Single U2OS cell D11_355


title: Single U2OS cell D12_356


title: Single U2OS cell D10_357


title: Single U2OS cell D10_356


title: Single U2OS cell D10_355


title: Single U2OS cell D11_357


title: Single U2OS cell C9_356


title: Single U2OS cell C8_355


title: Single U2OS cell C8_356


title: Single U2OS cell C7_357


title: Single U2OS cell C7_356


title: Single U2OS cell C9_357


title: Single U2OS cell C9_355


title: Single U2OS cell C6_357


title: Single U2OS cell C8_357


title: Single U2OS cell C6_355


title: Single U2OS cell C5_357


title: Single U2OS cell C5_356


title: Single U2OS cell C5_355


title: Single U2OS cell C4_357


title: Single U2OS cell C3_357


title: Single U2OS cell C3_355


title: Single U2OS cell C7_355


title: Single U2OS cell C4_356


title: Single U2OS cell C3_356


title: Single U2OS cell C2_357


title: Single U2OS cell C24_357


title: Single U2OS cell C2_355


title: Single U2OS cell C24_356


title: Single U2OS cell C24_355


title: Single U2OS cell C23_357


title: Single U2OS cell C2_356


title: Single U2OS cell C23_356


title: Single U2OS cell C22_357


title: Single U2OS cell C22_356


title: Single U2OS cell C6_356


title: Single U2OS cell C23_355


title: Single U2OS cell C21_357


title: Single U2OS cell C22_355


title: Single U2OS cell C20_357


title: Single U2OS cell C21_355


title: Single U2OS cell C20_356


title: Single U2OS cell C1_357


title: Single U2OS cell C1_355


title: Single U2OS cell C1_356


title: Single U2OS cell C19_357


title: Single U2OS cell C21_356


title: Single U2OS cell C20_355


title: Single U2OS cell C18_357


title: Single U2OS cell C18_356


title: Single U2OS cell C17_357


title: Single U2OS cell C18_355


title: Single U2OS cell C19_356


title: Single U2OS cell C17_355


title: Single U2OS cell C17_356


title: Single U2OS cell C16_357


title: Single U2OS cell C15_357


title: Single U2OS cell C16_356


title: Single U2OS cell C16_355


title: Single U2OS cell C15_356


title: Single U2OS cell C19_355


title: Single U2OS cell C14_357


title: Single U2OS cell C13_357


title: Single U2OS cell C14_356


title: Single U2OS cell C14_355


title: Single U2OS cell C15_355


title: Single U2OS cell C13_355


title: Single U2OS cell C12_356


title: Single U2OS cell C12_355


title: Single U2OS cell C11_355


title: Single U2OS cell C11_357


title: Single U2OS cell C11_356


title: Single U2OS cell C10_357


title: Single U2OS cell B9_356


title: Single U2OS cell B9_355


title: Single U2OS cell C10_355


title: Single U2OS cell B8_355


title: Single U2OS cell B8_357


title: Single U2OS cell B9_357


title: Single U2OS cell B6_357


title: Single U2OS cell B6_355


title: Single U2OS cell B6_356


title: Single U2OS cell C13_356


title: Single U2OS cell B7_357


title: Single U2OS cell B5_356


title: Single U2OS cell C12_357


title: Single U2OS cell B5_355


title: Single U2OS cell B8_356


title: Single U2OS cell C10_356


title: Single U2OS cell B4_355


title: Single U2OS cell B3_357


title: Single U2OS cell B3_355


title: Single U2OS cell B4_356


title: Single U2OS cell B4_357


title: Single U2OS cell B2_356


title: Single U2OS cell B2_355


title: Single U2OS cell B3_356


title: Single U2OS cell B2_357


title: Single U2OS cell B24_356


title: Single U2OS cell B7_356


title: Single U2OS cell B24_355


title: Single U2OS cell B7_355


title: Single U2OS cell B23_357


title: Single U2OS cell B23_356


title: Single U2OS cell B5_357


title: Single U2OS cell B23_355


title: Single U2OS cell B22_357


title: Single U2OS cell B22_356


title: Single U2OS cell B22_355


title: Single U2OS cell B21_356


title: Single U2OS cell B21_355


title: Single U2OS cell B20_357


title: Single U2OS cell B20_356


title: Single U2OS cell B20_355


title: Single U2OS cell B19_357


title: Single U2OS cell B1_356


title: Single U2OS cell B1_355


title: Single U2OS cell B19_355


title: Single U2OS cell B18_357


title: Single U2OS cell B19_356


title: Single U2OS cell B18_355


title: Single U2OS cell B24_357


title: Single U2OS cell B17_356


title: Single U2OS cell B17_355


title: Single U2OS cell B1_357


title: Single U2OS cell B17_357


title: Single U2OS cell B18_356


title: Single U2OS cell B16_357


title: Single U2OS cell B15_357


title: Single U2OS cell B16_355


title: Single U2OS cell B15_356


title: Single U2OS cell B21_357


title: Single U2OS cell B15_355


title: Single U2OS cell B14_357


title: Single U2OS cell B14_356


title: Single U2OS cell B14_355


title: Single U2OS cell B13_355


title: Single U2OS cell B12_357


title: Single U2OS cell B13_356


title: Single U2OS cell B12_356


title: Single U2OS cell B12_355


title: Single U2OS cell C4_355


title: Single U2OS cell B11_356


title: Single U2OS cell B11_355


title: Single U2OS cell B10_357


title: Single U2OS cell B10_356


title: Single U2OS cell B11_357


title: Single U2OS cell B10_355


title: Single U2OS cell A9_356


title: Single U2OS cell B16_356


title: Single U2OS cell A9_357


title: Single U2OS cell A7_356


title: Single U2OS cell A8_355


title: Single U2OS cell A7_355


title: Single U2OS cell A6_357


title: Single U2OS cell A6_356


title: Single U2OS cell A6_355


title: Single U2OS cell B13_357


title: Single U2OS cell A8_357


title: Single U2OS cell A5_355


title: Single U2OS cell A4_357


title: Single U2OS cell A5_357


title: Single U2OS cell A5_356


title: Single U2OS cell A3_357


title: Single U2OS cell A3_356


title: Single U2OS cell A2_357


title: Single U2OS cell A2_356


title: Single U2OS cell A3_355


title: Single U2OS cell A24_357


title: Single U2OS cell A2_355


title: Single U2OS cell A9_355


title: Single U2OS cell A8_356


title: Single U2OS cell A24_355


title: Single U2OS cell A23_357


title: Single U2OS cell A23_356


title: Single U2OS cell A22_357


title: Single U2OS cell A7_357


title: Single U2OS cell A23_355


title: Single U2OS cell A21_357


title: Single U2OS cell A22_356


title: Single U2OS cell A22_355


title: Single U2OS cell A21_356


title: Single U2OS cell A20_356


title: Single U2OS cell A4_356


title: Single U2OS cell A1_356


title: Single U2OS cell A1_357


title: Single U2OS cell A4_355


title: Single U2OS cell A20_357


title: Single U2OS cell A21_355


title: Single U2OS cell A20_355


title: Single U2OS cell A19_356


title: Single U2OS cell A19_357


title: Single U2OS cell A24_356


title: Single U2OS cell A18_357


title: Single U2OS cell A19_355


title: Single U2OS cell A18_356


title: Single U2OS cell A18_355


title: Single U2OS cell A16_356


title: Single U2OS cell A17_356


title: Single U2OS cell A1_355


title: Single U2OS cell A17_357


title: Single U2OS cell A17_355


title: Single U2OS cell A16_355


title: Single U2OS cell A15_357


title: Single U2OS cell A14_357


title: Single U2OS cell A14_355


title: Single U2OS cell A15_355


title: Single U2OS cell A13_357


title: Single U2OS cell A14_356


title: Single U2OS cell A16_357


title: Single U2OS cell A13_356


title: Single U2OS cell A15_356


title: Single U2OS cell A13_355


title: Single U2OS cell A12_357


title: Single U2OS cell A11_357


title: Single U2OS cell A11_356


title: Single U2OS cell A10_357


title: Single U2OS cell A10_356


title: Single U2OS cell A11_355


title: Single U2OS cell A10_355


title: CS23_12058_Input_ChIP-seq

status: Public on Jul 29 2020

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

country: USA

institute: Yale University

description:
CS23_12058_25state.bigBed
CS23_12058_18state.bigBed
CS23_12058_15state.bigBed
12058_DNase.imputed.bigWig
12058_H2A.Z.imputed.bigWig
12058_H3K27ac.imputed.bigWig
12058_H3K27me3.imputed.bigWig
12058_H3K36me3.imputed.bigWig
12058_H3K4me1.imputed.bigWig
12058_H3K4me2.imputed.bigWig
12058_H3K4me3.imputed.bigWig
12058_H3K79me2.imputed.bigWig
12058_H3K9ac.imputed.bigWig
12058_H3K9me3.imputed.bigWig
12058_H4K20me1.imputed.bigWig

