title: L04_AE06_MethodBlank_0

description:
L04_AE06
Hepatocyte_normcounts.csv


title: L04_AE07_087_kerosine_10

status: Public on Jan 01 2022

type: SRA

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

country: USA

institute: National Instititute of Environmental Health Sciences

description:
L04_AE07
Hepatocyte_normcounts.csv

library_source: transcriptomic

data_processing:
pipeline run to convert reads to counts https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672545/
samples with counts < 100 average reads per transcript removed
normalized counts generated by cell type in DESEQ2
Genome_build: NA – Targeted Reads by BioSpyder
Supplementary_files_format_and_content: 6 normalized count matrix files in CSV with genes as rows and columns as samples.  The sample information in the hashfile.csv

molecule: total RNA

organism: Homo sapiens

source_name: Hepatocyte

extract_protocol:
described in https://www.altex.org/index.php/altex/article/view/1994
described in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178302

tag: tissue/celltype

value: iCell Hepatocytes

tag: treatment

value: KER

tag: dose


title: mmusculus_K21

city: Uppsala

first: Henrik

last: Boije

address: Uppsala University, Dept. Of Neuroscience, Box 593, BMC

country: Sweden

institute: Uppsala University

description: mmusculus.loom

data_processing:
Alignment and mapping: Genome indexing and read alignment was performed using STAR v.2.5.4b and Velocyto v0.17.17 (La Manno et al., 2018). Fasta files for extra genes were manually added for eGFP 146 (LC337138.1), tdTomato (GeneBank: AY678269.1) and ERCC genes (Thermofisher assets: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and gene information was added to the species GTF file (Shaner et al., 2004; Nakajima et al., 2018). Reads were mapped to GRCm38.99 genome for mus musculus or GRCz11.98 genome for danio rerio. Genes were counted using featureCounts (subread V2.0.0) and Velocyto v0.17.17. Velocyto spliced and unspliced information was added to the final loom file as seperate layers. Full scripts are deposited at Github (http://github.com/jonetjakobsson/dmrt3-single-cell)
Genome_build: GRCm38.99
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Loom file containing layers; reads, RPKM, spliced and unspliced meassures. Each row represents a well and each column represents one gene.

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse spinal cord

extract_protocol:
For zebrafish, cells were collected 3 days post fertilization. The head and tail were removed and the middle part of the larvae was collected for sequencing. The yolk was removed by gently pipetting up and down in 100 μL of calcium-free Ringer’s solution. Larvae (n=20) were transferred to a protease solution (0.25% trypsin, 1mM EDTA, pH 8.0, PBS, 50 ml) pre-warmed at 28°C and 27 μL collagenase P in HBSS was added to the samples for 15 minutes at 28°C with homogenizing every 5 minutes by gently pipetting up and down. Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added to the tube and spun at 350 RCF for 5 minutes at 4°C. The resuspension was passed through a 20 μm cell strainer and the sample was placed on ice. Quality control was addressed by comparing live cells versus dead cells using a viability indicator for dead cells (NucRed™ Dead 647 ReadyProbes™ Reagent). For mice, the spinal cords from three E14.5 embryos were dissected in ice-cold 1X D-PBS (Thermofisher). Both the DRGs and vertebrae column were removed as much as possible. The spinal cords were pooled in one tube and dissociated using the adult brain dissociation kit (Milteny Biotec), adapted for spinal cord tissue. Briefly, 1 ml pre-heated (37ºC) enzyme solution 1 (50 µl enzyme P in 950ul buffer Z) was added to the spinal cords followed by 15ul enzyme solution 2 (5 µl enzyme A in 10 µl buffer Y). The tissue was incubated at 37ºC for 30 minutes. Every 10 minutes, the tissue was triturated 10 times with fire polished glass Pasteur pipettes pretreated in 0.5% BSA in 1X D-PBS. The pipets had a decreasing diameter staring with around 200% then 100% and finally around 20% of original opening diameter. Tissue was then transferred to 10 ml ice cold 1X D-PBS and filtered through a 40 µm cell strainer. The suspension was centrifuged at 300 RCF for 10 minutes at 4ºC and the supernatant was discarded. The cell pellet was resuspended in 900 µl 0.5% BSA in 1X D-PBS followed by 100 µl myelin removal beads (Milteny Biotec) and incubated for 15 min at 8ºC. 10 ml ice cold 1X D-PBS was added to the sample and centrifuged at 300 RCF for 10 minutes. Supernatant was discarded and the cell pellet was resuspended in 1 ml 0.5% BSA in 1X D-PBS. The sample was run through an LS-column (Milteny Biotec) on a magnetic stand and flushed with 2x1 ml 0.5% BSA in 1X D-PBS. Cell sorting was performed on a BD Melody cell sorter, and tomato positive cells were gated out in comparison to a non-fluorescent control.
cDNA synthesis and preamplification were performed using the SMART-seq2 method (Picelli et al., 2014). Briefly, cDNA was transcribed using SuperScript II reverse transcriptase, oligo(dT) primers and template switching oligonucleotides (TSO). Preamplification of the cDNA was facilitated by ISPCR primers that binds the TSO and oligo(dT). The cDNA was tagmented using the Tn5 transposase creating fragments of 200-600bp, followed by indexation using the Nextera XT sample preparation kits.

tag: developmental stage

tag: tissue

value: spinal cord

tag: strain


title: mmusculus_K20

description: mmusculus.loom


title: mmusculus_K2

description: mmusculus.loom


title: L04_AE03_076_gasoline_10

description:
L04_AE03
Hepatocyte_normcounts.csv

value: NAPTHA


title: L04_AE05_065_P_Hwax_10

description:
L04_AE05
Hepatocyte_normcounts.csv

value: WAX


title: mmusculus_K22

description: mmusculus.loom


title: mmusculus_K8

description: mmusculus.loom


title: L04_AF04_192_BITUMENS_10

description:
L04_AF04
Hepatocyte_normcounts.csv

value: BIT


title: mmusculus_K18

description: mmusculus.loom


title: mmusculus_K19

description: mmusculus.loom


title: mmusculus_K15

description: mmusculus.loom


title: L04_AD11_050_HFO_10

description:
L04_AD11
Hepatocyte_normcounts.csv

value: HFO


title: L04_AD10_089_UDAE_10

description:
L04_AD10
Hepatocyte_normcounts.csv

value: UDAE


title: mmusculus_K14

description: mmusculus.loom


title: L04_AD09_093_petrolatum_10

description:
L04_AD09
Hepatocyte_normcounts.csv


title: L04_AD08_103_gasoline_10

description:
L04_AD08
Hepatocyte_normcounts.csv


title: mmusculus_K17

description: mmusculus.loom


title: mmusculus_K12

description: mmusculus.loom


title: L04_AD07_008_HFO_10

description:
L04_AD07
Hepatocyte_normcounts.csv


title: L04_AD06_MethodBlank_0

description:
L04_AD06
Hepatocyte_normcounts.csv


title: mmusculus_K11

description: mmusculus.loom


title: L04_AE04_141_gasoline_10

description:
L04_AE04
Hepatocyte_normcounts.csv


title: L04_AD05_074_OLBO_10

description:
L04_AD05
Hepatocyte_normcounts.csv

value: BO


title: L04_AD02_127_slackwax_10

description:
L04_AD02
Hepatocyte_normcounts.csv


title: L04_AD01_081_OLBO_10

description:
L04_AD01
Hepatocyte_normcounts.csv


title: mmusculus_J9

description: mmusculus.loom


title: L04_AE01_169_SRGO_10

description:
L04_AE01
Hepatocyte_normcounts.csv

value: SRGO


title: mmusculus_K16

description: mmusculus.loom


title: L04_AB10_083_UATO_10

description:
L04_AB10
Hepatocyte_normcounts.csv

value: UATO


title: L04_AB11_063_P_Hwax_10

description:
L04_AB11
Hepatocyte_normcounts.csv


title: mmusculus_J7

description: mmusculus.loom


title: mmusculus_J8

description: mmusculus.loom


title: L04_AC06_MethodBlank_0

description:
L04_AC06
Hepatocyte_normcounts.csv


title: mmusculus_J6

description: mmusculus.loom


title: mmusculus_J5

description: mmusculus.loom


title: L04_AB08_080_HFO_10

description:
L04_AB08
Hepatocyte_normcounts.csv


title: L04_AB09_187_1__OGO_10

description:
L04_AB09
Hepatocyte_normcounts.csv

value: OGO


title: mmusculus_J4

description: mmusculus.loom


title: mmusculus_K13

description: mmusculus.loom


title: L04_AB07_129_HFO_10

description:
L04_AB07
Hepatocyte_normcounts.csv


title: mmusculus_J3

description: mmusculus.loom


title: mmusculus_J24

description: mmusculus.loom


title: L04_AB06_MethodBlank_0

description:
L04_AB06
Hepatocyte_normcounts.csv


title: mmusculus_J23

description: mmusculus.loom


title: mmusculus_K10

description: mmusculus.loom


title: mmusculus_K1

description: mmusculus.loom


title: mmusculus_J22

description: mmusculus.loom


title: L04_AB03_184_VHGO_10

description:
L04_AB03
Hepatocyte_normcounts.csv

value: VHGO


title: L04_AB05_059_dieselfuel_10

description:
L04_AB05
Hepatocyte_normcounts.csv


title: mmusculus_J20

description: mmusculus.loom


title: mmusculus_J2

description: mmusculus.loom


title: mmusculus_J21

description: mmusculus.loom


title: L04_AB01_041_CGO_10

description:
L04_AB01
Hepatocyte_normcounts.csv

value: CGO


title: L04_AB02_009_gasoline_10

description:
L04_AB02
Hepatocyte_normcounts.csv


title: mmusculus_J19

description: mmusculus.loom


title: mmusculus_J18

description: mmusculus.loom


title: L04_AA08_006_HFO_10

description:
L04_AA08
Hepatocyte_normcounts.csv


title: mmusculus_J17

description: mmusculus.loom


title: mmusculus_J16

description: mmusculus.loom


title: L04_AA05_151_OLBO_10

description:
L04_AA05
Hepatocyte_normcounts.csv


title: L04_AA10_180_VHGO_10

description:
L04_AA10
Hepatocyte_normcounts.csv


title: L04_AA06_MethodBlank_0

description:
L04_AA06
Hepatocyte_normcounts.csv


title: mmusculus_J15

description: mmusculus.loom


title: L04_AA09_082_UATO_10

description:
L04_AA09
Hepatocyte_normcounts.csv


title: L04_AA01_016_kerosine_10

description:
L04_AA01
Hepatocyte_normcounts.csv


title: mmusculus_J13

description: mmusculus.loom


title: L04_AB04_155_HFO_10

description:
L04_AB04
Hepatocyte_normcounts.csv


title: L04_AA03_043_kerosine_10

description:
L04_AA03
Hepatocyte_normcounts.csv


title: mmusculus_J14

description: mmusculus.loom


title: mmusculus_J12

description: mmusculus.loom


title: mmusculus_J10

description: mmusculus.loom


title: mmusculus_J11

description: mmusculus.loom


title: mmusculus_J1

description: mmusculus.loom


title: L03_DH06_MethodBlank_0

description:
L03_DH06
Hepatocyte_normcounts.csv


title: mmusculus_I9

description: mmusculus.loom


title: L03_DH08_084_UATO_100

description:
L03_DH08
Hepatocyte_normcounts.csv


title: L03_DH09_175_VHGO_100

description:
L03_DH09
Hepatocyte_normcounts.csv


title: L03_DH02_069_TDAE_100

description:
L03_DH02
Hepatocyte_normcounts.csv

value: TDAE


title: mmusculus_I6

description: mmusculus.loom


title: L03_DH04_149_OLBO_100

description:
L03_DH04
Hepatocyte_normcounts.csv


title: mmusculus_I8

description: mmusculus.loom


title: mmusculus_I5

description: mmusculus.loom


title: L03_DH05_085C_OLBO_100

description:
L03_DH05
Hepatocyte_normcounts.csv


title: mmusculus_I7

description: mmusculus.loom


title: L03_DH01_049_kerosine_100

description:
L03_DH01
Hepatocyte_normcounts.csv


title: L03_DG10_139_OLBO_100

description:
L03_DG10
Hepatocyte_normcounts.csv


title: L03_DG11_078_HFO_100

description:
L03_DG11
Hepatocyte_normcounts.csv


title: mmusculus_I4

description: mmusculus.loom


title: mmusculus_I23

description: mmusculus.loom


title: L03_DH11_185_RAE_100

description:
L03_DH11
Hepatocyte_normcounts.csv

value: RAE


title: L03_DG08_134_HFO_100

description:
L03_DG08
Hepatocyte_normcounts.csv


title: mmusculus_I22

description: mmusculus.loom


title: L03_DG04_073_OLBO_100

description:
L03_DG04
Hepatocyte_normcounts.csv


title: L03_DG09_056_gasoline_100

description:
L03_DG09
Hepatocyte_normcounts.csv


title: L03_DG03_072_OLBO_100

description:
L03_DG03
Hepatocyte_normcounts.csv


title: mmusculus_I3

description: mmusculus.loom


title: L03_DH10_172_SRGO_100

description:
L03_DH10
Hepatocyte_normcounts.csv


title: mmusculus_I24

description: mmusculus.loom


title: mmusculus_I20

description: mmusculus.loom


title: L03_DG02_064_UATO_100

description:
L03_DG02
Hepatocyte_normcounts.csv


title: mmusculus_I21

description: mmusculus.loom


title: L03_DG06_MethodBlank_0

description:
L03_DG06
Hepatocyte_normcounts.csv


title: L03_DF06_MethodBlank_0

description:
L03_DF06
Hepatocyte_normcounts.csv


title: L03_DG01_109_FO_100

description:
L03_DG01
Hepatocyte_normcounts.csv

value: FO


title: mmusculus_I18

description: mmusculus.loom


title: mmusculus_I16

description: mmusculus.loom


title: mmusculus_I17

description: mmusculus.loom


title: L03_DE10_177_VHGO_100

description:
L03_DE10
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: L03_DE11_131_HFO_100

