title: xl_els_pb_CEP5


title: TP0001651C04_2_0.100000uM_DMEM_24h_TC00283157_G10

status: Public on Dec 05 2023

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
TP0001651C04_2_0.100000uM_DMEM_24h
TC00283157_G10

library_source: transcriptomic

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv1
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 Cells

growth_protocol: Five vials of cryopreserved MCF7 (HTB-22TM) cells were purchased from American Tissue Culture Collection, designated as passage 0 (P0) and stored in vapor phase liquid nitrogen prior to initial thawing and expansion. A passage 3 (P3) MCF7 cryostock was generated by thawing and pooling all five original source vials and culturing through three consecutive passages in complete growth medium (DMEM + 10% FBS + 1% PSG). At each passage, cells from different culture vessels were pooled prior to re-seeding for subsequent expansion. At P3, cells were cryopreserved at 4 million cells per mL in complete growth medium + 5% DMSO according to manufacturer’s protocol. MCF7 cultures used in all phases of this study were maintained in humidified incubators with 5% CO2 atmosphere and internal temperature of 37°C. For chemical screening, MCF7 cells were thawed and subjected to a uniform expansion protocol from P3 to P6 through increasingly larger sizes of tissue culture vessels (T25 to T75 to T225) prior to plating in 384-well format. The three cultures were initiated on consecutive days and subject to uniform handling procedures to ensure that dosing and sample collection also occurred on consecutive days. All chemical screening experiments were performed on P7 cells.

extract_protocol:
Six hours after chemical treatment, HTTr assay plates were removed from the incubator and media in each assay well was drained to a residual volume of 10 µL using MultiFlo FX microdispenser equipped with a vacuum-driven aspiration manifold. To create cell lysates, 10 µL volumes of 2X BioSpyder lysis buffer were dispensed into each assay well using the same MultiFlo FX instrument equipped with 1 µL peristaltic pump dispensing cassette. Then, 20 µL volumes of UHRR, HBRR, BLDSMO, BLTSA and Lysis Buffer reference material were manually dispensed into duplicate wells of column 1 of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 minutes. The plates were then stored at -80°C prior to shipment to BioSpyder, Inc.
Samples were analyzed by BioSpyder using a custom-attenuated version of the TempO-Seq human whole transcriptome version 1 (hWTv1) assay, which includes 21,111 probes covering 19,287 genes. Lysates were processed as described in (House et al. 2017). In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv1 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 hours. Excess oligos were then removed via nuclease digestion (90 min at 37°C) and hybridized detector oligos were ligated (60 min at 37°) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification (10 min at 37°C, 2 min at 95°C, 6 cycles of 95°C for 30 s, 54°C for 30 s, 72°C for 120 s, 16 cycles of 95°C for 30s and 72°C for 120s, followed by 72°C for 60 s) with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were then pooled into a series of three sequencing libraries (1 for each plate). Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized chemical stock solutions were received frozen from the US EPA ToxCast chemical inventory management contractor (EvoTec, Princeton, NJ) and stored at -80°C prior to dose plate preparation. An eight-point dilution series (1/2 log10 spacing) of test chemicals was prepared in a LabCyte Echo-qualified 384-well polypropylene (384PP) plate at 200x the desired nominal test concentration for screening (0.03 – 100 µM). Singleton wells of dosing solutions for each test chemical concentration were arrayed in columns 2 through 23 of the dose plate (Figure 1A). Transcriptomics reference chemicals (genistein, trichostatin A, sirolimus) were solubilized as 200x dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the transcriptomic reference chemicals were added to the dose plate (column 24) along with quadruplicate wells of pure DMSO as a vehicle control. At 24 h post-plating, 200 nL of 200x dosing solutions were transferred to the assay plates using a LabCyte Echo 550 acoustic dispenser. The final concentration of DMSO in all treatment, reference treatment and vehicle control wells was 0.5%.  Well coordinates on each assay plate were uniquely randomized with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 24h exposure of 0.1 uM of Simvastatin

tag: chemical name

value: Simvastatin

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: TP0001651G02_8_100.000000uM_DMEM_24h_TC00283157_G11

description:
TP0001651G02_8_100.000000uM_DMEM_24h
TC00283157_G11

value: 24h exposure of 100 uM of Lovastatin

value: Lovastatin


title: xl_els_pb_HDP4

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

data_processing:
Reads were aligned using the Seq2Fun algorithm which translates raw reads to protein orthologs and maps them to a high-resolution protein-ortholog database - EcoOmicsDB available at www.expressanalyst.ca. The filtering parameters are provided below
Filtering: N. of amino acid mismatches was set at 2
Filtering: Minimum matching length was set at 19
Filtering: Minimum matching score was set at 80
Assembly: Mapping was species agnostic. Translated reads were mapped to the Vertebrate database
Raw fastq files were filtered as mentioned above and provided count matrices. These were analyzed for gene expression and pathway enrichment analysis.
Raw files and count files are provided as fastq files and .txt files, respectively.
Supplementary files format and content: Files here are from 49 datasets (datasets column below). Each dataset has a processed file which contains the counts for all samples within that dataset. Hence all samples (with unique title) from a dataset is present in the corresponding processed file. The title of the raw file for each sample is provided below as well. Some exposures were conducted together and hence had a common control exposure. Hence while 776 libraries are listed, they will correspond to fewer fastq files. But all fastq files are present.

organism: Xenopus laevis

source_name: embryo

extract_protocol:
RNA was extracted from Japanese quail and Double-crested cormorant samples using the Qiagen RNeasy mini kits; RNA was extracted from the fathead minnow, rainbow trout, African-clawed frog and the northern leopard frog using the Qiagen RNeasy Universal Mini kit.
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 or HiSeq 4000 PE100 101-bp paired-end reads.

tag: lifestage

value: els

tag: tissue

value: embryo

tag: chemical

value: pb

tag: concentration

value: HIGH


title: TSA_DMEM_24h_TC00283157_G09

description:
TSA_DMEM_24h
TC00283157_G09

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: xl_els_pb_HEP5


title: xl_els_pb_HCP3


title: TSA_DMEM_24h_TC00283157_G07

description:
TSA_DMEM_24h
TC00283157_G07


title: TP0001651C02_2_0.100000uM_DMEM_24h_TC00283157_G08

description:
TP0001651C02_2_0.100000uM_DMEM_24h
TC00283157_G08

value: 24h exposure of 0.1 uM of 4-Hydroxytamoxifen


title: TP0001651G05_4_1.000000uM_DMEM_24h_TC00283157_G06

description:
TP0001651G05_4_1.000000uM_DMEM_24h
TC00283157_G06

value: 24h exposure of 1 uM of Cyproterone acetate

value: Cyproterone acetate


title: xl_els_pb_CBP2

value: dmso

value: CTRL


title: xl_els_tb_SBP2


title: xl_els_tb_MDP4

value: tb

value: MED


title: xl_els_tb_MEP5


title: TP0001651A02_7_30.000000uM_DMEM_24h_TC00283157_G05

description:
TP0001651A02_7_30.000000uM_DMEM_24h
TC00283157_G05

value: DMEM + 10% HI-FBS

value: 24h exposure of 30 uM of Imazalil

value: Imazalil

value: 30 uM


title: TP0001651C06_2_0.100000uM_DMEM_24h_TC00283157_G04

description:
TP0001651C06_2_0.100000uM_DMEM_24h
TC00283157_G04

value: 24h exposure of 0.1 uM of Cycloheximide

value: Cycloheximide


title: xl_els_tb_HEP5

value: els

value: embryo

value: HIGH


title: xl_els_tb_MCP3


title: xl_els_tb_SAP1


title: TP0001651H03_5_3.000000uM_DMEM_24h_TC00283157_G03

description:
TP0001651H03_5_3.000000uM_DMEM_24h
TC00283157_G03

value: 24h exposure of 3 uM of Fomesafen

value: Fomesafen

value: 3 uM


title: TP0001651E02_5_3.000000uM_DMEM_24h_TC00283157_G02

description:
TP0001651E02_5_3.000000uM_DMEM_24h
TC00283157_G02

value: 24h exposure of 3 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched


title: xl_els_tb_MBP2


title: BL_TSA_TC00283157_G01

description:
BL_TSA
TC00283157_G01

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: xl_els_tb_HDP4

value: tb


title: TP0001651A02_4_1.000000uM_DMEM_24h_TC00283157_F24

description:
TP0001651A02_4_1.000000uM_DMEM_24h
TC00283157_F24

value: DMEM + 10% HI-FBS

value: 24h exposure of 1 uM of Imazalil


title: xl_els_tb_MAP1

value: MED


title: TP0001651C05_4_1.000000uM_DMEM_24h_TC00283157_F23

description:
TP0001651C05_4_1.000000uM_DMEM_24h
TC00283157_F23

value: 24h exposure of 1 uM of Bisphenol B

value: Bisphenol B


title: TP0001651B04_3_0.300000uM_DMEM_24h_TC00283157_F22

description:
TP0001651B04_3_0.300000uM_DMEM_24h
TC00283157_F22

value: 24h exposure of 0.3 uM of Propiconazole

value: Propiconazole


title: TP0001651B02_1_0.030000uM_DMEM_24h_TC00283157_F21

description:
TP0001651B02_1_0.030000uM_DMEM_24h
TC00283157_F21

value: 24h exposure of 0.03 uM of 3,5,3'-Triiodothyronine


title: xl_els_tb_HBP2

value: els

value: embryo

value: HIGH


title: xl_els_tb_SEP5

value: dmso

value: CTRL


title: TP0001651C02_3_0.300000uM_DMEM_24h_TC00283157_F20

description:
TP0001651C02_3_0.300000uM_DMEM_24h
TC00283157_F20

value: 24h exposure of 0.3 uM of 4-Hydroxytamoxifen


title: xl_els_tb_SDP4


title: xl_els_tb_HAP1


title: TP0001651C01_7_30.000000uM_DMEM_24h_TC00283157_F19

description:
TP0001651C01_7_30.000000uM_DMEM_24h
TC00283157_F19

value: 24h exposure of 30 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

value: 30 uM


title: xl_els_tb_SCP3


title: TP0001651E01_2_0.100000uM_DMEM_24h_TC00283157_F18

description:
TP0001651E01_2_0.100000uM_DMEM_24h
TC00283157_F18

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.1 uM of Bifenthrin

value: Bifenthrin


title: xl_els_seme_HEP5

value: seme


title: TP0001651D01_4_1.000000uM_DMEM_24h_TC00283157_F17

description:
TP0001651D01_4_1.000000uM_DMEM_24h
TC00283157_F17

value: 24h exposure of 1 uM of Lactofen

value: Lactofen

value: 1 uM


title: TP0001651F03_5_3.000000uM_DMEM_24h_TC00283157_F12

description:
TP0001651F03_5_3.000000uM_DMEM_24h
TC00283157_F12

value: 24h exposure of 3 uM of 4-Cumylphenol

value: 3 uM


title: xl_els_seme_MEP5

value: els

value: embryo

value: MED


title: TP0001651C02_6_10.000000uM_DMEM_24h_TC00283157_F15

description:
TP0001651C02_6_10.000000uM_DMEM_24h
TC00283157_F15

value: 24h exposure of 10 uM of 4-Hydroxytamoxifen

value: 10 uM


title: TP0001651C02_4_1.000000uM_DMEM_24h_TC00283157_F13

description:
TP0001651C02_4_1.000000uM_DMEM_24h
TC00283157_F13

value: 24h exposure of 1 uM of 4-Hydroxytamoxifen


title: TP0001651C03_5_3.000000uM_DMEM_24h_TC00283157_F09

description:
TP0001651C03_5_3.000000uM_DMEM_24h
TC00283157_F09

value: 24h exposure of 3 uM of Simazine

value: Simazine


title: xl_els_seme_HAP1

value: HIGH


title: TP0001651E01_6_10.000000uM_DMEM_24h_TC00283157_F10

description:
TP0001651E01_6_10.000000uM_DMEM_24h
TC00283157_F10

value: DMEM + 10% HI-FBS

value: 24h exposure of 10 uM of Bifenthrin


title: xl_els_seme_MBP2

value: seme


title: xl_els_seme_MAP1


title: DMSO_DMEM_24h_TC00283157_F16

description:
DMSO_DMEM_24h
TC00283157_F16

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: xl_els_seme_MCP3


title: xl_els_tb_HCP3

value: tb


title: TP0001651D03_4_1.000000uM_DMEM_24h_TC00283157_F14

description:
TP0001651D03_4_1.000000uM_DMEM_24h
TC00283157_F14

value: 24h exposure of 1 uM of Cypermethrin

value: Cypermethrin

value: 1 uM


title: TP0001651B04_5_3.000000uM_DMEM_24h_TC00283157_F11

description:
TP0001651B04_5_3.000000uM_DMEM_24h
TC00283157_F11

value: 24h exposure of 3 uM of Propiconazole

value: Propiconazole

value: 3 uM


title: TP0001651B02_7_30.000000uM_DMEM_24h_TC00283157_F06

description:
TP0001651B02_7_30.000000uM_DMEM_24h
TC00283157_F06

value: 24h exposure of 30 uM of 3,5,3'-Triiodothyronine

value: 30 uM


title: xl_els_seme_MDP4

value: els

value: embryo

value: MED


title: TP0001651D05_3_0.300000uM_DMEM_24h_TC00283157_F07

description:
TP0001651D05_3_0.300000uM_DMEM_24h
TC00283157_F07

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Thiram

value: Thiram


title: TP0001651H04_8_100.000000uM_DMEM_24h_TC00283157_F08

description:
TP0001651H04_8_100.000000uM_DMEM_24h
TC00283157_F08

value: 24h exposure of 100 uM of Bisphenol A

value: Bisphenol A


title: xl_els_seme_CBP2

value: dmso

value: CTRL


title: TP0001651E05_2_0.100000uM_DMEM_24h_TC00283157_F05

description:
TP0001651E05_2_0.100000uM_DMEM_24h
TC00283157_F05

value: 24h exposure of 0.1 uM of Atrazine

value: Atrazine


title: xl_els_seme_HCP3

value: seme

value: HIGH


title: xl_els_seme_CDP4


title: TP0001651F03_2_0.100000uM_DMEM_24h_TC00283157_F04

description:
TP0001651F03_2_0.100000uM_DMEM_24h
TC00283157_F04

value: 24h exposure of 0.1 uM of 4-Cumylphenol


title: xl_els_seme_CAP1


title: xl_els_seme_HDP4


title: xl_els_seme_CEP5


title: TP0001651C06_3_0.300000uM_DMEM_24h_TC00283157_F03

description:
TP0001651C06_3_0.300000uM_DMEM_24h
TC00283157_F03

value: 24h exposure of 0.3 uM of Cycloheximide

value: Cycloheximide


title: xl_els_seme_CCP3

value: els


title: xl_els_seme_HBP2

value: embryo


title: TP0001651G01_8_100.000000uM_DMEM_24h_TC00283157_E23

description:
TP0001651G01_8_100.000000uM_DMEM_24h
TC00283157_E23

value: 24h exposure of 100 uM of Vinclozolin

value: Vinclozolin


title: BL_DMSO_TC00283157_F01

description:
BL_DMSO
TC00283157_F01

value: untreated

value: 0 uM


title: xl_els_hbcd_HBP2

value: hbcd


title: xl_els_hbcd_HCP3


title: TP0001651F05_7_30.000000uM_DMEM_24h_TC00283157_F02

description:
TP0001651F05_7_30.000000uM_DMEM_24h
TC00283157_F02

value: DMEM + 10% HI-FBS

value: 24h exposure of 30 uM of Fenofibrate

value: Fenofibrate

value: 30 uM


title: xl_els_hbcd_MEP5

value: MED


title: TP0001651G02_3_0.300000uM_DMEM_24h_TC00283157_E24

description:
TP0001651G02_3_0.300000uM_DMEM_24h
TC00283157_E24

value: 24h exposure of 0.3 uM of Lovastatin

value: Lovastatin


title: TP0001651D04_5_3.000000uM_DMEM_24h_TC00283157_E20

description:
TP0001651D04_5_3.000000uM_DMEM_24h
TC00283157_E20

value: 24h exposure of 3 uM of Clofibrate

value: Clofibrate

value: 3 uM


title: xl_els_hbcd_MDP4

value: els


title: xl_els_hbcd_HDP4

value: embryo

value: HIGH


title: xl_els_hbcd_MCP3


title: xl_els_hbcd_HEP5


title: xl_els_hbcd_HAP1


title: TP0001651F05_5_3.000000uM_DMEM_24h_TC00283157_E21

description:
TP0001651F05_5_3.000000uM_DMEM_24h
TC00283157_E21

value: 24h exposure of 3 uM of Fenofibrate


title: DMSO_DMEM_24h_TC00283157_E16

description:
DMSO_DMEM_24h
TC00283157_E16

value: 0.5% DMSO vehicle control

value: DMSO


title: TP0001651H05_6_10.000000uM_DMEM_24h_TC00283157_E18

description:
TP0001651H05_6_10.000000uM_DMEM_24h
TC00283157_E18

value: 24h exposure of 10 uM of Trifloxystrobin

value: Trifloxystrobin

value: 10 uM


title: xl_els_hbcd_MAP1

value: hbcd


title: xl_els_hbcd_MBP2


title: xl_els_hbcd_CEP5

value: dmso

value: CTRL


title: TP0001651D06_4_1.000000uM_DMEM_24h_TC00283157_E22

description:
TP0001651D06_4_1.000000uM_DMEM_24h
TC00283157_E22

value: DMEM + 10% HI-FBS

value: 24h exposure of 1 uM of PFOS

value: PFOS

value: 1 uM


title: TP0001651C06_6_10.000000uM_DMEM_24h_TC00283157_E17

description:
TP0001651C06_6_10.000000uM_DMEM_24h
TC00283157_E17

value: 24h exposure of 10 uM of Cycloheximide

value: Cycloheximide


title: xl_els_hbcd_CDP4

value: els

value: embryo


title: TP0001651H05_5_3.000000uM_DMEM_24h_TC00283157_E15

description:
TP0001651H05_5_3.000000uM_DMEM_24h
TC00283157_E15

value: 24h exposure of 3 uM of Trifloxystrobin

value: 3 uM


title: TP0001651A04_6_10.000000uM_DMEM_24h_TC00283157_E19

description:
TP0001651A04_6_10.000000uM_DMEM_24h
TC00283157_E19

value: 24h exposure of 10 uM of Rotenone

value: Rotenone


title: TP0001651B05_5_3.000000uM_DMEM_24h_TC00283157_E14

description:
TP0001651B05_5_3.000000uM_DMEM_24h
TC00283157_E14

value: 24h exposure of 3 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: xl_els_hbcd_CCP3


title: TP0001651G02_5_3.000000uM_DMEM_24h_TC00283157_E13

description:
TP0001651G02_5_3.000000uM_DMEM_24h
TC00283157_E13

value: 24h exposure of 3 uM of Lovastatin

value: Lovastatin


title: xl_els_hbcd_CBP2

value: dmso

value: CTRL


title: TP0001651H02_3_0.300000uM_DMEM_24h_TC00283157_E12

description:
TP0001651H02_3_0.300000uM_DMEM_24h
TC00283157_E12

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Maneb

value: Maneb


title: xl_els_hbcd_CAP1


title: xl_els_flx_HCP3

value: flx

value: HIGH


title: xl_els_flx_CBP2

value: els


title: TP0001651D01_1_0.030000uM_DMEM_24h_TC00283157_E08

description:
TP0001651D01_1_0.030000uM_DMEM_24h
TC00283157_E08

value: 24h exposure of 0.03 uM of Lactofen

value: Lactofen


title: TP0001651D04_2_0.100000uM_DMEM_24h_TC00283157_E11

description:
TP0001651D04_2_0.100000uM_DMEM_24h
TC00283157_E11

value: 24h exposure of 0.1 uM of Clofibrate

value: Clofibrate


title: TP0001651F03_7_30.000000uM_DMEM_24h_TC00283157_E09

description:
TP0001651F03_7_30.000000uM_DMEM_24h
TC00283157_E09

value: 24h exposure of 30 uM of 4-Cumylphenol

value: 30 uM


title: TP0001651E02_4_1.000000uM_DMEM_24h_TC00283157_E07

description:
TP0001651E02_4_1.000000uM_DMEM_24h
TC00283157_E07

value: 24h exposure of 1 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

value: 1 uM


title: TP0001651E04_1_0.030000uM_DMEM_24h_TC00283157_E10

description:
TP0001651E04_1_0.030000uM_DMEM_24h
TC00283157_E10

value: 24h exposure of 0.03 uM of Farglitazar

value: Farglitazar


title: TP0001651B01_5_3.000000uM_DMEM_24h_TC00283157_E05

description:
TP0001651B01_5_3.000000uM_DMEM_24h
TC00283157_E05

value: DMEM + 10% HI-FBS

value: 24h exposure of 3 uM of Cyanazine

value: Cyanazine

value: 3 uM


title: xl_els_flx_HBP2

value: embryo

value: flx

value: HIGH


title: xl_els_flx_MCP3

value: els

value: MED


title: xl_els_flx_CDP4

value: dmso

value: CTRL


title: xl_els_flx_HDP4


title: xl_els_flx_MBP2


title: xl_els_flx_CCP3


title: xl_els_flx_MDP4


title: TP0001651B06_5_3.000000uM_DMEM_24h_TC00283157_E02

description:
TP0001651B06_5_3.000000uM_DMEM_24h
TC00283157_E02

value: 24h exposure of 3 uM of Troglitazone

value: Troglitazone


title: TP0001651D01_8_100.000000uM_DMEM_24h_TC00283157_E06

description:
TP0001651D01_8_100.000000uM_DMEM_24h
TC00283157_E06

value: 24h exposure of 100 uM of Lactofen

value: Lactofen


title: xl_els_flx_MEP5


title: xl_els_flx_HEP5


title: TP0001651D02_4_1.000000uM_DMEM_24h_TC00283157_E03

description:
TP0001651D02_4_1.000000uM_DMEM_24h
TC00283157_E03

value: 24h exposure of 1 uM of PFOA

value: PFOA

value: 1 uM


title: xl_els_flx_HAP1


title: BL_DMSO_TC00283157_E01

description:
BL_DMSO
TC00283157_E01

value: untreated

value: 0 uM


title: TP0001651C06_8_100.000000uM_DMEM_24h_TC00283157_D23

description:
TP0001651C06_8_100.000000uM_DMEM_24h
TC00283157_D23

value: DMEM + 10% HI-FBS

value: 24h exposure of 100 uM of Cycloheximide

value: Cycloheximide


title: xl_els_flx_MAP1

value: embryo

value: flx


title: TP0001651G02_1_0.030000uM_DMEM_24h_TC00283157_D24

description:
TP0001651G02_1_0.030000uM_DMEM_24h
TC00283157_D24

value: 24h exposure of 0.03 uM of Lovastatin

value: Lovastatin


title: xl_els_flx_CEP5

value: els

value: dmso

value: CTRL


title: TP0001651C05_7_30.000000uM_DMEM_24h_TC00283157_D22

description:
TP0001651C05_7_30.000000uM_DMEM_24h
TC00283157_D22

value: 24h exposure of 30 uM of Bisphenol B

value: Bisphenol B

value: 30 uM


title: xl_els_flx_CAP1


title: TP0001651E04_4_1.000000uM_DMEM_24h_TC00283157_D20

description:
TP0001651E04_4_1.000000uM_DMEM_24h
TC00283157_D20

value: 24h exposure of 1 uM of Farglitazar

value: Farglitazar


title: xl_els_ee2_HEP5

value: HIGH


title: TP0001651H01_5_3.000000uM_DMEM_24h_TC00283157_E04

description:
TP0001651H01_5_3.000000uM_DMEM_24h
TC00283157_E04

value: 24h exposure of 3 uM of Flutamide

value: Flutamide

value: 3 uM


title: TP0001651C02_8_100.000000uM_DMEM_24h_TC00283157_D19

description:
TP0001651C02_8_100.000000uM_DMEM_24h
TC00283157_D19

value: DMEM + 10% HI-FBS

value: 24h exposure of 100 uM of 4-Hydroxytamoxifen


title: xl_els_ee2_MDP4

value: embryo

value: MED


title: TP0001651D02_3_0.300000uM_DMEM_24h_TC00283157_D18

description:
TP0001651D02_3_0.300000uM_DMEM_24h
TC00283157_D18

value: 24h exposure of 0.3 uM of PFOA

value: PFOA


title: TP0001651C06_7_30.000000uM_DMEM_24h_TC00283157_D14

description:
TP0001651C06_7_30.000000uM_DMEM_24h
TC00283157_D14

value: 24h exposure of 30 uM of Cycloheximide

value: Cycloheximide


title: xl_els_ee2_SDP4

value: els

value: dmso

value: CTRL


title: xl_els_ee2_MAP1


title: xl_els_ee2_MBP2


title: TP0001651A02_6_10.000000uM_DMEM_24h_TC00283157_D11

description:
TP0001651A02_6_10.000000uM_DMEM_24h
TC00283157_D11

value: 24h exposure of 10 uM of Imazalil

value: Imazalil

value: 10 uM


title: xl_els_ee2_SBP2


title: TP0001651G02_2_0.100000uM_DMEM_24h_TC00283157_D17

description:
TP0001651G02_2_0.100000uM_DMEM_24h
TC00283157_D17

value: 24h exposure of 0.1 uM of Lovastatin

value: Lovastatin


title: xl_els_ee2_MCP3


title: TP0001651A05_6_10.000000uM_DMEM_24h_TC00283157_D16

description:
TP0001651A05_6_10.000000uM_DMEM_24h
TC00283157_D16

value: 24h exposure of 10 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: TP0001651C02_7_30.000000uM_DMEM_24h_TC00283157_D15

description:
TP0001651C02_7_30.000000uM_DMEM_24h
TC00283157_D15

value: DMEM + 10% HI-FBS

value: 24h exposure of 30 uM of 4-Hydroxytamoxifen

value: 30 uM


title: xl_els_ee2_MEP5

value: embryo

value: MED


title: TP0001651D04_8_100.000000uM_DMEM_24h_TC00283157_D13

description:
TP0001651D04_8_100.000000uM_DMEM_24h
TC00283157_D13

value: 24h exposure of 100 uM of Clofibrate

value: Clofibrate


title: xl_els_ee2_HBP2

value: els

value: HIGH


title: GEN_DMEM_24h_TC00283157_D12

description:
GEN_DMEM_24h
TC00283157_D12

value: 6h exposure of 10 uM of Genistein

value: Genistein


title: TP0001651A05_5_3.000000uM_DMEM_24h_TC00283157_D21

description:
TP0001651A05_5_3.000000uM_DMEM_24h
TC00283157_D21

value: 24h exposure of 3 uM of Clomiphene citrate (1:1)

