title: 43553_2_B4: SS2 Aged  Trem2ko White Matter A8 25

description: processed data file: 10xaged.tsv


title: 43553_2_A3: SS2 Aged  Trem2ko White Matter A8 23

status: Public on Feb 18 2021

type: SRA

city: Munich

first: Ozgun

last: Gokce

address: Feodor-Lynen-Strasse 17

country: Germany

institute: Institute for Stroke and Dementia Research

description: processed data file: 10xaged.tsv

library_source: transcriptomic

data_processing:
BCL files were demultiplexed with the bcl2fastq software from Illumina.
Quality was assessed with FastQC
Trimming and QC filtering was performed with trim-galore and following command trim_galore -j 2 --paired -q 20 --nextera --stringency 1
Reads were aligned using rnaSTAR (Dobin et al., 2013). Read counts were collected using the parameter “quantMode GeneCounts” of rnaSTAR and using the unstranded values.
For 10x datasets, fastq files were processed with Cell Ranger v4
Genome_build: mm10
Supplementary_files_format_and_content: 5x expression matrices of raw counts as tab-separated files, for each dataset. First (unnamed) column are the gene names, each column depicts a single-cell.

molecule: total RNA

organism: Mus musculus

extract_protocol:
The mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; grey matter was isolated from the frontal cortex and white matter form optic tract, medial lemniscus and corpus callosum (attached grey matter and choroid plexus were removed carefully) isolated. We developed and established a microglia isolation protocol that prevents ex-vivo transcription and automatizes the mechanical isolation parts using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D (Act-D, Sigma, No. A1410) to a final concentration of 45 μM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 μm cell strainer (Corning, 352350) before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody, eBioscience cat:14-0161-82,1100) and then stained for 15 min using 7AAD (Thermo Fisher, A1310, 25 ug/mL) and the antibodies against CD45 (eFluor 450, 30-F11, eBioscience，Cat.:48-0451-82, 1:200) and CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and after washed with PBS (Sigma, D8537). Viable (7AAD negative) single immune cells (CD45 and CD11b positive cells) were sorted by flow cytometry (SH800; Sony). For GFP positive microglia from CX3CR1GFP/+ mice, cells were either dissociated with Act-D or without and labeled with DAPI (4’,6-diamidino-2-phenylindole, 1:4000 dilution; Sigma) to label dead cells. After FSC-A/FSC-H selection of single-cells, DAPI negative and GFP positive cells were selected. Single immune cells (CD45 and CD11b positive cells) were sorted by flow cytometry (SH800; Sony). Flow cytometry data were analyzed using FlowJo v10. Single-cells were sorted into 96 well plates filled with 4 μL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC (External RNA Controls Consortium) RNA spike-in Mix (Ambion, Life Technologies) (1:24000000 dilution), 2.5 μM oligo-dT, 2.5 mM dNTP and 2 U/μL of recombinant RNase inhibitor (Clontech) then spun down and frozen at -80°C. Plates were thawed and libraries prepared as described below.
The 96-well plates containing the sorted single cells were first thawed and then incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added each well a mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Template-switching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reaction mixes were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; finally ending with 70°C for 5 min for enzyme inactivation. Pre-amplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5′ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure bead (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and also fluorometrically using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies) to measure the concentrations. Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/µL. Sequencing libraries were constructed by using in-house produced Tn5 transposase (Picelli et al., 2014). Libraries were barcoded and pooled then underwent three 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were sequenced 2x150 reads base pairs (bp) paired-end on Illumina HiSeq4000 to a depth of 3x105–6x105 reads/sample.
scRNA-seq with Smart-seq2