description:
L03_DE11
Hepatocyte_normcounts.csv


title: mmusculus_I15

description: mmusculus.loom


title: L03_DE09_012_CGO_100

description:
L03_DE09
Hepatocyte_normcounts.csv


title: L03_DE08_066_OLBO_100

description:
L03_DE08
Hepatocyte_normcounts.csv


title: L03_DE07_007_HFO_100

description:
L03_DE07
Hepatocyte_normcounts.csv


title: mmusculus_I14

description: mmusculus.loom


title: mmusculus_I13

description: mmusculus.loom


title: mmusculus_I12

description: mmusculus.loom


title: mmusculus_I2

description: mmusculus.loom


title: L03_DE05_173_OGO_100

description:
L03_DE05
Hepatocyte_normcounts.csv


title: L03_DE04_097_HFO_100

description:
L03_DE04
Hepatocyte_normcounts.csv


title: L03_DE03_113_OLBO_100

description:
L03_DE03
Hepatocyte_normcounts.csv


title: L03_DE02_192_BITUMENS_100

description:
L03_DE02
Hepatocyte_normcounts.csv


title: mmusculus_I11

description: mmusculus.loom


title: mmusculus_I10

description: mmusculus.loom


title: L03_DE01_111_petrolatum_100

description:
L03_DE01
Hepatocyte_normcounts.csv


title: mmusculus_H9

description: mmusculus.loom


title: mmusculus_H7

description: mmusculus.loom


title: mmusculus_H8

description: mmusculus.loom


title: mmusculus_I19

description: mmusculus.loom


title: L03_DD12_034_HFO_100

description:
L03_DD12
Hepatocyte_normcounts.csv


title: L03_DD11_189_BITUMEN_100

description:
L03_DD11
Hepatocyte_normcounts.csv


title: mmusculus_H6

description: mmusculus.loom


title: L03_DD07_024_HFO_100

description:
L03_DD07
Hepatocyte_normcounts.csv


title: L03_DD04_137_OLBO_100

description:
L03_DD04
Hepatocyte_normcounts.csv


title: L03_DD10_031_HFO_100

description:
L03_DD10
Hepatocyte_normcounts.csv


title: mmusculus_H5

description: mmusculus.loom


title: mmusculus_H24

description: mmusculus.loom


title: L03_DD06_MethodBlank_0

description:
L03_DD06
Hepatocyte_normcounts.csv


title: L03_DD05_112_OLBO_100

description:
L03_DD05
Hepatocyte_normcounts.csv


title: mmusculus_H3

description: mmusculus.loom


title: mmusculus_H22

description: mmusculus.loom


title: mmusculus_H20

description: mmusculus.loom


title: mmusculus_H21

description: mmusculus.loom


title: mmusculus_I1

description: mmusculus.loom


title: L03_DD02_020_HFO_100

description:
L03_DD02
Hepatocyte_normcounts.csv


title: L03_DD03_174_OGO_100

description:
L03_DD03
Hepatocyte_normcounts.csv


title: mmusculus_H2

description: mmusculus.loom


title: L03_DD01_003_CGO_100

description:
L03_DD01
Hepatocyte_normcounts.csv


title: L03_DC10_188_SRGO_10

description:
L03_DC10
Hepatocyte_normcounts.csv


title: L03_DD09_176_VHGO_100

description:
L03_DD09
Hepatocyte_normcounts.csv


title: mmusculus_H18

description: mmusculus.loom


title: L03_DC08_175_VHGO_10

description:
L03_DC08
Hepatocyte_normcounts.csv


title: mmusculus_H19

description: mmusculus.loom


title: mmusculus_H17

description: mmusculus.loom


title: L03_DC03_120_gasoline_10

description:
L03_DC03
Hepatocyte_normcounts.csv


title: L03_DC01_092_OLBO_10

description:
L03_DC01
Hepatocyte_normcounts.csv


title: mmusculus_H16

description: mmusculus.loom


title: mmusculus_H4

description: mmusculus.loom


title: L03_DC06_MethodBlank_0

description:
L03_DC06
Hepatocyte_normcounts.csv


title: mmusculus_H23

description: mmusculus.loom


title: L03_DC05_134_HFO_10

description:
L03_DC05
Hepatocyte_normcounts.csv


title: mmusculus_H15

description: mmusculus.loom


title: mmusculus_H13

description: mmusculus.loom


title: L03_DB11_186_RAE_100

description:
L03_DB11
Hepatocyte_normcounts.csv


title: L03_DB08_146_gasoline_100

description:
L03_DB08
Hepatocyte_normcounts.csv


title: mmusculus_H10

description: mmusculus.loom


title: L03_DB06_MethodBlank_0

description:
L03_DB06
Hepatocyte_normcounts.csv


title: L03_DB10_171_SRGO_100

description:
L03_DB10
Hepatocyte_normcounts.csv


title: mmusculus_G8

description: mmusculus.loom


title: L03_DB03_147_OLBO_100

description:
L03_DB03
Hepatocyte_normcounts.csv


title: mmusculus_H1

description: mmusculus.loom


title: L03_DB05_061_P_Hwax_100

description:
L03_DB05
Hepatocyte_normcounts.csv


title: L03_DB07_168_SRGO_100

description:
L03_DB07
Hepatocyte_normcounts.csv


title: mmusculus_H12

description: mmusculus.loom


title: mmusculus_G9

description: mmusculus.loom


title: L03_DB04_117_OLBO_100

description:
L03_DB04
Hepatocyte_normcounts.csv


title: mmusculus_G6

description: mmusculus.loom


title: mmusculus_G7

description: mmusculus.loom


title: L03_DA10_085D_OLBO_100

description:
L03_DA10
Hepatocyte_normcounts.csv


title: L03_DA11_028_HFO_100

description:
L03_DA11
Hepatocyte_normcounts.csv


title: L03_DA08_025_HFO_100

description:
L03_DA08
Hepatocyte_normcounts.csv


title: mmusculus_G24

description: mmusculus.loom


title: L03_DB01_152_slackwax_100

description:
L03_DB01
Hepatocyte_normcounts.csv


title: mmusculus_G23

description: mmusculus.loom


title: mmusculus_H14

description: mmusculus.loom


title: L03_DA05_138_OLBO_100

description:
L03_DA05
Hepatocyte_normcounts.csv


title: mmusculus_G5

description: mmusculus.loom


title: mmusculus_G3

description: mmusculus.loom


title: mmusculus_H11

description: mmusculus.loom


title: L03_DA06_MethodBlank_0

description:
L03_DA06
Hepatocyte_normcounts.csv


title: mmusculus_G22

description: mmusculus.loom


title: L03_DA07_018_HFO_100

description:
L03_DA07
Hepatocyte_normcounts.csv


title: mmusculus_G20

description: mmusculus.loom


title: L03_DA03_062_P_Hwax_100

description:
L03_DA03
Hepatocyte_normcounts.csv


title: mmusculus_G19

description: mmusculus.loom


title: L03_CH11_185_RAE_10

description:
L03_CH11
Hepatocyte_normcounts.csv


title: mmusculus_G4

description: mmusculus.loom


title: mmusculus_G17

description: mmusculus.loom


title: L03_CH09_175_VHGO_10

description:
L03_CH09
Hepatocyte_normcounts.csv


title: L03_DA01_046_gasoline_100

description:
L03_DA01
Hepatocyte_normcounts.csv


title: L03_CH05_085C_OLBO_10

description:
L03_CH05
Hepatocyte_normcounts.csv


title: mmusculus_G14

description: mmusculus.loom


title: L03_CH10_172_SRGO_10

description:
L03_CH10
Hepatocyte_normcounts.csv


title: L03_DA04_086_kerosine_100

description:
L03_DA04
Hepatocyte_normcounts.csv

value: KER


title: mmusculus_G18

description: mmusculus.loom

value: spinal cord


title: L03_CH04_149_OLBO_10

description:
L03_CH04
Hepatocyte_normcounts.csv


title: mmusculus_G11

description: mmusculus.loom


title: mmusculus_G16

description: mmusculus.loom


title: mmusculus_G13

description: mmusculus.loom


title: L03_CH08_084_UATO_10

description:
L03_CH08
Hepatocyte_normcounts.csv


title: L03_CG11_078_HFO_10

description:
L03_CG11
Hepatocyte_normcounts.csv


title: mmusculus_G1

description: mmusculus.loom


title: L03_DA02_160_FO_100

description:
L03_DA02
Hepatocyte_normcounts.csv


title: mmusculus_G15

description: mmusculus.loom


title: mmusculus_G12

description: mmusculus.loom


title: mmusculus_G21

description: mmusculus.loom


title: mmusculus_G10

description: mmusculus.loom


title: mmusculus_F9

description: mmusculus.loom


title: mmusculus_G2

description: mmusculus.loom


title: L03_CG08_134_HFO_10

description:
L03_CG08
Hepatocyte_normcounts.csv


title: L03_CG06_MethodBlank_0

description:
L03_CG06
Hepatocyte_normcounts.csv


title: mmusculus_F8

description: mmusculus.loom


title: L03_CH01_049_kerosine_10

description:
L03_CH01
Hepatocyte_normcounts.csv


title: L03_CH06_MethodBlank_0

description:
L03_CH06
Hepatocyte_normcounts.csv


title: L03_CG09_056_gasoline_10

description:
L03_CG09
Hepatocyte_normcounts.csv

value: NAPTHA


title: mmusculus_F7

description: mmusculus.loom


title: L03_CG10_139_OLBO_10

description:
L03_CG10
Hepatocyte_normcounts.csv


title: L03_CG05_183_VHGOa_10

description:
L03_CG05
Hepatocyte_normcounts.csv


title: mmusculus_F5

description: mmusculus.loom


title: mmusculus_F6

description: mmusculus.loom


title: mmusculus_F4

description: mmusculus.loom


title: mmusculus_F3

description: mmusculus.loom


title: L03_CG02_064_UATO_10

description:
L03_CG02
Hepatocyte_normcounts.csv


title: L03_CH02_069_TDAE_10

description:
L03_CH02
Hepatocyte_normcounts.csv


title: L03_CG03_072_OLBO_10

description:
L03_CG03
Hepatocyte_normcounts.csv


title: L03_CG04_073_OLBO_10

description:
L03_CG04
Hepatocyte_normcounts.csv


title: mmusculus_F24

description: mmusculus.loom


title: mmusculus_F23

description: mmusculus.loom


title: L03_CF06_MethodBlank_0

description:
L03_CF06
Hepatocyte_normcounts.csv


title: mmusculus_F22

description: mmusculus.loom


title: L03_CE09_012_CGO_10

description:
L03_CE09
Hepatocyte_normcounts.csv


title: L03_CE10_177_VHGO_10

description:
L03_CE10
Hepatocyte_normcounts.csv


title: mmusculus_F21

description: mmusculus.loom


title: L03_CE08_066_OLBO_10

description:
L03_CE08
Hepatocyte_normcounts.csv


title: mmusculus_F20

description: mmusculus.loom


title: mmusculus_F2

description: mmusculus.loom


title: mmusculus_F19

description: mmusculus.loom


title: L03_CE06_MethodBlank_0

description:
L03_CE06
Hepatocyte_normcounts.csv


title: mmusculus_F18

description: mmusculus.loom


title: L03_CE07_007_HFO_10

description:
L03_CE07
Hepatocyte_normcounts.csv


title: L03_CE04_097_HFO_10

description:
L03_CE04
Hepatocyte_normcounts.csv


title: mmusculus_F16

description: mmusculus.loom


title: L03_CE03_113_OLBO_10

description:
L03_CE03
Hepatocyte_normcounts.csv


title: mmusculus_F17

description: mmusculus.loom


title: L03_CE02_192_BITUMENS_10

description:
L03_CE02
Hepatocyte_normcounts.csv


title: L03_CE01_111_petrolatum_10

description:
L03_CE01
Hepatocyte_normcounts.csv


title: mmusculus_F14

description: mmusculus.loom


title: mmusculus_F15

description: mmusculus.loom


title: L03_CE11_131_HFO_10

description:
L03_CE11
Hepatocyte_normcounts.csv


title: L03_CD11_189_BITUMEN_10

description:
L03_CD11
Hepatocyte_normcounts.csv


title: L03_CD12_034_HFO_10

description:
L03_CD12
Hepatocyte_normcounts.csv


title: L03_CD10_031_HFO_10

description:
L03_CD10
Hepatocyte_normcounts.csv


title: mmusculus_F11

description: mmusculus.loom


title: mmusculus_F10

description: mmusculus.loom


title: mmusculus_F13

description: mmusculus.loom


title: L03_CD09_176_VHGO_10

description:
L03_CD09
Hepatocyte_normcounts.csv


title: L03_CD07_024_HFO_10

description:
L03_CD07
Hepatocyte_normcounts.csv


title: mmusculus_F1

description: mmusculus.loom


title: mmusculus_E9

description: mmusculus.loom


title: L03_CD05_112_OLBO_10

description:
L03_CD05
Hepatocyte_normcounts.csv


title: L03_CD04_137_OLBO_10

description:
L03_CD04
Hepatocyte_normcounts.csv


title: L03_CE05_173_OGO_10

description:
L03_CE05
Hepatocyte_normcounts.csv


title: mmusculus_F12

description: mmusculus.loom


title: mmusculus_E8

description: mmusculus.loom


title: mmusculus_E7

description: mmusculus.loom


title: L03_CD03_174_OGO_10

description:
L03_CD03
Hepatocyte_normcounts.csv