library_source: genomic

data_processing:
Align to genome using bowtie 2.3.1
Generate bam format and normalize with samtools 1.3.1
Sort bam with samtools 1.3.1
Index bam with samtools 1.3.1
Merged bams from alignment for 3 Replicates of 2N and 4N respectively to prepare for ChromImpute
Convert to tagAlign format for size estimation of combined and single replicates
Estimate fragment size using phantompeakqualtools for combined and single replicates
Call peaks with MACS2 2.1.1.20160309 for combined and single replicates
Convert combined bedGraph to binary for ChromImpute 1.0.3
Generate global distance measurements for ChromImpute
Generate features for training
Generate trained predictors
Generate imputed signal track
Convert imputed signals to ChromHMM singal format using DeepTOOLS 2.0
Binarize imputed signals for ChromHMM
Generate Chromatin State Segmentation with ChromHMM 1.12
Generate files for UCSC genome browser based on published Roadmap Epigenome Conventions
Convert segmentation beds to bigBed format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are the imputed bigWigs that are the output imputed signal tracks from ChromImpute, bigBed files are the 25 State chromatin segmentations that come from ChromHMM

molecule: genomic DNA

source_name: Embryonic Heart Tissue

growth_protocol: Samples flash frozen immediately after collection by HDBR

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
ChIP-seq libraries were prepared using the SMARTer® ThruPLEX® DNA-seq 48S Kit,  Cat No. R400427, Takara Bio USA.

treatment_protocol: Cotney and Noonan, CSHL Protocols 2015.

tag: developmental stage

tag: chip antibody vendor

tag: antibody catalog number


title: CS23_12058_H3K36me3_ChIP-seq

value: Diagenode


title: CS23_12058_H3K27me3_ChIP-seq


title: CS23_12058_H3K9me3_ChIP-seq


title: CS23_12058_H3K27ac_ChIP-seq


title: CS23_12151_H3K36me3_ChIP-seq

description:
CS23_12151_25state.bigBed
CS23_12151_18state.bigBed
CS23_12151_15state.bigBed
12151_DNase.imputed.bigWig
12151_H2A.Z.imputed.bigWig
12151_H3K27ac.imputed.bigWig
12151_H3K27me3.imputed.bigWig
12151_H3K36me3.imputed.bigWig
12151_H3K4me1.imputed.bigWig
12151_H3K4me2.imputed.bigWig
12151_H3K4me3.imputed.bigWig
12151_H3K79me2.imputed.bigWig
12151_H3K9ac.imputed.bigWig
12151_H3K9me3.imputed.bigWig
12151_H4K20me1.imputed.bigWig


title: CS23_12151_Input_ChIP-seq


title: CS23_12058_H3K4me1_ChIP-seq


title: CS23_12151_H3K27me3_ChIP-seq


title: CS23_12151_H3K4me2_ChIP-seq

value: Abcam


title: Single U2OS cell A12_356


title: CS23_12151_H3K4me3_ChIP-seq


title: CS23_12151_H3K27ac_ChIP-seq


title: CS21_12093_H3K9me3_ChIP-seq

description:
CS21_12093_25state.bigBed
CS21_12093_18state.bigBed
CS21_12093_15state.bigBed
12093_DNase.imputed.bigWig
12093_H2A.Z.imputed.bigWig
12093_H3K27ac.imputed.bigWig
12093_H3K27me3.imputed.bigWig
12093_H3K36me3.imputed.bigWig
12093_H3K4me1.imputed.bigWig
12093_H3K4me2.imputed.bigWig
12093_H3K4me3.imputed.bigWig
12093_H3K79me2.imputed.bigWig
12093_H3K9ac.imputed.bigWig
12093_H3K9me3.imputed.bigWig
12093_H4K20me1.imputed.bigWig


title: CS21_12093_H3K36me3_ChIP-seq


title: CS23_12058_H3K4me2_ChIP-seq


title: CS23_12151_H3K9me3_ChIP-seq


title: CS21_12093_Input_ChIP-seq


title: CS21_12093_H3K27ac_ChIP-seq


title: CS21_12093_H3K27me3_ChIP-seq


title: Single U2OS cell A12_355


title: CS21_12093_H3K4me1_ChIP-seq


title: CS23_12151_H3K4me1_ChIP-seq


title: CS21_12093_H3K4me3_ChIP-seq


title: CS21_12093_H3K4me2_ChIP-seq


title: CS21_11849_H3K27me3_ChIP-seq

description:
CS21_11849_25state.bigBed
CS21_11849_18state.bigBed
CS21_11849_15state.bigBed
11849_DNase.imputed.bigWig
11849_H2A.Z.imputed.bigWig
11849_H3K27ac.imputed.bigWig
11849_H3K27me3.imputed.bigWig
11849_H3K36me3.imputed.bigWig
11849_H3K4me1.imputed.bigWig
11849_H3K4me2.imputed.bigWig
11849_H3K4me3.imputed.bigWig
11849_H3K79me2.imputed.bigWig
11849_H3K9ac.imputed.bigWig
11849_H3K9me3.imputed.bigWig
11849_H4K20me1.imputed.bigWig


title: CS21_11849_H3K9me3_ChIP-seq


title: CS21_11849_Input_ChIP-seq


title: CS21_11849_H3K36me3_ChIP-seq


title: CS23_12058_H3K4me3_ChIP-seq


title: CS21_11849_H3K4me2_ChIP-seq


title: CS21_11849_H3K4me1_ChIP-seq


title: CS21_11849_H3K27ac_ChIP-seq


title: CS21_11849_H3K4me3_ChIP-seq


title: CS20_12448_H3K4me2_ChIP-seq

description:
CS20_12448_25state.bigBed
CS20_12448_18state.bigBed
CS20_12448_15state.bigBed
12448_DNase.imputed.bigWig
12448_H2A.Z.imputed.bigWig
12448_H3K27ac.imputed.bigWig
12448_H3K27me3.imputed.bigWig
12448_H3K36me3.imputed.bigWig
12448_H3K4me1.imputed.bigWig
12448_H3K4me2.imputed.bigWig
12448_H3K4me3.imputed.bigWig
12448_H3K79me2.imputed.bigWig
12448_H3K9ac.imputed.bigWig
12448_H3K9me3.imputed.bigWig
12448_H4K20me1.imputed.bigWig


title: CS20_12448_H3K36me3_ChIP-seq


title: CS20_12451_H3K9me3_ChIP-seq

description:
CS20_12451_25state.bigBed
CS20_12451_18state.bigBed
CS20_12451_15state.bigBed
12451_DNase.imputed.bigWig
12451_H2A.Z.imputed.bigWig
12451_H3K27ac.imputed.bigWig
12451_H3K27me3.imputed.bigWig
12451_H3K36me3.imputed.bigWig
12451_H3K4me1.imputed.bigWig
12451_H3K4me2.imputed.bigWig
12451_H3K4me3.imputed.bigWig
12451_H3K79me2.imputed.bigWig
12451_H3K9ac.imputed.bigWig
12451_H3K9me3.imputed.bigWig
12451_H4K20me1.imputed.bigWig


title: CS20_12451_H3K4me2_ChIP-seq


title: CS20_12448_H3K27ac_ChIP-seq


title: CS20_12448_H3K4me3_ChIP-seq


title: CS20_12451_Input_ChIP-seq


title: CS20_12448_H3K4me1_ChIP-seq


title: CS20_12451_H3K4me1_ChIP-seq


title: CS19_12135_Input_ChIP-seq

description:
CS19_12135_25state.bigBed
CS19_12135_18state.bigBed
CS19_12135_15state.bigBed
12135_DNase.imputed.bigWig
12135_H2A.Z.imputed.bigWig
12135_H3K27ac.imputed.bigWig
12135_H3K27me3.imputed.bigWig
12135_H3K36me3.imputed.bigWig
12135_H3K4me1.imputed.bigWig
12135_H3K4me2.imputed.bigWig
12135_H3K4me3.imputed.bigWig
12135_H3K79me2.imputed.bigWig
12135_H3K9ac.imputed.bigWig
12135_H3K9me3.imputed.bigWig
12135_H4K20me1.imputed.bigWig