tag: strain

tag: age

value: 20 months

tag: Sex

value: male

tag: genotype

tag: tissue

value: White Matter

value: Microglia

tag: technology

value: scRNA-seq Smart-seq2


title: 43553_2_A2: SS2 Aged  Trem2ko White Matter A8 22

description: processed data file: 10xaged.tsv


title: 43553_1_G3: SS2 Aged  Trem2ko Grey Matter A8 18

description: processed data file: 10xaged.tsv

value: Grey Matter


title: 43553_1_G4: SS2 Aged  Trem2ko Grey Matter A8 19

description: processed data file: 10xaged.tsv


title: 43553_2_B2: SS2 Aged  Trem2ko White Matter A8 24

description: processed data file: 10xaged.tsv


title: 43553_1_G2: SS2 Aged  Trem2ko Grey Matter A8 17

description: processed data file: 10xaged.tsv


title: 43553_1_H2: SS2 Aged  Trem2ko Grey Matter A8 20

description: processed data file: 10xaged.tsv


title: 43553_1_F3: SS2 Aged  Trem2ko Grey Matter A8 15

description: processed data file: 10xaged.tsv


title: 43553_1_E4: SS2 Aged  Trem2ko Grey Matter A8 13

description: processed data file: 10xaged.tsv


title: 43553_1_F2: SS2 Aged  Trem2ko Grey Matter A8 14

description: processed data file: 10xaged.tsv


title: 43553_2_A1: SS2 Aged  Trem2ko White Matter A8 21

description: processed data file: 10xaged.tsv


title: 43553_1_F4: SS2 Aged  Trem2ko Grey Matter A8 16

description: processed data file: 10xaged.tsv


title: 43553_1_E3: SS2 Aged  Trem2ko Grey Matter A8 12

description: processed data file: 10xaged.tsv


title: 43553_2_E4: SS2 Aged  Trem2ko White Matter A8 33

description: processed data file: 10xaged.tsv


title: 43553_1_D3: SS2 Aged  Trem2ko Grey Matter A8 10

description: processed data file: 10xaged.tsv


title: 43553_1_C3: SS2 Aged  Trem2ko Grey Matter A8 8

description: processed data file: 10xaged.tsv


title: 43553_1_C4: SS2 Aged  Trem2ko Grey Matter A8 9

description: processed data file: 10xaged.tsv


title: 43553_1_C2: SS2 Aged  Trem2ko Grey Matter A8 7

description: processed data file: 10xaged.tsv


title: 43553_1_D4: SS2 Aged  Trem2ko Grey Matter A8 11

description: processed data file: 10xaged.tsv


title: 43553_1_B3: SS2 Aged  Trem2ko Grey Matter A8 6

description: processed data file: 10xaged.tsv


title: 43553_1_B2: SS2 Aged  Trem2ko Grey Matter A8 5

description: processed data file: 10xaged.tsv


title: 43553_1_A4: SS2 Aged  Trem2ko Grey Matter A8 4

description: processed data file: 10xaged.tsv


title: 43553_1_A3: SS2 Aged  Trem2ko Grey Matter A8 3

description: processed data file: 10xaged.tsv


title: 43553_1_A1: SS2 Aged  Trem2ko Grey Matter A8 1

description: processed data file: 10xaged.tsv


title: 43517_2_H8: SS2 Aged  Wild type White Matter A7 53

description: processed data file: 10xaged.tsv

value: 18 months

value: Wild type


title: 43517_2_H9: SS2 Aged  Wild type White Matter A7 54

description: processed data file: 10xaged.tsv


title: 43517_2_H11: SS2 Aged  Wild type White Matter A7 51

description: processed data file: 10xaged.tsv


title: 43517_2_H10: SS2 Aged  Wild type White Matter A7 50

description: processed data file: 10xaged.tsv


title: 43517_2_G8: SS2 Aged  Wild type White Matter A7 49

description: processed data file: 10xaged.tsv


title: 43517_2_G7: SS2 Aged  Wild type White Matter A7 48

description: processed data file: 10xaged.tsv


title: 43517_2_G11: SS2 Aged  Wild type White Matter A7 47

description: processed data file: 10xaged.tsv


title: 43517_2_G10: SS2 Aged  Wild type White Matter A7 46

description: processed data file: 10xaged.tsv


title: 43517_2_E8: SS2 Aged  Wild type White Matter A7 39

description: processed data file: 10xaged.tsv


title: 43517_2_F11: SS2 Aged  Wild type White Matter A7 41

description: processed data file: 10xaged.tsv


title: 43517_2_E5: SS2 Aged  Wild type Grey Matter A7 37

description: processed data file: 10xaged.tsv


title: 43517_2_E7: SS2 Aged  Wild type White Matter A7 38

description: processed data file: 10xaged.tsv


title: 43517_2_F2: SS2 Aged  Wild type Grey Matter A7 42

description: processed data file: 10xaged.tsv


title: 43517_2_F4: SS2 Aged  Wild type Grey Matter A7 43

description: processed data file: 10xaged.tsv


title: 43517_2_E4: SS2 Aged  Wild type Grey Matter A7 36

description: processed data file: 10xaged.tsv


title: 43517_2_E2: SS2 Aged  Wild type Grey Matter A7 35

description: processed data file: 10xaged.tsv


title: 43517_2_H7: SS2 Aged  Wild type White Matter A7 52

description: processed data file: 10xaged.tsv


title: 43517_2_E10: SS2 Aged  Wild type White Matter A7 32

description: processed data file: 10xaged.tsv


title: 43517_2_D5: SS2 Aged  Wild type Grey Matter A7 29

description: processed data file: 10xaged.tsv


title: 43517_2_D9: SS2 Aged  Wild type White Matter A7 31

description: processed data file: 10xaged.tsv


title: 43517_2_E12: SS2 Aged  Wild type White Matter A7 34

description: processed data file: 10xaged.tsv


title: 43553_1_A2: SS2 Aged  Trem2ko Grey Matter A8 2

description: processed data file: 10xaged.tsv


title: 43517_2_D7: SS2 Aged  Wild type White Matter A7 30

description: processed data file: 10xaged.tsv


title: 43517_2_E11: SS2 Aged  Wild type White Matter A7 33

description: processed data file: 10xaged.tsv


title: 43517_2_D4: SS2 Aged  Wild type Grey Matter A7 28

description: processed data file: 10xaged.tsv


title: 43517_2_D12: SS2 Aged  Wild type White Matter A7 27

description: processed data file: 10xaged.tsv


title: 43517_2_D11: SS2 Aged  Wild type White Matter A7 26

description: processed data file: 10xaged.tsv


title: 43517_2_F9: SS2 Aged  Wild type White Matter A7 45

description: processed data file: 10xaged.tsv


title: 43517_2_F7: SS2 Aged  Wild type White Matter A7 44

description: processed data file: 10xaged.tsv


title: 43517_2_F10: SS2 Aged  Wild type White Matter A7 40

description: processed data file: 10xaged.tsv


title: 43517_2_D10: SS2 Aged  Wild type White Matter A7 25

description: processed data file: 10xaged.tsv


title: 43517_2_C8: SS2 Aged  Wild type White Matter A7 23

description: processed data file: 10xaged.tsv


title: 43517_2_C5: SS2 Aged  Wild type Grey Matter A7 22

description: processed data file: 10xaged.tsv


title: 43517_2_C3: SS2 Aged  Wild type Grey Matter A7 20

description: processed data file: 10xaged.tsv


title: 43517_2_C2: SS2 Aged  Wild type Grey Matter A7 19

description: processed data file: 10xaged.tsv


title: 43517_2_C12: SS2 Aged  Wild type White Matter A7 18

description: processed data file: 10xaged.tsv


title: 43517_2_C10: SS2 Aged  Wild type White Matter A7 17

description: processed data file: 10xaged.tsv


title: 43517_2_B4: SS2 Aged  Wild type Grey Matter A7 13

description: processed data file: 10xaged.tsv


title: 43517_2_B6: SS2 Aged  Wild type Grey Matter A7 14

description: processed data file: 10xaged.tsv


title: 43517_2_B9: SS2 Aged  Wild type White Matter A7 16

description: processed data file: 10xaged.tsv


title: 43517_2_B2: SS2 Aged  Wild type Grey Matter A7 11

description: processed data file: 10xaged.tsv


title: 43517_2_C9: SS2 Aged  Wild type White Matter A7 24

description: processed data file: 10xaged.tsv


title: 43517_2_B12: SS2 Aged  Wild type White Matter A7 10

description: processed data file: 10xaged.tsv


title: 43517_2_A9: SS2 Aged  Wild type White Matter A7 9

description: processed data file: 10xaged.tsv


title: 43517_2_A6: SS2 Aged  Wild type Grey Matter A7 7

description: processed data file: 10xaged.tsv


title: 43517_2_A11: SS2 Aged  Wild type White Matter A7 2

description: processed data file: 10xaged.tsv


title: 43517_2_A8: SS2 Aged  Wild type White Matter A7 8

description: processed data file: 10xaged.tsv


title: 43517_2_A12: SS2 Aged  Wild type White Matter A7 3

description: processed data file: 10xaged.tsv


title: 43517_2_A2: SS2 Aged  Wild type Grey Matter A7 4

description: processed data file: 10xaged.tsv


title: 43517_2_A4: SS2 Aged  Wild type Grey Matter A7 5

description: processed data file: 10xaged.tsv


title: 43517_2_A5: SS2 Aged  Wild type Grey Matter A7 6

description: processed data file: 10xaged.tsv


title: 43517_2_C4: SS2 Aged  Wild type Grey Matter A7 21

description: processed data file: 10xaged.tsv


title: 43546_2_E6: SS2 Aged  Wild type White Matter A6 21

description: processed data file: 10xaged.tsv

value: 19 months


title: 43517_2_A10: SS2 Aged  Wild type White Matter A7 1

description: processed data file: 10xaged.tsv


title: 43546_2_B6: SS2 Aged  Wild type White Matter A6 18

description: processed data file: 10xaged.tsv


title: 43546_2_C4: SS2 Aged  Wild type White Matter A6 19

description: processed data file: 10xaged.tsv


title: 43546_2_B4: SS2 Aged  Wild type White Matter A6 17

description: processed data file: 10xaged.tsv


title: 43517_2_B3: SS2 Aged  Wild type Grey Matter A7 12

description: processed data file: 10xaged.tsv


title: 43517_2_B8: SS2 Aged  Wild type White Matter A7 15

description: processed data file: 10xaged.tsv


title: 43546_2_A6: SS2 Aged  Wild type White Matter A6 16

description: processed data file: 10xaged.tsv


title: 43546_2_D6: SS2 Aged  Wild type White Matter A6 20

description: processed data file: 10xaged.tsv


title: 43546_2_A3: SS2 Aged  Wild type Grey Matter A6 15

description: processed data file: 10xaged.tsv


title: 43546_1_F5: SS2 Aged  Wild type White Matter A6 14

description: processed data file: 10xaged.tsv


title: 43546_1_F4: SS2 Aged  Wild type White Matter A6 13

description: processed data file: 10xaged.tsv


title: 43546_1_F1: SS2 Aged  Wild type Grey Matter A6 11

description: processed data file: 10xaged.tsv


title: 43546_1_D5: SS2 Aged  Wild type White Matter A6 10

description: processed data file: 10xaged.tsv


title: 43546_1_C5: SS2 Aged  Wild type White Matter A6 9

description: processed data file: 10xaged.tsv


title: 43546_1_B5: SS2 Aged  Wild type White Matter A6 7

description: processed data file: 10xaged.tsv


title: 43546_1_B6: SS2 Aged  Wild type White Matter A6 8

description: processed data file: 10xaged.tsv


title: 43546_1_B3: SS2 Aged  Wild type Grey Matter A6 6

description: processed data file: 10xaged.tsv


title: 43546_1_A4: SS2 Aged  Wild type White Matter A6 4

description: processed data file: 10xaged.tsv


title: 43546_1_F3: SS2 Aged  Wild type Grey Matter A6 12

description: processed data file: 10xaged.tsv


title: 43546_1_A2: SS2 Aged  Wild type Grey Matter A6 2

description: processed data file: 10xaged.tsv


title: 43546_1_A6: SS2 Aged  Wild type White Matter A6 5

description: processed data file: 10xaged.tsv


title: 43546_1_A1: SS2 Aged  Wild type Grey Matter A6 1

description: processed data file: 10xaged.tsv


title: 43517_1_H9: SS2 Aged  Wild type White Matter A5 49

description: processed data file: 10xaged.tsv


title: 43546_1_A3: SS2 Aged  Wild type Grey Matter A6 3

description: processed data file: 10xaged.tsv


title: 43517_1_H5_1: SS2 Aged  Wild type Grey Matter A5 47

description: processed data file: 10xaged.tsv


title: 43517_1_H6: SS2 Aged  Wild type Grey Matter A5 48

description: processed data file: 10xaged.tsv


title: 43517_1_H12: SS2 Aged  Wild type White Matter A5 44

description: processed data file: 10xaged.tsv


title: 43517_1_G4: SS2 Aged  Wild type Grey Matter A5 43

description: processed data file: 10xaged.tsv


title: 43517_1_G3: SS2 Aged  Wild type Grey Matter A5 42

description: processed data file: 10xaged.tsv


title: 43517_1_H5: SS2 Aged  Wild type Grey Matter A5 46

description: processed data file: 10xaged.tsv


title: 43517_1_G2: SS2 Aged  Wild type Grey Matter A5 41

description: processed data file: 10xaged.tsv


title: 43517_1_G10: SS2 Aged  Wild type White Matter A5 40

description: processed data file: 10xaged.tsv


title: 43517_1_H3: SS2 Aged  Wild type Grey Matter A5 45

description: processed data file: 10xaged.tsv


title: 43517_1_F6: SS2 Aged  Wild type Grey Matter A5 39

description: processed data file: 10xaged.tsv


title: 43517_1_F5: SS2 Aged  Wild type Grey Matter A5 38

description: processed data file: 10xaged.tsv


title: 43517_1_F2: SS2 Aged  Wild type Grey Matter A5 36

description: processed data file: 10xaged.tsv


title: 43517_1_F4: SS2 Aged  Wild type Grey Matter A5 37

description: processed data file: 10xaged.tsv