title: mmusculus_E6

description: mmusculus.loom


title: mmusculus_E5

description: mmusculus.loom


title: L03_CD06_MethodBlank_0

description:
L03_CD06
Hepatocyte_normcounts.csv


title: L03_CD02_020_HFO_10

description:
L03_CD02
Hepatocyte_normcounts.csv


title: L03_CD01_003_CGO_10

description:
L03_CD01
Hepatocyte_normcounts.csv


title: L03_CC10_188_SRGO_10

description:
L03_CC10
Hepatocyte_normcounts.csv


title: L03_CC08_175_VHGO_10

description:
L03_CC08
Hepatocyte_normcounts.csv


title: mmusculus_E4

description: mmusculus.loom


title: mmusculus_E24

description: mmusculus.loom


title: mmusculus_E23

description: mmusculus.loom


title: mmusculus_E22

description: mmusculus.loom


title: mmusculus_E3

description: mmusculus.loom


title: L03_CC06_MethodBlank_0

description:
L03_CC06
Hepatocyte_normcounts.csv


title: L03_CC03_120_gasoline_10

description:
L03_CC03
Hepatocyte_normcounts.csv


title: mmusculus_E21

description: mmusculus.loom


title: L03_CC01_092_OLBO_10

description:
L03_CC01
Hepatocyte_normcounts.csv


title: mmusculus_E2

description: mmusculus.loom


title: mmusculus_E20

description: mmusculus.loom


title: L03_CB11_186_RAE_10

description:
L03_CB11
Hepatocyte_normcounts.csv


title: L03_CC05_134_HFO_10

description:
L03_CC05
Hepatocyte_normcounts.csv


title: L03_CB10_171_SRGO_10

description:
L03_CB10
Hepatocyte_normcounts.csv


title: mmusculus_E18

description: mmusculus.loom


title: L03_CB08_146_gasoline_10

description:
L03_CB08
Hepatocyte_normcounts.csv


title: mmusculus_E17

description: mmusculus.loom


title: L03_CB07_168_SRGO_10

description:
L03_CB07
Hepatocyte_normcounts.csv


title: L03_CB06_MethodBlank_0

description:
L03_CB06
Hepatocyte_normcounts.csv


title: mmusculus_E15

description: mmusculus.loom


title: mmusculus_E19

description: mmusculus.loom


title: mmusculus_E14

description: mmusculus.loom


title: mmusculus_E13

description: mmusculus.loom


title: L03_CB04_117_OLBO_10

description:
L03_CB04
Hepatocyte_normcounts.csv


title: L03_CB05_061_P_Hwax_10

description:
L03_CB05
Hepatocyte_normcounts.csv

value: WAX


title: mmusculus_E11

description: mmusculus.loom


title: mmusculus_E10

description: mmusculus.loom


title: L03_CB02_011_kerosine_10

description:
L03_CB02
Hepatocyte_normcounts.csv


title: L03_CA08_025_HFO_10

description:
L03_CA08
Hepatocyte_normcounts.csv


title: mmusculus_D9

description: mmusculus.loom


title: L03_CA07_018_HFO_10

description:
L03_CA07
Hepatocyte_normcounts.csv


title: mmusculus_E1

description: mmusculus.loom


title: L03_CA11_028_HFO_10

description:
L03_CA11
Hepatocyte_normcounts.csv


title: L03_CA05_138_OLBO_10

description:
L03_CA05
Hepatocyte_normcounts.csv


title: mmusculus_D7

description: mmusculus.loom


title: L03_CA06_MethodBlank_0

description:
L03_CA06
Hepatocyte_normcounts.csv


title: L03_CA04_086_kerosine_10

description:
L03_CA04
Hepatocyte_normcounts.csv


title: mmusculus_D8

description: mmusculus.loom


title: mmusculus_E16

description: mmusculus.loom


title: L03_CA03_062_P_Hwax_10

description:
L03_CA03
Hepatocyte_normcounts.csv


title: mmusculus_D6

description: mmusculus.loom


title: mmusculus_D5

description: mmusculus.loom


title: mmusculus_D3

description: mmusculus.loom


title: L03_BG11_058_HFO_10

description:
L03_BG11
Hepatocyte_normcounts.csv


title: L03_BH06_MethodBlank_0

description:
L03_BH06
Hepatocyte_normcounts.csv


title: mmusculus_D24

description: mmusculus.loom


title: mmusculus_D4

description: mmusculus.loom


title: L03_CA02_160_FO_10

description:
L03_CA02
Hepatocyte_normcounts.csv


title: mmusculus_D23

description: mmusculus.loom


title: L03_CB03_147_OLBO_10

description:
L03_CB03
Hepatocyte_normcounts.csv


title: L03_BG10_123_kerosine_10

description:
L03_BG10
Hepatocyte_normcounts.csv


title: mmusculus_E12

description: mmusculus.loom


title: L03_BG09_170_SRGO_10

description:
L03_BG09
Hepatocyte_normcounts.csv


title: mmusculus_D22

description: mmusculus.loom


title: L03_CA10_085D_OLBO_10

description:
L03_CA10
Hepatocyte_normcounts.csv


title: mmusculus_D20

description: mmusculus.loom


title: mmusculus_D19

description: mmusculus.loom


title: mmusculus_D2

description: mmusculus.loom


title: L03_BG04_106_CGO_10

description:
L03_BG04
Hepatocyte_normcounts.csv


title: L03_BG06_MethodBlank_0

description:
L03_BG06
Hepatocyte_normcounts.csv


title: L03_BG03_153_OLBO_10

description:
L03_BG03
Hepatocyte_normcounts.csv


title: mmusculus_D18

description: mmusculus.loom


title: L03_BG01_121_CGO_10

description:
L03_BG01
Hepatocyte_normcounts.csv


title: mmusculus_D17

description: mmusculus.loom


title: L03_BF10_070_CGO_10

description:
L03_BF10
Hepatocyte_normcounts.csv


title: L03_BF09_096B_UDAE_10

description:
L03_BF09
Hepatocyte_normcounts.csv


title: mmusculus_D14

description: mmusculus.loom


title: L03_BF06_MethodBlank_0

description:
L03_BF06
Hepatocyte_normcounts.csv


title: L03_BF08_148_OLBO_10

description:
L03_BF08
Hepatocyte_normcounts.csv


title: mmusculus_D12

description: mmusculus.loom


title: mmusculus_D13

description: mmusculus.loom


title: L03_BF07_114_OLBO_10

description:
L03_BF07
Hepatocyte_normcounts.csv


title: mmusculus_D11

description: mmusculus.loom


title: mmusculus_D21

description: mmusculus.loom


title: mmusculus_D10

description: mmusculus.loom


title: L03_BG08_102_CGO_10

description:
L03_BG08
Hepatocyte_normcounts.csv


title: L03_BF05_196_petrolatum_10

description:
L03_BF05
Hepatocyte_normcounts.csv


title: mmusculus_D1

description: mmusculus.loom


title: L03_BF02_132_gasoline_10

description:
L03_BF02
Hepatocyte_normcounts.csv


title: L03_BF03_178_VHGO_10

description:
L03_BF03
Hepatocyte_normcounts.csv


title: mmusculus_C9

description: mmusculus.loom


title: L03_BF01_075_OLBO_10

description:
L03_BF01
Hepatocyte_normcounts.csv


title: mmusculus_C7

description: mmusculus.loom


title: mmusculus_C8

description: mmusculus.loom


title: mmusculus_C6

description: mmusculus.loom


title: L03_BG02_202_Paraffinwax_10

description:
L03_BG02
Hepatocyte_normcounts.csv


title: mmusculus_D16

description: mmusculus.loom


title: L03_BE10_188_SRGO_1

description:
L03_BE10
Hepatocyte_normcounts.csv


title: mmusculus_D15

description: mmusculus.loom


title: mmusculus_C5

description: mmusculus.loom


title: mmusculus_C4

description: mmusculus.loom


title: L03_BE08_175_VHGO_1

description:
L03_BE08
Hepatocyte_normcounts.csv


title: mmusculus_C3

description: mmusculus.loom


title: L03_BE06_MethodBlank_0

description:
L03_BE06
Hepatocyte_normcounts.csv


title: mmusculus_C23

description: mmusculus.loom


title: mmusculus_C24

description: mmusculus.loom


title: L03_BE09_175_VHGO_100

description:
L03_BE09
Hepatocyte_normcounts.csv


title: mmusculus_C22

description: mmusculus.loom


title: L03_BE05_134_HFO_1

description:
L03_BE05
Hepatocyte_normcounts.csv


title: L03_BE04_120_gasoline_100

description:
L03_BE04
Hepatocyte_normcounts.csv


title: L03_BF04_197_HFO_10

description:
L03_BF04
Hepatocyte_normcounts.csv


title: L03_BE03_120_gasoline_1

description:
L03_BE03
Hepatocyte_normcounts.csv


title: mmusculus_C21

description: mmusculus.loom


title: mmusculus_C20

description: mmusculus.loom


title: L03_BE02_092_OLBO_100

description:
L03_BE02
Hepatocyte_normcounts.csv


title: L03_BE01_092_OLBO_1

description:
L03_BE01
Hepatocyte_normcounts.csv


title: L03_BD03_020_HFO_10

description:
L03_BD03
Hepatocyte_normcounts.csv


title: mmusculus_C18

description: mmusculus.loom


title: mmusculus_C19

description: mmusculus.loom


title: L03_BE11_188_SRGO_100

description:
L03_BE11
Hepatocyte_normcounts.csv


title: mmusculus_C2

description: mmusculus.loom


title: L03_BD02_091_HFO_10

description:
L03_BD02
Hepatocyte_normcounts.csv


title: mmusculus_C16

description: mmusculus.loom


title: mmusculus_C15

description: mmusculus.loom


title: L03_BD01_184_VHGO_10

description:
L03_BD01
Hepatocyte_normcounts.csv


title: L03_BC11_193_OXASPH_10

description:
L03_BC11
Hepatocyte_normcounts.csv

value: BIT


title: L03_BC09_120_gasoline_10

description:
L03_BC09
Hepatocyte_normcounts.csv


title: mmusculus_C17

description: mmusculus.loom


title: mmusculus_C14

description: mmusculus.loom


title: L03_BC10_182_VHGO_10

description:
L03_BC10
Hepatocyte_normcounts.csv


title: L03_BC07_150_OLBO_10

description:
L03_BC07
Hepatocyte_normcounts.csv


title: mmusculus_C13

description: mmusculus.loom


title: L03_BC02_071_HFO_10

description:
L03_BC02
Hepatocyte_normcounts.csv

value: HFO


title: mmusculus_C11

description: mmusculus.loom


title: mmusculus_C10

description: mmusculus.loom


title: L03_BC01_179_VHGO_10

description:
L03_BC01
Hepatocyte_normcounts.csv


title: L03_BB11_115_OLBO_10

description:
L03_BB11
Hepatocyte_normcounts.csv


title: mmusculus_C1

description: mmusculus.loom


title: L03_BB10_085B_OLBO_10

description:
L03_BB10
Hepatocyte_normcounts.csv


title: mmusculus_B9

description: mmusculus.loom


title: mmusculus_B8

description: mmusculus.loom


title: L03_BB08_071_HFO_10

description:
L03_BB08
Hepatocyte_normcounts.csv


title: L03_BB09_190_BITUMENS_10

description:
L03_BB09
Hepatocyte_normcounts.csv


title: mmusculus_B7

description: mmusculus.loom


title: mmusculus_B5

description: mmusculus.loom


title: L03_BB07_166_HFO_10

description:
L03_BB07
Hepatocyte_normcounts.csv


title: L03_BB06_MethodBlank_0

description:
L03_BB06
Hepatocyte_normcounts.csv


title: L03_BB03_188_SRGO_10

description:
L03_BB03
Hepatocyte_normcounts.csv


title: mmusculus_B6

description: mmusculus.loom


title: mmusculus_B3

description: mmusculus.loom


title: mmusculus_C12

description: mmusculus.loom


title: L03_BC08_130_CGO_10

description:
L03_BC08
Hepatocyte_normcounts.csv


title: L03_AH11_090_FO_10

description:
L03_AH11
Hepatocyte_normcounts.csv


title: mmusculus_B24

description: mmusculus.loom


title: L03_AH10_067_P_Hwax_10

description:
L03_AH10
Hepatocyte_normcounts.csv


title: L03_BA06_MethodBlank_0

description:
L03_BA06
Hepatocyte_normcounts.csv


title: mmusculus_B23

description: mmusculus.loom


title: L03_BB01_154_OLBO_10

description:
L03_BB01
Hepatocyte_normcounts.csv


title: L03_AH09_079_HFO_10

description:
L03_AH09
Hepatocyte_normcounts.csv


title: mmusculus_B22

description: mmusculus.loom


title: L03_AH07_021_HFO_10

description:
L03_AH07
Hepatocyte_normcounts.csv


title: mmusculus_B21

description: mmusculus.loom


title: L03_AH06_MethodBlank_0

description:
L03_AH06
Hepatocyte_normcounts.csv


title: mmusculus_B20

description: mmusculus.loom


title: mmusculus_B2

description: mmusculus.loom


title: mmusculus_B19

description: mmusculus.loom


title: mmusculus_B18

description: mmusculus.loom


title: mmusculus_B17

description: mmusculus.loom


title: L03_AG11_191_BITUMEN_10

description:
L03_AG11
Hepatocyte_normcounts.csv


title: L03_AH01_195_UDAE_10

description:
L03_AH01
Hepatocyte_normcounts.csv