value: 3 uM


title: xl_els_ee2_HCP3


title: xl_els_ee2_SCP3WE4

value: dmso

value: CTRL


title: xl_els_ee2_HDP4


title: TP0001651D03_5_3.000000uM_DMEM_24h_TC00283157_D04

description:
TP0001651D03_5_3.000000uM_DMEM_24h
TC00283157_D04

value: 24h exposure of 3 uM of Cypermethrin

value: Cypermethrin


title: TP0001651H04_3_0.300000uM_DMEM_24h_TC00283157_D09

description:
TP0001651H04_3_0.300000uM_DMEM_24h
TC00283157_D09

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Bisphenol A

value: Bisphenol A


title: TP0001651C01_2_0.100000uM_DMEM_24h_TC00283157_D08

description:
TP0001651C01_2_0.100000uM_DMEM_24h
TC00283157_D08

value: 24h exposure of 0.1 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)


title: TP0001651B04_8_100.000000uM_DMEM_24h_TC00283157_D10

description:
TP0001651B04_8_100.000000uM_DMEM_24h
TC00283157_D10

value: 24h exposure of 100 uM of Propiconazole

value: Propiconazole


title: xl_els_ee2_HAP1

value: els

value: embryo


title: xl_els_ee2_SCP3


title: TP0001651D06_5_3.000000uM_DMEM_24h_TC00283157_D07

description:
TP0001651D06_5_3.000000uM_DMEM_24h
TC00283157_D07

value: 24h exposure of 3 uM of PFOS

value: PFOS


title: xl_els_bap_SHP3


title: TP0001651A03_3_0.300000uM_DMEM_24h_TC00283157_C24

description:
TP0001651A03_3_0.300000uM_DMEM_24h
TC00283157_C24

value: 24h exposure of 0.3 uM of Butafenacil

value: Butafenacil


title: xl_els_bap_MFP1

value: bap

value: HIGH


title: TP0001651F02_4_1.000000uM_DMEM_24h_TC00283157_C22

description:
TP0001651F02_4_1.000000uM_DMEM_24h
TC00283157_C22

value: 24h exposure of 1 uM of Ziram

value: Ziram

value: 1 uM


title: TP0001651G04_5_3.000000uM_DMEM_24h_TC00283157_D03

description:
TP0001651G04_5_3.000000uM_DMEM_24h
TC00283157_D03

value: DMEM + 10% HI-FBS

value: 24h exposure of 3 uM of Cladribine

value: Cladribine

value: 3 uM


title: xl_els_bap_LEP5

value: MED


title: xl_els_bap_MEP5


title: xl_els_bap_LHP3


title: xl_els_bap_SGP2

value: dmso

value: CTRL


title: TP0001651F05_6_10.000000uM_DMEM_24h_TC00283157_D02

description:
TP0001651F05_6_10.000000uM_DMEM_24h
TC00283157_D02

value: 24h exposure of 10 uM of Fenofibrate

value: Fenofibrate

value: 10 uM


title: HBRR_TC00283157_D01

description:
HBRR
TC00283157_D01

source_name: Human Brain Reference RNA

value: untreated


title: xl_els_ee2_SAP1

value: els

value: embryo


title: xl_els_bap_SFP1


title: TP0001651A06_6_10.000000uM_DMEM_24h_TC00283157_C21

description:
TP0001651A06_6_10.000000uM_DMEM_24h
TC00283157_C21

value: 24h exposure of 10 uM of Cyproconazole

value: Cyproconazole


title: xl_els_bap_LGP2

value: bap


title: xl_els_bap_LFP1


title: TP0001651F02_2_0.100000uM_DMEM_24h_TC00283157_D06

description:
TP0001651F02_2_0.100000uM_DMEM_24h
TC00283157_D06

value: 24h exposure of 0.1 uM of Ziram

value: Ziram


title: TP0001651F01_6_10.000000uM_DMEM_24h_TC00283157_C20

description:
TP0001651F01_6_10.000000uM_DMEM_24h
TC00283157_C20

value: DMEM + 10% HI-FBS

value: 24h exposure of 10 uM of Tetrac

value: Tetrac


title: xl_els_bap_SEP5


title: xl_els_bap_MIP4

value: HIGH


title: M3_DCCO_FLX

organism: Phalacrocorax auritus

source_name: liver

value: liver

value: flx

value: MED


title: TP0001651H02_2_0.100000uM_DMEM_24h_TC00283157_D05

description:
TP0001651H02_2_0.100000uM_DMEM_24h
TC00283157_D05

value: 24h exposure of 0.1 uM of Maneb

value: Maneb


title: TP0001651B01_4_1.000000uM_DMEM_24h_TC00283157_C23

description:
TP0001651B01_4_1.000000uM_DMEM_24h
TC00283157_C23

value: 24h exposure of 1 uM of Cyanazine

value: Cyanazine

value: 1 uM


title: H5_DCCO_FLX

value: els


title: TP0001651F04_4_1.000000uM_DMEM_24h_TC00283157_C19

description:
TP0001651F04_4_1.000000uM_DMEM_24h
TC00283157_C19

value: 24h exposure of 1 uM of Fulvestrant

value: Fulvestrant


title: TP0001651D03_6_10.000000uM_DMEM_24h_TC00283157_C18

description:
TP0001651D03_6_10.000000uM_DMEM_24h
TC00283157_C18

value: 24h exposure of 10 uM of Cypermethrin

value: Cypermethrin

value: 10 uM


title: M2_DCCO_FLX


title: xl_els_bap_MHP3

value: embryo

value: bap


title: TP0001651F01_5_3.000000uM_DMEM_24h_TC00283157_C17

description:
TP0001651F01_5_3.000000uM_DMEM_24h
TC00283157_C17

value: DMEM + 10% HI-FBS

value: 24h exposure of 3 uM of Tetrac

value: Tetrac

value: 3 uM


title: TSA_DMEM_24h_TC00283157_C15

description:
TSA_DMEM_24h
TC00283157_C15

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A


title: xl_els_bap_LIP4

value: MED


title: TP0001651D06_2_0.100000uM_DMEM_24h_TC00283157_C16

description:
TP0001651D06_2_0.100000uM_DMEM_24h
TC00283157_C16

value: 24h exposure of 0.1 uM of PFOS

value: PFOS


title: H4_DCCO_FLX

value: els

value: liver

value: flx

value: HIGH


title: TP0001651E04_5_3.000000uM_DMEM_12h_TC00283174_F20

description:
TP0001651E04_5_3.000000uM_DMEM_12h
TC00283174_F20

value: 12h exposure of 3 uM of Farglitazar

value: Farglitazar


title: TP0001651F02_7_30.000000uM_DMEM_24h_TC00283157_C13

description:
TP0001651F02_7_30.000000uM_DMEM_24h
TC00283157_C13

value: 24h exposure of 30 uM of Ziram

value: Ziram

value: 30 uM


title: xl_els_bap_SIP4

value: embryo

value: dmso

value: CTRL


title: TP0001651A01_8_100.000000uM_DMEM_24h_TC00283157_C14

description:
TP0001651A01_8_100.000000uM_DMEM_24h
TC00283157_C14

value: DMEM + 10% HI-FBS

value: 24h exposure of 100 uM of Pyraclostrobin

value: Pyraclostrobin


title: SIRO_DMEM_24h_TC00283157_C12

description:
SIRO_DMEM_24h
TC00283157_C12

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: S5_DCCO_FLX

value: els


title: H3_DCCO_FLX

value: liver


title: S3_DCCO_FLX


title: M5_DCCO_FLX

value: flx

value: MED


title: S4_DCCO_FLX


title: H1_DCCO_FLX

value: HIGH


title: S2_DCCO_FLX


title: xl_els_bap_MGP2

value: bap


title: NOK siLEF1 FL H327ac rep 2

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

library_source: genomic

data_processing:
Paired-end reads were aligned to the EBV Akata reference genome KC_207813 using Bowtie 2 (version 2.2.4).
Seq reads bettwen 40-300 bp in lengh were analyzed uisng the peteskene data analysis pipeline ( https://github.com/peteskene)
Bedtools (2.21.0) was used for peak calling. A threshold value was set based on the IgG controls (a threshold value of 40 was used for most samples, except for samples XXX where the threshold value was increased to 150 )
Assembly: KC_207813
Supplementary files format and content: Peak calling analysis of LEF1 binding to Epstein-Barr virus genome (KC_207813)
Supplementary files format and content: Begraph files of reads aligned to Epstein-Barr virus genome (KC_207813)
Library strategy: Cut-and-Run-Seq

molecule: genomic DNA

organism: human gammaherpesvirus 4

source_name: gingiva

growth_protocol: Akata BX1 Burkitt lymphoma (BL) cell line latently-infected with recombinant EBV encoding a GFP/Neomycin resistance cassette was grown in RPMI 1640 with glutamine [Corning # 10-040-CV] supplemented with 10% fetal bovine serum (FBS) and 350 µg/mL G418 sulfate. Akata BX1 cultures were passaged when cell density reached 1 x 106 cells/mL or approximately every 3 days. Human telomerase reverse transcriptase (hTERT)-immortalized normal oral keratinocytes (NOK) and NOKs-Akata were maintained in 1x Keratinocyte serum free medium [Gibco #10724-011] supplemented with human recombinant EGF and bovine pituitary extract [Gibco # 37000-015] with 50 µg/mL G418 sulfate (neomycin). NOKs-Akata were passaged every 4-5 days or when cells achieved 90% confluency within a 75 cm2 tissue culture flask (approximately 4.0 x 106 cells).  All cell lines were maintained in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
CUT&RUN experiments were performed using the CUT&RUN Assay kit (#86652) from Cell Signaling Technology (protocol no. 1884). Native chromatin-transcription factor footprint analysis was performed without prior crosslinking. Histone acetylation analysis of NOKs-Akata included formaldehyde crosslinking for 90 seconds with 0.1% formaldehyde followed by quenching with 135 mM Glycine for 7 minutes prior to Accutase treatment and lifting. 150,000 Akata BX1 or 250,000 EBV+NOKs per sample were washed twice in kit wash buffer. Cells were then captured with Concanavalin A magnetic beads (10 µL/sample) and re-suspended in the kit Antibody buffer at a total volume of 100 µL/sample. 500 ng of primary antibody was then added to the 100 μL sample and incubated for 12 hours at 4°C. Cell:Bead suspensions were then centrifuged at 200 x g for 1 min followed by magnetization and resuspended in 500 µL kit wash buffer for 2 X wash cycles. Following thorough washing, Cell:Beads were re-suspended in 100 µL wash buffer containing 0.2 mg of a donkey-anti rabbit secondary antibody (A16037, Thermo) and were incubated 1 hour at 4°C. Samples were then washed 2 X as described. Binding of pAG-micrococcal nuclease was performed following re-suspension of Cell:Beads in 50 µL wash buffer and supplemented with 1.5 µL pAG-MNase followed by incubation at 4°C for 1 hour. Cell:Beads were then thoroughly washed 2X times in wash buffer using centrifugation at 200 x g and magnetization. Cell:Beads were resuspended in 150 µL wash buffer and supplemented with 3 µL 100 mM CaCl2 at 4°C for 30min to promote cleavage of DNA.  Cleavage reactions were halted following addition of 150µL kit STOP Buffer containing S. cerevisiae Spike-In DNA (50 pg/sample) for sample normalization. Samples were incubated at 37°C for 20 min to release cleaved fragments, followed by centrifugation at 16,000 x g for 5 min enriched chromatin fractions were then collected following sample placement on magnet strip. 2 µL 10% SDS and 1.5 µL Proteinase K (20 mg/mL) was added to each sample and incubated for 1 hr at 50°C. CUT&RUN DNA was purified by phenol:chloroform:isoamyl alcohol (25:24:1) extraction. 300 µL PLC was added to enriched chromatin and vortexed followed by centrifugation at 16,000 x g for 5 min at room temperature. 300 µL chloroform was added to the centrifuged samples and inverted 10 X followed by centrifugation at 16,000 x g for 5 min at room temperature. The top liquid phase was then removed and transferred to a clean tube containing 2 µL 2 mg/mL Glycogen as carrier. 500 µL 100% ethanol was then added followed by vortexing and incubation at -80 °C for 1 hour. Samples were then centrifuged at 16,000 x g for 20 min at 4°C. Ethanol was removed and DNA pellets washed in additional 500 µL 100 % ethanol. Samples were re-centrifuged, ethanol was removed and pellets allowed to dry. CUT&RUN DNA pellets were dissolved in 50 μL 0.1× TE (1 mM Tris-HCl pH 8.0, 0.1mM EDTA) in preparation for down stream analysis.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) with protocol modifications described in (Kong NR, Chai L, Tenen DG, Bassal MA. A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines. STAR Protoc. 2021;2(3):100750). Samples were indexed with NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1, E7600). 4-6 ng of CUT&RUN DNA was processed for each sample. DNA was end repaired and adaptors were ligated. To clean up the reaction, 1.75× volume of Agencourt AMPure XP beads was added to retain short ligation products. PCR amplification was performed for 15 cycles. The resulting libraries were purified with 1.2× volume of AMPure beads then analyzed and quantified by Tapestation (D1000 screen Tape). Libraries were normalized to 4 nM and pooled. The library pool was denatured and diluted to approximately 12 pM and spiked with 10% PhiX as an internal control. Illumina paired-end sequencing (80x80 cycles) was performed using either on the MiSeq with the MiSeq Reagent kit v3 (150 cycles) or on the Nextseq 500 platform with NextSeq 500/550 High Output Kit v2 (150 cycles).