title: 43517_1_E6: SS2 Aged  Wild type Grey Matter A5 33

description: processed data file: 10xaged.tsv


title: 43517_1_E5: SS2 Aged  Wild type Grey Matter A5 32

description: processed data file: 10xaged.tsv


title: 43517_1_E4: SS2 Aged  Wild type Grey Matter A5 31

description: processed data file: 10xaged.tsv


title: 43517_1_E12: SS2 Aged  Wild type White Matter A5 29

description: processed data file: 10xaged.tsv


title: 43517_1_E11: SS2 Aged  Wild type White Matter A5 28

description: processed data file: 10xaged.tsv


title: 43517_1_D9: SS2 Aged  Wild type White Matter A5 25

description: processed data file: 10xaged.tsv


title: 43517_1_D3: SS2 Aged  Wild type Grey Matter A5 22

description: processed data file: 10xaged.tsv


title: 43517_1_D1: SS2 Aged  Wild type Grey Matter A5 20

description: processed data file: 10xaged.tsv


title: 43517_1_D5: SS2 Aged  Wild type Grey Matter A5 23

description: processed data file: 10xaged.tsv


title: 43517_1_C6_1: SS2 Aged  Wild type Grey Matter A5 19

description: processed data file: 10xaged.tsv


title: 43517_1_C6: SS2 Aged  Wild type Grey Matter A5 18

description: processed data file: 10xaged.tsv


title: 43517_1_C5: SS2 Aged  Wild type Grey Matter A5 17

description: processed data file: 10xaged.tsv


title: 43517_1_D7: SS2 Aged  Wild type White Matter A5 24

description: processed data file: 10xaged.tsv


title: 43517_1_D2: SS2 Aged  Wild type Grey Matter A5 21

description: processed data file: 10xaged.tsv


title: 43517_1_C1: SS2 Aged  Wild type Grey Matter A5 15

description: processed data file: 10xaged.tsv


title: 43517_1_B5: SS2 Aged  Wild type Grey Matter A5 13

description: processed data file: 10xaged.tsv


title: 43517_1_B3: SS2 Aged  Wild type Grey Matter A5 12

description: processed data file: 10xaged.tsv


title: 43517_1_E1: SS2 Aged  Wild type Grey Matter A5 26

description: processed data file: 10xaged.tsv


title: 43517_1_B2: SS2 Aged  Wild type Grey Matter A5 11

description: processed data file: 10xaged.tsv


title: 43517_1_C4: SS2 Aged  Wild type Grey Matter A5 16

description: processed data file: 10xaged.tsv


title: 43517_1_F10: SS2 Aged  Wild type White Matter A5 34

description: processed data file: 10xaged.tsv


title: 43517_1_B9: SS2 Aged  Wild type White Matter A5 14

description: processed data file: 10xaged.tsv


title: 43517_1_F12: SS2 Aged  Wild type White Matter A5 35

description: processed data file: 10xaged.tsv


title: 43517_1_B1: SS2 Aged  Wild type Grey Matter A5 9

description: processed data file: 10xaged.tsv


title: 43517_1_A8: SS2 Aged  Wild type White Matter A5 7

description: processed data file: 10xaged.tsv


title: 43517_1_A7: SS2 Aged  Wild type White Matter A5 6

description: processed data file: 10xaged.tsv


title: 43517_1_A9: SS2 Aged  Wild type White Matter A5 8

description: processed data file: 10xaged.tsv


title: 43517_1_A5: SS2 Aged  Wild type Grey Matter A5 5

description: processed data file: 10xaged.tsv


title: 43517_1_E10: SS2 Aged  Wild type White Matter A5 27

description: processed data file: 10xaged.tsv


title: 43517_1_E3: SS2 Aged  Wild type Grey Matter A5 30

description: processed data file: 10xaged.tsv


title: 43517_1_A4: SS2 Aged  Wild type Grey Matter A5 4

description: processed data file: 10xaged.tsv


title: 43517_1_A1: SS2 Aged  Wild type Grey Matter A5 1

description: processed data file: 10xaged.tsv


title: 43517_1_A11: SS2 Aged  Wild type White Matter A5 2

description: processed data file: 10xaged.tsv


title: 43552_3_H11: SS2 Aged  Wild type White Matter A4 85

description: processed data file: 10xaged.tsv


title: 43552_3_F4: SS2 Aged  Wild type Grey Matter A4 83

description: processed data file: 10xaged.tsv


title: 43552_3_F11: SS2 Aged  Wild type White Matter A4 82

description: processed data file: 10xaged.tsv


title: 43552_3_G12: SS2 Aged  Wild type White Matter A4 84

description: processed data file: 10xaged.tsv


title: 43552_3_E6: SS2 Aged  Wild type Grey Matter A4 80

description: processed data file: 10xaged.tsv


title: 43552_3_F10: SS2 Aged  Wild type White Matter A4 81

description: processed data file: 10xaged.tsv


title: 43517_1_B12: SS2 Aged  Wild type White Matter A5 10

description: processed data file: 10xaged.tsv


title: 43552_3_E5: SS2 Aged  Wild type Grey Matter A4 79

description: processed data file: 10xaged.tsv


title: 43552_3_E10: SS2 Aged  Wild type White Matter A4 75

description: processed data file: 10xaged.tsv


title: 43552_3_E11: SS2 Aged  Wild type White Matter A4 76

description: processed data file: 10xaged.tsv


title: 43552_3_D6: SS2 Aged  Wild type Grey Matter A4 74

description: processed data file: 10xaged.tsv


title: 43552_3_D4: SS2 Aged  Wild type Grey Matter A4 72

description: processed data file: 10xaged.tsv


title: 43552_3_D10: SS2 Aged  Wild type White Matter A4 70

description: processed data file: 10xaged.tsv


title: 43552_3_D5: SS2 Aged  Wild type Grey Matter A4 73

description: processed data file: 10xaged.tsv


title: 43517_1_A3: SS2 Aged  Wild type Grey Matter A5 3

description: processed data file: 10xaged.tsv


title: 43552_3_D11: SS2 Aged  Wild type White Matter A4 71

description: processed data file: 10xaged.tsv


title: 43552_3_C11: SS2 Aged  Wild type White Matter A4 66

description: processed data file: 10xaged.tsv


title: 43552_3_C6: SS2 Aged  Wild type Grey Matter A4 69

description: processed data file: 10xaged.tsv


title: 43552_3_C12: SS2 Aged  Wild type White Matter A4 67

description: processed data file: 10xaged.tsv


title: 43552_3_C4: SS2 Aged  Wild type Grey Matter A4 68

description: processed data file: 10xaged.tsv


title: 43552_3_B6: SS2 Aged  Wild type Grey Matter A4 65

description: processed data file: 10xaged.tsv


title: 43552_3_B11: SS2 Aged  Wild type White Matter A4 62

description: processed data file: 10xaged.tsv


title: 43552_3_B10: SS2 Aged  Wild type White Matter A4 61

description: processed data file: 10xaged.tsv


title: 43552_3_A6: SS2 Aged  Wild type Grey Matter A4 60

description: processed data file: 10xaged.tsv


title: 43552_3_B4: SS2 Aged  Wild type Grey Matter A4 63

description: processed data file: 10xaged.tsv


title: 43552_3_H12: SS2 Aged  Wild type White Matter A4 86

description: processed data file: 10xaged.tsv


title: 43552_3_A5: SS2 Aged  Wild type Grey Matter A4 59

description: processed data file: 10xaged.tsv


title: 43552_3_E4: SS2 Aged  Wild type Grey Matter A4 78

description: processed data file: 10xaged.tsv


title: 43552_3_E12: SS2 Aged  Wild type White Matter A4 77

description: processed data file: 10xaged.tsv


title: 43552_3_A11: SS2 Aged  Wild type White Matter A4 56

description: processed data file: 10xaged.tsv


title: 43552_3_A4: SS2 Aged  Wild type Grey Matter A4 58

description: processed data file: 10xaged.tsv


title: 43552_3_A10: SS2 Aged  Wild type White Matter A4 55

description: processed data file: 10xaged.tsv


title: 43552_3_A12: SS2 Aged  Wild type White Matter A4 57

description: processed data file: 10xaged.tsv


title: 43552_1_H9: SS2 Aged  Wild type White Matter A4 54

description: processed data file: 10xaged.tsv


title: 43552_1_H8: SS2 Aged  Wild type White Matter A4 53

description: processed data file: 10xaged.tsv


title: 43552_1_H4: SS2 Aged  Wild type Grey Matter A4 50

description: processed data file: 10xaged.tsv


title: 43552_1_H12: SS2 Aged  Wild type White Matter A4 49

description: processed data file: 10xaged.tsv


title: 43552_1_G9: SS2 Aged  Wild type White Matter A4 48

description: processed data file: 10xaged.tsv


title: 43552_1_G3: SS2 Aged  Wild type Grey Matter A4 46

description: processed data file: 10xaged.tsv


title: 43552_1_G11: SS2 Aged  Wild type White Matter A4 45

description: processed data file: 10xaged.tsv


title: 43552_1_H7: SS2 Aged  Wild type White Matter A4 52

description: processed data file: 10xaged.tsv


title: 43552_1_G8: SS2 Aged  Wild type White Matter A4 47

description: processed data file: 10xaged.tsv


title: 43552_1_G10: SS2 Aged  Wild type White Matter A4 44

description: processed data file: 10xaged.tsv


title: 43552_1_E9: SS2 Aged  Wild type White Matter A4 43

description: processed data file: 10xaged.tsv


title: 43552_1_H5: SS2 Aged  Wild type Grey Matter A4 51

description: processed data file: 10xaged.tsv


title: 43552_1_E6: SS2 Aged  Wild type Grey Matter A4 41

description: processed data file: 10xaged.tsv


title: 43552_1_E3: SS2 Aged  Wild type Grey Matter A4 38

description: processed data file: 10xaged.tsv


title: 43552_1_E5: SS2 Aged  Wild type Grey Matter A4 40

description: processed data file: 10xaged.tsv


title: 43552_1_E4: SS2 Aged  Wild type Grey Matter A4 39

description: processed data file: 10xaged.tsv


title: 43552_3_B5: SS2 Aged  Wild type Grey Matter A4 64

description: processed data file: 10xaged.tsv


title: 43552_1_E11: SS2 Aged  Wild type White Matter A4 37

description: processed data file: 10xaged.tsv


title: 43552_1_E10: SS2 Aged  Wild type White Matter A4 36

description: processed data file: 10xaged.tsv


title: 43552_1_E7: SS2 Aged  Wild type White Matter A4 42

description: processed data file: 10xaged.tsv


title: 43552_1_D7: SS2 Aged  Wild type White Matter A4 34

description: processed data file: 10xaged.tsv


title: 43552_1_D6: SS2 Aged  Wild type Grey Matter A4 33

description: processed data file: 10xaged.tsv


title: 43552_1_D5: SS2 Aged  Wild type Grey Matter A4 32

description: processed data file: 10xaged.tsv


title: 43552_1_D4: SS2 Aged  Wild type Grey Matter A4 31

description: processed data file: 10xaged.tsv


title: 43552_1_D3: SS2 Aged  Wild type Grey Matter A4 30

description: processed data file: 10xaged.tsv


title: 43552_1_C9: SS2 Aged  Wild type White Matter A4 28

description: processed data file: 10xaged.tsv


title: 43552_1_D10: SS2 Aged  Wild type White Matter A4 29

description: processed data file: 10xaged.tsv


title: 43552_1_C6: SS2 Aged  Wild type Grey Matter A4 26

description: processed data file: 10xaged.tsv


title: 43552_1_C5: SS2 Aged  Wild type Grey Matter A4 25

description: processed data file: 10xaged.tsv


title: 43552_1_C4: SS2 Aged  Wild type Grey Matter A4 24

description: processed data file: 10xaged.tsv


title: 43552_1_C3: SS2 Aged  Wild type Grey Matter A4 23

description: processed data file: 10xaged.tsv


title: 43552_1_C2: SS2 Aged  Wild type Grey Matter A4 22

description: processed data file: 10xaged.tsv


title: 43552_1_C11: SS2 Aged  Wild type White Matter A4 21

description: processed data file: 10xaged.tsv


title: 43552_1_B6: SS2 Aged  Wild type Grey Matter A4 17

description: processed data file: 10xaged.tsv


title: 43552_1_C10: SS2 Aged  Wild type White Matter A4 20

description: processed data file: 10xaged.tsv


title: 43552_1_B8: SS2 Aged  Wild type White Matter A4 18

description: processed data file: 10xaged.tsv


title: 43552_1_B5: SS2 Aged  Wild type Grey Matter A4 16

description: processed data file: 10xaged.tsv


title: 43552_1_B9: SS2 Aged  Wild type White Matter A4 19

description: processed data file: 10xaged.tsv


title: 43552_1_B2: SS2 Aged  Wild type Grey Matter A4 13

description: processed data file: 10xaged.tsv


title: 43552_1_B10: SS2 Aged  Wild type White Matter A4 12

description: processed data file: 10xaged.tsv


title: 43552_1_A8: SS2 Aged  Wild type White Matter A4 10

description: processed data file: 10xaged.tsv


title: 43552_1_B4: SS2 Aged  Wild type Grey Matter A4 15

description: processed data file: 10xaged.tsv


title: 43552_1_A4: SS2 Aged  Wild type Grey Matter A4 6

description: processed data file: 10xaged.tsv


title: 43552_1_A5: SS2 Aged  Wild type Grey Matter A4 7

description: processed data file: 10xaged.tsv


title: 43552_1_D8: SS2 Aged  Wild type White Matter A4 35

description: processed data file: 10xaged.tsv


title: 43552_1_A7: SS2 Aged  Wild type White Matter A4 9

description: processed data file: 10xaged.tsv


title: 43552_1_A3: SS2 Aged  Wild type Grey Matter A4 5

description: processed data file: 10xaged.tsv


title: 43552_1_A6: SS2 Aged  Wild type Grey Matter A4 8

description: processed data file: 10xaged.tsv


title: 43552_1_A2: SS2 Aged  Wild type Grey Matter A4 4

description: processed data file: 10xaged.tsv