value: UDAE


title: mmusculus_B4

description: mmusculus.loom


title: L03_AH02_119_OLBO_10

description:
L03_AH02
Hepatocyte_normcounts.csv

value: BO


title: L03_AG10_164_HFO_10

description:
L03_AG10
Hepatocyte_normcounts.csv


title: mmusculus_B16

description: mmusculus.loom


title: L03_AG09_104_kerosine_10

description:
L03_AG09
Hepatocyte_normcounts.csv


title: mmusculus_B14

description: mmusculus.loom


title: L03_AG07_136_slackwax_10

description:
L03_AG07
Hepatocyte_normcounts.csv


title: mmusculus_B15

description: mmusculus.loom


title: mmusculus_B13

description: mmusculus.loom


title: mmusculus_B12

description: mmusculus.loom


title: mmusculus_B11

description: mmusculus.loom


title: L03_AG04_181_VHGO_10

description:
L03_AG04
Hepatocyte_normcounts.csv


title: mmusculus_B10

description: mmusculus.loom


title: L03_AG06_MethodBlank_0

description:
L03_AG06
Hepatocyte_normcounts.csv


title: mmusculus_B1

description: mmusculus.loom


title: mmusculus_A9

description: mmusculus.loom


title: L03_AG01_118_OLBO_10

description:
L03_AG01
Hepatocyte_normcounts.csv


title: L03_AF06_MethodBlank_0

description:
L03_AF06
Hepatocyte_normcounts.csv


title: mmusculus_A8

description: mmusculus.loom


title: mmusculus_A7

description: mmusculus.loom


title: L03_AF05_183_VHGOa_10

description:
L03_AF05
Hepatocyte_normcounts.csv


title: L03_AF04_192_BITUMENS_10

description:
L03_AF04
Hepatocyte_normcounts.csv


title: mmusculus_A5

description: mmusculus.loom


title: L03_AF03_076_gasoline_10

description:
L03_AF03
Hepatocyte_normcounts.csv


title: mmusculus_A4

description: mmusculus.loom


title: L03_AG08_108_OLBO_10

description:
L03_AG08
Hepatocyte_normcounts.csv


title: mmusculus_A3

description: mmusculus.loom


title: L03_AF02_083_UATO_10

description:
L03_AF02
Hepatocyte_normcounts.csv


title: L03_AF01_043_kerosine_10

description:
L03_AF01
Hepatocyte_normcounts.csv


title: mmusculus_A24

description: mmusculus.loom


title: L03_AE11_124_gasoline_10

description:
L03_AE11
Hepatocyte_normcounts.csv


title: L03_AG03_017_HFO_10

description:
L03_AG03
Hepatocyte_normcounts.csv


title: mmusculus_A22

description: mmusculus.loom


title: L03_AG02_187_2__OGO_10

description:
L03_AG02
Hepatocyte_normcounts.csv


title: L03_AE08_107_P_Hwax_10

description:
L03_AE08
Hepatocyte_normcounts.csv


title: L03_AE09_092_OLBO_10

description:
L03_AE09
Hepatocyte_normcounts.csv


title: mmusculus_A20

description: mmusculus.loom


title: mmusculus_A21

description: mmusculus.loom


title: L03_AE10_085A_OLBO_10

description:
L03_AE10
Hepatocyte_normcounts.csv


title: mmusculus_A2

description: mmusculus.loom


title: L03_AE06_MethodBlank_0

description:
L03_AE06
Hepatocyte_normcounts.csv


title: mmusculus_A6

description: mmusculus.loom


title: mmusculus_A23

description: mmusculus.loom


title: mmusculus_A19

description: mmusculus.loom


title: mmusculus_A18

description: mmusculus.loom


title: L03_AE03_076_gasoline_10

description:
L03_AE03
Hepatocyte_normcounts.csv


title: mmusculus_A17

description: mmusculus.loom


title: L03_AE01_169_SRGO_10

description:
L03_AE01
Hepatocyte_normcounts.csv

value: SRGO


title: L03_AD11_050_HFO_10

description:
L03_AD11
Hepatocyte_normcounts.csv


title: mmusculus_A15

description: mmusculus.loom


title: L03_AD10_089_UDAE_10

description:
L03_AD10
Hepatocyte_normcounts.csv


title: mmusculus_A14

description: mmusculus.loom


title: L03_AD09_093_petrolatum_10

description:
L03_AD09
Hepatocyte_normcounts.csv


title: mmusculus_A13

description: mmusculus.loom


title: L03_AD08_103_gasoline_10

description:
L03_AD08
Hepatocyte_normcounts.csv


title: mmusculus_A12

description: mmusculus.loom


title: mmusculus_A11

description: mmusculus.loom


title: L03_AD07_008_HFO_10

description:
L03_AD07
Hepatocyte_normcounts.csv


title: L03_AE07_087_kerosine_10

description:
L03_AE07
Hepatocyte_normcounts.csv


title: mmusculus_A10

description: mmusculus.loom


title: L03_AD06_MethodBlank_0

description:
L03_AD06
Hepatocyte_normcounts.csv


title: mmusculus_A1

description: mmusculus.loom


title: L03_AE04_141_gasoline_10

description:
L03_AE04
Hepatocyte_normcounts.csv


title: NFATc1/aA-overexpressing+Blimp-1-deficient

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

description: Sample C

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file

source_name: B220-CD4+BlimpGFP+CXCR5+GITRhi TFR

growth_protocol: Mice were immunized i.p. with 125 µg NP-KLH (4-Hydroxy-3-Nitrophenylacetyl hapten conjugated to Keyhole Limpet Hemocyanin (24-32) (0.5 mg/ml in PBS) (Biosearch)) emulsified (1:1) in 250 µl of ImJectÒ Alum (ThermoScientific) and boosted on day 7.

extract_protocol:
Cells enriched by flow cytometry were directly collected in RNA extraction buffer
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 10 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

tag: model

value: immunization

tag: genotype

tag: cell type


title: NFATc1/aA-overexpressing

description: Sample B

value: Nfatc1caaA. Prdm1gfp/+.FIC


title: L03_AC06_MethodBlank_0

description:
L03_AC06
Hepatocyte_normcounts.csv


title: L03_AB11_063_P_Hwax_10

description:
L03_AB11
Hepatocyte_normcounts.csv


title: NFATc1-deficient

description: Sample A


title: L03_AG05_135_TDAE_10

description:
L03_AG05
Hepatocyte_normcounts.csv


title: mmusculus_A16

description: mmusculus.loom


title: L03_AB10_083_UATO_10

description:
L03_AB10
Hepatocyte_normcounts.csv

value: UATO


title: L03_AB07_129_HFO_10

description:
L03_AB07
Hepatocyte_normcounts.csv


title: PERK_WT_M2_1A

city: Columbus

first: Stanley

last: Huang

state: OH

address: 3113 Pelotonia Research Center, 2255 Kenny Road

department: Microbial Infection and Immunity

institute: The Ohio State University

data_processing:
We used HISAT to align the clean reads to the reference genome and then used StringTie to assemble. We used Bowtie2 to compare clean reads to the reference sequence, and then use RSEM to calculate the expression of genes and transcripts. We used Bowtie2 to align the clean reads to the gene reference sequence, and then count the coverage of the gene.
Genome_build: mm10
Supplementary_files_format_and_content: includes FPKM for each sample

source_name: Bone marrow

growth_protocol: Bone marrow cells were differentiated in the presence of recombinant mouse M-CSF (20 ng/ml) in complete medium (RPMI 1640 containing 10 mM glucose, 2 mM L-glutamine, 100 U/mL of penicillin/streptomycin and 10% FBS) for 7 days. Fresh complete medium with M-CSF was supplemented on day 6 prior to use.

extract_protocol:
Firstly, the biotin-labeled Ribo-Zero rRNA Removal Kit is used to remove ribosome rRNA of total RNA.Then the un-purified RNA is fragmented under a certain temperature and ion environment. Random primers and reverse transcriptase of TruSeq® Stranded kit are used to synthesize the first-strand cDNA. cDNA library sequencing was performed using Illumina HiSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 7 bone marrow-derived macrophages were washed and either untreated or stimulated with IL-4 (20 ng/mL) for 24 h at a density of 2 million cells per well in a 6-well plate.

value: bone marrow-derived macrophage

value: Eif2ak3 fl/fl


title: PERK_KO_M2_2A

value: LysMcre x Eif2ak3 fl/fl


title: PERK_WT_M2_2A


title: PERK_KO_M2_1A


title: L03_AB06_MethodBlank_0

description:
L03_AB06
Hepatocyte_normcounts.csv


title: L03_AB04_155_HFO_10

description:
L03_AB04
Hepatocyte_normcounts.csv


title: L03_AB05_059_dieselfuel_10

description:
L03_AB05
Hepatocyte_normcounts.csv


title: L03_AD02_127_slackwax_10

description:
L03_AD02
Hepatocyte_normcounts.csv


title: L03_AD01_081_OLBO_10

description:
L03_AD01
Hepatocyte_normcounts.csv


title: L03_AB03_184_VHGO_10

description:
L03_AB03
Hepatocyte_normcounts.csv

value: VHGO


title: L03_AB02_009_gasoline_10

description:
L03_AB02
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: V65_Dec_48h_B

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

library_source: genomic

data_processing:
Trimming using TrimGalore ! (v0.6.4), quality threshold 20, hard trimming 10bp
Reads were aligned against Mus musculus genome version 38 (GRCm38) using Bismark (v0.22.3)
BAM files were deduplicated and CpG calls were extracted using bismark_methylation_extractor
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed files contain individual CpG calls processed by Bismark

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Once a stable mTET3-CD complemented TET-TKO line was produced, media supplemented with 50 μg/ml ascorbate was added to cells plated at low-density in 12-well plates overnight. V6.5 hybrid embryonic stem cells (i.e. C57BL/6 X 129/sv cross) were seeded at low-density,

extract_protocol:
Total nucleic acids were purified using the Bio-On-Magnetic-Beads (BOMB) approach. Briefly, a guanidine isothiocyanate lysis buffer was used to homogenize cells, and then was combined with TE-diluted Sera-Mag Magnetic SpeedBeads (GE Healthcare, GEHE45152105050250) and isopropanol in volumetric ratio of 2:3:4 (beads:lysate:isopropanol). Beads were captured with a neodymium magnet and washed once with isopropanol, twice with 70% ethanol and resuspended in milliQ water.
Purified DNA was subjected to bisulfite conversion using the EZ-96 DNA methylation Direct™ MagPrep kit (Zymo Research, D5044), according to the manufacturer's user guide, however, reagent volumes were scaled down to 25% of the recommended volume, with the exception of the final elution step which remained at 25 μL. To synthesise the first strand, we used converted DNA and 5′-biotinylated adaptor primers containing seven random nucleotides at its 3′ end (BioP5N7, biotin- ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNN). The first strand product was purified using streptavidin-coated magnetic beads (ThermoFisher, 11205D) and alkaline denaturation. Second strand DNA was synthesised using the immobilised first strand DNA and another adaptor primer also containing seven random nucleotides at its 3′ end (P7N7, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNN). Unique molecular barcodes and sequences essential for binding to Illumina flow-cells were added to the second strand DNA by PCR using 1 x HiFi HotStart Uracil + Mix (KAPA, KK2801) and 10 μM indexed Truseq-type oligos, amplified by 15 cycles of PCR and size selected by PEG-diluted SPRI beads. Library integrity was determined by agarose gel electrophoresis and sequenced on an Illumina HiSeq using single-end 100 bp chemistry.

treatment_protocol: Mouse TET 1-3 triple-KO ESC line with doxycycline inducible mouse TET3 catalytic domain were treatet with 1 μM doxycycline. Wild-type V6.5 hybrid embryonic stem cells (i.e. C57BL/6 X 129/sv cross) were treated with 0.215µM of decitabine (5-aza-2’-deoxycytidine) over a period of 48 hours.

value: Wild type ESC derived from C57BL/6 x 129/sv cross

tag: dox inducible tet3-cd

tag: time treatment (h)