title: CS20_12448_H3K27me3_ChIP-seq


title: CS20_12451_H3K36me3_ChIP-seq


title: CS20_12448_H3K9me3_ChIP-seq


title: CS19_12135_H3K36me3_ChIP-seq


title: CS20_12451_H3K27me3_ChIP-seq


title: CS19_12135_H3K27ac_ChIP-seq


title: CS19_12135_H3K4me1_ChIP-seq


title: CS19_12135_H3K27me3_ChIP-seq


title: CS19_12135_H3K9me3_ChIP-seq


title: CS19_12135_H3K4me3_ChIP-seq


title: CS20_12448_Input_ChIP-seq


title: CS19_11914_H3K27ac_ChIP-seq

description:
CS19_11914_25state.bigBed
CS19_11914_18state.bigBed
CS19_11914_15state.bigBed
11914_DNase.imputed.bigWig
11914_H2A.Z.imputed.bigWig
11914_H3K27ac.imputed.bigWig
11914_H3K27me3.imputed.bigWig
11914_H3K36me3.imputed.bigWig
11914_H3K4me1.imputed.bigWig
11914_H3K4me2.imputed.bigWig
11914_H3K4me3.imputed.bigWig
11914_H3K79me2.imputed.bigWig
11914_H3K9ac.imputed.bigWig
11914_H3K9me3.imputed.bigWig
11914_H4K20me1.imputed.bigWig


title: CS19_11914_Input_ChIP-seq


title: CS19_11914_H3K36me3_ChIP-seq


title: CS19_11914_H3K9me3_ChIP-seq


title: CS19_11914_H3K27me3_ChIP-seq


title: CS19_11914_H3K4me3_ChIP-seq


title: CS20_12451_H3K27ac_ChIP-seq


title: CS20_12451_H3K4me3_ChIP-seq


title: CS19_12135_H3K4me2_ChIP-seq


title: CS18_12059_H3K36me3_ChIP-seq

description:
CS18_12059_25state.bigBed
CS18_12059_18state.bigBed
CS18_12059_15state.bigBed
12059_DNase.imputed.bigWig
12059_H2A.Z.imputed.bigWig
12059_H3K27ac.imputed.bigWig
12059_H3K27me3.imputed.bigWig
12059_H3K36me3.imputed.bigWig
12059_H3K4me1.imputed.bigWig
12059_H3K4me2.imputed.bigWig
12059_H3K4me3.imputed.bigWig
12059_H3K79me2.imputed.bigWig
12059_H3K9ac.imputed.bigWig
12059_H3K9me3.imputed.bigWig
12059_H4K20me1.imputed.bigWig


title: CS18_12456_Input_ChIP-seq

description:
CS18_12456_25state.bigBed
CS18_12456_18state.bigBed
CS18_12456_15state.bigBed
12456_DNase.imputed.bigWig
12456_H2A.Z.imputed.bigWig
12456_H3K27ac.imputed.bigWig
12456_H3K27me3.imputed.bigWig
12456_H3K36me3.imputed.bigWig
12456_H3K4me1.imputed.bigWig
12456_H3K4me2.imputed.bigWig
12456_H3K4me3.imputed.bigWig
12456_H3K79me2.imputed.bigWig
12456_H3K9ac.imputed.bigWig
12456_H3K9me3.imputed.bigWig
12456_H4K20me1.imputed.bigWig


title: CS18_12059_H3K4me1_ChIP-seq


title: CS19_11914_H3K4me1_ChIP-seq


title: CS18_12059_H3K4me3_ChIP-seq


title: CS18_12456_H3K36me3_ChIP-seq


title: CS19_11914_H3K4me2_ChIP-seq


title: CS18_12059_H3K27me3_ChIP-seq


title: CS18_12059_H3K27ac_ChIP-seq


title: CS18_12059_H3K9me3_ChIP-seq


title: CS18_12456_H3K4me3_ChIP-seq


title: CS17_12331_H3K27me3_ChIP-seq

description:
CS17_12331_25state.bigBed
CS17_12331_18state.bigBed
CS17_12331_15state.bigBed
12331_DNase.imputed.bigWig
12331_H2A.Z.imputed.bigWig
12331_H3K27ac.imputed.bigWig
12331_H3K27me3.imputed.bigWig
12331_H3K36me3.imputed.bigWig
12331_H3K4me1.imputed.bigWig
12331_H3K4me2.imputed.bigWig
12331_H3K4me3.imputed.bigWig
12331_H3K79me2.imputed.bigWig
12331_H3K9ac.imputed.bigWig
12331_H3K9me3.imputed.bigWig
12331_H4K20me1.imputed.bigWig


title: CS17_12331_H3K9me3_ChIP-seq


title: CS17_12331_H3K27ac_ChIP-seq


title: CS17_12331_H3K4me3_ChIP-seq


title: CS18_12059_Input_ChIP-seq


title: CS17_12331_H3K4me2_ChIP-seq


title: CS17_12991_Input_ChIP-seq

description:
CS17_12291_25state.bigBed
CS17_12291_18state.bigBed
CS17_12291_15state.bigBed
12291_DNase.imputed.bigWig
12291_H2A.Z.imputed.bigWig
12291_H3K27ac.imputed.bigWig
12291_H3K27me3.imputed.bigWig
12291_H3K36me3.imputed.bigWig
12291_H3K4me1.imputed.bigWig
12291_H3K4me2.imputed.bigWig
12291_H3K4me3.imputed.bigWig
12291_H3K79me2.imputed.bigWig
12291_H3K9ac.imputed.bigWig
12291_H3K9me3.imputed.bigWig
12291_H4K20me1.imputed.bigWig


title: CS18_12456_H3K27me3_ChIP-seq


title: CS17_12991_H3K9me3_ChIP-seq


title: CS18_12456_H3K4me1_ChIP-seq


title: CS17_12991_H3K36me3_ChIP-seq


title: CS17_12331_H3K4me1_ChIP-seq


title: CS17_12991_H3K27me3_ChIP-seq


title: CS18_12059_H3K4me2_ChIP-seq


title: CS18_12456_H3K9me3_ChIP-seq


title: CS17_12331_Input_ChIP-seq


title: CS18_12456_H3K27ac_ChIP-seq


title: CS17_12991_H3K27ac_ChIP-seq


title: CS18_12456_H3K4me2_ChIP-seq


title: CS17_12991_H3K4me3_ChIP-seq


title: CS16_14315_Input_ChIP-seq

description:
CS16_14315_25state.bigBed
CS16_14315_18state.bigBed
CS16_14315_15state.bigBed
14315_DNase.imputed.bigWig
14315_H2A.Z.imputed.bigWig
14315_H3K27ac.imputed.bigWig
14315_H3K27me3.imputed.bigWig
14315_H3K36me3.imputed.bigWig
14315_H3K4me1.imputed.bigWig
14315_H3K4me2.imputed.bigWig
14315_H3K4me3.imputed.bigWig
14315_H3K79me2.imputed.bigWig
14315_H3K9ac.imputed.bigWig
14315_H3K9me3.imputed.bigWig
14315_H4K20me1.imputed.bigWig


title: CS16_14315_H3K36me3_ChIP-seq


title: CS16_14315_H3K27ac_ChIP-seq


title: CS16_14315_H3K27me3_ChIP-seq


title: CS17_12331_H3K36me3_ChIP-seq


title: CS16_14315_H3K9me3_ChIP-seq


title: CS17_12991_H3K4me1_ChIP-seq


title: CS17_12991_H3K4me2_ChIP-seq


title: CS16_12997_Input_ChIP-seq

description:
CS16_12997_25state.bigBed
CS16_12997_18state.bigBed
CS16_12997_15state.bigBed
12997_DNase.imputed.bigWig
12997_H2A.Z.imputed.bigWig
12997_H3K27ac.imputed.bigWig
12997_H3K27me3.imputed.bigWig
12997_H3K36me3.imputed.bigWig
12997_H3K4me1.imputed.bigWig
12997_H3K4me2.imputed.bigWig
12997_H3K4me3.imputed.bigWig
12997_H3K79me2.imputed.bigWig
12997_H3K9ac.imputed.bigWig
12997_H3K9me3.imputed.bigWig
12997_H4K20me1.imputed.bigWig


title: CS16_14315_H3K4me3_ChIP-seq


title: CS16_14315_H3K4me2_ChIP-seq


title: CS16_12997_H3K36me3_ChIP-seq


title: CS16_12997_H3K9me3_ChIP-seq


title: CS16_12997_H3K27me3_ChIP-seq


title: CS16_12997_H3K4me3_ChIP-seq


title: CS16_12997_H3K4me2_ChIP-seq


title: CS16_12997_H3K27ac_ChIP-seq


title: CS16_14315_H3K4me1_ChIP-seq


title: CS16_12997_H3K4me1_ChIP-seq


title: CS14_14135_Input_ChIP-seq

description:
CS14_14135_25state.bigBed
CS14_14135_18state.bigBed
CS14_14135_15state.bigBed
14135_DNase.imputed.bigWig
14135_H2A.Z.imputed.bigWig
14135_H3K27ac.imputed.bigWig
14135_H3K27me3.imputed.bigWig
14135_H3K36me3.imputed.bigWig
14135_H3K4me1.imputed.bigWig
14135_H3K4me2.imputed.bigWig
14135_H3K4me3.imputed.bigWig
14135_H3K79me2.imputed.bigWig
14135_H3K9ac.imputed.bigWig
14135_H3K9me3.imputed.bigWig
14135_H4K20me1.imputed.bigWig