title: 43552_1_A11: SS2 Aged  Wild type White Matter A4 3

description: processed data file: 10xaged.tsv


title: 43552_1_A1: SS2 Aged  Wild type Grey Matter A4 1

description: processed data file: 10xaged.tsv


title: 43552_1_C7: SS2 Aged  Wild type White Matter A4 27

description: processed data file: 10xaged.tsv


title: 43552_1_A10: SS2 Aged  Wild type White Matter A4 2

description: processed data file: 10xaged.tsv


title: 43517_3_G7: SS2 Aged  Wild type White Matter A3 36

description: processed data file: 10xaged.tsv


title: 43517_3_F7: SS2 Aged  Wild type White Matter A3 35

description: processed data file: 10xaged.tsv


title: 43517_3_F6: SS2 Aged  Wild type Grey Matter A3 34

description: processed data file: 10xaged.tsv


title: 43517_3_F4: SS2 Aged  Wild type Grey Matter A3 32

description: processed data file: 10xaged.tsv


title: 43552_1_B3: SS2 Aged  Wild type Grey Matter A4 14

description: processed data file: 10xaged.tsv


title: 43517_3_F12: SS2 Aged  Wild type White Matter A3 29

description: processed data file: 10xaged.tsv


title: 43517_3_F3: SS2 Aged  Wild type Grey Matter A3 31

description: processed data file: 10xaged.tsv


title: 43552_1_A9: SS2 Aged  Wild type White Matter A4 11

description: processed data file: 10xaged.tsv


title: 43517_3_E9: SS2 Aged  Wild type White Matter A3 28

description: processed data file: 10xaged.tsv


title: 43517_3_E6: SS2 Aged  Wild type Grey Matter A3 27

description: processed data file: 10xaged.tsv


title: 43517_3_E3: SS2 Aged  Wild type Grey Matter A3 26

description: processed data file: 10xaged.tsv


title: 43517_3_E12: SS2 Aged  Wild type White Matter A3 25

description: processed data file: 10xaged.tsv


title: 43517_3_E10: SS2 Aged  Wild type White Matter A3 23

description: processed data file: 10xaged.tsv


title: 43517_3_D9: SS2 Aged  Wild type White Matter A3 22

description: processed data file: 10xaged.tsv


title: 43517_3_E11: SS2 Aged  Wild type White Matter A3 24

description: processed data file: 10xaged.tsv


title: 43517_3_D6: SS2 Aged  Wild type Grey Matter A3 20

description: processed data file: 10xaged.tsv


title: 43517_3_D8: SS2 Aged  Wild type White Matter A3 21

description: processed data file: 10xaged.tsv


title: 43517_3_D5: SS2 Aged  Wild type Grey Matter A3 19

description: processed data file: 10xaged.tsv


title: 43517_3_D3: SS2 Aged  Wild type Grey Matter A3 17

description: processed data file: 10xaged.tsv


title: 43517_3_D10: SS2 Aged  Wild type White Matter A3 15

description: processed data file: 10xaged.tsv


title: 43517_3_C4: SS2 Aged  Wild type Grey Matter A3 14

description: processed data file: 10xaged.tsv


title: 43517_3_C12: SS2 Aged  Wild type White Matter A3 12

description: processed data file: 10xaged.tsv


title: 43517_3_D4: SS2 Aged  Wild type Grey Matter A3 18

description: processed data file: 10xaged.tsv


title: 43517_3_C11: SS2 Aged  Wild type White Matter A3 11

description: processed data file: 10xaged.tsv


title: 43517_3_D11: SS2 Aged  Wild type White Matter A3 16

description: processed data file: 10xaged.tsv


title: 43517_3_B6: SS2 Aged  Wild type Grey Matter A3 10

description: processed data file: 10xaged.tsv


title: 43517_3_F5: SS2 Aged  Wild type Grey Matter A3 33

description: processed data file: 10xaged.tsv


title: 43517_3_C3: SS2 Aged  Wild type Grey Matter A3 13

description: processed data file: 10xaged.tsv


title: 43517_3_B4: SS2 Aged  Wild type Grey Matter A3 9

description: processed data file: 10xaged.tsv


title: 43517_3_F2: SS2 Aged  Wild type Grey Matter A3 30

description: processed data file: 10xaged.tsv


title: 43517_3_B12: SS2 Aged  Wild type White Matter A3 8

description: processed data file: 10xaged.tsv


title: 43517_3_A9: SS2 Aged  Wild type White Matter A3 7

description: processed data file: 10xaged.tsv


title: 43517_3_A6: SS2 Aged  Wild type Grey Matter A3 5

description: processed data file: 10xaged.tsv


title: 43517_3_A5: SS2 Aged  Wild type Grey Matter A3 4

description: processed data file: 10xaged.tsv


title: 43517_3_A4: SS2 Aged  Wild type Grey Matter A3 3

description: processed data file: 10xaged.tsv


title: 43552_4_H4: SS2 Aged  Wild type Grey Matter A2 22

description: processed data file: 10xaged.tsv


title: 43552_4_H3: SS2 Aged  Wild type Grey Matter A2 21

description: processed data file: 10xaged.tsv


title: 43552_4_H2: SS2 Aged  Wild type Grey Matter A2 20

description: processed data file: 10xaged.tsv


title: 43552_4_H10: SS2 Aged  Wild type White Matter A2 19

description: processed data file: 10xaged.tsv


title: 43552_4_H9: SS2 Aged  Wild type White Matter A2 23

description: processed data file: 10xaged.tsv


title: 43517_3_A10: SS2 Aged  Wild type White Matter A3 1

description: processed data file: 10xaged.tsv


title: 43517_3_A2: SS2 Aged  Wild type Grey Matter A3 2

description: processed data file: 10xaged.tsv


title: 43552_4_G10: SS2 Aged  Wild type White Matter A2 15

description: processed data file: 10xaged.tsv


title: 43552_4_G8: SS2 Aged  Wild type White Matter A2 18

description: processed data file: 10xaged.tsv


title: 43552_4_D3: SS2 Aged  Wild type Grey Matter A2 12

description: processed data file: 10xaged.tsv


title: 43552_4_E1: SS2 Aged  Wild type Grey Matter A2 13

description: processed data file: 10xaged.tsv


title: 43552_4_G4: SS2 Aged  Wild type Grey Matter A2 16

description: processed data file: 10xaged.tsv


title: 43552_4_E8: SS2 Aged  Wild type White Matter A2 14

description: processed data file: 10xaged.tsv


title: 43552_4_G5: SS2 Aged  Wild type Grey Matter A2 17

description: processed data file: 10xaged.tsv


title: 43552_4_D2: SS2 Aged  Wild type Grey Matter A2 11

description: processed data file: 10xaged.tsv


title: 43517_3_A8: SS2 Aged  Wild type White Matter A3 6

description: processed data file: 10xaged.tsv


title: 43552_4_B8: SS2 Aged  Wild type White Matter A2 8

description: processed data file: 10xaged.tsv


title: 43552_4_B2: SS2 Aged  Wild type Grey Matter A2 4

description: processed data file: 10xaged.tsv


title: 43552_4_B3: SS2 Aged  Wild type Grey Matter A2 5

description: processed data file: 10xaged.tsv


title: 43552_4_B4: SS2 Aged  Wild type Grey Matter A2 6

description: processed data file: 10xaged.tsv


title: 43552_4_B5: SS2 Aged  Wild type Grey Matter A2 7

description: processed data file: 10xaged.tsv


title: 43556_1_H3: SS2 Aged  Wild type Grey Matter A1 13

description: processed data file: 10xaged.tsv

value: female


title: 43552_4_B1: SS2 Aged  Wild type Grey Matter A2 3

description: processed data file: 10xaged.tsv


title: 43552_4_A9: SS2 Aged  Wild type White Matter A2 2

description: processed data file: 10xaged.tsv


title: 43556_1_H4: SS2 Aged  Wild type Grey Matter A1 14

description: processed data file: 10xaged.tsv


title: 43556_1_H1: SS2 Aged  Wild type Grey Matter A1 11

description: processed data file: 10xaged.tsv


title: 43556_1_H2: SS2 Aged  Wild type Grey Matter A1 12

description: processed data file: 10xaged.tsv


title: 43552_4_A8: SS2 Aged  Wild type White Matter A2 1

description: processed data file: 10xaged.tsv


title: 43556_1_G2: SS2 Aged  Wild type Grey Matter A1 9

description: processed data file: 10xaged.tsv


title: 43556_1_C2: SS2 Aged  Wild type Grey Matter A1 4

description: processed data file: 10xaged.tsv


title: 43556_1_D1: SS2 Aged  Wild type Grey Matter A1 5

description: processed data file: 10xaged.tsv


title: 43552_4_B9: SS2 Aged  Wild type White Matter A2 9

description: processed data file: 10xaged.tsv


title: 43556_1_E2: SS2 Aged  Wild type Grey Matter A1 7

description: processed data file: 10xaged.tsv


title: 43552_4_D10: SS2 Aged  Wild type White Matter A2 10

description: processed data file: 10xaged.tsv


title: 43556_1_E3: SS2 Aged  Wild type Grey Matter A1 8

description: processed data file: 10xaged.tsv


title: 43556_1_B1: SS2 Aged  Wild type Grey Matter A1 2

description: processed data file: 10xaged.tsv


title: 43556_1_E1: SS2 Aged  Wild type Grey Matter A1 6

description: processed data file: 10xaged.tsv


title: Paternal_FD_TG_1_eight_cell_RNA_Seq

city: Sainte-Anne-de-Bellevue

first: Sarah

last: Kimmins

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

data_processing:
Reads were trimmed using Trimmomatic (version 0.38, Bolger et al., 2014) in paired-end mode (TruSeq3-PE.fa:1:30:15 TRAILING:25 MINLEN:30). Reads were were mapped to the mm10 genome with Hisat2 (version 2.1.0, K in paired-end mode using the standard settings. SAMtools (version 1.7, Li et al., 2009) was then used to sort and convert SAM files into BAM files. Transcripts were called using Stringtie (version 2.0.4, Pertea et al., 2015). RPKM normalized bigwig coverage tracks were generated from aligned reads using DeepTools2 (Ramírez et al., 2016) using 10 bp windows.
Genome_build: mm10

molecule: polyA RNA

source_name: Pre-implantation embryo

extract_protocol:
Total RNA was extracted using Tri-Reagent
mRNA-Seq libraries were generated using the NEBNext Single Cell / Low Input RNA Library Preparation Kit for Illumina as per manufacturer recommendations

treatment_protocol: Wildtype or KDM1A transgenic male C57BL/6 mice were fed a folate sufficient (2.0 mg/kg) or folate deficient (0.3 mg/kg) for 9 - 11 weeks beginning at weaning. Males were then bred to wildtype females on a folate sufficient diet and 8-cell embryos were collected on embryonic day 2.5.

tag: developmental stage

value: 8-cell pre-implantation embryo

value: Transgenic (KDM1A overexpressing)

tag: diet

value: Folate deficient


title: 43556_1_A1: SS2 Aged  Wild type Grey Matter A1 1

description: processed data file: 10xaged.tsv


title: 43556_1_C1: SS2 Aged  Wild type Grey Matter A1 3

description: processed data file: 10xaged.tsv


title: Paternal_FD_WT_3_eight_cell_RNA_Seq

value: Wildtype


title: Paternal_FD_TG_3_eight_cell_RNA_Seq


title: Paternal_FD_TG_2_eight_cell_RNA_Seq


title: Paternal_FD_WT_2_eight_cell_RNA_Seq


title: Paternal_FD_WT_1_eight_cell_RNA_Seq


title: Paternal_FS_TG_3_eight_cell_RNA_Seq

value: Folate sufficient


title: Paternal_FS_TG_2_eight_cell_RNA_Seq


title: Paternal_FS_TG_1_eight_cell_RNA_Seq


title: Paternal_FS_WT_3_eight_cell_RNA_Seq


title: Paternal_FS_WT_1_eight_cell_RNA_Seq


title: Paternal_FS_WT_2_eight_cell_RNA_Seq


title: 43556_1_G4: SS2 Aged  Wild type Grey Matter A1 10

description: processed data file: 10xaged.tsv


title: Paternal_FS_A_eight_cell_H3K4me3

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic (version 0.38, Bolger et al., 2014). Reads were mapped to  the December 2011 assembly of the mouse genome downloaded from UCSC Genome Browser  (mm10, NCBI Build 38, Haeussler et al., 2019) with Bowtie2 (version 2.3.5, Ben et al., 2012). SAMtools (version 1.7, Li et al., 2012) was then used to sort and convert SAM files and RPKM normalized bigwig coverage tracks were generated from aligned reads using DeepTools2 (Fidel et al., 2016) using 10 bp windows.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

extract_protocol:
For Ultra-Low-Input ChIP-Sequencing (Brind'Amour et al., Nature Communications, 2015), embryos in nuclear isolation buffer were thawed on ice and embryos from the same breeding groups were pooled to obtain about 250 cells per immunoprecipitation (2 – 3 litters pooled per ChIP). Cells were lysed and MNase digestion was performed for 7.5 minutes at 21°C. Reaction was stopped by adding EDTA. Chromatin was pre-cleared for an hour and 0.125 μg of H3K4me3 antibody was added. Samples were pre-cleared and incubated overnight with the antibody. The next day, the samples were washed and DNA was eluted. RNase A and proteinase K treatments were performed. A phenol:chloroform extraction was done, followed by a chloroform extraction to remove any remnant traces of phenol. DNA was precipitated, pelleted and resuspended in elution buffer.
Qiagen Ultralow Input Library Kit as per manufacturer's instructions

treatment_protocol: Wildtype male C57BL/6 mice were fed a folate sufficient (2.0 mg/kg) or folate deficient (0.3 mg/kg) for 9 - 11 weeks beginning at weaning. Males were then bred to wildtype females on a folate sufficient diet and 8-cell embryos were collected on embryonic day 2.5.