title: V65_Dec_48h_C


title: L03_AA10_180_VHGO_10

description:
L03_AA10
Hepatocyte_normcounts.csv


title: L03_AB09_187_1__OGO_10

description:
L03_AB09
Hepatocyte_normcounts.csv

value: OGO


title: L03_AB01_041_CGO_10

description:
L03_AB01
Hepatocyte_normcounts.csv

value: CGO


title: V65_Dec_42h_B


title: L03_AB08_080_HFO_10

description:
L03_AB08
Hepatocyte_normcounts.csv


title: V65_Dec_36h_C


title: V65_Dec_42h_C


title: L03_AA09_082_UATO_10

description:
L03_AA09
Hepatocyte_normcounts.csv


title: L03_AA08_006_HFO_10

description:
L03_AA08
Hepatocyte_normcounts.csv


title: V65_Dec_36h_A


title: V65_Dec_36h_B


title: L03_AA03_043_kerosine_10

description:
L03_AA03
Hepatocyte_normcounts.csv

value: KER


title: L03_AA06_MethodBlank_0

description:
L03_AA06
Hepatocyte_normcounts.csv


title: V65_Dec_30h_C


title: V65_Dec_30h_B


title: L03_AA01_016_kerosine_10

description:
L03_AA01
Hepatocyte_normcounts.csv


title: V65_Dec_48h_A


title: L02_DG11_058_HFO_100

description:
L02_DG11
Hepatocyte_normcounts.csv


title: V65_Dec_30h_A


title: V65_Dec_24h_B


title: V65_Dec_24h_C


title: L02_DG10_123_kerosine_100

description:
L02_DG10
Hepatocyte_normcounts.csv


title: L02_DG09_170_SRGO_100

description:
L02_DG09
Hepatocyte_normcounts.csv


title: V65_Dec_24h_A


title: V65_Dec_42h_A


title: L02_DG08_102_CGO_100

description:
L02_DG08
Hepatocyte_normcounts.csv


title: V65_Dec_18h_B


title: L02_DG06_MethodBlank_0

description:
L02_DG06
Hepatocyte_normcounts.csv


title: V65_Dec_18h_C


title: V65_Dec_12h_B


title: V65_Dec_12h_C


title: L02_DG04_106_CGO_100

description:
L02_DG04
Hepatocyte_normcounts.csv


title: L02_DG03_153_OLBO_100

description:
L02_DG03
Hepatocyte_normcounts.csv


title: L02_DF10_070_CGO_100

description:
L02_DF10
Hepatocyte_normcounts.csv


title: L02_DF09_096B_UDAE_100

description:
L02_DF09
Hepatocyte_normcounts.csv


title: L02_DG01_121_CGO_100

description:
L02_DG01
Hepatocyte_normcounts.csv


title: L02_DG02_202_Paraffinwax_100

description:
L02_DG02
Hepatocyte_normcounts.csv

value: WAX


title: V65_Dec_18h_A


title: V65_Dec_12h_A


title: V65_Dec_6h_C


title: V65_Dec_0h_B


title: L02_DF08_148_OLBO_100

description:
L02_DF08
Hepatocyte_normcounts.csv


title: V65_Dec_0h_C


title: V65_Dec_6h_A


title: L02_DH06_MethodBlank_0

description:
L02_DH06
Hepatocyte_normcounts.csv


title: V65_Ctr_48h_C


title: V65_Ctr_48h_B


title: L02_DF07_114_OLBO_100

description:
L02_DF07
Hepatocyte_normcounts.csv


title: L02_DF06_MethodBlank_0

description:
L02_DF06
Hepatocyte_normcounts.csv


title: V65_Ctr_42h_B


title: L02_DF05_196_petrolatum_100

description:
L02_DF05
Hepatocyte_normcounts.csv


title: V65_Dec_0h_A


title: V65_Ctr_42h_C


title: L02_DE08_175_VHGO_1

description:
L02_DE08
Hepatocyte_normcounts.csv


title: V65_Ctr_42h_A


title: V65_Ctr_36h_C


title: L02_DF02_132_gasoline_100

description:
L02_DF02
Hepatocyte_normcounts.csv

value: NAPTHA


title: V65_Ctr_48h_A


title: L02_DE10_188_SRGO_1

description:
L02_DE10
Hepatocyte_normcounts.csv


title: L02_DF01_075_OLBO_100

description:
L02_DF01
Hepatocyte_normcounts.csv


title: L02_DE11_188_SRGO_100

description:
L02_DE11
Hepatocyte_normcounts.csv


title: V65_Ctr_36h_B


title: L02_DF03_178_VHGO_100

description:
L02_DF03
Hepatocyte_normcounts.csv


title: V65_Dec_6h_B


title: V65_Ctr_36h_A


title: L02_DE09_175_VHGO_100

description:
L02_DE09
Hepatocyte_normcounts.csv


title: L02_DE07_134_HFO_100

description:
L02_DE07
Hepatocyte_normcounts.csv

value: HFO


title: V65_Ctr_30h_C


title: L02_DE02_092_OLBO_100

description:
L02_DE02
Hepatocyte_normcounts.csv

value: BO


title: L02_DE06_MethodBlank_0

description:
L02_DE06
Hepatocyte_normcounts.csv


title: V65_Ctr_24h_C


title: L02_DF04_197_HFO_100

description:
L02_DF04
Hepatocyte_normcounts.csv


title: V65_Ctr_30h_B


title: L02_DE05_134_HFO_1

description:
L02_DE05
Hepatocyte_normcounts.csv


title: V65_Ctr_30h_A


title: L02_DE04_120_gasoline_100

description:
L02_DE04
Hepatocyte_normcounts.csv


title: L02_DE03_120_gasoline_1

description:
L02_DE03
Hepatocyte_normcounts.csv


title: V65_Ctr_24h_B


title: V65_Ctr_24h_A


title: V65_Ctr_18h_A


title: L02_DE01_092_OLBO_1

description:
L02_DE01
Hepatocyte_normcounts.csv


title: L02_DD04_177_VHGO_100

description:
L02_DD04
Hepatocyte_normcounts.csv


title: V65_Ctr_12h_C


title: L02_DD05_168_SRGO_100

description:
L02_DD05
Hepatocyte_normcounts.csv

value: SRGO


title: V65_Ctr_18h_C


title: V65_Ctr_12h_B


title: L02_DC11_193_OXASPH_100

description:
L02_DC11
Hepatocyte_normcounts.csv

value: BIT


title: V65_Ctr_18h_B


title: L02_DD01_184_VHGO_100

description:
L02_DD01
Hepatocyte_normcounts.csv


title: L02_DD06_MethodBlank_0

description:
L02_DD06
Hepatocyte_normcounts.csv


title: V65_Ctr_12h_A


title: V65_Ctr_6h_B


title: L02_DD03_020_HFO_100

description:
L02_DD03
Hepatocyte_normcounts.csv


title: L02_DD02_091_HFO_100

description:
L02_DD02
Hepatocyte_normcounts.csv


title: V65_Ctr_6h_A


title: V65_Ctr_0h_A


title: L02_DC10_182_VHGO_100

description:
L02_DC10
Hepatocyte_normcounts.csv


title: V65_Ctr_6h_C


title: L02_DC09_120_gasoline_100

description:
L02_DC09
Hepatocyte_normcounts.csv


title: L02_DC07_150_OLBO_100

description:
L02_DC07
Hepatocyte_normcounts.csv


title: L02_DC06_MethodBlank_0

description:
L02_DC06
Hepatocyte_normcounts.csv


title: V65_Ctr_0h_C


title: L02_DC08_130_CGO_100

description:
L02_DC08
Hepatocyte_normcounts.csv


title: V65_Ctr_0h_B


title: ESC_TET_TKO_TET3_Dox_66h_B

value: Mouse TET 1-3 triple-KO ESC line with doxycycline inducible mouse TET3 catalytic domain


title: L02_DC05_140_OLBO_100

description:
L02_DC05
Hepatocyte_normcounts.csv


title: L02_DC04_036_OLBO_100

description:
L02_DC04
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_60h_C


title: L02_DB10_085B_OLBO_100

description:
L02_DB10
Hepatocyte_normcounts.csv


title: L02_DB09_190_BITUMENS_100

description:
L02_DB09
Hepatocyte_normcounts.csv


title: L02_DB08_071_HFO_100

description:
L02_DB08
Hepatocyte_normcounts.csv


title: L02_DB07_166_HFO_100

description:
L02_DB07
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_66h_C


title: ESC_TET_TKO_TET3_Dox_72h_A


title: L02_DB11_115_OLBO_100

description:
L02_DB11
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_66h_A


title: L02_DB06_MethodBlank_0

description:
L02_DB06
Hepatocyte_normcounts.csv


title: L02_DB03_188_SRGO_100

description:
L02_DB03
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_60h_A


title: ESC_TET_TKO_TET3_Dox_54h_B


title: ESC_TET_TKO_TET3_Dox_72h_C


title: ESC_TET_TKO_TET3_Dox_54h_C


title: ESC_TET_TKO_TET3_Dox_54h_A


title: ESC_TET_TKO_TET3_Dox_72h_B


title: L02_DA06_MethodBlank_0

description:
L02_DA06
Hepatocyte_normcounts.csv


title: L02_CH11_185_RAE_1

description:
L02_CH11
Hepatocyte_normcounts.csv

value: RAE


title: ESC_TET_TKO_TET3_Dox_48h_B


title: L02_DB05_091_HFO_100

description:
L02_DB05
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_48h_C


title: L02_DC02_145_HRBO_100

description:
L02_DC02
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_42h_C


title: ESC_TET_TKO_TET3_Dox_48h_A


title: L02_CH09_175_VHGO_1

description:
L02_CH09
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_42h_B


title: ESC_TET_TKO_TET3_Dox_60h_B


title: L02_CH04_149_OLBO_1

description:
L02_CH04
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_36h_A


title: L02_CH02_069_TDAE_1

description:
L02_CH02
Hepatocyte_normcounts.csv

value: TDAE


title: L02_CH06_MethodBlank_0

description:
L02_CH06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_36h_C


title: L02_CH08_084_UATO_1

description:
L02_CH08
Hepatocyte_normcounts.csv

value: UATO


title: ESC_TET_TKO_TET3_Dox_30h_B


title: ESC_TET_TKO_TET3_Dox_24h_B


title: ESC_TET_TKO_TET3_Dox_24h_A


title: L02_CG09_056_gasoline_1

description:
L02_CG09
Hepatocyte_normcounts.csv


title: L02_CG06_MethodBlank_0

description:
L02_CG06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_36h_B


title: ESC_TET_TKO_TET3_Dox_18h_C


title: L02_CH05_085C_OLBO_1

description:
L02_CH05
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_30h_C


title: ESC_TET_TKO_TET3_Dox_30h_A


title: L02_CG10_139_OLBO_1

description:
L02_CG10
Hepatocyte_normcounts.csv


title: L02_CG11_078_HFO_1

description:
L02_CG11
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_24h_C


title: ESC_TET_TKO_TET3_Dox_18h_A


title: ESC_TET_TKO_TET3_Dox_12h_C


title: ESC_TET_TKO_TET3_Dox_12h_B


title: L02_CH10_172_SRGO_1

description:
L02_CH10
Hepatocyte_normcounts.csv


title: L02_CH01_049_kerosine_1

description:
L02_CH01
Hepatocyte_normcounts.csv


title: L02_CG05_183_VHGOa_1

description:
L02_CG05
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_18h_B


title: L02_CG08_134_HFO_1

description:
L02_CG08
Hepatocyte_normcounts.csv


title: L02_CE10_177_VHGO_1

description:
L02_CE10
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_6h_C


title: L02_CE09_012_CGO_1

description:
L02_CE09
Hepatocyte_normcounts.csv


title: L02_CG04_073_OLBO_1

description:
L02_CG04
Hepatocyte_normcounts.csv


title: L02_CG02_064_UATO_1

description:
L02_CG02
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_12h_A


title: ESC_TET_TKO_TET3_Dox_0h_C


title: ESC_TET_TKO_TET3_Dox_0h_B


title: ESC_TET_TKO_TET3_Dox_6h_B


title: L02_CE07_007_HFO_1

description:
L02_CE07
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_0h_A


title: L02_CE06_MethodBlank_0

description:
L02_CE06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Dox_6h_A


title: L02_CE05_173_OGO_1

description:
L02_CE05
Hepatocyte_normcounts.csv


title: L02_CE08_066_OLBO_1

description:
L02_CE08
Hepatocyte_normcounts.csv


title: L02_CE04_097_HFO_1

description:
L02_CE04
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_72h_B


title: L02_CF06_MethodBlank_0

description:
L02_CF06
Hepatocyte_normcounts.csv


title: L02_CE11_131_HFO_1

description:
L02_CE11
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_66h_C


title: L02_CG03_072_OLBO_1

description:
L02_CG03
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_72h_C


title: L02_CE03_113_OLBO_1

description:
L02_CE03
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_72h_A


title: L02_CE02_192_BITUMENS_1

description:
L02_CE02
Hepatocyte_normcounts.csv


title: L02_CD11_189_BITUMEN_1

description:
L02_CD11
Hepatocyte_normcounts.csv


title: L02_CD10_031_HFO_1

description:
L02_CD10
Hepatocyte_normcounts.csv


title: L02_CE01_111_petrolatum_1

description:
L02_CE01
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_66h_B


title: L02_CD09_176_VHGO_1

description:
L02_CD09
Hepatocyte_normcounts.csv


title: L02_CD12_034_HFO_1

description:
L02_CD12
Hepatocyte_normcounts.csv


title: L02_CD05_112_OLBO_1

description:
L02_CD05
Hepatocyte_normcounts.csv


title: L02_CD03_174_OGO_1

description:
L02_CD03
Hepatocyte_normcounts.csv


title: L02_CD04_137_OLBO_1

description:
L02_CD04
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_48h_B


title: ESC_TET_TKO_TET3_Ctr_54h_A


title: L02_CD01_003_CGO_1

description:
L02_CD01
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_48h_A


title: ESC_TET_TKO_TET3_Ctr_60h_A


title: L02_CD07_024_HFO_1

description:
L02_CD07
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_54h_C


title: ESC_TET_TKO_TET3_Ctr_42h_B


title: L02_CD06_MethodBlank_0

description:
L02_CD06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_66h_A


title: ESC_TET_TKO_TET3_Ctr_60h_C


title: L02_CC08_175_VHGO_10

description:
L02_CC08
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_42h_C


title: L02_CC10_188_SRGO_10

description:
L02_CC10
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_42h_A


title: ESC_TET_TKO_TET3_Ctr_30h_C


title: ESC_TET_TKO_TET3_Ctr_54h_B


title: L02_CC01_092_OLBO_10

description:
L02_CC01
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_36h_A


title: L02_CD02_020_HFO_1

description:
L02_CD02
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_48h_C


title: ESC_TET_TKO_TET3_Ctr_60h_B


title: L02_CC06_MethodBlank_0

description:
L02_CC06
Hepatocyte_normcounts.csv


title: L02_CC05_134_HFO_10

description:
L02_CC05
Hepatocyte_normcounts.csv


title: L02_CB07_168_SRGO_1

description:
L02_CB07
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_18h_A


title: L02_CC03_120_gasoline_10

description:
L02_CC03
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_12h_C


title: ESC_TET_TKO_TET3_Ctr_30h_A


title: L02_CB11_186_RAE_1

description:
L02_CB11
Hepatocyte_normcounts.csv


title: L02_CB10_171_SRGO_1

description:
L02_CB10
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_30h_B


title: L02_CB01_152_slackwax_1

description:
L02_CB01
Hepatocyte_normcounts.csv


title: L02_CB08_146_gasoline_1

description:
L02_CB08
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_24h_B


title: ESC_TET_TKO_TET3_Ctr_24h_C


title: L02_CA10_085D_OLBO_1

description:
L02_CA10
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_0h_B


title: L02_CB06_MethodBlank_0

description:
L02_CB06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_24h_A


title: ESC_TET_TKO_TET3_Ctr_0h_A


title: L02_CB04_117_OLBO_1

description:
L02_CB04
Hepatocyte_normcounts.csv


title: L02_CB05_061_P_Hwax_1

description:
L02_CB05
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_12h_A


title: L02_CB03_147_OLBO_1

description:
L02_CB03
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_6h_C


title: L02_CB02_011_kerosine_1

description:
L02_CB02
Hepatocyte_normcounts.csv


title: L02_CA06_MethodBlank_0

description:
L02_CA06
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_6h_B


title: L02_CA11_028_HFO_1

description:
L02_CA11
Hepatocyte_normcounts.csv


title: Old SNI rep2

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

source_name: whole sciatic Dorsal Root Ganglia

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 7.5 was used for library preparation.
Libraries were generated using the TruSeq mRNA Sample Preparation Kit  (Illumina, San Diego CA) at Ospedale San Raffaele according to the Sample Preparation Guide protocol. Ligation and library integrity was verified using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent). Sample libraries ligated with unique adapter sequences were multiplexed and were sequenced using Illumina HiSeq 2500 100-cycle, pair end sequencing.