treatment_protocol: For viral reactivation studies, 5x105 cells/mL Akata BX1 BL cells were induced for 4 hrs by the addition of 100 μg/ml goat anti-human IgG (Jackson ImmunoResearch) in RPMI1640 supplemented with 10% fetal bovine serum. For siRNA studies, NOKs-Akata were seeded at 1.5 × 105 cells/well in 12 well plates. 24 hours post-seeding, cells were transfected with 20 nM siRNA and 6.3 μL/mL Dharmafect 1 [Dharmacon/Horizon] in a total volume of 500 μL (250 µL KSFM+250 µL Opti-MEM) for 6 hours. 48 hours post siRNA transfection cells were harvested for CUT&RUN-seq. Akata BX1 cells were transfected via electroporation with either siLEF1 or NT siRNA using the Neon transfection system [Life Technologies], according to the manufacturer’s instructions. Briefly, cells were harvested, PBS washed, and resuspended in Neon buffer R at a density of 1 x 107 cells/mL. Neon 100 µL electroporation tips were used for each reaction with electrolytic buffer 2. siRNA was added to the buffer R/cell suspension for a final concentration of 20 nM (1 x 106 BX1 per 100 µL R buffer at siRNA 20 nM). Electroporation was performed with the following settings: 1375 V 10 ms 3 pulse. Electroporated cells were placed into 2 mL complete media (RPMI 10% FBS) and incubated at 37 °C with 5% CO2 atmosphere for 24 hrs prior to harvesting for CUT&RUN-seq.

tag: host

value: human

value: gingiva

value: human-Tert immortalized oral keratinocytes (NOK)

tag: cell type

value: keratinocyte

tag: genotype

value: EBV+ (Akata BX-1 strain)

tag: chromatin fixation

value: Yes

tag: cut-&-run antibody


title: NOK siLEF1 FL H3K9ac rep 2

tag: cell line

tag: treatment


title: NOK siLEF1 FL_DN H3K9ac rep 2


title: S1_DCCO_FLX

value: dmso

value: CTRL


title: NOK siNT H3K27ac rep2

value: transfectedsiRNAnontarget


title: NOK siLEF1 FL+DN H327ac rep 2


title: NOK siNT H3K9ac rep 2


title: TP0001651E04_8_100.000000uM_DMEM_24h_TC00283157_C09

description:
TP0001651E04_8_100.000000uM_DMEM_24h
TC00283157_C09

tag: media

value: DMEM + 10% HI-FBS

value: 24h exposure of 100 uM of Farglitazar

tag: chemical name

value: Farglitazar

tag: chemical sample id


title: M4_DCCO_FLX

value: els

value: liver


title: TP0001651G05_2_0.100000uM_DMEM_24h_TC00283157_C11

description:
TP0001651G05_2_0.100000uM_DMEM_24h
TC00283157_C11

value: 24h exposure of 0.1 uM of Cyproterone acetate

value: Cyproterone acetate

tag: chemical concentration

tag: dose level

tag: exposure time


title: M1_DCCO_FLX

tag: lifestage

value: flx

value: MED


title: M1_DCCO_EE2

tag: tissue


title: H4_DCCO_EE2

tag: chemical

value: HIGH


title: H3_DCCO_EE2

tag: concentration


title: H2_DCCO_FLX


title: H2_DCCO_EE2


title: NOK siNT IgG rep 2

tag: host

value: human

value: gingiva

value: human-Tert immortalized oral keratinocytes (NOK)

value: IgG


title: M5_DCCO_EE2


title: TP0001651G03_5_3.000000uM_DMEM_24h_TC00283157_C07

description:
TP0001651G03_5_3.000000uM_DMEM_24h
TC00283157_C07

value: 24h exposure of 3 uM of Nilutamide

value: Nilutamide

value: 3 uM

tag: assay plate

tag: assay plate well


title: M3_DCCO_EE2


title: TP0001651B03_4_1.000000uM_DMEM_24h_TC00283157_C05

description:
TP0001651B03_4_1.000000uM_DMEM_24h
TC00283157_C05

value: DMEM + 10% HI-FBS

value: 24h exposure of 1 uM of Reserpine

value: Reserpine

value: 1 uM


title: H5_DCCO_EE2

value: els

value: liver


title: M4_DCCO_EE2


title: TP0001651C05_6_10.000000uM_DMEM_24h_TC00283157_C06

description:
TP0001651C05_6_10.000000uM_DMEM_24h
TC00283157_C06

value: 24h exposure of 10 uM of Bisphenol B

value: Bisphenol B

value: 10 uM


title: NOK siLEF1 FL H327ac rep1

tag: cell type

value: keratinocyte

tag: genotype

value: EBV+ (Akata BX-1 strain)

tag: chromatin fixation

value: Yes


title: TP0001651E03_3_0.300000uM_DMEM_24h_TC00283157_C10

description:
TP0001651E03_3_0.300000uM_DMEM_24h
TC00283157_C10

tag: cell line

tag: treatment

value: 24h exposure of 0.3 uM of Prochloraz

value: Prochloraz


title: NOK siLEF1 FL_DN H3K9ac rep1

value: human

value: gingiva

value: human-Tert immortalized oral keratinocytes (NOK)

tag: cut-&-run antibody


title: TP0001651H04_6_10.000000uM_DMEM_24h_TC00283157_C04

description:
TP0001651H04_6_10.000000uM_DMEM_24h
TC00283157_C04

tag: media

value: DMEM + 10% HI-FBS

value: 24h exposure of 10 uM of Bisphenol A

tag: chemical name

value: Bisphenol A

tag: chemical sample id


title: NOK siLEF1 FL H3K9ac rep1


title: H5_DCCO_CPF

value: cpf

value: HIGH


title: M2_DCCO_CPF

value: els

value: liver

value: MED


title: TP0001651G03_3_0.300000uM_DMEM_24h_TC00283157_C03

description:
TP0001651G03_3_0.300000uM_DMEM_24h
TC00283157_C03

value: 24h exposure of 0.3 uM of Nilutamide

value: Nilutamide

tag: chemical concentration

tag: dose level

tag: exposure time


title: H4_DCCO_CPF

tag: lifestage

tag: tissue

tag: chemical


title: TP0001651C04_5_3.000000uM_DMEM_24h_TC00283157_C08

description:
TP0001651C04_5_3.000000uM_DMEM_24h
TC00283157_C08

value: 24h exposure of 3 uM of Simvastatin

value: Simvastatin

value: 3 uM

tag: assay plate


title: TP0001651B05_1_0.030000uM_DMEM_24h_TC00283157_C02

description:
TP0001651B05_1_0.030000uM_DMEM_24h
TC00283157_C02

value: 24h exposure of 0.03 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

tag: assay plate well


title: H3_DCCO_CPF

tag: concentration


title: H1_DCCO_EE2


title: S5_DCCO_CPF

value: dmso

value: CTRL


title: NOK siLEF1 FL+DN H327ac rep1

tag: host

value: human

value: gingiva

value: human-Tert immortalized oral keratinocytes (NOK)

tag: cell type

value: keratinocyte

tag: genotype

value: EBV+ (Akata BX-1 strain)

value: Yes


title: NOK siNT H3K9ac rep1

tag: cell line

tag: treatment

value: transfectedsiRNAnontarget

tag: chromatin fixation


title: S3_DCCO_CPF

value: els

value: liver


title: NOK siNT IgG rep1

tag: cut-&-run antibody

value: IgG


title: H2_DCCO_CPF

value: cpf

value: HIGH


title: TP0001651D02_1_0.030000uM_DMEM_24h_TC00283157_B24

description:
TP0001651D02_1_0.030000uM_DMEM_24h
TC00283157_B24

tag: media

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.03 uM of PFOA

tag: chemical name

value: PFOA

tag: chemical sample id


title: M2_DCCO_EE2

description:
S30, S33, S35, S37, S39
S1_DCCO_EE2, S2_DCCO_EE2, S3_DCCO_EE2, S4_DCCO_EE2, S5_DCCO_EE2
NS.1205.002.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.CE2-S1-LT-RNAseq_R1.fastq.gz, NS.1205.002.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.CE2-S2-LT-RNAseq_R1.fastq.gz, NS.1205.002.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.CE2-S3-LT-RNAseq_R1.fastq.gz, NS.1205.002.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.CE2-S4-LT-RNAseq_R1.fastq.gz, NS.1205.002.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.CE2-S5-LT-RNAseq_R1.fastq.gz
NS.1205.002.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.CE2-S1-LT-RNAseq_R2.fastq.gz, NS.1205.002.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.CE2-S2-LT-RNAseq_R2.fastq.gz, NS.1205.002.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.CE2-S3-LT-RNAseq_R2.fastq.gz, NS.1205.002.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.CE2-S4-LT-RNAseq_R2.fastq.gz, NS.1205.002.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.CE2-S5-LT-RNAseq_R2.fastq.gz
dcco_els_ee2.txt

value: MED


title: M4_DCCO_CPF


title: M5_DCCO_CPF


title: AkataBX1 4hr reativation LEF1 rep 2

source_name: Burkitt Lymphoma AkataBX-1

value: Burkitt Lymphoma AkataBX-1

value: B lymphocyte

value: No


title: M3_DCCO_CPF


title: TP0001651F01_1_0.030000uM_DMEM_24h_TC00283157_B23

description:
TP0001651F01_1_0.030000uM_DMEM_24h
TC00283157_B23

value: 24h exposure of 0.03 uM of Tetrac

value: Tetrac

tag: chemical concentration

tag: dose level

tag: exposure time


title: H1_DCCO_CPF

tag: lifestage

tag: tissue

tag: chemical


title: TP0001651F02_8_100.000000uM_DMEM_24h_TC00283157_B22

description:
TP0001651F02_8_100.000000uM_DMEM_24h
TC00283157_B22

value: 24h exposure of 100 uM of Ziram

value: Ziram

tag: assay plate

tag: assay plate well


title: S1_DCCO_CPF

value: dmso

tag: concentration

value: CTRL


title: NOK siNT H3K27ac rep1

tag: host

value: human

value: gingiva

value: human-Tert immortalized oral keratinocytes (NOK)

tag: cell type

value: keratinocyte

tag: genotype

value: EBV+ (Akata BX-1 strain)

value: transfectedsiRNAnontarget

value: Yes


title: M1_DCCO_CPF

value: els

value: liver

value: cpf

value: MED


title: TP0001651H01_6_10.000000uM_DMEM_24h_TC00283157_B21

description:
TP0001651H01_6_10.000000uM_DMEM_24h
TC00283157_B21

tag: cell line

value: DMEM + 10% HI-FBS

tag: treatment

value: 24h exposure of 10 uM of Flutamide

value: Flutamide

value: 10 uM


title: AkataBX1 uninduced control IgG rep 2

value: Burkitt Lymphoma AkataBX-1

value: B lymphocyte

value: untreated

tag: chromatin fixation

value: No

tag: cut-&-run antibody

value: IgG


title: AkataBX1 uninduced controlLEF1 rep 2

value: human


title: dcco.els.bap.H5

value: bap

value: HIGH


title: TP0001651B05_2_0.100000uM_DMEM_24h_TC00283157_B20

description:
TP0001651B05_2_0.100000uM_DMEM_24h
TC00283157_B20

tag: media

value: 24h exposure of 0.1 uM of Amiodarone hydrochloride

tag: chemical name

value: Amiodarone hydrochloride

tag: chemical sample id


title: dcco.els.bap.H4

value: els

value: liver


title: AkataBX1 2hr reativation LEF1 rep 2

value: EBV+ (Akata BX-1 strain)


title: dcco.els.bap.M3

value: MED


title: TP0001651F02_1_0.030000uM_DMEM_24h_TC00283157_B19

description:
TP0001651F02_1_0.030000uM_DMEM_24h
TC00283157_B19

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.03 uM of Ziram

value: Ziram

tag: chemical concentration

tag: dose level

tag: exposure time


title: AkataBX1 4hr reativation LEF1 rep 1

value: Burkitt Lymphoma AkataBX-1


title: dcco.els.bap.M2

tag: lifestage

tag: tissue

tag: chemical


title: HBRR_TC00283157_C01

description:
HBRR
TC00283157_C01

tag: assay plate

tag: assay plate well


title: dcco.els.bap.M1

tag: concentration


title: dcco.els.bap.H3


title: AkataBX1 uninduced control IgG rep 1

tag: host

tag: cell type

value: B lymphocyte

tag: genotype


title: AkataBX1 2hr reativation LEF1 rep 1

tag: cell line

tag: treatment

tag: chromatin fixation


title: TP0001651D05_8_100.000000uM_DMEM_24h_TC00283157_B18

description:
TP0001651D05_8_100.000000uM_DMEM_24h
TC00283157_B18

tag: media

value: 24h exposure of 100 uM of Thiram

tag: chemical name

value: Thiram


title: dcco.els.bap.S5

value: dmso

value: CTRL


title: S2_DCCO_CPF


title: dcco.els.bap.H2

value: bap


title: TP0001651A01_1_0.030000uM_DMEM_24h_TC00283157_B17

description:
TP0001651A01_1_0.030000uM_DMEM_24h
TC00283157_B17

value: 24h exposure of 0.03 uM of Pyraclostrobin

value: Pyraclostrobin

tag: chemical sample id

tag: chemical concentration


title: xl_els_cpf_SCP3

value: embryo


title: dcco.els.bap.H1

value: els

value: HIGH


title: dcco.els.bap.S1

value: liver


title: dcco.els.bap.S2


title: dcco.els.bap.M4

value: MED


title: AkataBX1 siLEF1 FL+DN LEF1 rep 1

value: human

value: EBV+ (Akata BX-1 strain)