title: CS14_14135_H3K36me3_ChIP-seq


title: CS14_14135_H3K9me3_ChIP-seq


title: CS14_14135_H3K27me3_ChIP-seq


title: CS14_14135_H3K4me3_ChIP-seq


title: CS14_14135_H3K27ac_ChIP-seq


title: CS14_14135_H3K4me2_ChIP-seq


title: CS14_14135_H3K4me1_ChIP-seq


title: CS14_12408_Input_ChIP-seq

description:
CS14_12408_25state.bigBed
CS14_12408_18state.bigBed
CS14_12408_15state.bigBed
12408_DNase.imputed.bigWig
12408_H2A.Z.imputed.bigWig
12408_H3K27ac.imputed.bigWig
12408_H3K27me3.imputed.bigWig
12408_H3K36me3.imputed.bigWig
12408_H3K4me1.imputed.bigWig
12408_H3K4me2.imputed.bigWig
12408_H3K4me3.imputed.bigWig
12408_H3K79me2.imputed.bigWig
12408_H3K9ac.imputed.bigWig
12408_H3K9me3.imputed.bigWig
12408_H4K20me1.imputed.bigWig


title: CS14_12408_H3K9me3_ChIP-seq


title: CS14_12408_H3K36me3_ChIP-seq


title: CS14_12408_H3K27ac_ChIP-seq


title: CS14_12408_H3K4me3_ChIP-seq


title: CS14_12408_H3K27me3_ChIP-seq


title: CS14_12408_H3K4me1_ChIP-seq


title: CS14_12408_H3K4me2_ChIP-seq


title: CS13_12690_H3K27me3_ChIP-seq

description:
CS13_12690_25state.bigBed
CS13_12690_18state.bigBed
CS13_12690_15state.bigBed
12690_DNase.imputed.bigWig
12690_H2A.Z.imputed.bigWig
12690_H3K27ac.imputed.bigWig
12690_H3K27me3.imputed.bigWig
12690_H3K36me3.imputed.bigWig
12690_H3K4me1.imputed.bigWig
12690_H3K4me2.imputed.bigWig
12690_H3K4me3.imputed.bigWig
12690_H3K79me2.imputed.bigWig
12690_H3K9ac.imputed.bigWig
12690_H3K9me3.imputed.bigWig
12690_H4K20me1.imputed.bigWig


title: CS13_12690_Input_ChIP-seq


title: CS13_12690_H3K27ac_ChIP-seq


title: CS13_12690_H3K4me2_ChIP-seq


title: CS13_12690_H3K9me3_ChIP-seq


title: CS13_12383_H3K9me3_ChIP-seq

description:
CS13_12383_25state.bigBed
CS13_12383_18state.bigBed
CS13_12383_15state.bigBed
12383_DNase.imputed.bigWig
12383_H2A.Z.imputed.bigWig
12383_H3K27ac.imputed.bigWig
12383_H3K27me3.imputed.bigWig
12383_H3K36me3.imputed.bigWig
12383_H3K4me1.imputed.bigWig
12383_H3K4me2.imputed.bigWig
12383_H3K4me3.imputed.bigWig
12383_H3K79me2.imputed.bigWig
12383_H3K9ac.imputed.bigWig
12383_H3K9me3.imputed.bigWig
12383_H4K20me1.imputed.bigWig


title: CS13_12383_Input_ChIP-seq


title: CS13_12383_H3K27me3_ChIP-seq


title: CS13_12690_H3K36me3_ChIP-seq


title: CS13_12383_H3K36me3_ChIP-seq


title: CS13_12383_H3K27ac_ChIP-seq


title: CS13_12690_H3K4me1_ChIP-seq


title: CS13_12383_H3K4me3_ChIP-seq


title: CS13_12690_H3K4me3_ChIP-seq


title: CS13_12383_H3K4me1_ChIP-seq


title: CS13_12383_H3K4me2_ChIP-seq


title: TET2_KO_LPS_285_TET2_LPS_RNA_Seq

status: Public on Jun 19 2020

city: Grand Rapids

first: Lee

last: Marshall

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description:
24hrs LPS injection in tet2 knock-out mice
TET2_KO_LPS_285_L001

data_processing:
Adapter sequences were removed from fastq files using TrimGalore (v0.4.4).
The remaining sequencing reads were then aligned to the reference genome (GRCm38/mm10) and the Gencode vM20 primary assembly transcriptome indexed by STAR (v2.3.5a).
Reads per gene were counted using STAR (v2.3.5a).
Gene counts matrix was imported into R (3.5.1) and low expressed genes (counts per million <1 in all samples) were removed prior to trimmed mean of M-values normalization in EdgeR (v3.24.3).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Each ReadsPerGene.txt file contains the following information in order: gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA

molecule: total RNA

organism: Mus musculus

growth_protocol: Tet2 knock-out mice were obtained from The Jackson Laboratory (strain 023359) and maintained in a pathogen-free barrier facility and provided with food (LabDiet 5021) and water for ad libitum consumption. The vivarium was maintained under controlled temperature (21°C±1°C) and humidity (50-60%), with a 12-h diurnal cycle (lights on: 0700-1900).

extract_protocol:
Mice were perfused with PBS and the midbrain was isolated and snap frozen. Midbrain tissue (25-50 mg) homogenized in TRIzol (Invitrogen) using a Precellys Lysing Kit (Bertin Technologies) with the MiniLys (Bertin). Total RNA was isolated and treated with DNase I (Qiagen), followed by a clean up using an RNeasy Mini Kit (Qiagen). The resulting RNA quantity was assessed by Nanodrop 8000 (Thermo Scientific) and quality was assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega Corp), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (single-end 75 bp) was performed on an Illumina NextSeq500 sequencer.

treatment_protocol: At two months of age mice received an intraperitoneal injection of saline (PBS) or lipopolysaccharide (LPS; 5 mg/kg) and brain tissues were harvested exactly 24 hours post-injection.

tag: sttrain background

value: knock-out

tag: Sex

value: M

tag: treatment

value: LPS

tag: tissue

value: Midbrain

tag: replicate

value: Biological Sample


title: TET2_KO_LPS_291_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 knock-out mice
TET2_KO_LPS_291_L001


title: TET2_KO_LPS_316_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 knock-out mice
TET2_KO_LPS_316_L001


title: TET2_KO_SAL_287_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 knock-out mice
TET2_KO_SAL_287_L001

value: saline


title: TET2_KO_SAL_284_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 knock-out mice
TET2_KO_SAL_284_L001


title: TET2_WT_LPS_302_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 wild-type mice
TET2_WT_LPS_302_L001

value: wild-type


title: TET2_WT_LPS_310_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 wild-type mice
TET2_WT_LPS_310_L001


title: TET2_WT_LPS_278_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 wild-type mice
TET2_WT_LPS_278_L001


title: TET2_WT_SAL_318_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 wild-type mice
TET2_WT_SAL_318_L001


title: TET2_WT_LPS_279_TET2_LPS_RNA_Seq

description:
24hrs LPS injection in tet2 wild-type mice
TET2_WT_LPS_279_L001


title: TET2_KO_SAL_295_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 knock-out mice
TET2_KO_SAL_295_L001


title: TET2_WT_SAL_289_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 wild-type mice
TET2_WT_SAL_289_L001


title: TET2_WT_SAL_277_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 wild-type mice
TET2_WT_SAL_277_L001


title: TET2_WT_SAL_299_TET2_LPS_RNA_Seq

description:
24hrs Saline injection in tet2 wild-type mice
TET2_WT_SAL_299_L001


title: PAC01404

status: Public on May 18 2020

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: biotin

source_name: Total RNA from cutaneous biopsy

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted using mirVana miRNA Isolation kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA), according to the manufacturer’s instructions