treatment_protocol: Young (8-10 weeks old) and aged Mice (20-22 months old)  underwent sham or sciatic nerve injury and sacrifized 24h after

value: whole sciatic Dorsal Root Ganglia

tag: age

value: 20-22 months old

value: sciatic nerve injury


title: Old SNI rep1


title: ESC_TET_TKO_TET3_Ctr_6h_A


title: Old Sham rep3

value: sham


title: ESC_TET_TKO_TET3_Ctr_0h_C


title: L02_CA08_025_HFO_1

description:
L02_CA08
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: Old Sham rep2


title: L02_CA07_018_HFO_1

description:
L02_CA07
Hepatocyte_normcounts.csv


title: L02_CA02_160_FO_1

description:
L02_CA02
Hepatocyte_normcounts.csv

value: FO


title: Old SNI rep3


title: L02_CA05_138_OLBO_1

description:
L02_CA05
Hepatocyte_normcounts.csv


title: ESC_TET_TKO_TET3_Ctr_12h_B


title: L02_CA04_086_kerosine_1

description:
L02_CA04
Hepatocyte_normcounts.csv

value: KER


title: L02_BG09_170_SRGO_1

description:
L02_BG09
Hepatocyte_normcounts.csv


title: L02_BG08_102_CGO_1

description:
L02_BG08
Hepatocyte_normcounts.csv

value: CGO


title: L02_CA03_062_P_Hwax_1

description:
L02_CA03
Hepatocyte_normcounts.csv

value: WAX


title: L02_BG06_MethodBlank_0

description:
L02_BG06
Hepatocyte_normcounts.csv


title: Old Sham rep1


title: Young Sham rep3

value: 8-10 weeks old


title: X3_76_IPF

city: New Haven

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5
After quality control for adapter contamination and trimming, fastq files were mapped on human genome (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM gene counts for every gene and every sample

source_name: Lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen) from each core. according the manufacture protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station
20 ng RNA input was used for library preparation by AmpliSeq Transcriptome Human Gene Expression kit. The cDNA was then amplified and barcoded using the Ion Xpress RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485).  The Ion Chip Kit v2 BC (Life Technologies) 4484270) was then loaded using the Ion Chef System (Life Technologies 4484177) with the Ion PI IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI IC 200 Kit.

treatment_protocol: Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor. The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 4 cores were randomly selected per lung.

value: lung

tag: disease

value: IPF

tag: subject

tag: surface density

tag: smoking ever

tag: age transplant

tag: gender

value: M

tag: cluster


title: L02_BG11_058_HFO_1

description:
L02_BG11
Hepatocyte_normcounts.csv

tag: tissue/celltype

tag: treatment

value: HFO

tag: dose


title: X3_26_IPF

tag: tissue


title: L02_BF10_070_CGO_1

description:
L02_BF10
Hepatocyte_normcounts.csv


title: X3_68_IPF


title: L02_BG01_121_CGO_1

description:
L02_BG01
Hepatocyte_normcounts.csv


title: X25_59_IPF


title: X3_45_IPF


title: Young Sham rep2

tag: strain


title: L02_BG10_123_kerosine_1

description:
L02_BG10
Hepatocyte_normcounts.csv


title: Young Sham rep1


title: X50_4_IPF


title: X50_46_IPF


title: X25_22_IPF


title: X50_25_IPF


title: L02_BF09_096B_UDAE_1

description:
L02_BF09
Hepatocyte_normcounts.csv

value: UDAE


title: X50_16_IPF


title: L02_BG04_106_CGO_1

description:
L02_BG04
Hepatocyte_normcounts.csv


title: L02_CA01_046_gasoline_1

description:
L02_CA01
Hepatocyte_normcounts.csv

value: NAPTHA


title: L02_BH06_MethodBlank_0

description:
L02_BH06
Hepatocyte_normcounts.csv


title: X25_15_IPF


title: L02_BG02_202_Paraffinwax_1

description:
L02_BG02
Hepatocyte_normcounts.csv


title: L02_BF06_MethodBlank_0

description:
L02_BF06
Hepatocyte_normcounts.csv


title: L02_BF05_196_petrolatum_1

description:
L02_BF05
Hepatocyte_normcounts.csv


title: X25_49_IPF


title: L02_BF08_148_OLBO_1

description:
L02_BF08
Hepatocyte_normcounts.csv

value: BO


title: L02_BF04_197_HFO_1

description:
L02_BF04
Hepatocyte_normcounts.csv


title: L02_BG03_153_OLBO_1

description:
L02_BG03
Hepatocyte_normcounts.csv


title: X190_36_IPF


title: L02_BF03_178_VHGO_1

description:
L02_BF03
Hepatocyte_normcounts.csv

value: VHGO


title: X190_24_IPF


title: X162_23_IPF


title: X162_11_IPF


title: X162_15_IPF


title: L02_BF07_114_OLBO_1

description:
L02_BF07
Hepatocyte_normcounts.csv


title: L02_BE10_188_SRGO_1

description:
L02_BE10
Hepatocyte_normcounts.csv

value: SRGO


title: L02_BE08_175_VHGO_1

description:
L02_BE08
Hepatocyte_normcounts.csv


title: L02_BE11_188_SRGO_100

description:
L02_BE11
Hepatocyte_normcounts.csv


title: L02_BF02_132_gasoline_1

description:
L02_BF02
Hepatocyte_normcounts.csv


title: L02_BE07_134_HFO_100

description:
L02_BE07
Hepatocyte_normcounts.csv


title: X162_12_IPF


title: L02_BE06_MethodBlank_0

description:
L02_BE06
Hepatocyte_normcounts.csv


title: X190_64_IPF


title: X147_10_IPF


title: X147_24_IPF


title: L02_BE05_134_HFO_1

description:
L02_BE05
Hepatocyte_normcounts.csv


title: L02_BE09_175_VHGO_100

description:
L02_BE09
Hepatocyte_normcounts.csv


title: L02_BE04_120_gasoline_100

description:
L02_BE04
Hepatocyte_normcounts.csv


title: L02_BE03_120_gasoline_1

description:
L02_BE03
Hepatocyte_normcounts.csv


title: X127_29_IPF


title: L02_BF01_075_OLBO_1

description:
L02_BF01
Hepatocyte_normcounts.csv


title: X190_4_IPF


title: L02_BE02_092_OLBO_100

description:
L02_BE02
Hepatocyte_normcounts.csv


title: X127_15_IPF


title: X127_4_IPF


title: L02_BE01_092_OLBO_1

description:
L02_BE01
Hepatocyte_normcounts.csv


title: L02_BD06_MethodBlank_0

description:
L02_BD06
Hepatocyte_normcounts.csv


title: X120_16_IPF


title: X120_110_IPF


title: L02_BD05_168_SRGO_1

description:
L02_BD05
Hepatocyte_normcounts.csv


title: X147_43_IPF


title: L02_BD04_177_VHGO_1

description:
L02_BD04
Hepatocyte_normcounts.csv


title: X120_100_IPF


title: L02_BD02_091_HFO_1

description:
L02_BD02
Hepatocyte_normcounts.csv


title: X11_30_IPF


title: X11_54_IPF


title: L02_BD03_020_HFO_1

description:
L02_BD03
Hepatocyte_normcounts.csv


title: L02_BD01_184_VHGO_1

description:
L02_BD01
Hepatocyte_normcounts.csv


title: X11_25_IPF


title: L02_BC11_193_OXASPH_1

description:
L02_BC11
Hepatocyte_normcounts.csv

value: BIT


title: X11_11_IPF


title: X127_37_IPF


title: X110_58_IPF


title: L02_BC10_182_VHGO_1

description:
L02_BC10
Hepatocyte_normcounts.csv


title: X110_30_IPF


title: L02_BC06_MethodBlank_0

description:
L02_BC06
Hepatocyte_normcounts.csv


title: X120_31_IPF


title: L02_BC07_150_OLBO_1

description:
L02_BC07
Hepatocyte_normcounts.csv


title: X110_12_IPF


title: X91_42_HP

value: HP

value: F


title: X91_36_HP


title: X91_21_HP


title: L02_BC04_036_OLBO_1

description:
L02_BC04
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: X40_82_HP