value: No

tag: cut-&-run antibody


title: AkataBX1 siNT IgG rep 2

value: Burkitt Lymphoma AkataBX-1

value: transfectedsiRNAnontarget

value: IgG


title: AkataBX1 siNT LEF1 rep 2

value: B lymphocyte


title: TP0001651G01_3_0.300000uM_DMEM_24h_TC00283157_B11

description:
TP0001651G01_3_0.300000uM_DMEM_24h
TC00283157_B11

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Vinclozolin

value: Vinclozolin

tag: dose level

tag: exposure time


title: AkataBX1 siNT LEF1 rep 1


title: dcco.els.bap.S4

tag: lifestage

tag: tissue

tag: chemical

value: dmso

value: CTRL


title: AkataBX1 siLEF1 FL+DN LEF1 rep 2


title: TP0001651B05_4_1.000000uM_DMEM_24h_TC00283157_B16

description:
TP0001651B05_4_1.000000uM_DMEM_24h
TC00283157_B16

value: 24h exposure of 1 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

value: 1 uM

tag: assay plate

tag: assay plate well


title: AkataBX1 siLEF1 FL LEF1 rep 2

tag: host

tag: cell type


title: xl_els_cpf_MCP3

value: els

value: embryo

value: cpf

tag: concentration


title: AkataBX1 siNT IgG rep 1

value: human

tag: cell line

tag: genotype

value: EBV+ (Akata BX-1 strain)

tag: treatment


title: dcco.els.bap.S3

value: liver


title: TP0001651E02_7_30.000000uM_DMEM_24h_TC00283157_B09

description:
TP0001651E02_7_30.000000uM_DMEM_24h
TC00283157_B09

tag: media

value: 24h exposure of 30 uM of 4-Nonylphenol, branched

tag: chemical name

value: 4-Nonylphenol, branched

value: 30 uM


title: dcco.els.bap.M5

value: bap

value: MED


title: xl_els_cpf_HCP3

value: HIGH


title: xl_els_cpf_SDP4

value: dmso


title: TP0001651E05_4_1.000000uM_DMEM_24h_TC00283157_B15

description:
TP0001651E05_4_1.000000uM_DMEM_24h
TC00283157_B15

value: DMEM + 10% HI-FBS

value: 24h exposure of 1 uM of Atrazine

value: Atrazine

tag: chemical sample id

tag: chemical concentration


title: TP0001651A03_7_30.000000uM_DMEM_24h_TC00283157_B14

description:
TP0001651A03_7_30.000000uM_DMEM_24h
TC00283157_B14

value: 24h exposure of 30 uM of Butafenacil

value: Butafenacil

tag: dose level


title: xl_els_cpf_MEP5

value: els

value: embryo


title: xl_els_cpf_MDP4

value: cpf


title: TP0001651D01_3_0.300000uM_DMEM_24h_TC00283157_B07

description:
TP0001651D01_3_0.300000uM_DMEM_24h
TC00283157_B07

value: 24h exposure of 0.3 uM of Lactofen

value: Lactofen

tag: exposure time


title: AkataBX1 siLEF1 FL LEF1 rep 1

value: human

value: Burkitt Lymphoma AkataBX-1

value: B lymphocyte

value: EBV+ (Akata BX-1 strain)

tag: chromatin fixation

value: No

tag: cut-&-run antibody


title: xl_els_cpf_HBP2

tag: lifestage

tag: tissue

tag: chemical

value: HIGH


title: xl_els_cpf_MBP2

value: MED


title: xl_els_cpf_SBP2

value: dmso

value: CTRL


title: xl_els_cpf_SEP5


title: VENTX-R121Q

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs). Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: PBMs were scanned in a GenePix 4400A microarray scanner. At least 3 scans were taken for each slide at different photomultiplier tube (PMT) gain settings. We refer to the set of array chambers for a single allelic series assayed on the same slide (up to 8 array chambers per slide) as an allelic replicate. For each allelic replicate, an optimal scan was selected, corresponding to the PMT gain with the lowest proportions of both over-saturated probes (over-saturated probes are defined here as having intensity levels of >215.5; the signal is completely saturated at 216 = 65,536 intensity levels) and under-saturated probes (defined as intensity levels < 25) across all chambers in the allelic replicate. Most often, this corresponded to PMT gains between 400 and 500. The same PMT gain value was typically used within an allelic series.

data_processing:
Pre-processing procedures, including background subtraction, and spatial de-biasing, were applied to each array independently as previously described . Probes with foreground intensities less than background intensities were excluded. An empirical reference generated by pooling across Cy3 scans from 90 arrays was used for Cy3 normalization. Probes with log2 Cy3 observed-to-expected ratios greater than 1 or less than -1 were also excluded. Arrays were normalized within allelic replicates against a single anchor sample within the replicate, typically the reference allele. A log-scale additive normalization factor was estimated for each non-anchor sample using the trimmed mean of M-values approach originally proposed for RNA-seq normalization. Arrays were then normalized across allelic replicates using a single anchor allele present in all allelic replicates considered, typically the reference allele, with the exception of two allelic series (HOXD13 and SIX6) for which we used multiple anchor variant alleles (and averaged normalization factors across these multiple anchors). First, a reference sample value was calculated for the anchor allele using the log-scale mean of the anchor samples across the replicates. Then, to account for both shift and scale differences between allelic replicates, both a log-scale additive and a log-scale multiplicative factor were calculated for each replicate against the cross-replicate normalization sample. The log-scale additive factor for each replicate was estimated as the difference in the log-scale median probe intensity of the corresponding anchor sample and log-scale median probe intensity of the cross-replicate reference sample value. The log-scale multiplicative factor for each replicate was estimated as the median ratio of the rank-ordered and median-centered log-probe intensities between the corresponding anchor sample and the cross-replicate reference sample value. This is approximately equivalent to the slope of the log-scale QQ plot of the anchor and cross-replicate reference samples. Allelic replicates with low relative signal (as compared to other replicates) were deemed as lower-quality experiments and therefore filtered out at this step. This was assessed by comparing the upper-tail width (90th to 99th percentile) of the distribution of probe intensities for reference TF DBD samples in each allelic replicate. In most cases, at least two replicates were assayed for each member of an allelic series; for a small number of published data 1 reanalyzed for inclusion in this set, a single variant array was analyzed by comparison with replicates of the reference allele. If the tail width of a reference TF sample in an allelic replicate was less than 25% of the maximum tail width (or 50% of the maximum, if the array had been used previously and then stripped for re-use of the array in a new experiment) of the reference TF DBD samples across all replicates of the allelic series, the entire allelic replicate was excluded due to it being deemed as a lower quality replicate. A threshold of 50% of the maximum tail width was applied if the array had previously been used and then stripped for re-use of the array in a new experiment. Normalization across allelic replicates was repeated as above after removing the lower-quality experiments. After cross-replicate normalization, mixed-effects models were fit for each 8-mer aggregating across allelic replicates and probes to calculate 8-mer-level affinity scores. Summarization was performed for each 8-mer by first estimating probe-level means and variances across replicates using the limma smoothed variance estimator. Each probe-level estimate was further corrected for sequence position bias to account for differences in measured binding due to the distance of the 8-mer from the beginning or end of the probe sequence. Finally, 8-mer-level affinity scores were calculated using the two-step DerSimonian and Laird estimator across all probes containing the respective 8-mer sequences. All inference was performed at the 8-mer-level.
"affiniteEstimate," an 8-mer-level affinity score

molecule: protein

source_name: IVT protein

label_protocol: Arrays were incubated with an Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen A-11131).

extract_protocol: TF DBD sequence plus 15 a.a. N- and C-terminal flanking sequences were cloned into the pDEST15 expression vector, conferring an N-terminal GST tag. N-terminal GST-fusion TF DBD proteins were expressed using the PURExpress in vitro transcription/translation kit (NEB) following the manufacturer’s recommendations.

treatment_protocol: n/a/

tag: sample type

value: Variant


title: TP0001651A05_3_0.300000uM_DMEM_24h_TC00283157_B06

description:
TP0001651A05_3_0.300000uM_DMEM_24h
TC00283157_B06

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

tag: assay plate

tag: assay plate well


title: xl_els_cpf_HDP4

value: els

value: embryo

tag: concentration


title: xl_els_cpf_SAP1


title: TP0001651A02_2_0.100000uM_DMEM_24h_TC00283157_B10

description:
TP0001651A02_2_0.100000uM_DMEM_24h
TC00283157_B10

tag: cell line

value: 24h exposure of 0.1 uM of Imazalil

value: Imazalil


title: TP0001651G02_6_10.000000uM_DMEM_24h_TC00283157_B13

description:
TP0001651G02_6_10.000000uM_DMEM_24h
TC00283157_B13

tag: treatment

value: 24h exposure of 10 uM of Lovastatin

value: Lovastatin

value: 10 uM


title: xl_els_cpf_HAP1

value: cpf


title: TP0001651B02_3_0.300000uM_DMEM_24h_TC00283157_B12

description:
TP0001651B02_3_0.300000uM_DMEM_24h
TC00283157_B12

tag: media

value: 24h exposure of 0.3 uM of 3,5,3'-Triiodothyronine


title: TP0001651B01_7_30.000000uM_DMEM_24h_TC00283157_B05

description:
TP0001651B01_7_30.000000uM_DMEM_24h
TC00283157_B05

value: 24h exposure of 30 uM of Cyanazine

tag: chemical name

value: Cyanazine

value: 30 uM


title: Bf, DNBS, scRNA-seq

city: La Jolla

first: Hiutung

last: Chu

state: CA

address: 9500 Gilman

institute: UC San Diego

library_source: transcriptomic single cell

data_processing:
FASTQ files were demultiplexed and aligned to the mouse reference genome (Cell Ranger 10x Genomics, v3.0.2). Cellranger count was run on each set of files. Cellranger aggr was used to combine all GEM wells from a single experiment.
Supplementary files format and content: Cell Ranger output includes a matrix where each row corresponds to a feature (gene), each column corresponds to a barcode (cell), a barcode tsv with information about each cell, and a feature tsv with information about each gene

organism: Mus musculus

source_name: MLNs

extract_protocol:
Mesenteric lymph nodes (MLN) were processed by mashing tissues through 100 µm cell strainer to generate single cell suspensions. Enrichment of CD4+ and Foxp3-hCD2+ cells were performed using MACS beads.
Mesenteric lymph nodes (MLN) were generated and approximately 8,000-10,000 cells were loaded onto a Chromium Single Cell Chip (10x Genomics), according to the manufacturer's protocol. mRNA was barcoded during cDNA synthesis and pooled for Illumina sequencing. Libraries were sequenced with an 8 base index read on a Novaseq 6000.

value: MLNs

tag: cell type

value: Lymphocytes

tag: strain

value: Bacteroides fragilis WT-monocolonized mice induced with DNBS colitis  (DNBS)


title: Bf, SS, scRNA-seq

value: Bacteroides fragilis WT-monocolonized mice at steady state (SS)


title: VENTX-REF

value: Reference


title: AkataBX1 untreated LEF1 rep 1

tag: host

value: human

value: Burkitt Lymphoma AkataBX-1

value: B lymphocyte

tag: genotype

value: EBV+ (Akata BX-1 strain)

value: untreated

value: No


title: GEN_DMEM_24h_TC00283157_B08

description:
GEN_DMEM_24h
TC00283157_B08

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Genistein

value: Genistein

tag: chemical sample id

tag: chemical concentration

value: 10 uM

tag: dose level

tag: exposure time


title: DES 20Hz, replicate 3, scRNA-seq

city: Suzhou

first: Yaobo

last: Liu

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Institute of neuroscience

country: China

institute: Soochow University

description:
Smart-seq2
EffectiveDES3

data_processing:
FPKM
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Spinal cord

extract_protocol:
Spinal cord motoneurons of mice in the sham group (n = 3 mice), untrained group (n = 3 mice), 10-20 Hz MS group (n = 3 mice),  10-20 Hz SCS group (n = 3 mice), 10-20 Hz DES group (n = 3 mice), 1-40 Hz DES group (n = 3 mice) were labeled with TRDA and sacrificed 4 weeks after SCI.  The freshly isolated spinal cord was sliced on a Vibratome (Leica, Germany) into 200- to 300-μm-thick coronal sections.  Fluorescence-labeled motoneurons were visualized under a fluorescence microscope (Zeiss) using a miniature operating system (Eppendorf, Germany), and the motoneurons were aspirated by glass electrodes and placed in preservation solution (Invitrogen, USA).  TRDA-labeled neurons were individually homogenized in 1 ml TRIzol (Invitrogen), and RNA was extracted with a RNeasy Mini Kit (Qiagen) or equivalent.  Total RNA (1 μg) was used to synthesize double-stranded cDNA.
First, reference genome sequences and gene model annotation files of related species were downloaded from genome websites such as UCSC, NCBI, and ENSEMBL. Second, Hisat2 software (v2.0.1, http://daehwankimlab.github.io/hisat2/) was used to index the reference genome sequence. Finally, clean data were aligned to the reference genome via Hisat2 software (v2.0.1). Then, transcripts in FASTA format were converted from known gff annotation files and indexed properly. Then, with the file that served as the reference genome file, HTSeq (v0.6.1, https://htseq.readthedocs.io/en/master/) was used to estimate gene and isoform expression levels from the paired-end clean data. Differential expression analysis was performed using the DESeq2 Bioconductor package, a model based on a negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporated data-driven prior distributions 63, and the adjusted p-value of the genes was set to <0.05 to detect differentially expressed genes.

tag: tissue

value: Spinal cord

value: Motoneurons

value: Neuron

value: WT

value: Spinal cord injury,dual electrical stimulation


title: xl_els_cpf_HEP5

tag: lifestage

value: els

value: embryo

tag: chemical

value: cpf

value: HIGH


title: VAX1-K157R

tag: sample type

value: Variant


title: TP0001651F04_6_10.000000uM_DMEM_24h_TC00283157_B03

description:
TP0001651F04_6_10.000000uM_DMEM_24h
TC00283157_B03

value: 24h exposure of 10 uM of Fulvestrant

value: Fulvestrant

tag: assay plate

tag: assay plate well


title: DES 10Hz, replicate 1, scRNA-seq

description:
Smart-seq2
EffectiveDES1

tag: cell line

tag: treatment


title: xl_els_cpf_MAP1

tag: concentration

value: MED


title: VENTX-Y115F


title: AkataBX1 untreated IgG rep 1

value: human

value: Burkitt Lymphoma AkataBX-1

tag: cell type

value: B lymphocyte

value: EBV+ (Akata BX-1 strain)

value: untreated

tag: chromatin fixation

value: No

tag: cut-&-run antibody

value: IgG


title: DES 30Hz, replicate 2, scRNA-seq

description:
Smart-seq2
IneffectiveDES2

value: Spinal cord

value: Motoneurons

value: Neuron

tag: genotype

value: WT


title: GF, DNBS, scRNA-seq

value: MLNs

value: Lymphocytes

tag: strain

value: Germ free mice induced with DNBS colitis (DNBS)


title: VAX1-REF

value: Reference


title: DES 1Hz, replicate 1, scRNA-seq

description:
Smart-seq2
IneffectiveDES1

value: Spinal cord injury,dual electrical stimulation


title: DES 40Hz, replicate 3, scRNA-seq

description:
Smart-seq2
IneffectiveDES3


title: GF, SS, scRNA-seq

value: Germ free mice at steady state (SS)


title: SIX6-L167V

value: Variant


title: TP0001651H04_1_0.030000uM_DMEM_24h_TC00283157_B04

description:
TP0001651H04_1_0.030000uM_DMEM_24h
TC00283157_B04

tag: media

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.03 uM of Bisphenol A

tag: chemical name

value: Bisphenol A

tag: chemical sample id

tag: chemical concentration


title: DES 15Hz, replicate 2, scRNA-seq

description:
Smart-seq2
EffectiveDES2

tag: tissue


title: TP0001651C03_2_0.100000uM_DMEM_24h_TC00283157_A24

description:
TP0001651C03_2_0.100000uM_DMEM_24h
TC00283157_A24

value: 24h exposure of 0.1 uM of Simazine

value: Simazine

tag: dose level

tag: exposure time


title: SCS 20Hz, replicate 3, scRNA-seq

description:
Smart-seq2
SCS3

value: Spinal cord injury,spinal cord stimulation


title: SIX6-L167M

tag: sample type


title: VAX1-T142I


title: SIX6-L167I


title: MS 10Hz, replicate 1, scRNA-seq

description:
Smart-seq2
MS1

value: Spinal cord

value: Spinal cord injury,muscle stimulation


title: SCS 10Hz, replicate 1, scRNA-seq

description:
Smart-seq2
SCS1

value: Motoneurons

value: Neuron


title: TP0001651E01_5_3.000000uM_DMEM_24h_TC00283157_A22

description:
TP0001651E01_5_3.000000uM_DMEM_24h
TC00283157_A22

value: 24h exposure of 3 uM of Bifenthrin

value: Bifenthrin

value: 3 uM

tag: assay plate

tag: assay plate well


title: UHRR_TC00283157_B01

description:
UHRR
TC00283157_B01

source_name: Universal Human Reference RNA

tag: cell line

tag: treatment

value: untreated


title: MS 20Hz, replicate 3, scRNA-seq

description:
Smart-seq2
MS3

tag: cell type

value: WT


title: SCS 15Hz, replicate 2, scRNA-seq

description:
Smart-seq2
SCS2


title: MS 15Hz, replicate 2, scRNA-seq

description:
Smart-seq2
MS2


title: TP0001651B02_6_10.000000uM_DMEM_24h_TC00283157_B02

description:
TP0001651B02_6_10.000000uM_DMEM_24h
TC00283157_B02

value: 24h exposure of 10 uM of 3,5,3'-Triiodothyronine

value: 10 uM


title: SIX6-T165P

value: Variant


title: Untrained,replicate 1, scRNA-seq

description:
Smart-seq2
Untrained1

value: Spinal cord injury


title: Untrained,replicate 2, scRNA-seq

description:
Smart-seq2
Untrained2


title: TP0001651G04_6_10.000000uM_DMEM_24h_TC00283157_A21

description:
TP0001651G04_6_10.000000uM_DMEM_24h
TC00283157_A21

value: DMEM + 10% HI-FBS

value: 24h exposure of 10 uM of Cladribine

value: Cladribine


title: TP0001651E05_6_10.000000uM_DMEM_24h_TC00283157_A20

description:
TP0001651E05_6_10.000000uM_DMEM_24h
TC00283157_A20

value: 24h exposure of 10 uM of Atrazine

value: Atrazine


title: Sham, replicate 3, scRNA-seq

description:
Smart-seq2
Sham3

value: Spinal cord


title: Sham, replicate 2, scRNA-seq

description:
Smart-seq2
Sham2

value: Motoneurons


title: MC38 tumor, unmasked positive control, Day 7, rep 5

city: Waltham

first: Damiano

last: Fantini

address: 828 Winter Street, Suite 300

institute: Xilio Therapeutics

data_processing:
FastQ files were analyzed by Rosalind Inc. (San Diego, CA). Reads were trimmed using cutadapt and then quality scores were assessed using FastQC (ver 0.11.9).
Reads were aligned to the Mus musculus genome build mm10 using STAR (ver 2.7.10a).
Gene expression counts in each sample were quantified using HTSeq (ver 0.11.1; parameters: -m intersection-nonempty -t exon).
Filtering, normalization, and downstream gene expression analyses were performed in R (version 4.1.0). Data normalization was performed via trimmed mean of M-values (TMM) using the edgeR (ver 3.34.0) R library.
Assembly: mm10
Supplementary files format and content: tab separated value file including raw counts for each gene and sample.
Supplementary files format and content: tab separated value file including TMM-normalized log2-transformed counts per million reads for each gene and sample.

molecule: polyA RNA

source_name: MC38 tumor

growth_protocol: 0.5x10^6 MC38 cells were subcutaneously injected in the right flank of 10wk old female C57BL/6J mice. Animals were treated when tumors reached 200-300mm3.

extract_protocol:
Tumor tissue samples were homogenized using a bead mill. RNA extractions were performed using the NucleoSpin RNA kit (Takara) which includes an on-column DNase treatment.
Libraries were prepared using the TrueSeq RNA library prep kit (Illumina) and following the manufacturer’s protocol.

treatment_protocol: Animals received one intravenous injection of mXTX301 (0.39mg/kg), unmasked positive control (0.03mg/kg) or vehicle. Mice were sacrificed 4 or 7 days after injection.

tag: Sex

value: Female

value: MC38 tumor

value: unmasked positive control

tag: time

value: Day 7

tag: replicate


title: TP0001651E03_6_10.000000uM_DMEM_24h_TC00283157_A19

description:
TP0001651E03_6_10.000000uM_DMEM_24h
TC00283157_A19

value: 24h exposure of 10 uM of Prochloraz

value: Prochloraz


title: SIX6-T165G


title: Sham, replicate 1, scRNA-seq

description:
Smart-seq2
Sham1

value: Neuron

tag: genotype

value: WT


title: TP0001651A05_1_0.030000uM_DMEM_24h_TC00283157_A23

description:
TP0001651A05_1_0.030000uM_DMEM_24h
TC00283157_A23

tag: media

value: 24h exposure of 0.03 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: SIX6-T165A

value: Variant


title: Untrained,replicate 3, scRNA-seq

description:
Smart-seq2
Untrained3

value: Spinal cord injury


title: TP0001651E01_1_0.030000uM_DMEM_24h_TC00283157_A18

description:
TP0001651E01_1_0.030000uM_DMEM_24h
TC00283157_A18

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.03 uM of Bifenthrin

tag: chemical name

value: Bifenthrin


title: MC38 tumor, unmasked positive control, Day 7, rep 4

tag: strain


title: TP0001651C04_1_0.030000uM_DMEM_24h_TC00283157_A17

description:
TP0001651C04_1_0.030000uM_DMEM_24h
TC00283157_A17

value: 24h exposure of 0.03 uM of Simvastatin

value: Simvastatin

tag: chemical sample id

tag: chemical concentration


title: SIX6-L143V


title: MC38 tumor, unmasked positive control, Day 7, rep 2

value: Female

tag: tissue


title: MC38 tumor, unmasked positive control, Day 4, rep 5

value: MC38 tumor

value: Day 4


title: MC38 tumor, unmasked positive control, Day 7, rep 1

value: unmasked positive control

value: Day 7


title: SIX6-L143M


title: TP0001651F01_3_0.300000uM_DMEM_24h_TC00283157_A16

description:
TP0001651F01_3_0.300000uM_DMEM_24h
TC00283157_A16

value: 24h exposure of 0.3 uM of Tetrac

value: Tetrac

tag: dose level

tag: exposure time


title: SIX6-T165I

tag: sample type


title: MC38 tumor, unmasked positive control, Day 4, rep 2


title: MC38 tumor, unmasked positive control, Day 4, rep 4


title: MC38 tumor, unmasked positive control, Day 4, rep 3


title: SIX6-L143I


title: TP0001651E05_7_30.000000uM_DMEM_24h_TC00283157_A15

description:
TP0001651E05_7_30.000000uM_DMEM_24h
TC00283157_A15

value: 24h exposure of 30 uM of Atrazine

value: Atrazine

value: 30 uM

tag: assay plate

tag: assay plate well


title: MC38 tumor, unmasked positive control, Day 4, rep 1

tag: treatment


title: TP0001651A06_3_0.300000uM_DMEM_24h_TC00283157_A14

description:
TP0001651A06_3_0.300000uM_DMEM_24h
TC00283157_A14

tag: cell line

value: 24h exposure of 0.3 uM of Cyproconazole

value: Cyproconazole


title: SIX6-H141N

value: Variant


title: SIX6-T139Q


title: MC38 tumor, unmasked positive control, Day 7, rep 3

tag: Sex


title: MC38 tumor, mXTX301, Day 7, rep 5

tag: time


title: MC38 tumor, mXTX301, Day 7, rep 3

tag: replicate


title: TP0001651F04_1_0.030000uM_DMEM_24h_TC00283157_A13

description:
TP0001651F04_1_0.030000uM_DMEM_24h
TC00283157_A13

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.03 uM of Fulvestrant

value: Fulvestrant


title: TP0001651G03_7_30.000000uM_DMEM_24h_TC00283157_A12

description:
TP0001651G03_7_30.000000uM_DMEM_24h
TC00283157_A12

value: 24h exposure of 30 uM of Nilutamide

value: Nilutamide


title: MC38 tumor, mXTX301, Day 7, rep 4

value: Female

value: MC38 tumor


title: SHOX-R173C


title: SIX6-REF

value: Reference


title: MC38 tumor, mXTX301, Day 4, rep 5

value: Day 4


title: MC38 tumor, mXTX301, Day 7, rep 2

value: Day 7


title: MC38 tumor, mXTX301, Day 4, rep 4


title: MC38 tumor, mXTX301, Day 4, rep 3


title: MC38 tumor, mXTX301, Day 7, rep 1


title: SHOX-REF


title: MC38 tumor, mXTX301, Day 4, rep 2


title: TP0001651C02_5_3.000000uM_DMEM_24h_TC00283157_A11

description:
TP0001651C02_5_3.000000uM_DMEM_24h
TC00283157_A11

value: 24h exposure of 3 uM of 4-Hydroxytamoxifen

value: 3 uM


title: TP0001651H04_4_1.000000uM_DMEM_24h_TC00283157_A10

description:
TP0001651H04_4_1.000000uM_DMEM_24h
TC00283157_A10

value: 24h exposure of 1 uM of Bisphenol A

value: Bisphenol A

value: 1 uM


title: MC38 tumor, mXTX301, Day 4, rep 1


title: MC38 tumor, Vehicle, Day 7, rep 5

value: vehicle


title: PROP1-R112Q

value: Variant


title: PRRX1-REF


title: MC38 tumor, Vehicle, Day 7, rep 3


title: TP0001651C05_3_0.300000uM_DMEM_24h_TC00283157_A08

description:
TP0001651C05_3_0.300000uM_DMEM_24h
TC00283157_A08

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.3 uM of Bisphenol B

value: Bisphenol B


title: TP0001651H05_3_0.300000uM_DMEM_24h_TC00283157_A07

description:
TP0001651H05_3_0.300000uM_DMEM_24h
TC00283157_A07

value: 24h exposure of 0.3 uM of Trifloxystrobin

value: Trifloxystrobin


title: PROP1-R99Q


title: PRRX1-F113S


title: MC38 tumor, Vehicle, Day 7, rep 4

value: Female


title: MC38 tumor, Vehicle, Day 4, rep 4

value: MC38 tumor


title: MC38 tumor, Vehicle, Day 4, rep 2


title: MC38 tumor, Vehicle, Day 4, rep 1


title: MC38 tumor, Vehicle, Day 7, rep 2


title: PROP1-F88S


title: MC38 tumor, Vehicle, Day 7, rep 1


title: GEN_DMEM_24h_TC00283157_A02

description:
GEN_DMEM_24h
TC00283157_A02

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: PITX2-R141K


title: PITX2-W132L


title: UHRR_TC00283157_A01

description:
UHRR
TC00283157_A01

value: untreated


title: Torin2

city: Miami

first: James

middle: S

last: Choi

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

description: Nugen Universal Plus mRNAseq library prep

data_processing:
Generation of raw FASTQ files utilizing BCL2FASTQ software
Raw FASTQ quality control via FASTQC algorithm
Adapter and quality trimming
Alignment to the mouse (mm10) genome with the STAR v2.5.2a algorithm
Gene count quantification against the mouse GENCODE vM25 gene release database
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Bone-marrow-derived macrophage