tag: disease state

value: actinic keratosis

tag: group

value: post-treatment

tag: patient

value: cutaneous biopsy


title: PAC02002

value: sun-exposed peri-lesional skin

value: pre-treatment


title: PAC02102


title: PAC02104


title: PAC01401

value: non-lesional non-sun-exposed skin


title: PAC01703


title: PAC01902_do


title: PAC01304


title: PAC01903


title: PAC02101


title: PAC01901


title: PAC02004


title: PAC01202


title: PAC01203


title: PAC01701


title: PAC01403


title: PAC01303


title: PAC01402


title: PAC01201


title: PAC01104


title: PAC01904


title: PAC01704


title: PAC02103


title: PAC01204


title: PAC01702


title: PAC02001


title: PAC01302


title: PAC01301


title: PAC01103


title: PAC02003


title: PAC01004


title: PAC01102


title: PAC00901


title: PAC01001


title: PAC01101


title: PAC00802


title: PAC00803


title: PAC01002


title: PAC00703


title: PAC00801


title: PAC00903


title: PAC00404


title: PAC00804


title: PAC00904


title: PAC00701


title: PAC00704


title: PAC01003


title: PAC00203


title: PAC00204


title: PAC00103


title: PAC00402


title: PAC00102


title: PAC00101


title: PAC00702


title: PAC00401


title: PAC00403


title: PAC00202


title: PAC00104


title: PAC00201


title: PAC00902


title: B6

status: Public on Feb 28 2020

city: Madrid

first: Ignacio

last: Benedicto

state: Madrid

address: Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description:
B6_S1_L005
mouse_eye_meta.data.txt (Metadata for both scRNA-seq samples, including columns for cell type annotation)
mouse_eyes_20180414.Rda (Seurat object including tsne coordinates of the clusters)

library_source: transcriptomic single cell

data_processing:
Single cell RNAseq: primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA). 10X Genomics Cell Ranger Single Cell Software suite v2.1.0 was used to perform sample de-multiplexing, alignment (mm10), filtering, UMI counting, single-cell 3’end gene counting and performing quality control using the manufacturer parameters. Unsupervised cell clustering analysis was carried out using the Seurat 2.1 R package. Cells with <1700 UMIs, <600 genes or >10% mitochondrial genes were excluded from the analysis, as well as genes detected in <3 cells. Gene expression raw counts were normalized following a global-scaling normalization method with a scale factor of 10,000 and a log transformation, using the Seurat NormalizeData function. The top 2000 highly variable genes from C57BL/6J and B6129PF1/J datasets were selected, followed by a canonical correlation analysis (CCA) to identify common sources of variation between the two datasets and minimize batch effect. The first 11 aligned CCA results were used to generate 2-dimensional t-Distributed Stochastic Neighbor Embedding (RunTSNE in Seurat, perplexity = 30) and unsupervised cell clustering by a shared nearest neighbor (FindClusters in Seurat, k.param = 30 and resolution = 0.8).
Bulk RNAseq: Illumina Casava 1.8.2 software used for basecalling. Upon quality control using FastQC, raw reads were aligned to the mouse genome (mm10) using STAR_2.4.0f1 and SAMTOOLS v0.1.19 for sorting and indexing reads. Cufflinks (2.0.2) was used to get the expression values (FPKM; Fragments Per Kilobase of transcripts per Million reads). To determine the genes differentially expressed between choroidal ECs and ECs from neural retina, lung, liver and heart, statistical significance was calculated using DEseq2 bioconductor package in R, which uses read counts (htseq-count).
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNAseq of RPE/choroid tissue: tab-delimited text files include gene ID, AdjP_val (P-value calculated using likelihood-ratio test and adjusted by the Benjamini-Hochberg method), avg_diff, (log e fold change between the average expression in a given cluster and the average expression of all cells in the rest of clusters) and avg_UMI (average normalized UMIs). Bulk RNAseq of tissue-specific ECs: tab-delimited text file includes gene ID, average FPKMs, fold change versus choroid ECs and adjusted P value versus choroid ECs. Bulk RNAseq of RPE/choroid tissue from Ihh+/+ and IhhiΔEC/ΔiEC mice and from cultured choroidal GLI1+ cells: tab-delimited text files include gene ID, log2 fold change, adjusted P value and average FPKMs.

source_name: RPE/choroid single cells

extract_protocol:
Single cell RNAseq: after eye enucleation, neural retina was removed and RPE/choroid was mechanically dissected from the sclera and digested in the presence of 1mM Hoechst to label nuclei during digestion. The cell suspension was pelleted, resuspended in sorting buffer (PBS plus 5% FBS and 2mM EDTA), filtered through a 70 µm cell strainer, stained with 1 µg/ml TO-PRO-3 and purified by fluorescence-activated cell sorting with gates set to include Hoechst+ nucleated particles and to exclude TO-PRO-3+ dead cells. Collected cells were pelleted, resuspended in sorting buffer at a concentration between 250-500 cells/µl and loaded onto the 10x Genomics Chromium platform. Bulk RNAseq of tissue-specific endothelial cells: after tissue digestion, ECs were isolated by fluorescence-activated cell sorting and RNA was extracted immediately with TRI Reagent (Molecular Research Center, Inc.) and purified with RNeasy Mini Kit (Qiagen). Bulk RNAseq of RPE/choroid tissue from Ihh+/+ and IhhiΔEC/ΔiEC mice: after eye enucleation, neural retina was removed and RPE/choroid was mechanically dissected and used for RNA extraction using the RNeasy Mini Kit (Qiagen). Bulk RNAseq of cultured choroidal GLI1+ cells: RNA was extracted with RNeasy Mini Kit (Qiagen). All cDNA libraries for bulk RNAseq assays were prepared with the TruSeq RNA Sample Preparation Kit (Illumina).
Single cell RNAseq: the 10x Genomics Chromium platform was used to generate barcoded single-cell GEMs, targeting about 5000 single cells per sample. GEM-reverse transcription (53 °C for 45 min, 85 °C for 5 min) was performed in a C1000 Touch thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules, CA). Next, GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified (98 °C for 3 min; 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min x 12 cycles) using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Quality of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1170 bp. Amplified cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min). Indexed libraries were subjected to a second double-sided size selection, and libraries were then quantified using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA). The quality was assessed on an Agilent Bioanalyzer 2100, obtaining an average library size of 455bp. Bulk RNAseq: RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: age

value: 3 month-old

tag: cell type

value: RPE/choroid single cells


title: allogeneic1 [A1]

status: Public on Jan 13 2020

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

growth_protocol: Recipient balb/c mice were lethally irradiated and transplanted with either syngeneic or allogeneic bone marrow (5 million cells) and T cells (300000). The mice were sacrificed by perfusion on day 14 and RNA was isolated from microglia. Four mice were analyzed per group

extract_protocol:
Microglia were sorted by FACS and RNA was isolated using the Picopure RNA extraction Kit as per manufacturer's instructions.RNA quality was accessed by bio-analyzer. The samples with an RNA integrity value of 8 and above were considered for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Post transplantation mouse were regularly checked until day 14 which is the peak stage of GvHD

value: Balb/c

tag: genotype/variation

value: WT

value: Allogeneic Bone Marrow and T cell Transplantation

value: brain

value: sorted microglia cells


title: MDS2: Bone marrow monocytes from Myelodysplastic syndrome patient, biological rep2

status: Public on Feb 10 2020

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Human Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven. Arrays were washed and stained in an Affymetrix Fluidics Station 450 according to Affymettix protocol.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and signal intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher Scientific).

data_processing: Array data quality analysis, normalization (RMA+DAGB) and statistical tests for differential expression (eBayes) were carried out with the Transcriptome Analysis Console software (TAC 4.0.1) (cut-off for significance p-value <0.05).

label: Biotin

label_protocol: labelled cRNAwas prepared according to the GeneChip Whole Transcript Expression Arrays protocol (Affymetrix, Thermo Fisher Scientific)

extract_protocol: RNA was extracted from monocytes (CD14+ cells), independently of their CD56 co-expression from two disease-free individuals and from two MDS patients (biological replicates) using the RNeasy kit (Qiagen).

value: Bone marrow monocytes

tag: disease status

value: Myelodysplastic syndrome


title: Control1: Bone marrow monocytes from disease-free individuals, biological rep1

value: Disease-free


title: MDS1: Bone marrow monocytes from Myelodysplastic syndrome patient, biological rep1


title: Control2: Bone marrow monocytes from disease-free individuals, biological rep2


title: MSC1

status: Public on Nov 18 2019

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

data_processing:
Demultiplexing, bcl2fastq v2.18.0.12 --no-lane-splitting --barcode-mismatches 1 -l INFO -r 4 -d 4 -p 4 -w 4 --minimum-trimmed-read-length 15 --mask-short-adapter-reads 15
Trim adapters and dereplicate reads using mirDeep2 mapper.pl -e -h -l 15 -m
Alignment to human rRNA (keeping unmapped reads for next step), bowtie -f -n 1 -e 80 -l 15 -a -m 5 --best --strata --sam --no-unal
Alignment to miRBase v22, bowtie -f -n 1 -e 80 -l 15 -a -m 5 --best --strata --sam --no-unal
miRNA counts were generated using a custom script, combining deplication information with the corresponding read mapping from the BAM files (using samtools v1.3.1)
Identified miRNAs were filtered, requiring at least ten read counts in at least two of the five samples
Differential expression analysis between MSC samples and LSC samples was performed using the edgeR and limma R packages and upper quantile normalized read counts
Supplementary_files_format_and_content: raw human miRNA count matrix (ASCII text)