tag: chip antibody

value: H3K4me3, Diagenode, catalogue #C15410003-10, lot #A1052D


title: Paternal_FD_B_eight_cell_H3K4me3


title: Paternal_FS_B_eigth_cell_H3K4me3


title: FD_TG_4_Sperm_H3K4me3

source_name: Mouse sperm

extract_protocol:
Sperm was collected from the caudal epididymis using a previously described swim-out procedure (Hisano et al., 2013). For ChIP-Sequencing on sperm (Hisano et al., 2013), 9 x 106 mouse spermatozoa from individual mice were washed three times in PBS and treated with dithiothreitol to open the chromatin. Mouse spermatozoa were lysed, washed with PBS, and aliquoted into three tubes per sample. Spermatozoa were lysed again and subject to MNase digestion using 15 units per tube for 5 minutes. Reaction was stopped by adding EDTA. After spinning at maximum speed for 10 minutes, supernatants were pooled on ice. Samples were pre-cleared and incubated overnight with 5 μg of H3K4me3 antibody. The next day, samples were washed, eluted, and treated with RNase A and Proteinase K. DNA was extracted with the Zymo Kit ChIP DNA Clean and Concentrator. For 8-cell embryo collection, wildtype males on a folate sufficient or folate deficient diet were bred to C57BL/6 females on a folate sufficient diet and 8-cell embryos were collected on embryonic day E2.5. 8-cell embryos were washed in drops of M2/Penicillin-Streptomycin media and passed through drops of Acidic Tyrode's to remove the zona pellucida. 8-cell embryos were subsequently washed in M2/Penicillin-Streptomycin media and treated with lysis buffer before
Qiagen Ultralow Input Library Kit as per manufacturer's instructions

treatment_protocol: Wildtype or KDM1A overexpressing transgenic male C57BL/6 mice were fed a folate sufficient (2.0 mg/kg) or folate deficient (0.3 mg/kg) for 9 - 11 weeks beginning at weaning.

value: Mature sperm

value: H3K4me3, Cell Signaling, catalogue #9751, lot #10


title: FS_WT_5_Sperm_H3K4me3


title: FS_TG_4_Sperm_H3K4me3


title: FS_WT_4_Sperm_H3K4me3


title: FS_TG_2_Sperm_H3K4me3


title: FD_WT_3_Sperm_H3K4me3


title: FD_WT_4_Sperm_H3K4me3


title: FD_TG_5_Sperm_H3K4me3


title: FD_WT_5_Sperm_H3K4me3


title: FD_TG_3_Sperm_H3K4me3


title: FS_TG_1_Sperm_H3K4me3

value: Trangenic (KDM1A overexpressing)


title: FD_WT_1_Sperm_H3K4me3


title: FD_TG_1_Sperm_H3K4me3


title: FS_WT_2_Sperm_H3K4me3


title: FS_WT_3_Sperm_H3K4me3


title: FS_TG_3_Sperm_H3K4me3


title: FD_WT_2_Sperm_H3K4me3


title: FD_TG_2_Sperm_H3K4me3


title: FS_WT_1_Sperm_H3K4me3


title: FS_TG_5_Sperm_H3K4me3


title: Spt4 NETseq Replicate 1

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

country: USA

institute: University of Alabama at Birmingham

data_processing:
Library strategy: NET-seq
Base calling was performed using bcl2fastq software (version 2.20.00).
Reads were deduplicated using the UMI sequence with fqtrim (version 0.9.7) by adding the "-C" option.
Reads that contained the sequence 5’-AGNNNNNNNNTG-3’ at the 5' end were isolated, and these twelve nucleotides were removed using cutadapt (version 1.12). The parameters "-g -no-indels" were used.
The 3' sequence 5’-CTGTAGGCACCAT-3’ was removed using cutadapt (version 1.12), with the parameters "-a -no-indels".
Reads were aligned to the Saccharomyces cerevisiae genome assembly R64-1-1 with STAR (version 2.7.1a). The alignIntronMax parameter was set to 1.
Output BAM files were sorted and indexed using SAMtools (version 1.6).
The BAM files were converted to BED files using BEDTools (version 2.26.0).
Genome coverage files were created using BEDTools (version 2.26.0), with the genomecov function and parameters "- strand" and "+strand".
Data visualization was performed using R (version 3.6.2).
Genome_build: S. cerevisiae R64-1-1

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cells were grown at 30ºC until OD600 reached 0.3.

extract_protocol:
Extraction methods were based on Clarke et. al., NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I, PNAS, 2018. 115 (50), E11633-E11641. In brief, cells were harvested by filtration and flash frozen. Then, cells were lysed for 10-one minute cycles with a mikro dismembranator II under cryogenic conditions. Immnoprecipitation was performed as previously described, by incubating samples with anti-HA magnetic beads for 3 hours. RNA was extracted with an acidic phenol-chloroform extraction, then RNA was precipitated at -80ºC with ammonium acetate ethanol solution.
Libraries were constructed based on previous methods in  Clarke et. al., NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I, PNAS, 2018. 115 (50), E11633-E11641. To summarize, a DNA linker containing a UMI sequence (5’-/5rApp/CANNNNNNNNCTCCACGAGTCATCCGC /3ddC/-3’) was ligated to the 3' end of the isolated RNA transcripts. A gel extraction was performed to remove residual linker from the sample. Samples underwent reverse transcription to produce cDNA, then another gel extraction was used to remove excess reverse transcription primer from sample. Finally, samples were circularized, libraries were amplified, and PCRCleanDX magnetic beads were used to prepare libraries for sequencing.


title: Spt4 NETseq Replicate 2


title: Spt4 NETseq Replicate 3


title: Wild-Type NETseq Replicate 3

value: wild-type


title: TDF cells GFP KO experiment 2 biological replicate 10 (DNA-seq)

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Library strategy: DNA-Seq
Raw sequenced reads were adapter/quality trimmed using TrimGalore 0.6.0 and then aligned to the GRCh37/hg19 genome using bwa mem (bwa 0.7.15) 58 with subsequent sorting and merging of replicates performed using samtools 0.1.19 65 (total coverage per sample: ~8x)
Paired (relative) copy number analysis directly comparing wild-type or cntr-KO cells and MSL-disrupted cells was performed using CNVKit (0.9.5) (Talevich et al. PLoS computational biology 2016) with –target-avg-size set to 3,000 nucleotides
For each chromosome, adjacent segments with common estimated absolute copy number were merged if their boundaries were no more than 5 Mb apart. Merged segments of total length < 2Mb were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing CNV detected in the MSL3_KO sample relative to WT or cntr_KO. Each segment logR is reported as the mean logR of the intervals it contains.

organism: Homo sapiens

source_name: Transformed Dermal Fibroblast cells

growth_protocol: Cells were grown in MEM medium containing Tet-free 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
DNA was extracted from the cells using DNAeasy Blood and Tissue kit (Qiagen).
Whole-genome sequencing libraries were generated using the Nextera DNA Flex Library Prep Kit (Illumina 20018705) and were confirmed to be of good quality using a TapeStation 4200 with D1000 ScreenTape (Agilent G2991AA). Libraries were equalized in DNA quantity, pooled and sequenced on an Illumina HiSeq 2500 platform generating ~ 250 million paired-end 100 bp reads per sample.

treatment_protocol: Cells were treated with 1µg/ml Doxycicline (dox) for 14 days to induce target gene KO.

tag: cell type

value: Transformed Dermal Fibroblast cells

value: GFP KO


title: TDF cells GFP KO experiment 2 biological replicate 8 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 6 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 5 (DNA-seq)


title: Wild-Type NETseq Replicate 1


title: TDF cells GFP KO experiment 2 biological replicate 9 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 3 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 10 (DNA-seq)

value: MSL3 KO


title: TDF cells MSL3 KO experiment 2 biological replicate 9 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 1 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 8 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 2 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 7 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 5 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 4 (DNA-seq)


title: Wild-Type NETseq Replicate 2


title: TDF cells MSL3 KO experiment 2 biological replicate 1 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 2 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 3 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 7 (DNA-seq)


title: TDF cells GFP KO experiment 2 biological replicate 4 (DNA-seq)


title: TDF cells MSL3 KO experiment 2 biological replicate 6 (DNA-seq)


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  9 days post infection replicate 1

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 9 days post infection replicate 1

hyb_protocol: Following fragmentation, samples were hybridized for 16 hr at 45C on GeneChip Rhesus Macaque.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

label: biotin

organism: Macaca mulatta

label_protocol: The cDNA (3.75 μg) was fragmented and labeled using the Encore Biotin Labeling Kit

extract_protocol: The miRNeasy Mini kit (Qiagen) was used to extract total RNA

treatment_protocol: Rhesus monkeys (Macaca mulatta; WNV-seronegative; 2–3-year-old) were inoculated intrathalamically (bilaterally) with a dose of 5.0 log10 PFU of wild-type WNV strain NY99-35262. CNS tissue from these animals was systematically collected for downstream analyses

tag: time point

value: 9 days post infection

value: lumbar cord

tag: infection


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  9 days post infection replicate 2

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 9 days post infection replicate 2


description: Gene expression data from Rhesus Macaque lumbar cord with mock infected day 14 rep 1

value: day 14

value: mock


description: Gene expression data from Rhesus Macaque lumbar cord with mock infected day 10 rep 1

value: day 10


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  7 days post infection replicate 2

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 2

value: 7 days post infection


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  7 days post infection replicate 1

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 1


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 7 days post infection replicate 2

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 2

value: cerebellum

tag: days post-infection


description: Gene expression data from Rhesus Macaque lumbar cord with mock infected day 7 rep 1

value: day 7


title: Rhesus Macaque cerebellum with mock infected day 10 rep 1

description: Gene expression data from Rhesus Macaque with mock infected day 10 rep 1

value: mock - day 10


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 9 days post infection replicate 1

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 9 days post infection replicate 1


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 9 days post infection replicate 2

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 9 days post infection replicate 2


description: Gene expression data from Rhesus Macaque lumbar cord with mock infected day 21 rep 1

value: day 21


title: Rhesus Macaque cerebellum with mock infected day 14 rep 1

description: Gene expression data from Rhesus Macaque with mock infected day 14 rep 1

value: mock - day 14


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  10 days post infection replicate 1

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 10 days post infection replicate 1

value: 10 days post infection


title: Rhesus Macaque cerebellum with mock infected day 21 rep 1

description: Gene expression data from Rhesus Macaque with mock infected day 21 rep 1

value: mock - day 21


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  3 days post infection replicate 2