growth_protocol: After anesthetizing with avertin (250mg/kg, i.p), 8-12-week-old male and female C57BL/6J mice (Jackson Strain 000664) were sacrificed by cervical dislocation and sprayed down with 70% ethanol. Skin on lower back was pinched and cut with small scissors to expose muscles. Skin was pulled down to each leg and removed with scissors. Once skin was fully flayed and removed, muscles were trimmed down to the bone. Legs were removed from the body by grabbing the leg at the hip and pulling away from the body, ensuring that the femur remained intact. With each leg removed, remaining muscle was cleared away using scissors and wiped dry with Kimwipes. While holding near the joints, bones were gently twisted to separate the tibia from the ankle and the knee, and the femur from the hip bone and knee. The kneecap was removed and discarded. Bones were placed in ice cold 70% ethanol in a Petri dish for ~1 minute to sterilize and then placed in ice cold RPMI in a Petri dish for remainder of dissection. Bones from different animals were kept in separate dishes to maintain biological replicates. Once finished with dissection, bones were brought to the tissue culture hood. Using clean and sterilized forceps, tips of bones were cut to expose marrow, held above an open 50 mL conical, and flushed with a 10 mL syringe filled with cold RPMI and a 25-gauge needle. Once all the bones were flushed, marrow was triturated with 1000 μL pipette until in a single-cell suspension. This suspension was passed through a pre-wet 70 μM filter into a new conical tube. These suspensions were spun down at 300 g for 10 minutes (4°C) and supernatant carefully aspirated. The pellet was esuspended in 3 mL ACK lysis buffer to lyse red blood cells and incubated for 1-2 minutes at room temperature. 20 mL of RPMI was added to dilute the lysis buffer, and ells spun down again at 300 g for 10 minutes. Cells were resuspended for direct plating in regular BMDM media. Cells were counted and plated in a TC-treated T75 flask in 20 mL at 10 million cells per flask. Regular BMDM media contained 20% L929 conditioned media, 10% FBS, 50 μM BME, 1X antibiotic and antifungal in RPMI supplemented with L-glutamine, HEPES, Phenol Red, Sodium Pyruvate, High glucose, Low sodium bicarbonate (Gibco, Catalog# A1049101,). Alternatively, extra cells not used for immediate culture were frozen in freezing media (10% DMSO, 90% FBS) at 6-8 million cells per mL, 1 mL per cryotube. To culture at a later time, cells were thawed in 10 mL pre-warmed HBSS (-/-) and spun down at 300 g, 10 minutes. Cells were plated in same manner as above. After isolation (Day 0), cells were grown in the regular BMDM media for 5 days with media change every other day. On day 5 (or day 6 if cell number appeared low), cells were trypsinized by first washing the T75 flask well with HBSS (-/-) three times, ensuring complete removal of serum. ~7mL of prewarmed trypsin (Corning, Catalog# 25053CI) was added and incubated for 15-30 minutes, depending on when cells start to detach. Trypsin was neutralized by adding at least 2X volume of FBS-containing media. Cells were spun down at 300 g, 10 minutes and resuspended in 3 mL of BMDM growth media. Cells were counted using Trypan Blue and a hemacytometer and plated at a density of 60,000 cells in 100 μL per well in a 96 well plate with μCLEAR bottom (Greiner, Catalog# 655090). Cells were placed in an incubator at 37°C (5% CO2) overnight to be stimulated the following day.

extract_protocol:
For RNA sequencing, cells were washed and resuspended in RLT Lysis Buffer plus beta-mercaptoethanol (10 μL per 1 mL of buffer, Sigma, Catalog# M6250). RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer instructions with a genomic DNA elimination column step.
We utilized the Nugen Universal Plus mRNAseq (input >10ng) for library preparation.
RNA-seq: we sequenced 20 million 100bp paired end reads per sample with three biological  replicates in three conditions (Homogenate + Vehicle, Homogenate + Torin-2, Homogenate + Rapamycin).

treatment_protocol: Whole spinal cord from male and female 8-20 week old C57BL/6 mice was dissected after transcardial perfusion with cold PBS. Meninges were removed to prevent fibroblast contamination in culture, and then cords placed in a 1.5 mL tube and frozen on dry ice. Cords were stored at -80°C until ready to prepare spinal cord homogenate. Spinal cords were isolated in bulk (20-30 mice at a time) to generate homogenate lot for multiple experiments and reduce variability between spinal cord preps. Multiple cords were pooled together, diced with a razor blade, and then separated into aliquots and frozen. When ready to treat cells with homogenate, cords were thawed, weighed, and homogenized with a Dounce homogenizer in cell culture media to produce a 10X suspension equaling 100 mg cord/mL media (10% weight/volume). To homogenize, cord was transferred to the Dounce grinder and appropriate volume of complete media was added. Both A and B pestles were used sequentially for 15 strokes each, ensuring no bubbles were generated in the homogenate. After cells were treated for 2 hours with Torin-2/Rapamycin/Vehicle, 10 μL of this 10X homogenate suspension was directly added to each well with vehicle/compounds for final concentration of 10 mg/mL or 1% w/v in the well. After 24 hours of incubation, homogenate and media were removed, and cells were washed gently three times with HBSS (no calcium, no magnesium, no phenol red, Gibco, Catalog# 14175095) to ensure complete removal of residual homogenate without disrupting the cell monolayer.

value: Bone-marrow-derived macrophage

tag: cell type

tag: genotype

value: WT


title: Torin3


title: Veh2

value: Vehicle media


title: MC38 tumor, Vehicle, Day 4, rep 5

value: Day 4


title: TP0001651G05_8_100.000000uM_DMEM_24h_TC00283157_A06

description:
TP0001651G05_8_100.000000uM_DMEM_24h
TC00283157_A06

tag: media

value: 24h exposure of 100 uM of Cyproterone acetate

tag: chemical name

value: Cyproterone acetate


title: PROP1-R99H

value: Variant


title: Rapa3

value: Rapamycin


title: TP0001651E04_5_3.000000uM_DMEM_24h_TC00283157_A09

description:
TP0001651E04_5_3.000000uM_DMEM_24h
TC00283157_A09

value: DMEM + 10% HI-FBS

value: 24h exposure of 3 uM of Farglitazar

value: Farglitazar

tag: chemical sample id

value: 3 uM


title: PITX2-T114P


title: Rapa1


title: MC38 tumor, Vehicle, Day 4, rep 3

tag: strain

value: Female

value: MC38 tumor

value: vehicle


title: TP0001651A01_7_30.000000uM_DMEM_24h_TC00283157_A05

description:
TP0001651A01_7_30.000000uM_DMEM_24h
TC00283157_A05

value: 24h exposure of 30 uM of Pyraclostrobin

value: Pyraclostrobin

tag: chemical concentration

value: 30 uM


title: TP0001651A03_8_100.000000uM_DMEM_24h_TC00283157_A04

description:
TP0001651A03_8_100.000000uM_DMEM_24h
TC00283157_A04

value: 24h exposure of 100 uM of Butafenacil

value: Butafenacil

tag: dose level


title: PROP1-REF

value: Reference


title: Veh3

tag: tissue

value: Bone-marrow-derived macrophage

value: WT

value: Vehicle media


title: TP0001651D06_6_10.000000uM_DMEM_12h_TC00283154_P23

description:
TP0001651D06_6_10.000000uM_DMEM_12h
TC00283154_P23

value: 12h exposure of 10 uM of PFOS

value: PFOS

value: 10 uM

tag: exposure time


title: PITX2-R108H

tag: sample type

value: Variant


title: TP0001651A04_2_0.100000uM_DMEM_24h_TC00283157_A03

description:
TP0001651A04_2_0.100000uM_DMEM_24h
TC00283157_A03

value: DMEM + 10% HI-FBS

value: 24h exposure of 0.1 uM of Rotenone

value: Rotenone

tag: assay plate

tag: assay plate well


title: Veh1

tag: treatment


title: PITX2-R130W


title: Torin1


title: adBNST, male control, 10

city: New Brunswick

first: Thomas

last: Degroat

state: NJ

address: 10 Suydam Street, Apt 12

department: Animal Sciences

institute: Rutgers University

data_processing:
Reads were quality trimmed with the FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with a minimum quality score of 20.0.
Trimmed reads were aligned to the mm10 reference genome using STAR and the NCBI RefSeq mm10 gene annotation.
Reads were counted with FeatureCounts.
Data was imported to R and differential expression was analyzed using DESeq2 with the following design parameters: (design ~ sex + condition + sex:condition).
Principle component analyses (PCA) were also generated by PCAExplorer to check for outliers.
Assembly: mm10
Supplementary files format and content: Raw counts for each sample is included in a tab-delimited text file

source_name: adBNST

extract_protocol:
Total RNA was extracted from anterdorsal bed nuceleus of the stria terminalis microdissections using the RNAqueous Micro Isolation kit (Invitrogen; AM1931) and following manufacturer's instructions.
RNA was sent to JPSulzberger Columbia Genome Center for library prep and sequencing. The Center uses STRPOLYA which enriches mRNA through a poly-A pull down method. All transcripts that were pulled down were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Chronic variable mild stress was conducted over 6 weeks on the stressed mice which included alteration of the light/dark cycle (light on overnight or lights off during the day for 180 min), temperature alteration (15 min of cold stress), bedding alteration for 8 h (removing the bedding, replacing the bedding with wet bedding, replacing the bedding with a centimeter of room-temperature water, or housing them in the bedding of a novel mouse of the same sex), frequent cage changes (5 or 6 times that day), forced swim (in room-temperature water for 4 min or 4C water for 2 min), isolation stress for 8 h, restraint stress for 1 h, cage tilting at a 45 angle for 8 h, and predator sounds for 15 min. The stressors are randomized during the 6-week paradigm to ensure that the mice do not get accustomed to any one stressor.

value: adBNST

tag: Sex

value: male

value: control


title: TP0001651D05_3_0.300000uM_DMEM_12h_TC00283154_P24

description:
TP0001651D05_3_0.300000uM_DMEM_12h
TC00283154_P24

tag: cell line

value: 12h exposure of 0.3 uM of Thiram

value: Thiram


title: Rapa2

value: Rapamycin


title: TP0001651D05_5_3.000000uM_DMEM_12h_TC00283154_P20

description:
TP0001651D05_5_3.000000uM_DMEM_12h
TC00283154_P20

value: 12h exposure of 3 uM of Thiram

value: 3 uM


title: TP0001651G05_5_3.000000uM_DMEM_12h_TC00283154_P19

description:
TP0001651G05_5_3.000000uM_DMEM_12h
TC00283154_P19

value: 12h exposure of 3 uM of Cyproterone acetate

value: Cyproterone acetate


title: adBNST, female control, 8

value: WT

value: female


title: adBNST, male control, 7


title: PBX4-REF

value: Reference


title: adBNST, female stressed, 8

value: stressed


title: adBNST, female control, 10


title: adBNST, male stressed, 9


title: adBNST, female stressed, 9


title: adBNST, female stressed, 7


title: PITX2-L100Q

value: Variant


title: adBNST, male control, 9


title: TP0001651D03_1_0.030000uM_DMEM_12h_TC00283154_P22

description:
TP0001651D03_1_0.030000uM_DMEM_12h
TC00283154_P22

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Cypermethrin

value: Cypermethrin


title: TP0001651B03_2_0.100000uM_DMEM_12h_TC00283154_P17

description:
TP0001651B03_2_0.100000uM_DMEM_12h
TC00283154_P17

value: 12h exposure of 0.1 uM of Reserpine

value: Reserpine


title: adBNST, female stressed, 6

value: adBNST


title: PAX4-R200Q


title: TP0001651H01_5_3.000000uM_DMEM_12h_TC00283154_P21

description:
TP0001651H01_5_3.000000uM_DMEM_12h
TC00283154_P21

value: 12h exposure of 3 uM of Flutamide

value: Flutamide


title: adBNST, male stressed, 7

value: male


title: adBNST, male control, 8

value: control


title: PAX4-R200K


title: adBNST, male control, 6


title: adBNST, male stressed, 8


title: PITX2-REF


title: TP0001651F04_5_3.000000uM_DMEM_12h_TC00283154_P15

description:
TP0001651F04_5_3.000000uM_DMEM_12h
TC00283154_P15

value: 12h exposure of 3 uM of Fulvestrant

value: Fulvestrant

value: 3 uM


title: PBX4-R215Q


title: TP0001651C01_5_3.000000uM_DMEM_12h_TC00283154_P18

description:
TP0001651C01_5_3.000000uM_DMEM_12h
TC00283154_P18

value: 12h exposure of 3 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)


title: adBNST, female control, 7

value: WT

value: female


title: PAX4-R227W

value: Variant


title: TP0001651G02_5_3.000000uM_DMEM_12h_TC00283154_P14

description:
TP0001651G02_5_3.000000uM_DMEM_12h
TC00283154_P14

value: DMEM + 10% HI-FBS

value: 12h exposure of 3 uM of Lovastatin

value: Lovastatin


title: adBNST, female control, 9


title: adBNST, male stressed, 3

value: stressed


title: adBNST, male stressed, 5

value: adBNST


title: TP0001651C06_4_1.000000uM_DMEM_12h_TC00283154_P13

description:
TP0001651C06_4_1.000000uM_DMEM_12h
TC00283154_P13

value: 12h exposure of 1 uM of Cycloheximide

value: Cycloheximide

value: 1 uM


title: TP0001651E02_2_0.100000uM_DMEM_12h_TC00283154_P16

description:
TP0001651E02_2_0.100000uM_DMEM_12h
TC00283154_P16

value: 12h exposure of 0.1 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched


title: adBNST, male stressed, 1

value: male


title: adBNST, male stressed, 2


title: TP0001651B05_3_0.300000uM_DMEM_12h_TC00283154_P11

description:
TP0001651B05_3_0.300000uM_DMEM_12h
TC00283154_P11

value: 12h exposure of 0.3 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: adBNST, female stressed, 4


title: adBNST, female stressed, 3


title: PAX4-F177Y


title: adBNST, female control, 6

value: control


title: adBNST, male stressed, 4

value: WT


title: PAX4-F177V


title: adBNST, female stressed, 5

value: female


title: TP0001651C05_1_0.030000uM_DMEM_12h_TC00283154_P12

description:
TP0001651C05_1_0.030000uM_DMEM_12h
TC00283154_P12

value: 12h exposure of 0.03 uM of Bisphenol B

value: Bisphenol B


title: adBNST, male stressed, 6


title: NKX2-6-R150C

value: Variant


title: adBNST, male control, 3


title: adBNST, female stressed, 1


title: NKX2-6-F151L


title: adBNST, male control, 5


title: NKX2-5-R190C


title: adBNST, female stressed, 2


title: adBNST, male control, 2


title: adBNST, female control, 5


title: TP0001651F03_6_10.000000uM_DMEM_12h_TC00283154_P09

description:
TP0001651F03_6_10.000000uM_DMEM_12h
TC00283154_P09

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of 4-Cumylphenol

value: 10 uM


title: adBNST, male control, 4

value: adBNST


title: NKX3-2-REF

value: Reference


title: NKX2-5-K183E


title: TP0001651C03_7_30.000000uM_DMEM_12h_TC00283154_P08

description:
TP0001651C03_7_30.000000uM_DMEM_12h
TC00283154_P08

value: 12h exposure of 30 uM of Simazine

value: Simazine

value: 30 uM


title: adBNST, female control, 1


title: NKX3-2-P234S


title: adBNST, male control, 1

value: male


title: Sperm from Dnmt3L WT on MCD sample 5

city: Montreal

first: Jacquetta

last: Trasler

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome (mm10) and get methylation calls with bsmap-2.6
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Sperm

extract_protocol:
Frozen sperm samples  were thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits  according to the manufacturer’s guide, with modifications. Sperm was incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , DTT and proteinase K . The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, ~500ng of  DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.

treatment_protocol: Both WT and Dnmt3L Het male mice, starting at 8 weeks of age, were fed either a high-fat diet (HFD) with 60% kcal from fat or a matched-control-diet (MCD) with 10% kcal from fat; both diets contained 2 mg/kg folate.  Males were fed the diets for 11-13 weeks, before breeding, ART or sperm collections. Males were sacrificed and mature sperm from the cauda epididymides were collected with the swim-out method and kept at -80°C until DNA isolation was performed

value: Sperm

value: MCD


title: Sperm from Dnmt3L WT on MCD sample 4


title: TP0001651A01_7_30.000000uM_DMEM_12h_TC00283154_P07

description:
TP0001651A01_7_30.000000uM_DMEM_12h
TC00283154_P07

value: 12h exposure of 30 uM of Pyraclostrobin

value: Pyraclostrobin


title: adBNST, female control, 4

value: WT

value: female

value: control


title: PAX4-REF


title: Sperm from Dnmt3L WT on MCD sample 3


title: adBNST, female control, 2


title: Sperm from Dnmt3L WT on MCD sample 2


title: TP0001651E04_1_0.030000uM_DMEM_12h_TC00283154_P02

description:
TP0001651E04_1_0.030000uM_DMEM_12h
TC00283154_P02

value: 12h exposure of 0.03 uM of Farglitazar

value: Farglitazar


title: TP0001651F01_3_0.300000uM_DMEM_12h_TC00283154_P06

description:
TP0001651F01_3_0.300000uM_DMEM_12h
TC00283154_P06

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Tetrac

value: Tetrac


title: adBNST, female control, 3

value: adBNST


title: TP0001651C01_1_0.030000uM_DMEM_12h_TC00283154_P05

description:
TP0001651C01_1_0.030000uM_DMEM_12h
TC00283154_P05

value: 12h exposure of 0.03 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)


title: Sperm from Dnmt3L WT on MCD sample 6


title: Sperm from Dnmt3L Het on MCD sample 5

value: Dnmt3L Het


title: NKX2-4-T231S

value: Variant


title: TP0001651G05_1_0.030000uM_DMEM_12h_TC00283154_P04

description:
TP0001651G05_1_0.030000uM_DMEM_12h
TC00283154_P04

value: 12h exposure of 0.03 uM of Cyproterone acetate

value: Cyproterone acetate


title: TP0001651C01_3_0.300000uM_DMEM_12h_TC00283154_P10

description:
TP0001651C01_3_0.300000uM_DMEM_12h
TC00283154_P10

value: 12h exposure of 0.3 uM of Fenpyroximate (Z,E)


title: NKX2-5-REF

value: Reference


title: NKX2-5-R139K


title: NKX2-5-R161P


title: NKX2-6-REF


title: Sperm from Dnmt3L Het on MCD sample 3

value: Sperm

value: MCD


title: Sperm from Dnmt3L Het on MCD sample 2


title: TP0001651B06_8_100.000000uM_DMEM_12h_TC00283154_P03

description:
TP0001651B06_8_100.000000uM_DMEM_12h
TC00283154_P03

value: 12h exposure of 100 uM of Troglitazone

value: Troglitazone


title: Sperm from Dnmt3L WT on MCD sample 1

value: WT


title: NKX2-4-R246Q


title: TP0001651H03_7_30.000000uM_DMEM_12h_TC00283154_O24

description:
TP0001651H03_7_30.000000uM_DMEM_12h
TC00283154_O24

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Fomesafen

value: Fomesafen

value: 30 uM


title: TP0001651H02_1_0.030000uM_DMEM_12h_TC00283154_O23

description:
TP0001651H02_1_0.030000uM_DMEM_12h
TC00283154_O23

value: 12h exposure of 0.03 uM of Maneb

value: Maneb


title: NKX2-4-P217L


title: Sperm from Dnmt3L WT on HFD sample 5

value: HFD


title: Sperm from Dnmt3L WT on HFD sample 3


title: TP0001651B03_5_3.000000uM_DMEM_12h_TC00283154_O22

description:
TP0001651B03_5_3.000000uM_DMEM_12h
TC00283154_O22

value: 12h exposure of 3 uM of Reserpine

value: Reserpine

value: 3 uM


title: Sperm from Dnmt3L Het on MCD sample 6

value: Dnmt3L Het


title: TP0001651A02_6_10.000000uM_DMEM_12h_TC00283154_O20

description:
TP0001651A02_6_10.000000uM_DMEM_12h
TC00283154_O20

value: 12h exposure of 10 uM of Imazalil

value: Imazalil

value: 10 uM


title: Sperm from Dnmt3L Het on MCD sample 1

value: Sperm

value: MCD


title: Sperm from Dnmt3L WT on HFD sample 4

value: WT


title: Sperm from Dnmt3L Het on MCD sample 4


title: Sperm from Dnmt3L WT on HFD sample 2


title: Sperm from Dnmt3L WT on HFD sample 6


title: TP0001651D02_1_0.030000uM_DMEM_12h_TC00283154_O21

description:
TP0001651D02_1_0.030000uM_DMEM_12h
TC00283154_O21

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of PFOA

value: PFOA


title: MSX2-R199I

value: Variant


title: TP0001651H01_7_30.000000uM_DMEM_12h_TC00283154_O19

description:
TP0001651H01_7_30.000000uM_DMEM_12h
TC00283154_O19

value: 12h exposure of 30 uM of Flutamide

value: Flutamide

value: 30 uM


title: Sperm from Dnmt3L WT on HFD sample 1

value: HFD


title: TP0001651C06_3_0.300000uM_DMEM_12h_TC00283154_O17

description:
TP0001651C06_3_0.300000uM_DMEM_12h
TC00283154_O17

value: 12h exposure of 0.3 uM of Cycloheximide

value: Cycloheximide


title: NKX2-4-REF

value: Reference


title: MSX2-F161Y


title: MSX2-REF


title: Sperm from Dnmt3L Het on HFD sample 5

value: Dnmt3L Het


title: Sperm from Dnmt3L Het on HFD sample 6


title: Sperm from Dnmt3L Het on HFD sample 4


title: ISX-R83Q


title: ISX-REF


title: TP0001651A05_7_30.000000uM_DMEM_12h_TC00283154_O16

description:
TP0001651A05_7_30.000000uM_DMEM_12h
TC00283154_O16

value: 12h exposure of 30 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: Sperm from Dnmt3L Het on HFD sample 3

value: Sperm


title: Sperm from Dnmt3L Het on HFD sample 1


title: TP0001651G02_4_1.000000uM_DMEM_12h_TC00283154_O15

description:
TP0001651G02_4_1.000000uM_DMEM_12h
TC00283154_O15

value: 12h exposure of 1 uM of Lovastatin

value: Lovastatin

value: 1 uM


title: TP0001651H05_1_0.030000uM_DMEM_12h_TC00283154_O18

description:
TP0001651H05_1_0.030000uM_DMEM_12h
TC00283154_O18

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Trifloxystrobin

value: Trifloxystrobin


title: Sperm from Dnmt3L Het on HFD sample 2


title: TP0001651G03_5_3.000000uM_DMEM_12h_TC00283154_O13

description:
TP0001651G03_5_3.000000uM_DMEM_12h
TC00283154_O13

value: 12h exposure of 3 uM of Nilutamide

value: Nilutamide

value: 3 uM


title: HOXD13-Q325R

value: Variant


title: HOXD13-S316C


title: S9_S9

first: Allan

middle: M

last: Goldstein

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
Sequencing performed using Illumina NovaSeq platform
Assembly: mm10, GRCh38
Library strategy: CUT&RUN

source_name: Neuro 2a cells – CUT&RUN

extract_protocol: Qiagen RNEasy kit (RNAseq) or Cell Signaling CUT&RUN kit (CUT&RUN)

value: Neuroblastoma

value: A/J

tag: antibody

value: Neuro 2a


title: IH_S13

tag: cell type

value: input


title: S12_S12


title: S10_S10


title: TP0001651C02_7_30.000000uM_DMEM_12h_TC00283154_O12

description:
TP0001651C02_7_30.000000uM_DMEM_12h
TC00283154_O12

value: 12h exposure of 30 uM of 4-Hydroxytamoxifen

value: 30 uM


title: TP0001651B05_7_30.000000uM_DMEM_12h_TC00283154_O14

description:
TP0001651B05_7_30.000000uM_DMEM_12h
TC00283154_O14

value: 12h exposure of 30 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: S11_S11


title: HOXD13-Q325K


title: HOXD13-T313R


title: TP0001651H05_6_10.000000uM_DMEM_12h_TC00283154_O11

description:
TP0001651H05_6_10.000000uM_DMEM_12h
TC00283154_O11

value: 12h exposure of 10 uM of Trifloxystrobin

value: 10 uM


title: S5_S5


title: S7_S7


title: S6_S6


title: TP0001651D02_7_30.000000uM_DMEM_12h_TC00283154_O10

description:
TP0001651D02_7_30.000000uM_DMEM_12h
TC00283154_O10

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of PFOA

value: PFOA


title: S4_S4


title: HOXD13-T313A


title: S1_S1


title: S1_S2


title: IL_S14


title: S3_S3