title: L02_BC01_179_VHGO_1

description:
L02_BC01
Hepatocyte_normcounts.csv


title: X91_12_HP


title: L02_BB11_115_OLBO_1

description:
L02_BB11
Hepatocyte_normcounts.csv


title: L02_BB10_085B_OLBO_1

description:
L02_BB10
Hepatocyte_normcounts.csv


title: X40_36_HP


title: X147_69_IPF


title: X40_23_HP


title: X40_46_HP


title: X216_95_HP


title: L02_BB08_071_HFO_1

description:
L02_BB08
Hepatocyte_normcounts.csv


title: L02_BB09_190_BITUMENS_1

description:
L02_BB09
Hepatocyte_normcounts.csv


title: L02_BB07_166_HFO_1

description:
L02_BB07
Hepatocyte_normcounts.csv


title: L02_BC09_120_gasoline_1

description:
L02_BC09
Hepatocyte_normcounts.csv


title: L02_BC08_130_CGO_1

description:
L02_BC08
Hepatocyte_normcounts.csv


title: L02_BB06_MethodBlank_0

description:
L02_BB06
Hepatocyte_normcounts.csv


title: X216_34_HP


title: X216_86_HP


title: L02_BB05_091_HFO_1

description:
L02_BB05
Hepatocyte_normcounts.csv


title: L02_BC02_145_HRBO_1

description:
L02_BC02
Hepatocyte_normcounts.csv


title: L02_BB03_188_SRGO_1

description:
L02_BB03
Hepatocyte_normcounts.csv


title: X216_17_HP


title: X213_51_HP


title: L02_BA06_MethodBlank_0

description:
L02_BA06
Hepatocyte_normcounts.csv


title: X213_64_HP


title: L02_AH11_090_FO_1

description:
L02_AH11
Hepatocyte_normcounts.csv

value: FO


title: X213_40_HP


title: L02_AH10_067_P_Hwax_1

description:
L02_AH10
Hepatocyte_normcounts.csv


title: X110_16_IPF


title: L02_BC05_140_OLBO_1

description:
L02_BC05
Hepatocyte_normcounts.csv


title: L02_AH09_079_HFO_1

description:
L02_AH09
Hepatocyte_normcounts.csv


title: L02_BB01_154_OLBO_1

description:
L02_BB01
Hepatocyte_normcounts.csv


title: X213_23_HP


title: X212_53_HP


title: X212_8_HP


title: L02_AH07_021_HFO_1

description:
L02_AH07
Hepatocyte_normcounts.csv


title: X212_4_HP


title: L02_AH05_096A_UDAE_1

description:
L02_AH05
Hepatocyte_normcounts.csv


title: X212_40_HP


title: X209_57_HP


title: L02_AH06_MethodBlank_0

description:
L02_AH06
Hepatocyte_normcounts.csv


title: L02_AH04_128_kerosine_1

description:
L02_AH04
Hepatocyte_normcounts.csv

value: KER


title: X209_47_HP


title: X209_21_HP


title: L02_AH03_060_OLBO_1

description:
L02_AH03
Hepatocyte_normcounts.csv


title: L02_AH02_119_OLBO_1

description:
L02_AH02
Hepatocyte_normcounts.csv


title: X209_34_HP


title: X144_96_HP


title: L02_AG11_191_BITUMEN_1

description:
L02_AG11
Hepatocyte_normcounts.csv


title: X144_94_HP


title: L02_AG10_164_HFO_1

description:
L02_AG10
Hepatocyte_normcounts.csv


title: L02_AH01_195_UDAE_1

description:
L02_AH01
Hepatocyte_normcounts.csv


title: X144_53_HP


title: L02_AG09_104_kerosine_1

description:
L02_AG09
Hepatocyte_normcounts.csv


title: L02_AG08_108_OLBO_1

description:
L02_AG08
Hepatocyte_normcounts.csv


title: X144_33_HP


title: X113_54_HP


title: L02_AG07_136_slackwax_1

description:
L02_AG07
Hepatocyte_normcounts.csv

value: WAX


title: X113_3_HP


title: X113_4_HP


title: X107_9_HP


title: L02_AG06_MethodBlank_0

description:
L02_AG06
Hepatocyte_normcounts.csv


title: X113_27_HP


title: L02_AG05_135_TDAE_1

description:
L02_AG05
Hepatocyte_normcounts.csv

value: TDAE


title: L02_AG04_181_VHGO_1

description:
L02_AG04
Hepatocyte_normcounts.csv


title: X107_52_HP

value: lung


title: L02_AG03_017_HFO_1

description:
L02_AG03
Hepatocyte_normcounts.csv


title: L02_AG02_187_2__OGO_1

description:
L02_AG02
Hepatocyte_normcounts.csv

value: OGO


title: L02_AG01_118_OLBO_1

description:
L02_AG01
Hepatocyte_normcounts.csv


title: L02_AF06_MethodBlank_0

description:
L02_AF06
Hepatocyte_normcounts.csv


title: L02_AF04_192_BITUMENS_1

description:
L02_AF04
Hepatocyte_normcounts.csv


title: L02_AF05_183_VHGOa_1

description:
L02_AF05
Hepatocyte_normcounts.csv


title: L02_AF01_043_kerosine_1

description:
L02_AF01
Hepatocyte_normcounts.csv


title: L02_AE11_124_gasoline_1

description:
L02_AE11
Hepatocyte_normcounts.csv


title: X107_38_HP

value: M


title: L02_AF03_076_gasoline_1

description:
L02_AF03
Hepatocyte_normcounts.csv


title: L02_AE06_MethodBlank_0

description:
L02_AE06
Hepatocyte_normcounts.csv


title: L02_AE10_085A_OLBO_1

description:
L02_AE10
Hepatocyte_normcounts.csv


title: L02_AE07_087_kerosine_1

description:
L02_AE07
Hepatocyte_normcounts.csv


title: L02_AE08_107_P_Hwax_1

description:
L02_AE08
Hepatocyte_normcounts.csv


title: L02_AF02_083_UATO_1

description:
L02_AF02
Hepatocyte_normcounts.csv

value: UATO


title: L02_AE09_092_OLBO_1

description:
L02_AE09
Hepatocyte_normcounts.csv


title: L02_AE03_076_gasoline_1

description:
L02_AE03
Hepatocyte_normcounts.csv


title: L02_AE05_065_P_Hwax_1

description:
L02_AE05
Hepatocyte_normcounts.csv


title: L02_AD09_093_petrolatum_1

description:
L02_AD09
Hepatocyte_normcounts.csv


title: L02_AE01_169_SRGO_1

description:
L02_AE01
Hepatocyte_normcounts.csv


title: L02_AD11_050_HFO_1

description:
L02_AD11
Hepatocyte_normcounts.csv

value: HFO


title: L02_AD05_074_OLBO_1

description:
L02_AD05
Hepatocyte_normcounts.csv


title: X107_78_HP


title: L02_AD10_089_UDAE_1

description:
L02_AD10
Hepatocyte_normcounts.csv

value: UDAE


title: L02_AD01_081_OLBO_1

description:
L02_AD01
Hepatocyte_normcounts.csv

value: BO


title: L02_AD08_103_gasoline_1

description:
L02_AD08
Hepatocyte_normcounts.csv

value: NAPTHA


title: GFP-FOXR1 rep3

city: Boston

first: Uwe

last: Beffert

state: MA

address: 24 Cummington Mall

department: Biology

institute: Boston University

data_processing:
Reads alignment using hisat2/2.0.3 with default parameter. The bam files were sorted by read names instead of chromosome coordinates by SAMtools
Gene count matrix of each sample was generated by HTSeq/0.6.1
Downstream analysis was performed with the DEseq2. Genes that were not expressed in any cell were removed from downstream analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: transiently transfected HEK-293 cells

growth_protocol: HEK293T (ATCC CRL-3216) cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS; Hyclone) and 1% Penicillin/Streptomycin in a 5% CO2 incubator at 37oC.

extract_protocol:
HEK293T were transfected with GFP, GFP-FOXR1 or GFP-M280L mutant using FuGENE6.  Forty-eight hours after transfection, total RNA was purified using the QIAshredder and RNeasy Mini Kit (QIAGEN) and samples were processed with Trizol (Invitrogen). Three biological replicates were processed independently. RNA samples were suspended in DEPC-treated water and concentrations were determined using the Nanodrop ND-1000 (Thermo Scientific) where all samples showed A260/A280 ratios higher than 2.0. RNA integrity was also checked in a bioanalyzer (Agilent 2100).
Library preparations and sequencing were performed by The Broad Institute, Cambridge, MA using Illumina HiSeq 2000 technology.

treatment_protocol: Cells at 60% confluency were transfected with GFP, GFP-FOXR1 or GFP-M280L plasmids using FuGENE6 transfection reagent (Promega) according to the manufacturer’s instructions.

tag: transfection

value: GFP-human FOXR1 fusion


title: L02_AD07_008_HFO_1

description:
L02_AD07
Hepatocyte_normcounts.csv


title: L02_AD06_MethodBlank_0

description:
L02_AD06
Hepatocyte_normcounts.csv


title: GFP-FOXR1 rep2


title: L02_AC06_MethodBlank_0

description:
L02_AC06
Hepatocyte_normcounts.csv


title: GFP-CTL rep3

value: GFP


title: GFP-FOXR1-M280L rep1

value: GFP-human FOXR1 M280L fusion


title: L02_AB08_080_HFO_1

description:
L02_AB08
Hepatocyte_normcounts.csv


title: L02_AB07_129_HFO_1

description:
L02_AB07
Hepatocyte_normcounts.csv


title: GFP-CTL rep2


title: L02_AB09_187_1__OGO_1

description:
L02_AB09
Hepatocyte_normcounts.csv


title: L02_AB04_155_HFO_1

description:
L02_AB04
Hepatocyte_normcounts.csv


title: L02_AB05_059_dieselfuel_1

description:
L02_AB05
Hepatocyte_normcounts.csv


title: L02_AB10_083_UATO_1

description:
L02_AB10
Hepatocyte_normcounts.csv


title: L02_AE04_141_gasoline_1

description:
L02_AE04
Hepatocyte_normcounts.csv


title: H3.3-G34R rep 2

city: Ann Arbor

first: Margaret

last: Hartlage

state: MI

address: 1150 W Medical Center Dr.

department: Neurosurgery

institute: University of Michigan

data_processing:
Indexing using kallisto version 0.45.1 on Ensembl v96 Homo sapeins transcriptome.
Quantification using kallisto version 0.45.1 with 100 bootstrap samples.
Estimated counts used for further analysis.
Genome_build: Ensembl v96 Homo sapeins
Supplementary_files_format_and_content: counts (gene x sample)

source_name: Human pHGG cells stably tranfected to express3X-FLAG-tagged H3.3 harboring the G34R mutation

growth_protocol: We developed a model based on the human primary pHGG cell culture, SJ-GBM2. These cells harbor inactivating mutations in P53 and ATRX and were obtained from a patient harboring a hemispheric pHGG. SJ-GBM2 cells were stably transfected with constructs to express a 3X-FLAG-tagged wild type H3.3 (generating the SJ-GBM2-H3.3-Wt cells) or a 3X-FLAG-tagged H3.3 harboring the G34R mutation (generating the SJ-GBM2-H3.3-G34R cells).

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Cat #74134)
RNA quality was assessed using a TapeStation (Agilent Technologies) following the manufacturer's recommended protocol. RNA sequencing libraries were prepared according to the TruSeq Stranded Total RNA Human/Mouse/Rat (Illumina) and were sequenced on the HiSeq 2000 platform.

treatment_protocol: For human pHGG cells, 4 independently generated stably transfected cultures of SJ-GBM2-H3.3-Wt and 3 independently generated stably transfected cultures of SJ-GBM2-H3.3-G34R were used. Biological replicates were grown in T25 flasks, and 2 million cells were used for RNA purification.

value: brain tumor cells

tag: genotype

value: mutated P53 + mutated ATRX + 3X-FLAG tagged hsitone H3.3 harboring G34R mutation


title: H3.3-G34R rep 3


title: GFP-CTL rep1


title: L02_AB03_184_VHGO_1

description:
L02_AB03
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: VHGO


title: H3.3-G34R rep 1


title: L02_AB02_009_gasoline_1

description:
L02_AB02
Hepatocyte_normcounts.csv


title: H3.3-Wt rep 3

source_name: Human pHGG cells stably tranfected to express 3X-FLAG-tagged wild type H3.3

value: mutated P53 + mutated ATRX + 3X-FLAG tagged wildtype H3.3


title: H3.3-Wt rep 4


title: L02_AD02_127_slackwax_1

description:
L02_AD02
Hepatocyte_normcounts.csv

value: WAX


title: L02_AB11_063_P_Hwax_1

description:
L02_AB11
Hepatocyte_normcounts.csv


title: L02_AB01_041_CGO_1

description:
L02_AB01
Hepatocyte_normcounts.csv

value: CGO


title: H3.3-Wt rep 2


title: L02_AA10_180_VHGO_1

description:
L02_AA10
Hepatocyte_normcounts.csv


title: GFP-FOXR1-M280L rep2


title: NLN-4_LN_mix

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Reads were aligned to hg38 using STAR (Dobin et al., 2013), summarized by featureCounts (Liao et al., 2014),
and normalized across samples (Law et al., 2014). Counts per million (CPM) were used to measure gene expression.
Genes with CPM > 1 in ≥ 3 samples were analyzed in downstream analysis.
Paired gene-level differential analysis was conducted using the limma package (Law et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: log2CPM Text format

extract_protocol:
RNA was extracted from CD19+ cells or snap frozen lymph node biopsies using RNeasy kits (Qiagen, Germantown, MD, USA).
Total RNA libraries were prepared according to the Illumina TruSeq protocol.

value: lymph node

tag: cd19+ selection

value: no

tag: diagnosis

value: Normal


title: L02_AA09_082_UATO_1

description:
L02_AA09
Hepatocyte_normcounts.csv

value: UATO


title: H3.3-Wt rep 1


title: L02_AA08_006_HFO_1

description:
L02_AA08
Hepatocyte_normcounts.csv

value: HFO


title: NLN-3_LN_mix


title: L02_AB06_MethodBlank_0

description:
L02_AB06
Hepatocyte_normcounts.csv


title: L01_DH10_067_P_Hwax_100

description:
L01_DH10
Hepatocyte_normcounts.csv


title: CLL-C53_LN_mix

tag: age

tag: Sex

value: F

value: SLL

tag: ighv

value: M


title: NLN-1_LN_mix


title: L02_AA06_MethodBlank_0

description:
L02_AA06
Hepatocyte_normcounts.csv


title: NLN-2_LN_mix


title: L02_AA05_151_OLBO_1

description:
L02_AA05
Hepatocyte_normcounts.csv

value: BO


title: L02_AA03_043_kerosine_1

description:
L02_AA03
Hepatocyte_normcounts.csv

value: KER


title: L01_DH07_021_HFO_100

description:
L01_DH07
Hepatocyte_normcounts.csv


title: L01_DH11_090_FO_100

description:
L01_DH11
Hepatocyte_normcounts.csv

value: FO


title: CLL-C42_LN_mix


title: CLL-C39_LN_mix


title: L01_DH09_079_HFO_100

description:
L01_DH09
Hepatocyte_normcounts.csv


title: CLL-C55_LN_mix

value: U


title: CLL-C46_LN_mix

value: CLL


title: L01_DH06_MethodBlank_0

description:
L01_DH06
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: L01_DH04_128_kerosine_100

description:
L01_DH04
Hepatocyte_normcounts.csv


title: L01_DH05_096A_UDAE_100

description:
L01_DH05
Hepatocyte_normcounts.csv

value: UDAE


title: CLL-C41_LN_mix


title: CLL-C34_LN_mix


title: CLL-C32_LN_mix


title: CLL-C45_LN_mix


title: L01_DH02_119_OLBO_100

description:
L01_DH02
Hepatocyte_normcounts.csv


title: CLL-C43_LN_mix


title: CLL-C35_LN_mix


title: L01_DH01_195_UDAE_100

description:
L01_DH01
Hepatocyte_normcounts.csv


title: CLL-C51_LN_mix


title: L01_DG10_164_HFO_100

description:
L01_DG10
Hepatocyte_normcounts.csv


title: L02_AA01_016_kerosine_1

description:
L02_AA01
Hepatocyte_normcounts.csv


title: CLL-C210_LN_mix


title: CLL-C30_LN_mix


title: L01_DG09_104_kerosine_100

description:
L01_DG09
Hepatocyte_normcounts.csv


title: CLL-C14_LN_mix


title: L01_DG11_191_BITUMEN_100

description:
L01_DG11
Hepatocyte_normcounts.csv

value: BIT


title: L01_DG08_108_OLBO_100

description:
L01_DG08
Hepatocyte_normcounts.csv


title: CLL-C08_LN_mix


title: L01_DH03_060_OLBO_100

description:
L01_DH03
Hepatocyte_normcounts.csv


title: L01_DG07_136_slackwax_100

description:
L01_DG07
Hepatocyte_normcounts.csv

value: WAX


title: CLL-C24_LN_mix

value: lymph node


title: L01_DG03_017_HFO_100

description:
L01_DG03
Hepatocyte_normcounts.csv


title: CLL-C05_LN_mix

value: no


title: L01_DG06_MethodBlank_0

description:
L01_DG06
Hepatocyte_normcounts.csv


title: L01_DG02_187_2__OGO_100

description:
L01_DG02
Hepatocyte_normcounts.csv

value: OGO


title: L01_DG05_135_TDAE_100

description:
L01_DG05
Hepatocyte_normcounts.csv

value: TDAE


title: CLL-C11_LN_mix


title: CLL-C03_LN_mix


title: CLL-C33_LN_mix


title: CLL-C44_LN_mix


title: L01_DG04_181_VHGO_100

description:
L01_DG04
Hepatocyte_normcounts.csv

value: VHGO


title: CLL-C47_LN_mix

value: F


title: L01_DG01_118_OLBO_100

description:
L01_DG01
Hepatocyte_normcounts.csv


title: L01_DF05_183_VHGOa_100

description:
L01_DF05
Hepatocyte_normcounts.csv


title: L01_DF04_192_BITUMENS_100

description:
L01_DF04
Hepatocyte_normcounts.csv


title: CLL-C37_LN_mix


title: L01_DF06_MethodBlank_0

description:
L01_DF06
Hepatocyte_normcounts.csv


title: L01_DF03_076_gasoline_100

description:
L01_DF03
Hepatocyte_normcounts.csv

value: NAPTHA


title: CLL-C36_LN_mix


title: CLL-C31_LN_mix

value: M


title: CLL-C01_LN_mix


title: L01_DF01_043_kerosine_100

description:
L01_DF01
Hepatocyte_normcounts.csv


title: L01_DF02_083_UATO_100

description:
L01_DF02
Hepatocyte_normcounts.csv

value: UATO


title: L01_DE11_124_gasoline_100

description:
L01_DE11
Hepatocyte_normcounts.csv


title: CLL-C13_LN_mix


title: CLL-C07_LN_mix


title: CLL-C04_LN_mix


title: L01_DE07_087_kerosine_100

description:
L01_DE07
Hepatocyte_normcounts.csv

value: KER


title: L01_DE10_085A_OLBO_100

description:
L01_DE10
Hepatocyte_normcounts.csv

value: BO


title: CLL-C06_LN_mix

value: U


title: L01_DE06_MethodBlank_0

description:
L01_DE06
Hepatocyte_normcounts.csv


title: L01_DE09_092_OLBO_100

description:
L01_DE09
Hepatocyte_normcounts.csv


title: CLL-C49_LN_mix

value: CLL


title: L01_DE04_141_gasoline_100

description:
L01_DE04
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: CLL-C02_LN_mix