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 2

value: 3 days post infection


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 10 days post infection replicate 1

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 10 days post infection replicate 1


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  7 days post infection replicate 3

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 3


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 3 days post infection replicate 3

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 3


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 3 days post infection replicate 2

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 2


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 7 days post infection replicate 1

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 1


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 3 days post infection replicate 1

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 1


title: Rhesus Macaque cerebellum with West Nile virus neuroinvasive disease 7 days post infection replicate 3

description: Gene expression data from Rhesus Macaque with West Nile virus neuroinvasive disease from 1999 outbreak in New York 7 days post infection replicate 3


title: TDF cells MSL3 KO experiment 1 biological replicate 10 (DNA-seq)

value: Transformed Dermal Fibroblast cells


title: TDF cells MSL3 KO experiment 1 biological replicate 9 (DNA-seq)


description: Gene expression data from Rhesus Macaque cerebellum with mock infected day 7 rep 1


title: TDF cells MSL3 KO experiment 1 biological replicate 8 (DNA-seq)


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  3 days post infection replicate 1

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 1


title: Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease  3 days post infection replicate 3

description: Gene expression data from Rhesus Macaque lumbar cord with West Nile virus neuroinvasive disease from 1999 outbreak in New York 3 days post infection replicate 3


title: TDF cells MSL3 KO experiment 1 biological replicate 6 (DNA-seq)


title: TDF cells MSL3 KO experiment 1 biological replicate 7 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 10 (DNA-seq)

value: WT


title: TDF cells WT experiment 1 biological replicate 8 (DNA-seq)


title: TDF cells MSL3 KO experiment 1 biological replicate 2 (DNA-seq)

value: MSL3 KO


title: TDF cells MSL3 KO experiment 1 biological replicate 5 (DNA-seq)


title: TDF cells MSL3 KO experiment 1 biological replicate 3 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 6 (DNA-seq)


title: TDF cells MSL3 KO experiment 1 biological replicate 4 (DNA-seq)


title: TDF cells MSL3 KO experiment 1 biological replicate 1 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 5 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 9 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 3 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 7 (DNA-seq)


title: MCF7_HJT_rep1

city: Hangzhou

first: shujing

last: zhang

address: Xihu district

department: College of Pharmaceutical Sciences

country: China

institute: Zhejiang University

description: Gene expression data from MCF7 after HJT treatment

hyb_protocol: On completion of the fragmentation reaction,array hybridizations was proceeded using the GeneChip® Hybridization, Wash, and Stain Kit, (30 rxns),according to the manufacturer's instructions.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: The scanned images were analyzed with Affymetrix GeneChip Command Console(version4.0, Affymetrix)using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring (version 13.1, Agilent Technologies).

label: Biotin

source_name: MCF7 cell,HJT,replicate4

label_protocol: Biotin labeled cRNA was prepared from 0.2 ug RNA using GeneChip® 3’ IVT Express Kit according to the manufacturer's instructions, followed by aRNA Purification(Components of the GeneChip® IVT Express Kit, box 1, are used for this step).aRNA quantitation and expected yield were checked with NanoDrop Spectrophotometers according to the manufacturer's instructions

growth_protocol: MCF7 cells were cultured in DMEM medium (Corning), containing 10% fetal bovine serum and 0.1% antibiotics in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: MCF7 cells were sham washed or treated with HJT(dilution ratio=1/10) for 6 h

tag: cell line

tag: treatment

value: HJT


title: MCF7_HJT_rep2

source_name: MCF7 cell,HJT,replicate5


title: MCF7_Control_rep2

description: Gene expression data from MCF7

source_name: MCF7 cell,control,replicate2

value: control


title: MCF7_Control_rep1

description: Gene expression data from MCF7

source_name: MCF7 cell,control,replicate1


title: MCF7_HJT_rep3

source_name: MCF7 cell,HJT,replicate6


title: TDF cells WT experiment 1 biological replicate 4 (DNA-seq)


title: PHH - S1423T_TUN_10_TP-8_REP-2 [2b20_8hrDonor3TM10]

city: Leiden

first: Bob

last: van de Water

address: Einsteinweg 55

department: Division of Drug Discovery and Safety

country: Netherlands

institute: Leiden Academic Centre for Drug Research (LACDR), Leiden University

description:
2b20_8hrDonor3TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

source_name: PHH - S1423T

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

value: Primary human hepatocytes

tag: compound

value: Tunicamycin (TUN)

tag: concentration

value: 10 uM

value: 8 hr

tag: replicate


title: PHH - S1423T_TUN_100_TP-8_REP-1 [1b21_8hrDonor3TM100]

description:
1b21_8hrDonor3TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_100_TP-8_REP-2 [2b21_8hrDonor3TM100]

description:
2b21_8hrDonor3TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: TDF cells WT experiment 1 biological replicate 2 (DNA-seq)


title: TDF cells WT experiment 1 biological replicate 1 (DNA-seq)


title: PHH - S1423T_TUN_100_TP-8_REP-3 [3b21_8hrDonor3TM100]

description:
3b21_8hrDonor3TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_10_TP-8_REP-3 [3b20_8hrDonor3TM10]

description:
3b20_8hrDonor3TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_10_TP-8_REP-1 [1b20_8hrDonor3TM10]

description:
1b20_8hrDonor3TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_1_TP-8_REP-1 [1b19_8hrDonor3TM1]

description:
1b19_8hrDonor3TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: PHH - S1423T_TUN_1_TP-8_REP-2 [2b19_8hrDonor3TM1]

description:
2b19_8hrDonor3TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_1_TP-8_REP-3 [3b19_8hrDonor3TM1]

description:
3b19_8hrDonor3TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.001_TP-8_REP-2 [2b16_8hrDonor3TM0.001]

description:
2b16_8hrDonor3TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.001_TP-8_REP-3 [3b16_8hrDonor3TM0.001]

description:
3b16_8hrDonor3TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.01_TP-8_REP-1 [1b17_8hrDonor3TM0.01]

description:
1b17_8hrDonor3TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.01_TP-8_REP-2 [2b17_8hrDonor3TM0.01]

description:
2b17_8hrDonor3TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_50_TP-8_REP-2 [2d21_8hrDonor3TNF50]

description:
2d21_8hrDonor3TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: PHH - S1423T_TUN_0.1_TP-8_REP-2 [2b18_8hrDonor3TM0.1]

description:
2b18_8hrDonor3TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.1_TP-8_REP-3 [3b18_8hrDonor3TM0.1]

description:
3b18_8hrDonor3TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.01_TP-8_REP-3 [3b17_8hrDonor3TM0.01]

description:
3b17_8hrDonor3TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_50_TP-8_REP-1 [1d21_8hrDonor3TNF50]

description:
1d21_8hrDonor3TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.001_TP-8_REP-1 [1b16_8hrDonor3TM0.001]

description:
1b16_8hrDonor3TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_50_TP-8_REP-3 [3d21_8hrDonor3TNF50]

description:
3d21_8hrDonor3TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_10_TP-8_REP-3 [3d20_8hrDonor3TNF10]

description:
3d20_8hrDonor3TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: PHH - S1423T_TNF_10_TP-8_REP-1 [1d20_8hrDonor3TNF10]

description:
1d20_8hrDonor3TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_10_TP-8_REP-2 [2d20_8hrDonor3TNF10]

description:
2d20_8hrDonor3TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_7.5_TP-8_REP-3 [3d19_8hrDonor3TNF7.5]

description:
3d19_8hrDonor3TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: PHH - S1423T_TNF_7.5_TP-8_REP-2 [2d19_8hrDonor3TNF7.5]

description:
2d19_8hrDonor3TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_5_TP-8_REP-3 [3d18_8hrDonor3TNF5]

description:
3d18_8hrDonor3TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: PHH - S1423T_TNF_7.5_TP-8_REP-1 [1d19_8hrDonor3TNF7.5]

description:
1d19_8hrDonor3TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TUN_0.1_TP-8_REP-1 [1b18_8hrDonor3TM0.1]

description:
1b18_8hrDonor3TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_5_TP-8_REP-2 [2d18_8hrDonor3TNF5]

description:
2d18_8hrDonor3TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_2.5_TP-8_REP-1 [1d17_8hrDonor3TNF2.5]

description:
1d17_8hrDonor3TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: PHH - S1423T_TNF_1_TP-8_REP-3 [3d16_8hrDonor3TNF1]

description:
3d16_8hrDonor3TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: PHH - S1423T_TNF_1_TP-8_REP-2 [2d16_8hrDonor3TNF1]

description:
2d16_8hrDonor3TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_1_TP-8_REP-1 [1d16_8hrDonor3TNF1]

description:
1d16_8hrDonor3TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-6 [3mWc06_8hrDonor3]

description:
3mWc06_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: PHH - S1423T_MEDIUM_0_TP-8_REP-3 [3c15_8hrDonor3CPT0]

description:
3c15_8hrDonor3CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-3 [2mWc05_8hrDonor3]

description:
2mWc05_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-3 [3d15_8hrDonor3TNF0]

description:
3d15_8hrDonor3TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-1 [1d15_8hrDonor3TNF0]

description:
1d15_8hrDonor3TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-4 [2mWc06_8hrDonor3]

description:
2mWc06_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-2 [1mWc06_8hrDonor3]

description:
1mWc06_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-1 [1c15_8hrDonor3CPT0]

description:
1c15_8hrDonor3CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-1 [1mWc05_8hrDonor3]

description:
1mWc05_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-2 [2c15_8hrDonor3CPT0]

description:
2c15_8hrDonor3CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_5_TP-8_REP-1 [1d18_8hrDonor3TNF5]

description:
1d18_8hrDonor3TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_2.5_TP-8_REP-3 [3d17_8hrDonor3TNF2.5]

description:
3d17_8hrDonor3TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DMSO_0.2_TP-8_REP-3 [3a15_8hrDonor3DEM0]

description:
3a15_8hrDonor3DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: PHH - S1423T_DMSO_0.2_TP-8_REP-2 [2b15_8hrDonor3TM0]

description:
2b15_8hrDonor3TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DMSO_0.2_TP-8_REP-2 [2a15_8hrDonor3DEM0]

description:
2a15_8hrDonor3DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DMSO_0.2_TP-8_REP-1 [1b15_8hrDonor3TM0]

description:
1b15_8hrDonor3TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DMSO_0.2_TP-8_REP-3 [3b15_8hrDonor3TM0]

description:
3b15_8hrDonor3TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DMSO_0.2_TP-8_REP-1 [1a15_8hrDonor3DEM0]

description:
1a15_8hrDonor3DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_3300_TP-8_REP-1 [1a21_8hrDonor3DEM3300]

description:
1a21_8hrDonor3DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: PHH - S1423T_DEM_3300_TP-8_REP-2 [2a21_8hrDonor3DEM3300]

description:
2a21_8hrDonor3DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_1000_TP-8_REP-3 [3a20_8hrDonor3DEM1000]

description:
3a20_8hrDonor3DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_TNF_2.5_TP-8_REP-2 [2d17_8hrDonor3TNF2.5]

description:
2d17_8hrDonor3TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_1000_TP-8_REP-2 [2a20_8hrDonor3DEM1000]

description:
2a20_8hrDonor3DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_3300_TP-8_REP-3 [3a21_8hrDonor3DEM3300]