source_name: exosomes

extract_protocol:
Exosomal RNA was isolated using a commercially available total exosome RNA isolation kit (Qiagen’s exoRNeasy Serum Plasma Kit).
Small RNA libraries were prepared according to the manufacturer's protocol using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) and were size selected using a Pippen Prep (Sage Science)

value: Mesenchymal stem cells


title: LSC3

value: Lung spheroid cells


title: tg3

status: Public on Dec 17 2019

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
Sequencing reads (fastq) were filtered by Trimmomatic program, discarding all reads contaminated by sequencing adapter sequence as well as discarding reads whose mean quality in a bin of 20 bp was below Q30. Minimal length of read used for mapping was set as 65 bp
Quality filtered reads were aligned to mouse genome (mm10) by STAR program
Featurecounts analysis
Genome_build: mm10
Supplementary_files_format_and_content: feature_counts produced by featurecounst software from STAR aligned bam files

source_name: hippocampus

extract_protocol:
Total RNA was extracted from three individual hippocampi per variant using RNeasy Lipid Mini Kit (Qiagen: 74804) and treated on-column with DNase using the RNase-Free DNase Set (Qiagen: 79254).
Preparation of cDNA libraries and sequencing by Illumina HighSeq 1500 (run type: Paired-end sequencing, read length: 1 × 76 bp) were carried out in cooperation with Core Facility of IIMCB and the Nencki Institute.

tag: genotype


title: wt3

value: wild-type


title: wt1


title: tg1


title: tg2


title: MSC2


title: LSC1


title: KO_5

status: Public on Feb 04 2020

description: Gene expression data from total RNA

hyb_protocol: Sample was hybridized to the mouse Clariom S Array (ThermoFisher) in a GeneChip hybridization oven 640

scan_protocol: GeneChip was scanned using the Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (ThermoFisher) using a GeneChip Scanner 3000 7G

source_name: P6 Intestinal organoid IκBa KO

label_protocol: 100ng of total RNA from each sample was processed and labelled according to Affymetrix protocol GeneChip WT   PLUS Reagent kit (P/N 703174 2017) (ThermoFisher)

extract_protocol: Direct isolation from intestinal organoid culture with RNeasy Mini Kit [Qiagen Ref. 74004]

value: Intestine

tag: type

value: Organoid

value: KO


title: WT_3

description: Gene expression data from total RNA

source_name: P6 Intestinal organoid IκBa WT


title: WT_2

description: Gene expression data from total RNA


title: WT_1

description: Gene expression data from total RNA


title: KO_2

description: Gene expression data from total RNA


title: KO_1

description: Gene expression data from total RNA


title: KO_4

description: Gene expression data from total RNA


title: WT_4

description: Gene expression data from total RNA


title: WT_5

description: Gene expression data from total RNA


title: KO_3

description: Gene expression data from total RNA


title: Syngeneic1 [S1]

value: Syngeneic Bone Marrow and T cell Transplantation


title: wt2


title: LSC2


title: 9ZNC: 46mCHAVI009

status: Public on Sep 11 2019

data_processing:
Demultiplexing, bcl2fastq v2.18.0.12 --no-lane-splitting --barcode-mismatches 1 -l INFO -r 4 -d 4 -p 4 -w 4
Technical replicates (named with 170712, 170713, 170714, 170717, 170719, or 170817 prefix) for each sample are processed separately and pooled after generation of human read count matrices
Alignment to rRNA (all samples), STAR v2.5.2b --outSAMunmapped None --outSAMattributes Standard --outSAMtype BAM Unsorted --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Alignment to hemoglobin (all samples), STAR v2.5.2b --outSAMunmapped None --outSAMattributes Standard --outSAMtype BAM Unsorted --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Alignment to hg38 (all samples), STAR v2.5.2b --outSAMunmapped None --outSAMattributes Standard  --limitOutSAMoneReadBytes 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 25 --quantMode GeneCounts --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx
Pool technical replicates for each sample and merge count matrices for each sample to generate raw count matrix with gene counts for all samples
Genome_build: hg38 with gencode v25 primary assembly annotation
Supplementary_files_format_and_content: human count matrix (ASCII text) by running STAR alignment with --quantmode GeneCounts parameter

source_name: placental biopsy from HIV-infected Malawian woman

extract_protocol:
Placental biopsy samples in RNAlater from HIV-infected Malawian women were thawed on ice. Fifty mg of tissue was homogenized in Trizol (Invitrogen), and total RNA was purified with miRNeasy extraction kit (Qiagen) according to the manufacturer guidelines.
Total RNA libraries were prepared from 500 ng purified RNA using TruSeq Stranded Total RNA with Ribo-Zero Gold Kit (Illumina).

tag: gender

value: female

tag: nationality

value: Malawian

value: placenta


title: B6CX: 44mCHAVI009


title: DHLW: 42mCHAVI009


title: B7WZ: 45mCHAVI009


title: B8CY: 43mCHAVI009


title: C3FP: 47mCHAVI009


title: C65N: 40mCHAVI009


title: C36J: 41mCHAVI009


title: DH2F: 39mCHAVI009


title: BLX0: 38mCHAVI009


title: K88_pic_1

status: Public on Nov 13 2019

description:
Condition: KO (NFAT5-deficient) poly(I:C) 1 ug/ml
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

hyb_protocol: Sample was hybridized to Affymetrix Mouse Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.0.2) with aroma.affymetrix and bioconductor packages.

source_name: NFAT5-deficient BMDM stimulated with pIC 1 microgram/ml 6h

label_protocol: 100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® WT PLUS Reagent kit (P/N 703174 Rev. 2).

extract_protocol: RNA was extracted following the RNeasy Qiagen protocol.

tag: strain/background

value: NFAT5 KO

value: Bone marrow-derived macrophage (BMDM)

value: Poly(I:C) 1 ug/ml

tag: sample


title: BT4B: 37mCHAVI009


title: K44_pic_1

tag: treatment


title: W45_pic_1

description:
Condition: WT (wild-type) poly(I:C) 1 ug/ml
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

source_name: Wild-type BMDM stimulated with pIC 1 microgram/ml 6h

value: WT


title: K44_pic_02

description:
Condition: KO (NFAT5-deficient) poly(I:C) 0.2 ug/ml
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

source_name: NFAT5-deficient BMDM stimulated with pIC 0.2 micrograms/ml 6h

value: Poly(I:C) 0.2 ug/ml


title: K88_pic_02


title: W47_pic_1


title: K88_neg

description:
Condition: KO (NFAT5-deficient)
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

source_name: Unstimulated NFAT5-deficient BMDM

value: Unstimulated


title: W47_neg

description:
Condition: WT (wild-type)
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

source_name: Unstimulated wild-type BMDM


title: W87_neg


title: W47_pic_02

description:
Condition: WT (wild-type) poly(I:C) 0.2 ug/ml
NFAT5-deficient mice and BMDM have been described in Buxadé et al., 2012, J Exp Med, 209:379–393.

source_name: Wild-type BMDM stimulated with pIC 0.2 micrograms/ml 6h


title: K40_pic_02


title: W87_pic_1


title: W87_pic_02


title: K40_neg


title: K40_pic_1


title: K44_neg


title: W45_neg


title: W45_pic_02


title: BS03: 36mCHAVI009

tag: tissue


title: BZCH: 33mCHAVI009


title: B9F1: 32mCHAVI009


title: BJC2: 28mCHAVI009


title: 9FCR: 29mCHAVI009


title: BQD0: 31mCHAVI009


title: BJZP: 34mCHAVI009


title: B640: 26mCHAVI009


title: B6B9: 25mCHAVI009


title: 9Z8Q: 24mCHAVI009


title: 9YZ8: 21mCHAVI009


title: 96ZK: 22mCHAVI009


title: B3LH: 20mCHAVI009


title: BDN9: 35mCHAVI009


title: 9PN4: 17mCHAVI009


title: BBHW: 30mCHAVI009


title: 9NMN: 9mCHAVI009


title: BNDH: 13mCHAVI009


title: C2Y0: 7mCHAVI009


title: 9TBM: 8mCHAVI009


title: 9R4Z: 16mCHAVI009


title: BBNY: 12mCHAVI009


title: C659: 6mCHAVI009


title: B87D: 18mCHAVI009


title: C3YT: 4mCHAVI009


title: B16F: 5mCHAVI009


title: BLMP: 14mCHAVI009


title: BZYD: 3mCHAVI009


title: B2MF: 1mCHAVI009


title: BBH9: 2mCHAVI009


title: B36C: 23mCHAVI009


title: MEF-HiC-Arima rep2

status: Public on Sep 06 2019

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

description:
MEF-HiC-Arima_TADs.bed
Hi-C

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the mm10 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<10 kb)
Matrix generation: HicBench. For each replicate and each chromosome, a matrix with binned interactions (bin-size 10kb) was generated.
Normalization: custom script. Each loop with > 1 read across all replicates of the same condition was kept. We applied normalization by sequencing depth per replicate to raw read-counts (both Hi-C and HiChIP; leading to counts-per-million; CPM). Hi-C data only was additionally distance-normalized as recently described (Gong et al., 2018)
High-confidence interactions: custom script. We have applied an approach similar to mango, which employs a binomial test per diagnoal in the normalized counts-matrix. To define significant HiChIP loops, we have filtered all interactions for CPM>3 in all available replicates and p<0.1. For significant Hi-C loops, we have filtered more stringently using CPM>15 in all replicates and p<0.01.
Topologically associated domains (TADs): We called TADs from normalized corrected Hi-C matrices in PSCs processed at 10kb resolution using a recently published software (Ramirez et al., Nat Comm, 2018) with the use of the following parameters: --minDepth 120000 --maxDepth 420000 --thresholdComparison 0.001 --delta 0.01 --correctForMultipleTesting fdr
genome build: mm10
processed data files format and content: custom tsv: left anchor coordinates; right anchor coordiantes; raw read-counts per replicate; normalized read-counts (CPM) for all replicates; distance-normalized read-counts as described before (Gong et al., 2018).

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF were grown in low oxygen incubator with DMEM media, V6.5 were grown in KO-DMEM media in 2i conditions (TKO samples-with or without dox for 24 hrs) , MEF at different times of reprogramming were grown in the presence of dox and ascorbic acid

extract_protocol:
cells were collected with trypsin and fixed with 1% formaldehyde
Hi-C libraries were prepared using the KAPA Hyper prep kit following Arima's manufacturer's instructions.

treatment_protocol: dox was added for reprogramming samples and TKO samples for the amount of time indicated

tag: cell tye

value: Reprogrammable mouse embryonic fibroblasts (MEFs) prepared from rtTA3-OKSM embryos (embryonic day-E13.5) that were heterozygous for the Oct4-GFP reporter, OKSM cassette and rtTA3.

tag: culture condition

value: collected at passage 3


title: ES-HiC-Arima rep2

description:
ES-HiC-Arima_TADs.bed
Hi-C

source_name: Embryonic stem cells

value: cultured in 2i condition


title: ES-HiC-Arima rep1

description:
ES-HiC-Arima_TADs.bed
Hi-C


title: MEF-HiC-Arima rep1

description:
MEF-HiC-Arima_TADs.bed
Hi-C


title: B2S1: 19mCHAVI009


title: TKO-24h H3K27ac rep3

description:
TKO-24h-H3K27ac_high-confidence_interactions.tsv
HiChIP

extract_protocol:
cells were collected with trypsin and fixed with 1% formaldehyde
HiChIP libraries were prepared using nextera primers, after size selection they were sequenced on HiSeq 2500 platform on PE75 mode.

value: cultured in 2i condition and dox for 24hrs

tag: antibody


title: TKO-24h H3K27ac rep2


title: TKO-24h H3K27ac rep1


title: 9V34: 15mCHAVI009


title: TKO-0h H3K27ac rep3

description:
TKO-0h-H3K27ac_high-confidence_interactions.tsv
HiChIP


title: TKO-0h H3K27ac rep2


title: TKO-0h H3K27ac rep1


title: iPSC H3k27ac B ChiP-seq

data_processing:
Alignment of the ChIP-seq data was performed with bowtie2 algorithm (--very-sensitive option). Filtering of mitochondial reads, duplicate and low quality mapped reads was performed with the use of samtools and bedtools while peak calling was done with MACS2 (--nomodel –shift 37 –extsize 73  -p 1e-3). For all biological replicates we selected the common peaks
Genome_build: mm10
Supplementary_files_format_and_content: Only peaks common between the replicates were used for downstream analysis.

source_name: Induced Pluripotent Stem cells

growth_protocol: Mouse ES V6.5 were cultured on irradiated feeder cells in KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, β-mercaptoethanol and 1000 U/ml LIF, with or without the presence of 2i (1uM MEKinhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004)).

extract_protocol: ChiP-seq: iPSC and ESC cells were crosslinked in 1% formaldehyde at RT for 10 minutes and quenched with 125mM glycine for 5 mins at RT. 50 million cells were used for KLF4 ChIPs and 10 million for H3K27acetylation ChIP. Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer (10mM Tris pH8, 1mM EDTA, 0.5% SDS) per 20 million cells. Cells were sonicated in a bioruptor device (30 cycles 30sec on/off, high setting) and spun down 10 minutes at 4°C at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with the respective antibody (2-3ug/10M cells) (KLF4 R&D #3158, H3K27ac  ab4729) O/N with rotation at 4°C. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4°C. Beads were immobilized on a magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65°C (vortexing every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65°C O/N in presence of proteinase K. After RNase A treatment for 1hr at 37°C, DNA was purified using the minElute kit (Qiagen). 6-10ng of immunoprecipitated material was used for ChIP-seq library preparation using the KAPA Hyper prep kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq 2500 platform on SE50 mode.

treatment_protocol: V6.5 cells were infected using lentiviruses harboring the c3GIC9 vector76  (TRE3G-Cas9-P2A-GFP-PGK-Puro-IRES-rtta) containing gRNA/s targeting either KLF4 only or KLF2, KLF4 and KLF5 in tandem. Following infection cells were selected using Puromycin (LifeTech K210015) and clonal populations were manually picked. Expression of CRISPR-Cas9 from these stable cell lines was induced by addition of Doxycycline for 24hrs (1:1000 dilution of 2mg/ml stock) and KO efficiency in each clonal population was verified by WB: KLF4 (R&D, AF3158) KLF5 (R&D AF3758) KLF2 (Novus biologicals, NBP6181) ESRRB (PPMX, PPH6705) NANOG (Bethyl laboratories, A300-397A) ACTIN (abcam, ab49900). Successful KO clones were then used for subsequent experiments (qPCR, ChIP-seq, RNA-seq, 3C and HiChIP) after induction with doxycycline for the indicated time points (ESC TKO 0 hours and ESC TKO 24 hours).

value: Induced Pluripotent Stem cells

tag: culture


title: iPSC H3K27ac A ChiP-seq


title: Input iPSC KLF4


title: Input H3K27ac TKO 2

source_name: Embryonic Stem Cells (V 6.5)

value: Embryonic Stem Cells (V 6.5)


title: TKO 0h B: H3K27ac WT ChIP-seq

description: V6.5 cells were infected using lentiviruses harboring the c3GIC9 vector76  (TRE3G-Cas9-P2A-GFP-PGK-Puro-IRES-rtta) containing gRNA/s targeting either KLF4 only or KLF2, KLF4 and KLF5 in tandem.


title: Input H3K27ac TKO 1


title: TKO 24h B: H3K27ac KLF4 KO ChIP-seq

description: V6.5 cells were infected using lentiviruses harboring the c3GIC9 vector76  (TRE3G-Cas9-P2A-GFP-PGK-Puro-IRES-rtta) containing gRNA/s targeting either KLF4 only or KLF2, KLF4 and KLF5 in tandem.  Expression of CRISPR-Cas9 from these stable cell lines was induced by addition of Doxycycline for 24 hours.


title: iPSC KLF4 A ChiP-seq


title: Input iPSC H3K27ac


title: TKO 24h A: H3K27ac KLF4 KO ChIP-seq


title: iPSC KLF4 B ChiP-seq


title: TKO 0h A: H3K27ac WT ChIP-seq


title: EC-EA-3702-INPUT_ESC_2I

data_processing:
Reads were trimmed for residual adapters (cutadapt version 1.8.1).
Alignment to the mouse reference genome version mm10 was performed using standard parameters, permitting maximum one mismatch in seed alignment (Bowtie version 2.2.5).
Reads marked as positional duplicates or falling into mouseENCODE blacklisted genomic regions (liftOver to mm10; Consortium, 2012) were filtered out.
Coverage tracks in RPKM were generated from alignments using bamCoverage (V2.3.6).
ChIP-seq peaks (enrichment of signals over background) were called at 10^-2 (MACS version 2.1.1), and peaks detected in more than half of biological replicates were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for coverage tracks; BED files for peak coordinates.

growth_protocol: Mouse ES V6.5 were cultured on irradiated feeder cells in KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, β-mercaptoethanol and 1000 U/ml LIF (ESC medium).  All V6.5 samples for HiCHIP and two replicates of ChIPseq were cultured in the presence of 2i  (1uM MEKinhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004)). Mouse embryonic fibroblasts (MEFs) were isolated from a "reprogrammable" mouse harboring a polycystronic OKSM cassette in the Col1a1 locus and M2rtTA in the Rosa26 locus. Cells were reprogrammed in the presence of 1ug/ml doxycycline and 50ug/ml ascorbic acid and cultured in ES medium as described above.

extract_protocol:
Cells were crosslinked in 1% formaldehyde at RT for 10 minutes and quenched with 125mM glycine for 5 mins at RT. 50 million cells were used for KLF4 ChIPs and 10 million for H3K27acetylation ChIP. Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer (10mM Tris pH8, 1mM EDTA, 0.5% SDS) per 20 million cells. Cells were sonicated in a bioruptor device (30 cycles 30sec on/off, high setting) and spun down 10 minutes at 4°C at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with the respective antibody (2-3ug/10M cells) (KLF4 R&D #3158, H3K27ac  ab4729) O/N with rotation at 4°C. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4°C. Beads were immobilized on a magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65°C (vortexing every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65°C O/N in presence of proteinase K. After RNase A treatment for 1hr at 37°C, DNA was purified using the minElute kit (Qiagen).
6-10ng of immunoprecipitated material was used for ChIP-seq library preparation using the KAPA Hyper prep kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq 2500 platform on SE50 mode.

tag: strain

tag: Stage

value: ESC

tag: medium

value: ESC medium with 2i (1uM MEK inhibitor) and 3uM GSK3 inhibitor

tag: marker

value: unsorted

tag: batch


title: EC-DG-3458-INPUT_ESC

source_name: ESC

tag: genotype

value: ESC medium


title: EC-EA-2643-INPUT_ESC


title: EC-DG-3012-INPUT_ESC_2I


title: EC-DG-3458-INPUT_DAY6

value: OKSM Col1a1/M2rtTA ROSA26

value: ESC medium with 1ug/ml doxycycline and 50ug/ml ascorbic acid

value: sorted for SSEA+


title: EC-DG-4040-INPUT_DAY6


title: EC-DG-4040-INPUT_DAY3


title: EC-DG-3458-INPUT_MEF

source_name: MEF

value: MEF


title: EC-EA-3702-INPUT_DAY6


title: EC-EA-3702-INPUT_DAY3


title: MEF-Tbx3_enhancer_rep2

description: processed data file: Tbx3_enhancer_cpm.tsv

data_processing:
library strategy: 4C-seq
Read trimming: seqtk. Known adapter sequences were trimmed off the reads.
Read alignment: bowtie 1.0.0. Reads were mapped against redcued mm10 reference sequence using bowtie. Reduced reference genome only consists of sequences adjacent to DpnII cut-sites. Multi-mapped reads were discarded.
Read counts: custom script. The genome was binned in successively overlapping 10kb bins, with each bin overlapping by 9kb with the next bin. Read-mates were counted per bin if second mate mapped within +/-5kb around virtual viewpoint.
Normalization: edgeR. Raw read counts were normalized with R library edgeR function cpm.
Genome_build: mm10
Supplementary_files_format_and_content: custom tsv: counts-per-million (CPM) per 10kb bin

extract_protocol:
cells were collected with trypsin and fixed with 1% formaldehyde
Cell pellets were lysed in 1ml Lysis Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA; 1x complete protease inhibitor, 0.5% NP-40, 1% triton) and incubated on ice for 15 min. The samples were centrifuged at 2500xG for 5min at 4°C and the pellet was then resuspended in 360µl milli-Q, 60µl 10X DpnII restriction buffer and 15ul 10%SDS. After 1 hour incubation at 37ºC, 150ul of 10% Triton was added and samples were incubated again at 37ºC for 1 hour. 4ul DpnII enzyme (#R0543M, NEB) were added and samples were incubated at 37ºC over night while shaking in a thermomixer (9000rpm). After confirming the digestion efficiency, the enzyme was inactivated by adding 80ul 10% SDS and incubating at 65 ºC for 30 mins. The digested samples were then diluted with 4860ul Milli-Q, 700ul ligation buffer (500mM Tris pH 7.5, 100mM DTT, 100mM MgCl2,10mM ATP), and 750ul of Triton and incubated at 37ºC for 1 hour. Then 2ul Ligase (NEB M0202M) were added and samples were incubated over night at 16 ºC. Next morning, after testing the ligation efficiency, we reversed the crosslinks by adding 30ul of proteinase K (10mg/ml) and incubating over night at 65ºC. Subsequently the RNA was removed using 30ul of RNase A (10mg/ml) for 45mins at 37ºC. Extensive phenol/chloroform extraction was followed by EtOH precipitation and two washes with 70% EtOH. The pellets were dissolved in 150ul 10mM Tris pH 7.5 by incubating at 37 ºC. We then added 50ul 10x buffer B (Fermentas), 5ul Csp6I (Fermentas, ER0211) and 299ul milli-Q water and samples were digested at 37ºC over night. After determining digestion efficiency, the restriction enzyme was inactivated by incubating the tubes at 65ºC for 25 mins. Samples were diluted in 12ml milli-Q, 3ul ligase (NEB, M0202M) and 1.4ml 10X ligation buffer (500mM Tris pH7.5, 100mM DTT, 100mM MgCl2, 10mMATP) and incubated over night at 65ºC. Following phenol/chloroform and EtOH precipitation the pellets were dissolved in 300ul 10mM Tris pH7.5 and DNA was further purified using 4 Zymo columns per sample (Zymo, D4014). Each sample was eluted in 200ul total of 10mM Tris pH7.5
PCR-amplification  using the KAPA HiFi enzyme (KAPA biosystem, 07958927001).  Four PCR reactions were combined per sample, following column purification using the ZYMO kit (Zymo, D4014).

value: cultured in DMEM


title: MEF-Tbx3_enhancer_rep1


title: ES-Tbx3_enhancer_rep2

value: Embryonic stem cells


title: EC-DG-3012-KLF4_ESC_2I_1


title: EC-EA-3702-KLF4_ESC_2I_1


title: EC-EA-3702-KLF4_DAY9_2


title: EC-DG-4040-KLF4_DAY6_1


title: ES-Ets1_promoter_rep2

description: processed data file: Ets1_promoter_cpm.tsv

tag: cell line


title: MEF-Ets1_promoter_rep2


title: ES-Tbx3_enhancer_rep1


title: ES-Ets1_promoter_rep1


title: EC-EA-3702-KLF4_DAY9_1


title: EC-EA-2697-INPUT_ESC


title: MEF-Mycn_enhancer_rep2

description: processed data file: Mycn_enhancer_cpm.tsv


title: 129_B6

description:
129_B6_S2_L005
mouse_eye_meta.data.txt (Metadata for both scRNA-seq samples, including columns for cell type annotation)
mouse_eyes_20180414.Rda (Seurat object including tsne coordinates of the clusters)

source_name: RPE/choroid single cells

tag: strain background

tag: age

value: 3 month-old

tag: cell type

value: RPE/choroid single cells


title: MEF-Ets1_promoter_rep1

value: Reprogrammable mouse embryonic fibroblasts (MEFs) prepared from rtTA3-OKSM embryos (embryonic day-E13.5) that were heterozygous for the Oct4-GFP reporter, OKSM cassette and rtTA3.


title: EC-DG-3458-INPUT_DAY3


title: EC-EA-2697-KLF4_ESC_1


title: EC-EA-2643-KLF4_ESC_1


title: ES-Mycn_enhancer_rep2

value: cultured in 2i condition


title: ES-Mycn_enhancer_rep1


title: EC-EA-3702-KLF4_DAY6_1


title: EC-EA-3702-INPUT_DAY9

value: OKSM Col1a1/M2rtTA ROSA27


title: EC-DG-3458-H3K27AC_ESC_2


title: EC-EA-3702-KLF4_DAY3_1


title: EC-DG-4040-KLF4_DAY3_1


title: MEF-Mycn_enhancer_rep1


title: EC-EA-3702-H3K27AC_DAY9_1


title: EC-EA-3702-H3K27AC_DAY9_2


title: EC-DG-3458-H3K27AC_ESC_1


title: TKO 24h B: RNA-seq in ESCs after KLF4 KO

data_processing:
Alignment of the RNAseq data was performed with tophat2 algorithm (--very-sensitive option) while gene expression quantification and differential expression was performed with the use of Htseq-count and DESeq algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts per transcript as generated from Htseq-countare submitted in the raw.csv file

extract_protocol: RNA-seq: Total RNA was prepared with TRIZOL (Life technologies #15596018) following manufacturer’s instructions. Libraries were generated by the Weill Cornell Genomics core facility using the Illumina TruSeq stranded mRNA library preparation kit (#20020594) and sequenced on an Illumina HiSeq4000 platform on SE50 mode.

value: KLF KO


title: EC-DG-3458-H3K27AC_DAY6_2


title: EC-DG-3458-H3K27AC_DAY6_1


title: TKO 24h A: RNA-seq in ESCs after KLF4 KO

value: Embryonic Stem Cells (V 6.5)


title: EC-EA-3702-H3K27AC_DAY6_1


title: EC-DG-3458-H3K27AC_DAY3_2