title: L01_DE05_065_P_Hwax_100

description:
L01_DE05
Hepatocyte_normcounts.csv


title: L01_DE08_107_P_Hwax_100

description:
L01_DE08
Hepatocyte_normcounts.csv


title: L01_DE03_076_gasoline_100

description:
L01_DE03
Hepatocyte_normcounts.csv


title: CLL-C210_LN_CD19

value: yes

value: SLL


title: CLL-C43_LN_CD19


title: CLL-C45_LN_CD19


title: L01_DD11_050_HFO_100

description:
L01_DD11
Hepatocyte_normcounts.csv

value: HFO


title: CLL-C35_LN_CD19

value: lymph node


title: CLL-C25_LN_mix

value: no


title: L01_DD10_089_UDAE_100

description:
L01_DD10
Hepatocyte_normcounts.csv

value: UDAE


title: CLL-C46_LN_CD19


title: CLL-C41_LN_CD19


title: L01_DD09_093_petrolatum_100

description:
L01_DD09
Hepatocyte_normcounts.csv


title: CLL-C34_LN_CD19


title: L01_DD08_103_gasoline_100

description:
L01_DD08
Hepatocyte_normcounts.csv


title: L01_DD06_MethodBlank_0

description:
L01_DD06
Hepatocyte_normcounts.csv


title: CLL-C32_LN_CD19


title: CLL-C30_LN_CD19


title: CLL-C14_LN_CD19


title: L01_DD07_008_HFO_100

description:
L01_DD07
Hepatocyte_normcounts.csv


title: L01_DD05_074_OLBO_100

description:
L01_DD05
Hepatocyte_normcounts.csv


title: L01_DD02_127_slackwax_100

description:
L01_DD02
Hepatocyte_normcounts.csv

value: WAX


title: CLL-C08_LN_CD19


title: CLL-C01_LN_CD19


title: CLL-C05_LN_CD19


title: L01_DD01_081_OLBO_100

description:
L01_DD01
Hepatocyte_normcounts.csv


title: L01_DE01_169_SRGO_100

description:
L01_DE01
Hepatocyte_normcounts.csv

value: SRGO


title: Skin BPL4

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a ZR proprietary analysis pipeline, which is written in Python and used Bismark  to perform the alignment.
Index files were constructed using the bismark_genome_preparation command and the entire reference genome.
The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off during methylation calling.
The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
The methylation ratio (Mr) is defined as the number of reads overlapping a particular CpG comprising a C or a T at the first position of the CpG. If x is the number of C's and y the number of T's, the formula Mr = x/(x + y) then gives the methylation ratio for each CpG.
Genome_build: BalAcu1.0
Supplementary_files_format_and_content: Excel file including methylation data for every C for each sample including methylation differentiation and p value related to Comparison (group1 vs group2)
Supplementary_files_format_and_content: Matrix table with raw methylation counts for every gene and every sample
Supplementary_files_format_and_content: Comparison 1 CHH_result_table.xls: Comparison CHH
Supplementary_files_format_and_content: Comparison 1 CHG_top result_table.xls: Comparison CHG
Supplementary_files_format_and_content: Comparison CpG_top result_table.xls: Comparison CpG
Supplementary_files_format_and_content: CHH_all result_table.txt: All data CHH
Supplementary_files_format_and_content: CHG_all result_table.txt: All data CHG
Supplementary_files_format_and_content: CpG_all result_table.txt: All data CpG
Supplementary_files_format_and_content: Strongly Hypo-Hyper_CpG_CHH_CHG-xls: Selected data files for CpG_CHH_CHG

organism: Balaenoptera physalus

source_name: Skin tissue

extract_protocol:
DNA extraction with Quick-DNA Miniprep Plus Kit (Zymo Research, ZR).
Libraries were prepared from 300 ng of genomic DNA digested with 30 units of MspI (NEB) and then extracted with Zymo Research DNA Clean & Concentrator™-5 kit. The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR) for sequencing on an Illumina HiSeq.
Reduced representation bisulfite sequencing (RRBS)

tag: oc concentration

value: low

tag: group


title: L01_DB11_063_P_Hwax_100

description:
L01_DB11
Hepatocyte_normcounts.csv


title: L01_DB10_083_UATO_100

description:
L01_DB10
Hepatocyte_normcounts.csv


title: Skin BPT17

value: high


title: Skin BPT19


title: L01_DB09_187_1__OGO_100

description:
L01_DB09
Hepatocyte_normcounts.csv

value: OGO


title: Skin BPT16


title: CLL-C03_LN_CD19

value: M


title: CLL-C33_LN_CD19


title: BB17_GGCTAC

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and B. cinerea with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism:
Solanum lycopersicum
Botrytis cinerea

source_name: Inoculated fruit

extract_protocol:
At 3 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, mock-inoculated, and inoculated fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was ground to a fine powder in liquid nitrogen. 2 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were barcoded individually and analyzed for quantity and quality with the High Sensitivity DNA Analysis Kit in the Agilent 2100 Bioanalyzer (Agilent, USA). cDNA libraries were pooled in equal amounts for sequencing (single end, 50 bp) at the Expression Analysis Core Facility (UC Davis, CA, USA) in an Illumina HiSeq 2000 sequencer.

value: Ailsa Craig

tag: ripening stage

value: RR

value: B. cinerea inoculation


title: BB16_TAGCTT


title: L01_DC06_MethodBlank_0

description:
L01_DC06
Hepatocyte_normcounts.csv


title: Skin BPL1


title: CLL-C37_LN_CD19

value: CLL


title: Skin BPL6


title: CLL-C24_LN_CD19

value: U


title: L01_DB08_080_HFO_100

description:
L01_DB08
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: CLL-C11_LN_CD19

value: yes

value: F


title: CLL-C49_LN_CD19

value: lymph node


title: recovery_48h_40C_C

city: St. Louis

first: Ru

last: Zhang

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
Samples were quality control filtered using the JGI BBDuk and BBMap pipelines
Samples were quality assessed using FastQC
Reads were mapped to the Chlamydomonas reinhardtii v5.6 genome (Merchant et al., 2007) using STAR (Dobin and Gingeras, 2015; Dobin et al., 2013) with the maximum number of mapped loci set to 1 and the maximum mismatches per read set to 1, resulting in >92% of all reads being uniquely mapped to the Chlamydomonas reinhardtii v5.6 genome.
Reads per feature were counted via HT-seq count (Anders et al., 2014).
The dataset was filtered for genes that met minimum read count cutoffs of at least 10 mapped reads in at least 10% of the samples, resulting in 15,541 genes for downstream analyses
Differential expression modeling was performed on transcripts per million (TPM) normalized read counts using a generalized linear mixed-effect model and a negative binomial distribution. Treatment time points were compared to pre-heat controls. Significant differential expression was defined as |log2 fold-change > 1, FDR < 0.05, and |(control mean TPM) – (treatment mean TPM)| ≥ 1. FDR correction was performed using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995).
Genome_build: Chlamydomonas reinhardtii v5.6 genome
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Chlamydomonas reinhardtii

growth_protocol: Chlamydomonas reinhardtii wildtype strain (cc1690, also called 21gr, mt+) was used in all experiments. CC1690 were grown in standard Tris-acetate-phosphate (TAP) medium in 400mL photobioreactors (PBRs) (Photon System Instruments, FMT 150/400-RB). Cultures were illuminated with constant 100 µmol photons m-2 s-1 light (50% red: 50% blue), mixed by bubbling with filtered air at a flow rate of 1 L/minute. Algal growth was turbidostatically maintained using OD680 during the experiments, so the algal cultures were not limited by nutrients or light. After PBR inoculation, cultures were allowed to grow to a target cell density of 2.00x106 cells/mL corresponding to around 4.0 ug/mL chlorophyll content in log-phase growth at 25oC. The steady condition was maintained turbidostatically using OD680 for 4 days to allow cultures to adapt to steady growth conditions at 25oC before heat treatments

extract_protocol:
At each time point, approximately 4x106 cells were pelleted with Tween-20 (0.005%, v/v) by centrifugation at 1,100 x g and 4oC for 2 min. The cell pellet was flash frozen in liquid nitrogen and stored at -80oC before processing. Total RNA was extracted with the TRIzol reagent (Thermo Fisher Scientific, Cat No. 15596026) as described before with some modifications (Zones et al., 2015). RNA was purified by RNeasy mini-column (Qiagen, Cat No. 74106) after on column digestion with RNase-free DNase (Qiagen, Cat No. 79256) according to the manufacturer’s instructions. RNA was quantified with Qubit™ RNA BR Assay Kit, (Life technology, Cat No. Q10210). Total 0.4 μg RNA was reverse transcribed with oligo dT primers using SuperScript® III First-Strand Synthesis System (Life technology, Cat No. 18080-051) according to the manufacturer’s instructions. Quantitative real-time PCR (RT-qPCR) analysis was carried out using a CFX384 Real-Time System (C 1000 Touch Thermal Cycler, Bio-Rad, Hercules, California) using SensiFAST SYBR No-ROS kit (Bioline, BIO-98020). PCR was set up as follows: 2 min at 95˚C, followed by 40 cycles of 5 s at 95oC, 10 s at 60oC and 15 s at 72oC. Melting curve was checked right after all PCR cycles to make sure there are no primer dimers or unspecific PCR products. Expression of G-protein β-subunit-like polypeptide CBLP (Cre06.g278222), (Schloss, 1990) remain stable among all time points, and were used as internal controls (Xie et al., 2013). The relative expressions were calculated relative to its expression in pre-heat by the ΔΔCT method (Livak and Schmittgen, 2001b). The qPCR primers for tested genes (CBLP, HSP22A, HSP90A, and others) are listed in Supplementary Table 1. PCR efficiencies were checked and were employed to the 2−ΔΔCT method to calculate the relative expression as described previously (Livak and Schmittgen, 2001; Hellemans et al., 2007; Remans et al., 2014). Three biological replicates for each time point and treatment were conducted.
Library construction was perfored at the Department of Energy (DOE) Joint Genome Institute (JGI)

treatment_protocol: PBR temperatures were shifted to moderate or acute heat stress conditions (35oC and 40oC respectively in different PBRs) for 24 hours, then shifted back to 25oC for 48 hours for recovery.

value: recovery following 40C high temperature

tag: time point


title: CLL-C36_LN_CD19


title: recovery_48h_40C_A


title: recovery_24h_40C_B


title: recovery_24h_40C_C


title: BB9_TTAGGC

value: MG


title: L01_DB03_184_VHGO_100

description:
L01_DB03
Hepatocyte_normcounts.csv

value: VHGO


title: L01_DB07_129_HFO_100

description:
L01_DB07
Hepatocyte_normcounts.csv

value: HFO


title: BB8_CGATGT


title: CLL-C44_LN_CD19


title: BB7_ATCACG


title: L01_DB05_059_dieselfuel_100

description:
L01_DB05
Hepatocyte_normcounts.csv

value: KER


title: CLL-C47_LN_CD19

value: SLL


title: L01_DB04_155_HFO_100

description:
L01_DB04
Hepatocyte_normcounts.csv


title: L01_DB06_MethodBlank_0

description:
L01_DB06
Hepatocyte_normcounts.csv


title: CLL-C31_LN_CD19


title: BB18_CTTGTA


title: recovery_8h_40C_C


title: L01_DB02_009_gasoline_100

description:
L01_DB02
Hepatocyte_normcounts.csv

value: NAPTHA


title: CLL-C25_LN_CD19

value: M


title: recovery_48h_40C_B


title: L01_DB01_041_CGO_100

description:
L01_DB01
Hepatocyte_normcounts.csv

value: CGO


title: CLL-C13_LN_CD19


title: recovery_8h_40C_A


title: recovery_8h_40C_B


title: recovery_4h_40C_B


title: recovery_4h_40C_C


title: CLL-C07_LN_CD19


title: L01_DA09_082_UATO_100

description:
L01_DA09
Hepatocyte_normcounts.csv

value: UATO


title: recovery_24h_40C_A


title: recovery_4h_40C_A


title: CLL-C06_LN_CD19


title: recovery_2h_40C_B


title: recovery_2h_40C_A


title: CLL-C04_LN_CD19