description:
3a21_8hrDonor3DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_1000_TP-8_REP-1 [1a20_8hrDonor3DEM1000]

description:
1a20_8hrDonor3DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-2 [2d15_8hrDonor3TNF0]

description:
2d15_8hrDonor3TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_MEDIUM_0_TP-8_REP-5 [3mWc05_8hrDonor3]

description:
3mWc05_8hrDonor3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_333_TP-8_REP-3 [3a19_8hrDonor3DEM333]

description:
3a19_8hrDonor3DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_333_TP-8_REP-1 [1a19_8hrDonor3DEM333]

description:
1a19_8hrDonor3DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_100_TP-8_REP-3 [3a18_8hrDonor3DEM100]

description:
3a18_8hrDonor3DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_333_TP-8_REP-2 [2a19_8hrDonor3DEM333]

description:
2a19_8hrDonor3DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_100_TP-8_REP-2 [2a18_8hrDonor3DEM100]

description:
2a18_8hrDonor3DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_100_TP-8_REP-1 [1a18_8hrDonor3DEM100]

description:
1a18_8hrDonor3DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_10_TP-8_REP-2 [2a17_8hrDonor3DEM10]

description:
2a17_8hrDonor3DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_1_TP-8_REP-1 [1a16_8hrDonor3DEM1]

description:
1a16_8hrDonor3DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_DEM_1_TP-8_REP-2 [2a16_8hrDonor3DEM1]

description:
2a16_8hrDonor3DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_100_TP-8_REP-3 [3c21_8hrDonor3CPT100]

description:
3c21_8hrDonor3CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: PHH - S1423T_CPT_100_TP-8_REP-2 [2c21_8hrDonor3CPT100]

description:
2c21_8hrDonor3CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_100_TP-8_REP-1 [1c21_8hrDonor3CPT100]

description:
1c21_8hrDonor3CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_33_TP-8_REP-2 [2c20_8hrDonor3CPT33]

description:
2c20_8hrDonor3CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: PHH - S1423T_DEM_10_TP-8_REP-3 [3a17_8hrDonor3DEM10]

description:
3a17_8hrDonor3DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Primary human hepatocytes


title: PHH - S1423T_CPT_33_TP-8_REP-1 [1c20_8hrDonor3CPT33]

description:
1c20_8hrDonor3CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_10_TP-8_REP-2 [2c19_8hrDonor3CPT10]

description:
2c19_8hrDonor3CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_10_TP-8_REP-1 [1c19_8hrDonor3CPT10]

description:
1c19_8hrDonor3CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_10_TP-8_REP-3 [3c19_8hrDonor3CPT10]

description:
3c19_8hrDonor3CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_3.3_TP-8_REP-3 [3c18_8hrDonor3CPT3.3]

description:
3c18_8hrDonor3CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_3.3_TP-8_REP-2 [2c18_8hrDonor3CPT3.3]

description:
2c18_8hrDonor3CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MCF7_Control_rep3

description: Gene expression data from MCF7

source_name: MCF7 cell,control,replicate3

value: control


title: PHH - S1423T_CPT_3.3_TP-8_REP-1 [1c18_8hrDonor3CPT3.3]

description:
1c18_8hrDonor3CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_0.01_TP-8_REP-3 [3c16_8hrDonor3CPT0.01]

description:
3c16_8hrDonor3CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_0.01_TP-8_REP-2 [2c16_8hrDonor3CPT0.01]

description:
2c16_8hrDonor3CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_0.01_TP-8_REP-1 [1c16_8hrDonor3CPT0.01]

description:
1c16_8hrDonor3CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_1_TP-8_REP-2 [2c17_8hrDonor3CPT1]

description:
2c17_8hrDonor3CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_1_TP-8_REP-3 [3c17_8hrDonor3CPT1]

description:
3c17_8hrDonor3CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_1_TP-8_REP-1 [1c17_8hrDonor3CPT1]

description:
1c17_8hrDonor3CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_100_TP-8_REP-2 [2b14_8hrDonor2TM100]

description:
2b14_8hrDonor2TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: PHH - S1307T

value: Tunicamycin (TUN)


title: PHH - S1423T_DEM_1_TP-8_REP-3 [3a16_8hrDonor3DEM1]

description:
3a16_8hrDonor3DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: PHH - S1423T_DEM_10_TP-8_REP-1 [1a17_8hrDonor3DEM10]

description:
1a17_8hrDonor3DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: PHH - S1307T_TUN_10_TP-8_REP-2 [2b13_8hrDonor2TM10]

description:
2b13_8hrDonor2TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_100_TP-8_REP-1 [1b14_8hrDonor2TM100]

description:
1b14_8hrDonor2TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_10_TP-8_REP-3 [3b13_8hrDonor2TM10]

description:
3b13_8hrDonor2TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_100_TP-8_REP-3 [3b14_8hrDonor2TM100]

description:
3b14_8hrDonor2TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1423T_CPT_33_TP-8_REP-3 [3c20_8hrDonor3CPT33]

description:
3c20_8hrDonor3CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_10_TP-8_REP-1 [1b13_8hrDonor2TM10]

description:
1b13_8hrDonor2TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_1_TP-8_REP-2 [2b12_8hrDonor2TM1]

description:
2b12_8hrDonor2TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: PHH - S1307T_TUN_0.1_TP-8_REP-2 [2b11_8hrDonor2TM0.1]

description:
2b11_8hrDonor2TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_1_TP-8_REP-1 [1b12_8hrDonor2TM1]

description:
1b12_8hrDonor2TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.1_TP-8_REP-3 [3b11_8hrDonor2TM0.1]

description:
3b11_8hrDonor2TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.1_TP-8_REP-1 [1b11_8hrDonor2TM0.1]

description:
1b11_8hrDonor2TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.01_TP-8_REP-3 [3b10_8hrDonor2TM0.01]

description:
3b10_8hrDonor2TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.01_TP-8_REP-2 [2b10_8hrDonor2TM0.01]

description:
2b10_8hrDonor2TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.01_TP-8_REP-1 [1b10_8hrDonor2TM0.01]

description:
1b10_8hrDonor2TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.001_TP-8_REP-1 [1b09_8hrDonor2TM0.001]

description:
1b09_8hrDonor2TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.001_TP-8_REP-3 [3b09_8hrDonor2TM0.001]

description:
3b09_8hrDonor2TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_0.001_TP-8_REP-2 [2b09_8hrDonor2TM0.001]

description:
2b09_8hrDonor2TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_50_TP-8_REP-3 [3d14_8hrDonor2TNF50]

description:
3d14_8hrDonor2TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: PHH - S1307T_TNF_50_TP-8_REP-2 [2d14_8hrDonor2TNF50]

description:
2d14_8hrDonor2TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_50_TP-8_REP-1 [1d14_8hrDonor2TNF50]

description:
1d14_8hrDonor2TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_10_TP-8_REP-2 [2d13_8hrDonor2TNF10]

description:
2d13_8hrDonor2TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: PHH - S1307T_TNF_10_TP-8_REP-3 [3d13_8hrDonor2TNF10]

description:
3d13_8hrDonor2TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_7.5_TP-8_REP-2 [2d12_8hrDonor2TNF7.5]

description:
2d12_8hrDonor2TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: PHH - S1307T_TNF_7.5_TP-8_REP-1 [1d12_8hrDonor2TNF7.5]

description:
1d12_8hrDonor2TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_5_TP-8_REP-2 [2d11_8hrDonor2TNF5]

description:
2d11_8hrDonor2TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: PHH - S1307T_TNF_5_TP-8_REP-3 [3d11_8hrDonor2TNF5]

description:
3d11_8hrDonor2TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TUN_1_TP-8_REP-3 [3b12_8hrDonor2TM1]

description:
3b12_8hrDonor2TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_5_TP-8_REP-1 [1d11_8hrDonor2TNF5]

description:
1d11_8hrDonor2TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_2.5_TP-8_REP-2 [2d10_8hrDonor2TNF2.5]

description:
2d10_8hrDonor2TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: PHH - S1307T_TNF_1_TP-8_REP-3 [3d09_8hrDonor2TNF1]

description:
3d09_8hrDonor2TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: PHH - S1307T_TNF_2.5_TP-8_REP-1 [1d10_8hrDonor2TNF2.5]

description:
1d10_8hrDonor2TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_2.5_TP-8_REP-3 [3d10_8hrDonor2TNF2.5]

description:
3d10_8hrDonor2TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_1_TP-8_REP-2 [2d09_8hrDonor2TNF1]

description:
2d09_8hrDonor2TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-6 [3mWc04_8hrDonor2]

description:
3mWc04_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: PHH - S1307T_MEDIUM_0_TP-8_REP-3 [2mWc03_8hrDonor2]

description:
2mWc03_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-3 [3c08_8hrDonor2CPT0]

description:
3c08_8hrDonor2CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-5 [3mWc03_8hrDonor2]

description:
3mWc03_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-3 [3d08_8hrDonor2TNF0]

description:
3d08_8hrDonor2TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-2 [2c08_8hrDonor2CPT0]

description:
2c08_8hrDonor2CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-2 [1mWc04_8hrDonor2]

description:
1mWc04_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-4 [2mWc04_8hrDonor2]

description:
2mWc04_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-1 [1mWc03_8hrDonor2]

description:
1mWc03_8hrDonor2
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-1 [1d08_8hrDonor2TNF0]

description:
1d08_8hrDonor2TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_7.5_TP-8_REP-3 [3d12_8hrDonor2TNF7.5]

description:
3d12_8hrDonor2TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-1 [1c08_8hrDonor2CPT0]

description:
1c08_8hrDonor2CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_10_TP-8_REP-1 [1d13_8hrDonor2TNF10]

description:
1d13_8hrDonor2TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DMSO_0.2_TP-8_REP-3 [3b08_8hrDonor2TM0]

description:
3b08_8hrDonor2TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: PHH - S1307T_DMSO_0.2_TP-8_REP-3 [3a08_8hrDonor2DEM0]

description:
3a08_8hrDonor2DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DMSO_0.2_TP-8_REP-2 [2b08_8hrDonor2TM0]

description:
2b08_8hrDonor2TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DMSO_0.2_TP-8_REP-2 [2a08_8hrDonor2DEM0]

description:
2a08_8hrDonor2DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DMSO_0.2_TP-8_REP-1 [1b08_8hrDonor2TM0]

description:
1b08_8hrDonor2TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DMSO_0.2_TP-8_REP-1 [1a08_8hrDonor2DEM0]

description:
1a08_8hrDonor2DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_TNF_1_TP-8_REP-1 [1d09_8hrDonor2TNF1]

description:
1d09_8hrDonor2TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_3300_TP-8_REP-1 [1a14_8hrDonor2DEM3300]

description:
1a14_8hrDonor2DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: PHH - S1307T_DEM_3300_TP-8_REP-3 [3a14_8hrDonor2DEM3300]

description:
3a14_8hrDonor2DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_3300_TP-8_REP-2 [2a14_8hrDonor2DEM3300]

description:
2a14_8hrDonor2DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1000_TP-8_REP-1 [1a13_8hrDonor2DEM1000]

description:
1a13_8hrDonor2DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1000_TP-8_REP-3 [3a13_8hrDonor2DEM1000]

description:
3a13_8hrDonor2DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_333_TP-8_REP-3 [3a12_8hrDonor2DEM333]

description:
3a12_8hrDonor2DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_MEDIUM_0_TP-8_REP-2 [2d08_8hrDonor2TNF0]

description:
2d08_8hrDonor2TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_333_TP-8_REP-2 [2a12_8hrDonor2DEM333]

description:
2a12_8hrDonor2DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_333_TP-8_REP-1 [1a12_8hrDonor2DEM333]

description:
1a12_8hrDonor2DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1000_TP-8_REP-2 [2a13_8hrDonor2DEM1000]

description:
2a13_8hrDonor2DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_100_TP-8_REP-2 [2a11_8hrDonor2DEM100]

description:
2a11_8hrDonor2DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_100_TP-8_REP-1 [1a11_8hrDonor2DEM100]

description:
1a11_8hrDonor2DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_10_TP-8_REP-2 [2a10_8hrDonor2DEM10]

description:
2a10_8hrDonor2DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_10_TP-8_REP-3 [3a10_8hrDonor2DEM10]

description:
3a10_8hrDonor2DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1_TP-8_REP-3 [3a09_8hrDonor2DEM1]

description:
3a09_8hrDonor2DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1_TP-8_REP-2 [2a09_8hrDonor2DEM1]

description:
2a09_8hrDonor2DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_1_TP-8_REP-1 [1a09_8hrDonor2DEM1]

description:
1a09_8hrDonor2DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_100_TP-8_REP-2 [2c14_8hrDonor2CPT100]

description:
2c14_8hrDonor2CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: PHH - S1307T_CPT_33_TP-8_REP-2 [2c13_8hrDonor2CPT33]

description:
2c13_8hrDonor2CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Primary human hepatocytes

value: 33 uM


title: PHH - S1307T_CPT_100_TP-8_REP-1 [1c14_8hrDonor2CPT100]

description:
1c14_8hrDonor2CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_33_TP-8_REP-3 [3c13_8hrDonor2CPT33]

description:
3c13_8hrDonor2CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_33_TP-8_REP-1 [1c13_8hrDonor2CPT33]

description:
1c13_8hrDonor2CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_10_TP-8_REP-2 [2c12_8hrDonor2CPT10]

description:
2c12_8hrDonor2CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_10_TP-8_REP-3 [3c12_8hrDonor2CPT10]

description:
3c12_8hrDonor2CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_10_TP-8_REP-1 [1c12_8hrDonor2CPT10]

description:
1c12_8hrDonor2CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_100_TP-8_REP-3 [3a11_8hrDonor2DEM100]

description:
3a11_8hrDonor2DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_3.3_TP-8_REP-1 [1c11_8hrDonor2CPT3.3]

description:
1c11_8hrDonor2CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_1_TP-8_REP-3 [3c10_8hrDonor2CPT1]

description:
3c10_8hrDonor2CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_3.3_TP-8_REP-2 [2c11_8hrDonor2CPT3.3]

description:
2c11_8hrDonor2CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_100_TP-8_REP-3 [3c14_8hrDonor2CPT100]

description:
3c14_8hrDonor2CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_0.01_TP-8_REP-1 [1c09_8hrDonor2CPT0.01]

description:
1c09_8hrDonor2CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_100_TP-8_REP-3 [3b07_8hrDonor1TM100]

description:
3b07_8hrDonor1TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: PHH - S1295T

value: Tunicamycin (TUN)


title: PHH - S1295T_TUN_100_TP-8_REP-1 [1b07_8hrDonor1TM100]

description:
1b07_8hrDonor1TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: PHH - S1307T_CPT_0.01_TP-8_REP-3 [3c09_8hrDonor2CPT0.01]

description:
3c09_8hrDonor2CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_DEM_10_TP-8_REP-1 [1a10_8hrDonor2DEM10]

description:
1a10_8hrDonor2DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: PHH - S1295T_TUN_10_TP-8_REP-3 [3b06_8hrDonor1TM10]

description:
3b06_8hrDonor1TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_100_TP-8_REP-2 [2b07_8hrDonor1TM100]

description:
2b07_8hrDonor1TM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_1_TP-8_REP-3 [3b05_8hrDonor1TM1]

description:
3b05_8hrDonor1TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: PHH - S1295T_TUN_10_TP-8_REP-1 [1b06_8hrDonor1TM10]

description:
1b06_8hrDonor1TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_1_TP-8_REP-2 [2b05_8hrDonor1TM1]

description:
2b05_8hrDonor1TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_1_TP-8_REP-1 [1b05_8hrDonor1TM1]

description:
1b05_8hrDonor1TM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_10_TP-8_REP-2 [2b06_8hrDonor1TM10]

description:
2b06_8hrDonor1TM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.1_TP-8_REP-3 [3b04_8hrDonor1TM0.1]

description:
3b04_8hrDonor1TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.1_TP-8_REP-2 [2b04_8hrDonor1TM0.1]

description:
2b04_8hrDonor1TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.01_TP-8_REP-3 [3b03_8hrDonor1TM0.01]

description:
3b03_8hrDonor1TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.01_TP-8_REP-2 [2b03_8hrDonor1TM0.01]

description:
2b03_8hrDonor1TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.1_TP-8_REP-1 [1b04_8hrDonor1TM0.1]

description:
1b04_8hrDonor1TM0.1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.01_TP-8_REP-1 [1b03_8hrDonor1TM0.01]

description:
1b03_8hrDonor1TM0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.001_TP-8_REP-3 [3b02_8hrDonor1TM0.001]

description:
3b02_8hrDonor1TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_1_TP-8_REP-1 [1c10_8hrDonor2CPT1]

description:
1c10_8hrDonor2CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_1_TP-8_REP-2 [2c10_8hrDonor2CPT1]

description:
2c10_8hrDonor2CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_0.01_TP-8_REP-2 [2c09_8hrDonor2CPT0.01]

description:
2c09_8hrDonor2CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.001_TP-8_REP-2 [2b02_8hrDonor1TM0.001]

description:
2b02_8hrDonor1TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TUN_0.001_TP-8_REP-1 [1b02_8hrDonor1TM0.001]

description:
1b02_8hrDonor1TM0.001
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_50_TP-8_REP-3 [3d07_8hrDonor1TNF50]

description:
3d07_8hrDonor1TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: PHH - S1295T_TNF_10_TP-8_REP-2 [2d06_8hrDonor1TNF10]

description:
2d06_8hrDonor1TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_50_TP-8_REP-2 [2d07_8hrDonor1TNF50]

description:
2d07_8hrDonor1TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 50 ng/mL


title: PHH - S1295T_TNF_10_TP-8_REP-3 [3d06_8hrDonor1TNF10]

description:
3d06_8hrDonor1TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: PHH - S1295T_TNF_7.5_TP-8_REP-3 [3d05_8hrDonor1TNF7.5]

description:
3d05_8hrDonor1TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: PHH - S1295T_TNF_5_TP-8_REP-3 [3d04_8hrDonor1TNF5]

description:
3d04_8hrDonor1TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: PHH - S1295T_TNF_7.5_TP-8_REP-1 [1d05_8hrDonor1TNF7.5]

description:
1d05_8hrDonor1TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_5_TP-8_REP-2 [2d04_8hrDonor1TNF5]

description:
2d04_8hrDonor1TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_2.5_TP-8_REP-3 [3d03_8hrDonor1TNF2.5]

description:
3d03_8hrDonor1TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: PHH - S1295T_TNF_5_TP-8_REP-1 [1d04_8hrDonor1TNF5]

description:
1d04_8hrDonor1TNF5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_2.5_TP-8_REP-1 [1d03_8hrDonor1TNF2.5]

description:
1d03_8hrDonor1TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_10_TP-8_REP-1 [1d06_8hrDonor1TNF10]

description:
1d06_8hrDonor1TNF10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_1_TP-8_REP-3 [3d02_8hrDonor1TNF1]

description:
3d02_8hrDonor1TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: PHH - S1295T_TNF_50_TP-8_REP-1 [1d07_8hrDonor1TNF50]

description:
1d07_8hrDonor1TNF50
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_2.5_TP-8_REP-2 [2d03_8hrDonor1TNF2.5]

description:
2d03_8hrDonor1TNF2.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_1_TP-8_REP-1 [1d02_8hrDonor1TNF1]

description:
1d02_8hrDonor1TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_1_TP-8_REP-2 [2d02_8hrDonor1TNF1]

description:
2d02_8hrDonor1TNF1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-6 [3mWc02_8hrDonor1]

description:
3mWc02_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: PHH - S1295T_MEDIUM_0_TP-8_REP-3 [3c01_8hrDonor1CPT0]

description:
3c01_8hrDonor1CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-5 [3mWc01_8hrDonor1]

description:
3mWc01_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-3 [2mWc01_8hrDonor1]

description:
2mWc01_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-2 [2c01_8hrDonor1CPT0]

description:
2c01_8hrDonor1CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-2 [1mWc02_8hrDonor1]

description:
1mWc02_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-2 [2d01_8hrDonor1TNF0]

description:
2d01_8hrDonor1TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_TNF_7.5_TP-8_REP-2 [2d05_8hrDonor1TNF7.5]

description:
2d05_8hrDonor1TNF7.5
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-4 [2mWc02_8hrDonor1]

description:
2mWc02_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-1 [1mWc01_8hrDonor1]

description:
1mWc01_8hrDonor1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-1 [1c01_8hrDonor1CPT0]

description:
1c01_8hrDonor1CPT0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1307T_CPT_3.3_TP-8_REP-3 [3c11_8hrDonor2CPT3.3]

description:
3c11_8hrDonor2CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_MEDIUM_0_TP-8_REP-1 [1d01_8hrDonor1TNF0]

description:
1d01_8hrDonor1TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DMSO_0.2_TP-8_REP-2 [2a01_8hrDonor1DEM0]

description:
2a01_8hrDonor1DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: PHH - S1295T_DMSO_0.2_TP-8_REP-3 [3b01_8hrDonor1TM0]

description:
3b01_8hrDonor1TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DMSO_0.2_TP-8_REP-1 [1a01_8hrDonor1DEM0]

description:
1a01_8hrDonor1DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DMSO_0.2_TP-8_REP-2 [2b01_8hrDonor1TM0]

description:
2b01_8hrDonor1TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DMSO_0.2_TP-8_REP-3 [3a01_8hrDonor1DEM0]

description:
3a01_8hrDonor1DEM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DMSO_0.2_TP-8_REP-1 [1b01_8hrDonor1TM0]

description:
1b01_8hrDonor1TM0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_3300_TP-8_REP-2 [2a07_8hrDonor1DEM3300]

description:
2a07_8hrDonor1DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: PHH - S1295T_DEM_1000_TP-8_REP-2 [2a06_8hrDonor1DEM1000]

description:
2a06_8hrDonor1DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_3300_TP-8_REP-1 [1a07_8hrDonor1DEM3300]

description:
1a07_8hrDonor1DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_3300_TP-8_REP-3 [3a07_8hrDonor1DEM3300]

description:
3a07_8hrDonor1DEM3300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_333_TP-8_REP-3 [3a05_8hrDonor1DEM333]

description:
3a05_8hrDonor1DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_1000_TP-8_REP-3 [3a06_8hrDonor1DEM1000]

description:
3a06_8hrDonor1DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt