title: TP0001651A05_6_10.000000uM_DMEM_12h_TC00283154_O09

description:
TP0001651A05_6_10.000000uM_DMEM_12h
TC00283154_O09

value: 12h exposure of 10 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: HOXD13-R306W

status: Public on Dec 05 2023

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

country: USA

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

organism: Homo sapiens

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: HOXD13-N298S


title: S12_N2a_high

type: SRA

first: Allan

middle: M

last: Goldstein

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Sequencing performed using Illumina NovaSeq platform
Assembly: mm10, GRCh38

molecule: total RNA

organism: Mus musculus

source_name: Neuro 2a cells – RNAseq

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

tag: tissue

value: Neuroblastoma

tag: cell type

tag: strain

value: A/J

tag: cell line

value: Neuro 2a


title: TP0001651C04_7_30.000000uM_DMEM_12h_TC00283154_O08

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
TP0001651C04_7_30.000000uM_DMEM_12h
TC00283154_O08

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

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: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 30 uM of Simvastatin

tag: chemical name

value: Simvastatin

tag: chemical sample id

tag: chemical concentration

value: 30 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: S11_N2a_high


title: HOXD13-I322L


title: S8_S8

library_source: genomic

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

molecule: genomic DNA

source_name: Neuro 2a cells – CUT&RUN

tag: antibody


title: TP0001651D05_7_30.000000uM_DMEM_12h_TC00283154_O07

description:
TP0001651D05_7_30.000000uM_DMEM_12h
TC00283154_O07

value: 12h exposure of 30 uM of Thiram

value: Thiram


title: S10_N2a_high


title: HOXD13-I297V


title: S9_N2a_low


title: TP0001651E01_7_30.000000uM_DMEM_12h_TC00283154_O05

description:
TP0001651E01_7_30.000000uM_DMEM_12h
TC00283154_O05

value: 12h exposure of 30 uM of Bifenthrin

value: Bifenthrin


title: HOXD13-REF

value: Reference


title: TP0001651H03_3_0.300000uM_DMEM_12h_TC00283154_O06

description:
TP0001651H03_3_0.300000uM_DMEM_12h
TC00283154_O06

value: 12h exposure of 0.3 uM of Fomesafen

value: Fomesafen


title: CAL + DLL4 inhibition 3

city: Daegu

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

country: South Korea

institute: Keimyung University Dongsan Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 with HISAT2, and assembled with StringTie program.
Read count and FPKM(Fragment per Kilobase of transcript per Million mapped reads) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, TPM, raw counts

source_name: Adipose tissue

extract_protocol:
RNA was harvested using Trizol reagent. SureSelectXT RNA Direct Reagent Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose tissue

tag: age

value: 16 weeks

tag: genotype

value: wild type

tag: group

value: ASC added fat graft with Dll4 inhibition


title: S8_N2a_low

tag: tissue

value: Neuroblastoma

value: A/J


title: S7_N2a_low

tag: cell type

value: Neuro 2a


title: CAL + DLL4 inhibition 1

tag: strain


title: HOXC10-REF

tag: sample type


title: CAL + DLL4 inhibition 2


title: TP0001651G02_2_0.100000uM_DMEM_12h_TC00283154_O04

description:
TP0001651G02_2_0.100000uM_DMEM_12h
TC00283154_O04

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Lovastatin

value: Lovastatin


title: TP0001651H02_7_30.000000uM_DMEM_12h_TC00283154_O02

description:
TP0001651H02_7_30.000000uM_DMEM_12h
TC00283154_O02

tag: treatment

value: 12h exposure of 30 uM of Maneb

tag: chemical name

value: Maneb

value: 30 uM


title: HOXC9-R222W

value: Variant


title: Control 4

value: control fat grafts


title: CAL 3

value: ASC added fat graft


title: CAL 4


title: HOXC9-R193K


title: Control 3


title: TP0001651C06_5_3.000000uM_DMEM_12h_TC00283154_N24

description:
TP0001651C06_5_3.000000uM_DMEM_12h
TC00283154_N24

value: 12h exposure of 3 uM of Cycloheximide

value: Cycloheximide

tag: chemical sample id

tag: chemical concentration

value: 3 uM


title: HOXC9-K195R


title: CAL 1

value: Adipose tissue

value: 16 weeks

value: wild type


title: HOXC10-K271E


title: CAL + DLL4 inhibition 4

value: ASC added fat graft with Dll4 inhibition


title: HOXC9-REF

value: Reference


title: Control 1


title: Control 2


title: TP0001651E01_3_0.300000uM_DMEM_12h_TC00283154_N23

description:
TP0001651E01_3_0.300000uM_DMEM_12h
TC00283154_N23

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Bifenthrin

value: Bifenthrin

tag: dose level

tag: exposure time


title: fhm_els_bap_MEP

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: Pimephales promelas

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

value: embryo

tag: chemical

value: bap

tag: concentration

value: MED


title: HOXB9-T197M

value: Variant


title: TP0001651C01_8_100.000000uM_DMEM_12h_TC00283154_N22

description:
TP0001651C01_8_100.000000uM_DMEM_12h
TC00283154_N22

value: 12h exposure of 100 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

tag: assay plate

tag: assay plate well


title: HOXB9-R186Q


title: TP0001651H03_1_0.030000uM_DMEM_12h_TC00283154_N21

description:
TP0001651H03_1_0.030000uM_DMEM_12h
TC00283154_N21

value: 12h exposure of 0.03 uM of Fomesafen

value: Fomesafen


title: fhm_els_bap_HBP

tag: tissue

value: HIGH


title: fhm_els_bap_SEP

value: dmso

value: CTRL


title: HOXB9-REF


title: fhm_els_bap_MBP


title: TP0001651F04_2_0.100000uM_DMEM_12h_TC00283154_N20

description:
TP0001651F04_2_0.100000uM_DMEM_12h
TC00283154_N20

value: 12h exposure of 0.1 uM of Fulvestrant

value: Fulvestrant


title: CAL 2

value: Adipose tissue

tag: age

value: 16 weeks

tag: genotype

value: wild type

tag: group

value: ASC added fat graft


title: fhm_els_bap_HDP

value: els

value: embryo


title: HOXB6-K202E

tag: sample type


title: HOXB6-REF

value: Reference


title: fhm_els_bap_SBP


title: fhm_els_bap_SDP


title: TP0001651F04_7_30.000000uM_DMEM_12h_TC00283154_N18

description:
TP0001651F04_7_30.000000uM_DMEM_12h
TC00283154_N18

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Fulvestrant

value: 30 uM


title: HOXB4-V174I

value: Variant


title: fhm_els_bap_MAP

value: bap

value: MED


title: TP0001651D06_3_0.300000uM_DMEM_12h_TC00283154_N19

description:
TP0001651D06_3_0.300000uM_DMEM_12h
TC00283154_N19

tag: treatment

value: 12h exposure of 0.3 uM of PFOS

tag: chemical name

value: PFOS


title: HOXB4-REF


title: TP0001651F01_8_100.000000uM_DMEM_12h_TC00283154_N17

description:
TP0001651F01_8_100.000000uM_DMEM_12h
TC00283154_N17

value: 12h exposure of 100 uM of Tetrac

value: Tetrac

tag: chemical sample id

tag: chemical concentration


title: fhm_els_bap_HCP

value: HIGH


title: fhm_els_bap_SAP

value: dmso

value: CTRL


title: TP0001651A05_5_3.000000uM_DMEM_12h_TC00283154_N16

description:
TP0001651A05_5_3.000000uM_DMEM_12h
TC00283154_N16

value: 12h exposure of 3 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

value: 3 uM

tag: dose level

tag: exposure time


title: fhm_els_bap_MCP

tag: lifestage

value: els

value: embryo

tag: chemical


title: TP0001651G03_7_30.000000uM_DMEM_12h_TC00283154_N15

description:
TP0001651G03_7_30.000000uM_DMEM_12h
TC00283154_N15

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Nilutamide

value: Nilutamide

tag: assay plate


title: HOXA7-REF

value: Reference


title: HOXA4-W262R

value: Variant


title: fhm_els_bap_MDP

value: bap

tag: concentration

value: MED


title: BDA1-tech-rep2: IhhE95K/E95K/Lgr5DTR-GFP/+ technical replicate 2

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: 10X Genomics single-cell RNA-seq

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples. An average of 72% of the bases achieved a quality score1 of Q30 where Q30 denotes the accuracy of a base call to be 99.9%.
The demultiplexed FASTQ files were then processed with cellranger-2.1.0 (10X Genomics, Inc), a proprietary pipeline that perform alignment, quantification, and light-weight analyses in one go.
technical repl1 and technical replicate 2 were aggregated
Genome_build: Grcm38(mm10)
Supplementary_files_format_and_content: space-delimited text files containing gene expression table of the cells in sparse format (gene-id, cell-id, number-of-UMIs)

source_name: pool of 14 digits in 7 embryos

extract_protocol:
Dissected tissues were dissociated with 0.02% collagenase P (Roche 11213865001) for 45 mins at 37oC, followed by 40μm cell strainer.
Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 3’ Reagent Kits v2 and Chromium™ Single Cell A Chip Kit. Cells in suspension are counted and loaded into individual wells of 10X Chromium Single Cell chip. Single cells are then encapsulated into Gel in-beads emulsions (GEM) by 10X Chromium Controller. Single Cell 3’ Reagent Kits v2 is used to perform downstream steps, in brief as follows: reverse transcription is performed on GEMs, followed by cDNA clean up and amplification. The double-stranded cDNA will then go through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection per manufacturer’s protocol. Library size and concentration is determined by Qubit and Bioanalyzer assays.
The libraries are denatured and diluted to optimal concentration. Cluster generation is performed on the flow cell with HiSeq PE Cluster Kit v4 by cbot. Illumina HiSeq SBS Kit v4 is used for sequencing run at 100 bp for read 1 and read 2.

tag: mouse line

tag: tissues

value: Digit III M/P1 interzones

tag: number of cells captured

tag: median number of genes per cell


title: fhm_els_tb_MDP

tag: tissue

value: tb


title: TP0001651D04_6_10.000000uM_DMEM_12h_TC00283154_O03

description:
TP0001651D04_6_10.000000uM_DMEM_12h
TC00283154_O03

tag: cell line

value: 12h exposure of 10 uM of Clofibrate

value: Clofibrate

value: 10 uM

tag: assay plate well


title: fhm_els_bap_SCP

value: dmso

value: CTRL


title: TP0001651F02_5_3.000000uM_DMEM_12h_TC00283154_N14

description:
TP0001651F02_5_3.000000uM_DMEM_12h
TC00283154_N14

tag: media

tag: treatment

value: 12h exposure of 3 uM of Ziram

value: Ziram

value: 3 uM


title: HOXA4-W262F

tag: sample type


title: fhm_els_tb_SDP

value: els

value: embryo


title: fhm_els_tb_HAP

value: HIGH


title: fhm_els_bap_HAP


title: TP0001651D03_8_100.000000uM_DMEM_12h_TC00283154_N13

description:
TP0001651D03_8_100.000000uM_DMEM_12h
TC00283154_N13

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Cypermethrin

tag: chemical name

value: Cypermethrin

tag: chemical sample id

tag: chemical concentration


title: fhm_els_tb_MAP

tag: lifestage

value: MED


title: HOXA7-W177C

value: Variant


title: TP0001651F03_1_0.030000uM_DMEM_12h_TC00283154_N11

description:
TP0001651F03_1_0.030000uM_DMEM_12h
TC00283154_N11

value: 12h exposure of 0.03 uM of 4-Cumylphenol

tag: dose level

tag: exposure time


title: fhm_els_tb_SCP

tag: chemical

tag: concentration


title: TP0001651C03_4_1.000000uM_DMEM_12h_TC00283154_N10

description:
TP0001651C03_4_1.000000uM_DMEM_12h
TC00283154_N10

value: 12h exposure of 1 uM of Simazine

value: Simazine

value: 1 uM

tag: assay plate


title: TP0001651F03_5_3.000000uM_DMEM_12h_TC00283154_N12

description:
TP0001651F03_5_3.000000uM_DMEM_12h
TC00283154_N12

value: 12h exposure of 3 uM of 4-Cumylphenol


title: HOXA4-REF

value: Reference


title: fhm_els_tb_SAP

value: dmso

value: CTRL


title: HOXA4-R217L


title: TP0001651G04_4_1.000000uM_DMEM_12h_TC00283154_N09

description:
TP0001651G04_4_1.000000uM_DMEM_12h
TC00283154_N09

value: 12h exposure of 1 uM of Cladribine

value: Cladribine


title: fhm_els_tb_MCP

value: els

value: embryo

value: tb


title: fhm_els_tb_HEP

value: HIGH


title: fhm_els_bap_HEP

value: bap


title: TP0001651A01_2_0.100000uM_DMEM_12h_TC00283154_N08

description:
TP0001651A01_2_0.100000uM_DMEM_12h
TC00283154_N08

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Pyraclostrobin

value: Pyraclostrobin


title: fhm_els_tb_MBP

value: MED


title: HOXA2-R185T

value: Variant


title: fhm_els_tb_HBP


title: fhm_els_tb_SEP


title: fhm_els_tb_HDP


title: HOXA2-R185K


title: fhm_els_seme_MDP1

value: seme


title: HOXA2-REF


title: HOXA2-Y150S


title: fhm_els_seme_LDP1

value: LOW


title: fhm_els_seme_MBP1


title: fhm_els_tb_HCP


title: TP0001651H01_8_100.000000uM_DMEM_12h_TC00283154_N06

description:
TP0001651H01_8_100.000000uM_DMEM_12h
TC00283154_N06

value: 12h exposure of 100 uM of Flutamide

value: Flutamide


title: fhm_els_tb_SBP

value: dmso

value: CTRL


title: fhm_els_tb_MEP


title: fhm_els_seme_LBP1


title: HESX1-R165K


title: TP0001651G05_3_0.300000uM_DMEM_12h_TC00283154_N05

description:
TP0001651G05_3_0.300000uM_DMEM_12h
TC00283154_N05

value: 12h exposure of 0.3 uM of Cyproterone acetate

value: Cyproterone acetate


title: fhm_els_seme_SBP1

value: els

value: embryo


title: HESX1-R160C


title: TP0001651H04_3_0.300000uM_DMEM_12h_TC00283154_N04

description:
TP0001651H04_3_0.300000uM_DMEM_12h
TC00283154_N04

value: 12h exposure of 0.3 uM of Bisphenol A

value: Bisphenol A


title: fhm_els_seme_SDP1


title: fhm_els_seme_HCP1

value: HIGH


title: fhm_els_seme_HAP1


title: HESX1-E149K


title: fhm_els_seme_MCP1


title: TP0001651C04_1_0.030000uM_DMEM_12h_TC00283154_N03

description:
TP0001651C04_1_0.030000uM_DMEM_12h
TC00283154_N03

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Simvastatin

value: Simvastatin


title: fhm_els_seme_MAP1

value: MED


title: HESX1-N125S

value: Variant


title: HESX1-F115L


title: TP0001651D03_6_10.000000uM_DMEM_12h_TC00283154_N02

description:
TP0001651D03_6_10.000000uM_DMEM_12h
TC00283154_N02

value: 12h exposure of 10 uM of Cypermethrin

value: Cypermethrin

value: 10 uM


title: fhm_els_seme_LAP1

value: seme

value: LOW


title: fhm_els_seme_LCP1


title: TP0001651C03_5_3.000000uM_DMEM_12h_TC00283154_N07

description:
TP0001651C03_5_3.000000uM_DMEM_12h
TC00283154_N07

value: 12h exposure of 3 uM of Simazine

value: Simazine

value: 3 uM


title: TP0001651H03_4_1.000000uM_DMEM_12h_TC00283154_M24

description:
TP0001651H03_4_1.000000uM_DMEM_12h
TC00283154_M24

value: 12h exposure of 1 uM of Fomesafen

value: Fomesafen

value: 1 uM


title: HESX1-P111T


title: fhm_els_seme_SCP1

value: els

value: embryo

value: dmso

value: CTRL


title: fhm_els_seme_HBP1

value: HIGH


title: fhm_els_pb_HFP

value: pb


title: TP0001651B06_2_0.100000uM_DMEM_12h_TC00283154_M23

description:
TP0001651B06_2_0.100000uM_DMEM_12h
TC00283154_M23

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Troglitazone

value: Troglitazone


title: TP0001651A06_2_0.100000uM_DMEM_12h_TC00283154_M22

description:
TP0001651A06_2_0.100000uM_DMEM_12h
TC00283154_M22

value: 12h exposure of 0.1 uM of Cyproconazole

value: Cyproconazole


title: fhm_els_seme_HDP1

value: seme


title: HESX1-R109Q

value: Variant


title: HESX1-REF

value: Reference


title: CRX-E42D


title: fhm_els_pb_HEP


title: TP0001651B06_7_30.000000uM_DMEM_12h_TC00283154_M20

description:
TP0001651B06_7_30.000000uM_DMEM_12h
TC00283154_M20

value: 12h exposure of 30 uM of Troglitazone

value: 30 uM


title: TP0001651G03_2_0.100000uM_DMEM_12h_TC00283154_M21

description:
TP0001651G03_2_0.100000uM_DMEM_12h
TC00283154_M21

value: 12h exposure of 0.1 uM of Nilutamide

value: Nilutamide


title: fhm_els_pb_HAP

value: els

value: embryo


title: fhm_els_pb_HBP


title: CRX-R41L


title: fhm_els_pb_MFP

value: MED


title: TP0001651H03_5_3.000000uM_DMEM_12h_TC00283154_M19

description:
TP0001651H03_5_3.000000uM_DMEM_12h
TC00283154_M19

value: 12h exposure of 3 uM of Fomesafen

value: Fomesafen

value: 3 uM


title: CRX-REF


title: fhm_els_pb_MEP

value: pb


title: fhm_els_pb_MCP


title: TP0001651E05_6_10.000000uM_DMEM_12h_TC00283154_M18

description:
TP0001651E05_6_10.000000uM_DMEM_12h
TC00283154_M18

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Atrazine

value: Atrazine

value: 10 uM


title: fhm_els_pb_MBP


title: ARX-P353R

value: Variant


title: fhm_els_pb_MAP


title: ARX-P353L


title: TP0001651C05_6_10.000000uM_DMEM_12h_TC00283154_M17

description:
TP0001651C05_6_10.000000uM_DMEM_12h
TC00283154_M17

value: 12h exposure of 10 uM of Bisphenol B

value: Bisphenol B


title: fhm_els_pb_CFP

value: dmso

value: CTRL


title: fhm_els_pb_CEP


title: fhm_els_seme_SAP1


title: TP0001651G01_5_3.000000uM_DMEM_12h_TC00283154_M16

description:
TP0001651G01_5_3.000000uM_DMEM_12h
TC00283154_M16

value: 12h exposure of 3 uM of Vinclozolin

value: Vinclozolin


title: fhm_els_pb_HCP

value: els

value: embryo

value: HIGH


title: ARX-L343Q


title: fhm_els_pb_CCP


title: TP0001651A06_1_0.030000uM_DMEM_12h_TC00283154_M15

description:
TP0001651A06_1_0.030000uM_DMEM_12h
TC00283154_M15

value: 12h exposure of 0.03 uM of Cyproconazole

value: Cyproconazole


title: fhm_els_pb_CBP


title: ARX-T333N


title: fhm_els.hbcd_LEP

value: hbcd

value: MED


title: fhm_els_pb_CAP


title: fhm_els.hbcd_MEP


title: TP0001651C01_7_30.000000uM_DMEM_12h_TC00283154_M14

description:
TP0001651C01_7_30.000000uM_DMEM_12h
TC00283154_M14

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

value: 30 uM


title: fhm_els.hbcd_SCP


title: TP0001651C04_3_0.300000uM_DMEM_12h_TC00283154_M13

description:
TP0001651C04_3_0.300000uM_DMEM_12h
TC00283154_M13

value: 12h exposure of 0.3 uM of Simvastatin

value: Simvastatin


title: ARX-R332H

value: Variant


title: fhm_els.hbcd_SEP

value: dmso

value: CTRL


title: fhm_els.hbcd_MBP


title: ALX4-Q225E


title: ARX-REF

value: Reference


title: fhm_els.hbcd_MDP

value: els


title: TP0001651G01_3_0.300000uM_DMEM_12h_TC00283154_M12

description:
TP0001651G01_3_0.300000uM_DMEM_12h
TC00283154_M12

value: 12h exposure of 0.3 uM of Vinclozolin

value: Vinclozolin


title: TP0001651D06_1_0.030000uM_DMEM_12h_TC00283154_M11

description:
TP0001651D06_1_0.030000uM_DMEM_12h
TC00283154_M11

value: 12h exposure of 0.03 uM of PFOS

value: PFOS


title: fhm_els.hbcd_LDP

value: embryo

value: hbcd


title: fhm_els.hbcd_SBP


title: fhm_els.hbcd_LBP

value: MED


title: ALX4-REF


title: TP0001651B02_8_100.000000uM_DMEM_12h_TC00283154_M10

description:
TP0001651B02_8_100.000000uM_DMEM_12h
TC00283154_M10

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of 3,5,3'-Triiodothyronine


title: fhm_els.hbcd_SDP


title: ALX3-N203S


title: TP0001651H05_7_30.000000uM_DMEM_12h_TC00283154_M09

description:
TP0001651H05_7_30.000000uM_DMEM_12h
TC00283154_M09

value: 12h exposure of 30 uM of Trifloxystrobin

value: Trifloxystrobin

value: 30 uM


title: ALX3-N203Q

value: Variant


title: fhm_els.hbcd_MCP

value: HIGH


title: TP0001651G01_6_10.000000uM_DMEM_12h_TC00283154_M08

description:
TP0001651G01_6_10.000000uM_DMEM_12h
TC00283154_M08

value: 12h exposure of 10 uM of Vinclozolin

value: 10 uM


title: fhm_els.hbcd_LAP

value: els


title: TP0001651D03_7_30.000000uM_DMEM_12h_TC00283154_M07

description:
TP0001651D03_7_30.000000uM_DMEM_12h
TC00283154_M07

value: 12h exposure of 30 uM of Cypermethrin

value: Cypermethrin


title: ALX3-L168V


title: fhm_els_flx_232

value: flx


title: fhm_els.hbcd_LCP


title: TP0001651F05_6_10.000000uM_DMEM_12h_TC00283154_M06

description:
TP0001651F05_6_10.000000uM_DMEM_12h
TC00283154_M06

value: 12h exposure of 10 uM of Fenofibrate

value: Fenofibrate


title: fhm_els.hbcd_SAP

value: embryo

value: dmso

value: CTRL


title: ALX3-L168Q


title: fhm_els_flx_233


title: fhm_els_flx_231


title: ALX3-REF

value: Reference


title: fhm_els_flx_229


title: fhm_els_flx_227


title: fhm_els_flx_230


title: TP0001651F04_6_10.000000uM_DMEM_12h_TC00283154_M04

description:
TP0001651F04_6_10.000000uM_DMEM_12h
TC00283154_M04

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Fulvestrant

value: Fulvestrant


title: ALX1-L144R

value: Variant


title: fhm_els.hbcd_MAP

value: hbcd

value: HIGH


title: fhm_els_flx_226


title: fhm_els_flx_228


title: TP0001651C05_5_3.000000uM_DMEM_12h_TC00283154_M03

description:
TP0001651C05_5_3.000000uM_DMEM_12h
TC00283154_M03

value: 12h exposure of 3 uM of Bisphenol B

value: Bisphenol B

value: 3 uM


title: ALX1-REF


title: fhm_els_flx_224

value: els


title: TP0001651D05_2_0.100000uM_DMEM_12h_TC00283154_M02

description:
TP0001651D05_2_0.100000uM_DMEM_12h
TC00283154_M02

value: 12h exposure of 0.1 uM of Thiram

value: Thiram


title: fhm_els_flx_225

value: flx


title: fhm_els_flx_223

value: embryo


title: TP0001651G01_4_1.000000uM_DMEM_12h_TC00283154_L24

description:
TP0001651G01_4_1.000000uM_DMEM_12h
TC00283154_L24

value: 12h exposure of 1 uM of Vinclozolin

value: Vinclozolin

value: 1 uM


title: SWI4-LUTI∆_Whi5-anchor-away_rep2

city: Berkeley

first: Elcin

last: Unal

state: California

address: 1 Barker Hall

department: MCB

institute: UC Berkeley

data_processing:
reads aligned to genome using Hisat2 and quantification of RNA transcripts per million with StringTie.
fold change quantification performed with DESeq2 with default settings
Assembly: sk1_pacbio (Tresenrider et. Al, Mol Cell, 2021)
Supplementary files format and content: First tab of processed data is TPM table of all genes. Second tab is fold change as caculated by DESeq2

molecule: polyA RNA

organism: Saccharomyces cerevisiae SK1

growth_protocol: cells transferred to sporulate in SPO media and collected at 2 hours post transfer. See Su et al 2023 methods section for more detail. Cells for samples 6-12 were all treated with 1uM final rapamycin at 0H post transfer.

extract_protocol:
Cells were collected by centrifugation and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alchohol isolation.
PolyA selection and library generation was performed on 10ug of total RNA using NEXTflexTM Rapid Directional mRNA-Seq Kit

tag: strain

tag: genotype

value: cells transferred to sporulate in SPO media and collected at 2 hours post transfer. 1uM rapamycin treated 0H post transfer.


title: fhm_els_ee2_222_10b

tag: tissue


title: TP0001651A01_8_100.000000uM_DMEM_12h_TC00283154_L23

description:
TP0001651A01_8_100.000000uM_DMEM_12h
TC00283154_L23

tag: cell line

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Pyraclostrobin

value: Pyraclostrobin


title: SWI4-LUTI∆_Whi5-anchor-away_rep1


title: TP0001651B01_7_30.000000uM_DMEM_12h_TC00283154_M05

description:
TP0001651B01_7_30.000000uM_DMEM_12h
TC00283154_M05

value: 12h exposure of 30 uM of Cyanazine

value: Cyanazine

value: 30 uM

tag: assay plate well


title: TP0001651H04_4_1.000000uM_DMEM_12h_TC00283154_L22

description:
TP0001651H04_4_1.000000uM_DMEM_12h
TC00283154_L22

tag: media

value: 12h exposure of 1 uM of Bisphenol A

value: Bisphenol A


title: ALX1-L144V

value: Variant


title: Whi5-anchor-away_rep1

tag: treatment


title: Whi5-anchor-away_rep2


title: fhm_els_ee2_221_10a

value: els


title: SWI4-LUTI∆_rep2


title: fhm_els_ee2_220_4e


title: SWI4-LUTI∆_rep1


title: TP0001651B04_5_3.000000uM_DMEM_12h_TC00283154_L21

description:
TP0001651B04_5_3.000000uM_DMEM_12h
TC00283154_L21

value: 12h exposure of 3 uM of Propiconazole

value: Propiconazole

value: 3 uM


title: HCT116_2_155_Rep1_RNA_Fig2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9. Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2. Only uniquely mapping reads with at most two mismatches were retained.
For PRO-seq, following the removal of low-quality bases, adapters and ribosomal RNA signal, the paired-end reads with length of 15-51 nt were aligned to a concatenated genome comprised of human hg19 and fly dm3 assemblies using bowtie 2.4.5 with --very-sensitive option. To obtain PRO-seq signal in bigwig format, 5’ ends of R1 reads with MAPQ ≥ 20 were assigned to the opposite strand. Read counts were normalized to total reads aligned to the spike-in genome. Heatmaps and metaplots were generated using deepTools 3.5.1.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg19, dm3
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: HCT116 cells are cultured in DMEM+10%FBS.

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter) for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
PRO-seq: Libraries are prepped as in "A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)".

treatment_protocol: For lometrexol treatment, cells were treated with 0, 50, or 100 nM for 72 hours before cells are harvested for RNA extraction.

tag: cell type

value: colorectal cancer

value: MLL4 knockout


title: fhm_els_ee2_218_4c

value: embryo


title: HCT116_2_155_Rep2_RNA_Fig2


title: HCT116_2_82_Rep2_RNA_Fig2

value: MLL4 mutant allele only


title: TP0001651D06_7_30.000000uM_DMEM_12h_TC00283154_L19

description:
TP0001651D06_7_30.000000uM_DMEM_12h
TC00283154_L19

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of PFOS

tag: chemical name

value: PFOS


title: wild-type_rapamycin_rep2

source_name: wild-type

value: wild-type

value: cells transferred to sporulate in SPO media and collected at 2 hours post transfer. 1uM rapamycin treated 0H post transfer.


title: HCT116_2_82_Rep1_RNA_Fig2


title: fhm_els_ee2_217_4b


title: TP0001651A02_7_30.000000uM_DMEM_12h_TC00283154_L18

description:
TP0001651A02_7_30.000000uM_DMEM_12h
TC00283154_L18

value: 12h exposure of 30 uM of Imazalil

value: Imazalil

tag: chemical sample id

value: 30 uM


title: wild-type_rapamycin_rep1


title: fhm_els_ee2_216_4a


title: pATG8-SWI4_rep3

value: cells transferred to sporulate in SPO media and collected at 2 hours post transfer.


title: Untrtd_DMEM_12h_TC00283154_L16

description:
Untrtd_DMEM_12h
TC00283154_L16

value: untreated

tag: chemical concentration


title: pATG8-SWI4_rep2


title: fhm_els_ee2_219_4d

tag: lifestage

value: els


title: fhm_els_ee2_215_1c


title: fhm_els_ee2_214_1b


title: HCT116_1_94_Rep1_RNA_Fig2

value: MLL4 WT allele only


title: TSA_DMEM_12h_TC00283154_L20

description:
TSA_DMEM_12h
TC00283154_L20

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM

tag: dose level


title: HCT116_1_88_Rep2_RNA_Fig2

value: colorectal cancer


title: pATG8-SWI4_rep1


title: TP0001651F04_8_100.000000uM_DMEM_12h_TC00283154_L14

description:
TP0001651F04_8_100.000000uM_DMEM_12h
TC00283154_L14

value: 12h exposure of 100 uM of Fulvestrant

value: Fulvestrant

tag: exposure time


title: TP0001651C03_1_0.030000uM_DMEM_12h_TC00283154_L12

description:
TP0001651C03_1_0.030000uM_DMEM_12h
TC00283154_L12

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Simazine

value: Simazine


title: HCT116_2_115_Rep2_RNA_Fig2

value: MLL4 knockout


title: wild-type_rep1

value: wild-type


title: HCT116_1_88_Rep1_RNA_Fig2


title: HCT116_2_115_Rep1_RNA_Fig2


title: fhm_adult_seme_HE45

source_name: liver

value: adult

value: liver

tag: chemical

value: seme

value: HIGH


title: HCT116_1_77_Rep2_RNA_Fig2


title: fhm_adult_seme_ME45

tag: concentration

value: MED


title: wild-type_rep2

value: cells transferred to sporulate in SPO media and collected at 2 hours post transfer.


title: HCT116_1_94_Rep2_RNA_Fig2

value: MLL4 WT allele only


title: NK Pt11 Pop4  [CHIP_S144]

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
library strategy: CUT&RUN
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (hg38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38
Supplementary files format and content: peaks

source_name: PBMC

extract_protocol:
Briefly, isolated NK cells from ECs, HAARTs and HIVNs were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac, H3K27me3 and H3K4me3 histone marks (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

value: PBMC

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HAART

tag: antibody

value: IgG


title: fhm_adult_seme_CC45

tag: tissue

value: dmso

value: CTRL


title: TP0001651G04_6_10.000000uM_DMEM_12h_TC00283154_L17

description:
TP0001651G04_6_10.000000uM_DMEM_12h
TC00283154_L17

tag: cell line

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Cladribine

value: Cladribine

value: 10 uM

tag: assay plate


title: TP0001651B02_7_30.000000uM_DMEM_12h_TC00283154_L15

description:
TP0001651B02_7_30.000000uM_DMEM_12h
TC00283154_L15

tag: media

value: 12h exposure of 30 uM of 3,5,3'-Triiodothyronine

value: 30 uM

tag: assay plate well


title: fhm_els_ee2_213_1a

value: els

value: embryo


title: TP0001651G01_2_0.100000uM_DMEM_12h_TC00283154_L11

description:
TP0001651G01_2_0.100000uM_DMEM_12h
TC00283154_L11

tag: treatment

value: 12h exposure of 0.1 uM of Vinclozolin

value: Vinclozolin


title: TP0001651G03_8_100.000000uM_DMEM_12h_TC00283154_L13

description:
TP0001651G03_8_100.000000uM_DMEM_12h
TC00283154_L13

value: 12h exposure of 100 uM of Nilutamide

tag: chemical name

value: Nilutamide


title: TP0001651D01_6_10.000000uM_DMEM_12h_TC00283154_L10

description:
TP0001651D01_6_10.000000uM_DMEM_12h
TC00283154_L10

value: 12h exposure of 10 uM of Lactofen

value: Lactofen

tag: chemical sample id


title: fhm_adult_seme_CE45

value: adult

value: liver


title: HCT116_1_108_Rep2_RNA_Fig2

tag: cell type

value: colorectal cancer

tag: genotype

value: MLL4 mutant allele only


title: HCT116_1_77_Rep1_RNA_Fig2

value: MLL4 knockout


title: fhm_adult_seme_HD45

tag: lifestage

value: seme

value: HIGH


title: TP0001651E03_2_0.100000uM_DMEM_12h_TC00283154_L09

description:
TP0001651E03_2_0.100000uM_DMEM_12h
TC00283154_L09

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Prochloraz

value: Prochloraz

tag: chemical concentration

tag: dose level

tag: exposure time


title: HCT116_1_101_Rep2_RNA_Fig2

value: MLL4 WT allele only


title: NK Pt11 Pop2 [CHIP_S140]

value: PBMC

value: CD56bri CD16- NK cells

tag: participant id

value: HAART

value: IgG


title: fhm_adult_seme_MB45

tag: chemical

tag: concentration

value: MED


title: NK Pt11 Pop4 [CHIP_S142]

tag: tissue

value: CD56dim CD16+ NK cells

tag: participant phenotype

tag: antibody


title: TP0001651A03_6_10.000000uM_DMEM_12h_TC00283154_L08

description:
TP0001651A03_6_10.000000uM_DMEM_12h
TC00283154_L08

tag: cell line

tag: media

value: 12h exposure of 10 uM of Butafenacil

value: Butafenacil

value: 10 uM

tag: assay plate


title: fhm_adult_seme_HA45

value: adult

value: liver


title: HCT116_1_101_Rep1_RNA_Fig2

value: colorectal cancer

tag: treatment


title: TP0001651A03_7_30.000000uM_DMEM_12h_TC00283154_L07

description:
TP0001651A03_7_30.000000uM_DMEM_12h
TC00283154_L07

value: 12h exposure of 30 uM of Butafenacil

tag: chemical name

tag: chemical sample id

value: 30 uM

tag: assay plate well


title: NK Pt11 Pop2 [CHIP_S139]

tag: cell type


title: fhm_adult_seme_MC45

tag: lifestage

value: seme


title: HCT116_1_108_Rep1_RNA_Fig2

tag: genotype

value: MLL4 mutant allele only


title: HCT116_parental_Rep3_RNA_Fig2

value: wild type


title: TP0001651A06_8_100.000000uM_DMEM_12h_TC00283154_L06

description:
TP0001651A06_8_100.000000uM_DMEM_12h
TC00283154_L06

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Cyproconazole

value: Cyproconazole

tag: chemical concentration

tag: dose level

tag: exposure time


title: fhm_adult_seme_CA4

tag: chemical

value: dmso

tag: concentration

value: CTRL


title: NK Pt11 Pop2 [CHIP_S138]

tag: tissue

value: PBMC

value: CD56bri CD16- NK cells

tag: participant id

tag: participant phenotype

value: HAART


title: HCT116_parental_Rep2_RNA_Fig2

tag: cell line


title: TP0001651A05_2_0.100000uM_DMEM_12h_TC00283154_L05

description:
TP0001651A05_2_0.100000uM_DMEM_12h
TC00283154_L05

tag: media

value: 12h exposure of 0.1 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

tag: assay plate


title: STAT3-negative gastric cancer patient samples

type: genomic

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

description: pooled 3 patient samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Analysis by Microsoft Excel. Raw data selected by Detection pval and removed missing values.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Genomic DNA mini Kit (Geneaid) according to standard instructions

value: tumor

tag: disease

value: gastric cancer

tag: stat3 status

value: negative


title: NK Pt11 Pop4 [CHIP_S141]

value: CD56dim CD16+ NK cells

tag: antibody


title: NK Pt11 Pop2 [CHIP_S137]

tag: cell type


title: HCT116_parental_Rep1_RNA_Fig2

value: colorectal cancer

tag: treatment


title: TP0001651F02_7_30.000000uM_DMEM_12h_TC00283154_L04

description:
TP0001651F02_7_30.000000uM_DMEM_12h
TC00283154_L04

value: 12h exposure of 30 uM of Ziram

tag: chemical name

value: Ziram

tag: chemical sample id

value: 30 uM

tag: assay plate well


title: fhm_adult_seme_HC45

tag: lifestage

value: adult

value: liver

value: seme

value: HIGH


title: fhm_adult_seme_MD15

tag: chemical

value: MED


title: TP0001651C02_4_1.000000uM_DMEM_12h_TC00283154_L03

description:
TP0001651C02_4_1.000000uM_DMEM_12h
TC00283154_L03

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of 4-Hydroxytamoxifen

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time


title: NK Pt17 Pop4 [CHIP_S136]

tag: tissue

value: PBMC

tag: participant id

tag: participant phenotype

value: HIVN

value: IgG


title: Adrenal Demedullated-IUGR Fetus 2

city: Tucson

first: Sean

middle: W

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

data_processing:
Paired reads were filtered to remove reads less than 65 nt using Trimmomatic
Tophat 2.0.14 was used to map reads using parameters -a 20  -m 1 -I 10^5  -g 9 -N 3 --read-gap-length 1 --read-edit-dist 4  --read-realign-edit-dist 0 --library-type fr-unstranded
Cufflinks 2.2.1 was used to determine the transcriptome (annotation only)  using parameters -G oar3174.gtf -b genome.fa -u -N -F 0.05
A unified non-redundant transcriptome (merge.gtf) was determined for all samples using Cuffmerge 2.2.1
Quantification of gene expression for all samples was determined using Cuffquant 2.2.1 with parameters -u -library-type fr-unstranded -b genome.fa -max-bundle-frags 10^7  merged.gtf
Cuffdiff 2.2.1 was used to determine statistical differences in gene expression between treatments using parameters -u -c 24 -FDR 0.05 -b genome.fa --max-bundle-frags 10^7 -compatible-hits-norm --library-type fr-unstranded merged.gtf
Genome_build: Genome Ensembl release 74 Ovis_aries.Oar_v3.1.dna_sm.toplevel.fa; annotation Ensembl Ovis_aries.Oar_v3.1.74.gtf
Supplementary_files_format_and_content: gene_exp.diff.gz: Tab separated values contains the gene level statistical analysis unmodified from Cuffdiff 2.2.1
Supplementary_files_format_and_content: gene.FPKM.tsv.gz: Tab separated values containing columns with tracking_id, gene_id and locus along with FPKM values for each treatment.

organism: Ovis aries

source_name: Isolated Perirenal Adipose

growth_protocol: Columbia-Rambouillet crossbred ewes carrying singleton pregnancies.

extract_protocol:
The entire perirenal adipose depot above the left kidney was removed, snap frozen in liquid nitrogen and stored at -80C for RNA extraction with Qiagen Microprep RNAeasy.
mRNA was selected and double-stranded cDNA libraries with ligated sequencing adapters was constructed with the Illumina TruSeq RNA Sample Prep Kit. Cluster generation was conducted with Illumina TruSeq 100bp PE (paired end) cluster kit

treatment_protocol: IUGR fetuses were generated by exposing pregnant ewes to elevated ambient temperatures (40°C for 12h; 35°C for 12h; dew point 22°C) from 38 ± 1 days gestation age (dGA) until 94 ± 2 dGA. Control fetuses were from pregnant ewes that were maintained in a thermoneutral environment (22°C) and pair fed to the average daily dietary intake of the heat stressed ewes.

tag: internal animal id

tag: age (day in gestation)

tag: Sex

value: M

tag: weight at necropsy (kg)


title: Adrenal Demedullated-IUGR Fetus 1


title: Adrenal Demedullated-IUGR Fetus 0

value: F


title: fhm_adult_seme_CB45

value: dmso

tag: concentration

value: CTRL


title: TP0001651B02_4_1.000000uM_DMEM_12h_TC00283154_L02

description:
TP0001651B02_4_1.000000uM_DMEM_12h
TC00283154_L02

tag: cell line

tag: media

tag: treatment

value: 12h exposure of 1 uM of 3,5,3'-Triiodothyronine

tag: assay plate


title: NK Pt17 Pop4 [CHIP_S134]

tag: cell type

value: CD56dim CD16+ NK cells

tag: antibody


title: NK Pt17 Pop4 [CHIP_S133]


title: fhm_adult_seme_MA45

tag: lifestage

value: adult

tag: chemical


title: Sham-IUGR Fetus 3


title: Sham-IUGR Fetus 2


title: NK Pt17 Pop2 [CHIP_S132]

value: CD56bri CD16- NK cells


title: STAT3-positive gastric cancer patient samples

description: pooled 3 patient samples

value: tumor

tag: disease

value: gastric cancer

tag: stat3 status

value: positive


title: TP0001651B06_1_0.030000uM_DMEM_12h_TC00283154_K22

description:
TP0001651B06_1_0.030000uM_DMEM_12h
TC00283154_K22

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Troglitazone

tag: chemical name

value: Troglitazone

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate well


title: TP0001651H02_5_3.000000uM_DMEM_12h_TC00283154_K23

description:
TP0001651H02_5_3.000000uM_DMEM_12h
TC00283154_K23

value: 12h exposure of 3 uM of Maneb

value: Maneb

value: 3 uM


title: fhm_adult_seme_HB45

tag: tissue

value: liver

value: seme

tag: concentration

value: HIGH


title: fhm_adult_ee2_SALT4

value: dmso

value: CTRL


title: NK Pt17 Pop4 [CHIP_S135]

value: PBMC

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HIVN


title: NK Pt17 Pop2 [CHIP_S131]

value: CD56bri CD16- NK cells


title: NK Pt17 Pop2 [CHIP_S130]


title: NK Pt17 Pop2 [CHIP_S129]


title: TP0001651E03_8_100.000000uM_DMEM_12h_TC00283154_K21

description:
TP0001651E03_8_100.000000uM_DMEM_12h
TC00283154_K21

tag: cell line

tag: media

tag: treatment

value: 12h exposure of 100 uM of Prochloraz

value: Prochloraz

tag: assay plate


title: Sham-IUGR Fetus 0

tag: internal animal id

tag: age (day in gestation)

tag: Sex

value: M

tag: weight at necropsy (kg)


title: Sham-IUGR Fetus 1


title: fhm_adult_seme_CD45

tag: lifestage

value: adult

tag: chemical


title: Adrenal Demedullated-Control Fetus 2


title: fhm_adult_ee2_LD12

value: LOW


title: fhm_adult_ee2_LB12


title: TP0001651A06_5_3.000000uM_DMEM_12h_TC00283154_K24

description:
TP0001651A06_5_3.000000uM_DMEM_12h
TC00283154_K24

value: DMEM + 10% HI-FBS

value: 12h exposure of 3 uM of Cyproconazole

tag: chemical name

value: Cyproconazole

tag: chemical sample id

tag: chemical concentration

tag: dose level


title: TP0001651A05_1_0.030000uM_DMEM_12h_TC00283154_K20

description:
TP0001651A05_1_0.030000uM_DMEM_12h
TC00283154_K20

value: 12h exposure of 0.03 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

tag: exposure time

tag: assay plate well


title: TP0001651D04_1_0.030000uM_DMEM_12h_TC00283154_K19

description:
TP0001651D04_1_0.030000uM_DMEM_12h
TC00283154_K19

value: 12h exposure of 0.03 uM of Clofibrate

value: Clofibrate


title: fhm_adult_ee2_SD12

tag: tissue

value: liver

value: dmso

tag: concentration

value: CTRL


title: TP0001651F05_2_0.100000uM_DMEM_12h_TC00283154_K18

description:
TP0001651F05_2_0.100000uM_DMEM_12h
TC00283154_K18

tag: cell line

tag: media

value: 12h exposure of 0.1 uM of Fenofibrate

value: Fenofibrate


title: Adrenal Demedullated-Control Fetus 0


title: NK Pt02 Pop4 [CHIP_S128]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HAART

tag: antibody

value: IgG


title: fhm_adult_ee2_SB12

value: adult


title: NK Pt02 Pop4 [CHIP_S127]


title: TP0001651D06_8_100.000000uM_DMEM_12h_TC00283154_K17

description:
TP0001651D06_8_100.000000uM_DMEM_12h
TC00283154_K17

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 100 uM of PFOS

value: PFOS

tag: assay plate


title: fhm_adult_ee2_HE12

tag: lifestage

tag: chemical

value: HIGH


title: Sham-Control Fetus 3

tag: internal animal id

tag: age (day in gestation)

tag: Sex

value: M

tag: weight at necropsy (kg)


title: NK Pt02 Pop4 [CHIP_S126]


title: TP0001651A01_4_1.000000uM_DMEM_12h_TC00283154_K16

description:
TP0001651A01_4_1.000000uM_DMEM_12h
TC00283154_K16

value: 12h exposure of 1 uM of Pyraclostrobin

tag: chemical name

value: Pyraclostrobin

tag: chemical sample id

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time

tag: assay plate well


title: Sham-Control Fetus 1


title: NK Pt02 Pop2 [CHIP_S124]

tag: tissue

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id


title: NK Pt02 Pop4 [CHIP_S125]

tag: participant phenotype

tag: antibody


title: fhm_adult_ee2_ME12

tag: lifestage

value: liver

tag: concentration

value: MED


title: Sham-Control Fetus 2

tag: internal animal id


title: TSA_DMEM_12h_TC00283154_K15

description:
TSA_DMEM_12h
TC00283154_K15

tag: cell line

tag: media

tag: treatment

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

tag: assay plate


title: fhm_adult_ee2_HC12

tag: chemical


title: TP0001651C06_7_30.000000uM_DMEM_12h_TC00283154_K13

description:
TP0001651C06_7_30.000000uM_DMEM_12h
TC00283154_K13

value: 12h exposure of 30 uM of Cycloheximide

tag: chemical name

value: Cycloheximide

tag: chemical sample id

tag: chemical concentration

value: 30 uM


title: MK5

city: Moscow

first: Alexander

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

country: Russia

institute: EIMB

data_processing:
Read trimming (Trimmomatic)
Read alignment (STAR)
Read counting (FeatureCounts)
Assembly: mm10
Supplementary files format and content: Read counts assigned to exonic regions of genes

source_name: Cerebellum

extract_protocol:
For the transcriptomic analysis, three brain tissues (hippocampus, cortex and cerebellum) from two groups (OBX and sham-operated) were used. Brains were dissected and stored at 800C until the RNA isolation. The extraction RNA was made using RNAzol RT (Molecular Research Center, Cincinnati, OH, USA) according to the company’s protocol. The concentration and quality of RNA were determined via Qubit Fluorometer (Invitrogen) and an Agilent BioAnalyzer 2100, respectively, using RNA 6000 nano kit (Agilent technologies, Santa-Clara, CA, USA).
For libraries RNA with Integrity Number (RIN), no less than 8 were taken. Illumina NEB Next Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) was used for mRNA libraries preparation. The sequencing was performed on the Illumina NextSeq 2000 platform

value: Cerebellum

tag: genotype

value: Wild-type

value: Sham-operated


title: TP0001651C02_8_100.000000uM_DMEM_12h_TC00283154_K14

description:
TP0001651C02_8_100.000000uM_DMEM_12h
TC00283154_K14

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of 4-Hydroxytamoxifen

tag: dose level

tag: exposure time

tag: assay plate well


title: Sham-Control Fetus 0

tag: age (day in gestation)

tag: Sex

value: M

tag: weight at necropsy (kg)


title: fhm_adult_ee2_MC12

tag: lifestage

value: adult

tag: tissue

tag: concentration


title: MK4


title: NK Pt02 Pop2 [CHIP_S122]

value: PBMC

tag: cell type

tag: participant id

tag: participant phenotype

value: HAART

tag: antibody


title: Adrenal Demedullated-Control Fetus 1

tag: internal animal id


title: TP0001651G01_7_30.000000uM_DMEM_12h_TC00283154_K11

description:
TP0001651G01_7_30.000000uM_DMEM_12h
TC00283154_K11

tag: cell line

tag: media

tag: treatment

value: 12h exposure of 30 uM of Vinclozolin

tag: chemical name

value: Vinclozolin

tag: chemical sample id

tag: assay plate


title: MK3

tag: genotype


title: NK Pt02 Pop2 [CHIP_S121]

value: CD56bri CD16- NK cells


title: fhm_adult_ee2_LC12

value: liver

tag: chemical

value: LOW


title: TP0001651F05_4_1.000000uM_DMEM_12h_TC00283154_K12

description:
TP0001651F05_4_1.000000uM_DMEM_12h
TC00283154_K12

value: 12h exposure of 1 uM of Fenofibrate

value: Fenofibrate

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time

tag: assay plate well


title: fhm_adult_ee2_LE12

tag: lifestage

tag: tissue

tag: concentration


title: NK Pt09 Pop4 [CHIP_S120]

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HIVN

tag: antibody

value: IgG


title: TP0001651F01_6_10.000000uM_DMEM_12h_TC00283154_K10

description:
TP0001651F01_6_10.000000uM_DMEM_12h
TC00283154_K10

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 10 uM of Tetrac

value: Tetrac

value: 10 uM


title: MK2

value: Cerebellum

value: Wild-type

value: Sham-operated


title: fhm_adult_ee2_LA12

value: adult


title: fhm_adult_ee2_SE12

value: dmso

value: CTRL


title: TP0001651D01_8_100.000000uM_DMEM_12h_TC00283154_K09

description:
TP0001651D01_8_100.000000uM_DMEM_12h
TC00283154_K09

value: 12h exposure of 100 uM of Lactofen

tag: chemical name

value: Lactofen

tag: chemical sample id

tag: assay plate


title: NK Pt02 Pop2 [CHIP_S123]

value: PBMC

value: CD56bri CD16- NK cells

value: HAART


title: MK1

tag: genotype


title: fhm_adult_ee2_SC12

value: liver

tag: chemical


title: TP0001651C01_2_0.100000uM_DMEM_12h_TC00283154_K08

description:
TP0001651C01_2_0.100000uM_DMEM_12h
TC00283154_K08

value: 12h exposure of 0.1 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

tag: chemical concentration

tag: dose level

tag: exposure time


title: NK Pt09 Pop4 [CHIP_S117]

tag: tissue

value: CD56dim CD16+ NK cells

value: HIVN


title: NK Pt09 Pop4 [CHIP_S118]


title: NK Pt09 Pop2 [CHIP_S116]

value: IgG


title: fhm_adult_ee2_HD12

tag: lifestage

tag: concentration

value: HIGH


title: TP0001651A04_1_0.030000uM_DMEM_12h_TC00283154_K07

description:
TP0001651A04_1_0.030000uM_DMEM_12h
TC00283154_K07

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Rotenone

value: Rotenone

tag: assay plate well


title: MF1

value: Cerebellum

value: Wild-type

value: Olfactory bulbectomy


title: TP0001651F02_3_0.300000uM_DMEM_12h_TC00283154_K06

description:
TP0001651F02_3_0.300000uM_DMEM_12h
TC00283154_K06

value: 12h exposure of 0.3 uM of Ziram

value: Ziram


title: MF2


title: KK4

source_name: Cortex

value: Cortex

value: Sham-operated


title: Untrtd_DMEM_12h_TC00283154_K05

description:
Untrtd_DMEM_12h
TC00283154_K05

value: untreated


title: SIRO_DMEM_12h_TC00283154_K04

description:
SIRO_DMEM_12h
TC00283154_K04

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: NK Pt09 Pop4 [CHIP_S119]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype


title: fhm_adult_ee2_MB12

value: adult

value: liver

value: MED


title: NK Pt09 Pop2 [CHIP_S114]

value: CD56bri CD16- NK cells

value: HIVN

tag: antibody


title: KK3

tag: treatment


title: KK5


title: NK Pt09 Pop2 [CHIP_S115]


title: NK Pt09 Pop2 [CHIP_S113]


title: TP0001651G04_1_0.030000uM_DMEM_12h_TC00283154_K03

description:
TP0001651G04_1_0.030000uM_DMEM_12h
TC00283154_K03

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Cladribine

tag: chemical name

value: Cladribine


title: fhm_adult_ee2_MD12


title: fhm_adult_tb_SD124

value: dmso

value: CTRL


title: fhm_adult_tb_HB123

value: tb

value: HIGH


title: NK Pt05 Pop4 [CHIP_S112]

value: HAART

value: IgG


title: TP0001651G02_3_0.300000uM_DMEM_12h_TC00283154_K02

description:
TP0001651G02_3_0.300000uM_DMEM_12h
TC00283154_K02

value: 12h exposure of 0.3 uM of Lovastatin

value: Lovastatin

tag: chemical sample id

tag: assay plate


title: TP0001651G03_4_1.000000uM_DMEM_12h_TC00283154_J24

description:
TP0001651G03_4_1.000000uM_DMEM_12h
TC00283154_J24

value: 12h exposure of 1 uM of Nilutamide

value: Nilutamide

tag: chemical concentration

value: 1 uM


title: fhm_adult_tb_HE123

value: adult

value: liver

tag: chemical


title: KK1

value: Cortex

tag: genotype

value: Wild-type

value: Sham-operated


title: NK Pt05 Pop4 [CHIP_S111]

tag: tissue

value: PBMC

value: CD56dim CD16+ NK cells


title: NK Pt11 Pop4 [CHIP_S143]


title: TP0001651B06_3_0.300000uM_DMEM_12h_TC00283154_J23

description:
TP0001651B06_3_0.300000uM_DMEM_12h
TC00283154_J23

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Troglitazone

value: Troglitazone

tag: dose level

tag: exposure time


title: KF4

value: Olfactory bulbectomy


title: NK Pt05 Pop4 [CHIP_S110]

value: HAART


title: KF2


title: NK Pt05 Pop4 [CHIP_S109]


title: fhm_adult_tb_ME123

tag: lifestage

value: tb

tag: concentration

value: MED


title: TP0001651A05_4_1.000000uM_DMEM_12h_TC00283154_J22

description:
TP0001651A05_4_1.000000uM_DMEM_12h
TC00283154_J22

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

value: Clomiphene citrate (1:1)

tag: assay plate well


title: KF1


title: NK Pt05 Pop2 [CHIP_S108]

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id

tag: participant phenotype

value: IgG


title: TP0001651B06_4_1.000000uM_DMEM_12h_TC00283154_J21

description:
TP0001651B06_4_1.000000uM_DMEM_12h
TC00283154_J21

tag: cell line

tag: treatment

value: 12h exposure of 1 uM of Troglitazone

value: 1 uM


title: KK2

value: Cortex

value: Wild-type


title: fhm_adult_tb_SB123

value: adult

value: liver

value: dmso

value: CTRL


title: fhm_adult_tb_SE1235


title: GK5

source_name: Hippocampus

value: Hippocampus

value: Sham-operated


title: NK Pt05 Pop2 [CHIP_S107]

value: PBMC

value: HAART

tag: antibody


title: NK Pt05 Pop2 [CHIP_S106]


title: fhm_adult_tb_HC134

value: tb

value: HIGH


title: NK Pt05 Pop2 [CHIP_S105]


title: GK3


title: fhm_adult_tb_MC1234

value: MED


title: GK2


title: TP0001651H04_7_30.000000uM_DMEM_12h_TC00283154_J18

description:
TP0001651H04_7_30.000000uM_DMEM_12h
TC00283154_J18

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Bisphenol A

tag: chemical name

value: Bisphenol A

tag: chemical sample id

value: 30 uM


title: fhm_adult_tb_HA123

tag: chemical


title: NK Pt03 Pop4 [CHIP_S104]

value: CD56dim CD16+ NK cells

value: HIVN

value: IgG


title: fhm_adult_tb_SC13

value: adult

value: liver


title: TP0001651A03_1_0.030000uM_DMEM_12h_TC00283154_J16

description:
TP0001651A03_1_0.030000uM_DMEM_12h
TC00283154_J16

value: 12h exposure of 0.03 uM of Butafenacil

value: Butafenacil

tag: chemical concentration

tag: assay plate


title: GK1

tag: tissue

value: Hippocampus

tag: genotype

value: Wild-type

value: Sham-operated


title: GF4

value: Olfactory bulbectomy


title: TP0001651H04_1_0.030000uM_DMEM_12h_TC00283154_J17

description:
TP0001651H04_1_0.030000uM_DMEM_12h
TC00283154_J17

value: 12h exposure of 0.03 uM of Bisphenol A

tag: dose level

tag: exposure time


title: NK Pt03 Pop4 [CHIP_S103]

value: PBMC


title: fhm_adult_tb_MA123

tag: lifestage

value: tb

tag: concentration

value: MED


title: TP0001651B02_3_0.300000uM_DMEM_12h_TC00283154_J15

description:
TP0001651B02_3_0.300000uM_DMEM_12h
TC00283154_J15

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of 3,5,3'-Triiodothyronine

tag: assay plate well


title: fhm_adult_ee2_HB12

value: HIGH


title: NK Pt03 Pop4 [CHIP_S102]

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HIVN


title: GF3

tag: treatment


title: fhm_adult_tb_HD123

value: adult


title: TP0001651F01_1_0.030000uM_DMEM_12h_TC00283154_J19

description:
TP0001651F01_1_0.030000uM_DMEM_12h
TC00283154_J19

tag: cell line

tag: media

value: 12h exposure of 0.03 uM of Tetrac

value: Tetrac


title: SIRO_DMEM_12h_TC00283154_J14

description:
SIRO_DMEM_12h
TC00283154_J14

value: 6h exposure of 0.1 uM of Sirolimus

tag: chemical name

value: Sirolimus

tag: chemical sample id


title: NK Pt03 Pop4 [CHIP_S101]

tag: antibody


title: GF2

value: Hippocampus

value: Wild-type


title: TP0001651A03_4_1.000000uM_DMEM_12h_TC00283154_J20

description:
TP0001651A03_4_1.000000uM_DMEM_12h
TC00283154_J20

value: 12h exposure of 1 uM of Butafenacil

value: Butafenacil

tag: chemical concentration

value: 1 uM

tag: assay plate


title: fhm_adult_tb_SA123

tag: tissue

value: liver

tag: chemical

value: dmso

value: CTRL


title: GK4

tag: genotype

value: Sham-operated


title: NK Pt03 Pop2 [CHIP_S100]

value: PBMC

value: CD56bri CD16- NK cells

value: IgG


title: GF1

value: Olfactory bulbectomy


title: TP0001651F03_8_100.000000uM_DMEM_12h_TC00283154_J13

description:
TP0001651F03_8_100.000000uM_DMEM_12h
TC00283154_J13

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of 4-Cumylphenol

tag: dose level

tag: exposure time


title: NK Pt03 Pop2 [CHIP_S099]

value: HIVN


title: TP0001651H05_2_0.100000uM_DMEM_12h_TC00283154_J12

description:
TP0001651H05_2_0.100000uM_DMEM_12h
TC00283154_J12

value: 12h exposure of 0.1 uM of Trifloxystrobin

value: Trifloxystrobin

tag: assay plate well


title: NK Pt03 Pop2 [CHIP_S098]

tag: cell type


title: TP0001651B02_1_0.030000uM_DMEM_12h_TC00283154_J11

description:
TP0001651B02_1_0.030000uM_DMEM_12h
TC00283154_J11

value: 12h exposure of 0.03 uM of 3,5,3'-Triiodothyronine


title: Sample_8_IP-SHOCK2

city: seoul

first: Hakyun

last: Ryu

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk univ.

data_processing:
Quality control and analysis of sequenced data were performed by commercial service (SYSOFT, Daegu, South Korea) using FastQC (Wingett & Andrews, 2018) and HTseq (Anders et al., 2015).
Assembly: mm10
Supplementary files format and content: text files representing counts, RPKMs, and TPMs

source_name: Brain

extract_protocol:
RNA purified using the RNeasy Mini Kit (QIAGEN). RNA assessed using an Agilent Fragment Analyzer system.
cDNA was synthesized using the Ovation RNA Amplification System V2 (NuGEN) and then sequenced using an Illumina HiSeq 2000.

value: Brain

value: WT

tag: stress

value: shock

tag: fraction

value: IP


title: fhm_adult_flx_HB4

tag: lifestage

value: adult

value: liver

value: flx

tag: concentration

value: HIGH


title: Sample_7_Total-SHOCK2

value: Total


title: NK Pt03 Pop2 [CHIP_S097]

value: PBMC

value: CD56bri CD16- NK cells

tag: participant id

tag: participant phenotype


title: fhm_adult_flx_CE4

value: dmso

value: CTRL


title: NK Pt12 Pop4 [CHIP_S096]

value: CD56dim CD16+ NK cells

value: HIVN

value: IgG


title: TP0001651C04_8_100.000000uM_DMEM_12h_TC00283154_J10

description:
TP0001651C04_8_100.000000uM_DMEM_12h
TC00283154_J10

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 100 uM of Simvastatin

tag: chemical name

value: Simvastatin

tag: chemical sample id


title: fhm_adult_flx_CD4

tag: tissue

tag: chemical


title: NK Pt12 Pop4 [CHIP_S095]

tag: antibody


title: TP0001651A01_5_3.000000uM_DMEM_12h_TC00283154_J09

description:
TP0001651A01_5_3.000000uM_DMEM_12h
TC00283154_J09

value: 12h exposure of 3 uM of Pyraclostrobin

value: Pyraclostrobin

tag: chemical concentration

value: 3 uM

tag: dose level

tag: exposure time

tag: assay plate


title: Sample_4_IP-SHOCK1

value: Brain

tag: genotype

value: WT

tag: stress

value: shock

tag: fraction

value: IP


title: TP0001651C01_6_10.000000uM_DMEM_12h_TC00283154_J08

description:
TP0001651C01_6_10.000000uM_DMEM_12h
TC00283154_J08

value: 12h exposure of 10 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

value: 10 uM

tag: assay plate well


title: Sample_5_Total-CON2

value: control

value: Total


title: fhm_adult_flx_CC4

tag: lifestage

value: adult

value: liver

value: dmso

tag: concentration

value: CTRL


title: TP0001651C06_6_10.000000uM_DMEM_12h_TC00283154_J07

description:
TP0001651C06_6_10.000000uM_DMEM_12h
TC00283154_J07

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Cycloheximide

value: Cycloheximide


title: Sample_3_Total-SHOCK1


title: fhm_adult_flx_HE4

value: flx

value: HIGH


title: NK Pt12 Pop4 [CHIP_S093]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HIVN


title: NK Pt12 Pop4 [CHIP_S094]

tag: tissue


title: TP0001651E03_5_3.000000uM_DMEM_12h_TC00283154_J06

description:
TP0001651E03_5_3.000000uM_DMEM_12h
TC00283154_J06

tag: treatment

value: 12h exposure of 3 uM of Prochloraz

tag: chemical name

value: Prochloraz

tag: chemical sample id

value: 3 uM


title: fhm_adult_tb_MD123

tag: chemical

value: tb

value: MED


title: Sample_2_IP-CON1

value: Brain

value: WT

value: control

value: IP


title: fhm_adult_flx_MC4

value: adult

value: liver


title: fhm_adult_flx_CA4

value: dmso

value: CTRL


title: TP0001651G05_7_30.000000uM_DMEM_12h_TC00283154_J05

description:
TP0001651G05_7_30.000000uM_DMEM_12h
TC00283154_J05

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Cyproterone acetate

value: Cyproterone acetate

tag: chemical concentration

value: 30 uM

tag: dose level

tag: exposure time

tag: assay plate


title: NK Pt12 Pop2 [CHIP_S092]

value: PBMC

value: CD56bri CD16- NK cells

value: HIVN

tag: antibody

value: IgG


title: Sample_1_Total-CON1

tag: genotype

tag: stress

tag: fraction

value: Total


title: NK Pt12 Pop2 [CHIP_S091]


title: TP0001651B04_1_0.030000uM_DMEM_12h_TC00283154_J04

description:
TP0001651B04_1_0.030000uM_DMEM_12h
TC00283154_J04

tag: cell line

tag: media

value: 12h exposure of 0.03 uM of Propiconazole

value: Propiconazole

tag: assay plate well


title: fhm_adult_flx_CB4

tag: lifestage

tag: concentration


title: Ctrl - treated hippocampal neurons 9Ctrl

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Ctrl - treated hippocampal neurons
RNA sequencing
9Ctrl_mm_rna_sr_kauranil_A_2_S5_L002_R1_001

data_processing:
An in-house developed pipeline was used to analyze the small RNAome. Quality check and demultiplexing were performed using the CASAVA 1.8.2 software (Illumina)
smallRNA seq: To quantify small RNAome, reads were first mapped to mature miRNA sequences obtained by miRBase (http://www.mirbase.org/) followed by further mapping to other small non coding RNA sequences (http://www.ensembl.org/info/data/ftp/index.html). Reads were then mapped to the mm10 reference genome.
RNA seq: Demultiplexing was performed using Illumina CASAVA version 1.8. Cutadapt-1.8.1 was used to remove sequencing adapters.
smallRNA seq DESeq2: We used raw counts for DE analysis. We adjusted the raw read counts for library size and log2 transformed them prior to doing DE analysis. Each sample was assigned a quality z-score, and those with a low quality (Z > 2.5 or Z -2.5) were classified as outliers and excluded from further analysis. Further DE analysis was performed on samples with read counts greater than 5 in at least 50% of the analyzed samples. To adjust for hidden batch effects and to remove unwanted variation, the RUVSeq package was used.
RNA seq: We used raw counts for the DE analysis. Prior to performing DE analysis, we normalized the raw read counts for library size and converted them using the log2 transformation. Each sample was assigned a quality z-score, and samples with a low quality (Z > 2.5 or Z -2.5) were identified as outliers and excluded from further analysis. Additionally, read counts 10 in at least 50% of examined samples were used in DE analysis. The RUVSeq package was used to account for and eliminate undesired variance due to hidden batch effects. The data were corrected for batch effect. DESeq22 was used to conduct differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts txt files

source_name: Primary hippocampal neurons

growth_protocol: primary neurons were derived from mouse embryos at embryonic day 16 according to Animal Welfare regulations. Neurons were seeded onto poly-D-lysine-coated cell culture dishes in plating medium (Basal medium Eagle’s containing Eagle’s salts, 0.45% glucose, 10% horse serum (Capricorn; HOS-1A), 1mM sodium pyruvate, 100U/ml Penicillin and 0,1mg/ml Streptomycin). Plating medium was replaced with maintenance medium (MEM supplemented with 0.6% glucose, 0,2% sodium bicarbonate, 1mM sodium pyruvate, 2% B27 supplement (Gibco), 2mM Glutamax, 100U/ml Penicillin and 0,1mg/ml Streptomycin) 2-3 hours later and kept in a humidified incubator, 37C, 5% CO2.

extract_protocol:
After washing with cold PBS, cells and EVs were lysed directly in homogenization buffer provided by RNeasy or miRNeasy RNA isolation kits (Qiagen)
smallRNA sequencing: control- or BDNF-treated cortical neurons and corresponding sEVs were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) as per manufacturer’s instructions and sequenced in Illumina HiSeq2000. 150 ng of RNA was used as input material. RNA sequencing: Total RNA was used to prepare the sequencing library according to the manufacturer's protocol using the TrueSeq RNA library prep kit v2 (Illumina, USA). As a starting material, 500ng RNA was used. Multiplexed libraries were directly loaded onto an Ilumina Hiseq2000 using a 50 bp single read setup.
smallRNA sequencing and RNA sequencing

treatment_protocol: Cells were treated with BDNF (50ng/ml, 20min) or control vehicle at 6-7 days in vitro, after which cells were washed three times with maintenance medium.

tag: strain

value: NMRI

tag: treatment

value: Cell lysate

tag: batch

value: b


title: NK Pt12 Pop2 [CHIP_S090]

tag: tissue

tag: cell type

tag: participant id

tag: participant phenotype


title: fhm_adult_flx_ME4

value: adult

value: liver

tag: chemical

value: flx

value: MED


title: SIRO_DMEM_12h_TC00283154_J03

description:
SIRO_DMEM_12h
TC00283154_J03

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Sirolimus

tag: chemical name

value: Sirolimus

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate


title: Ctrl - treated hippocampal neurons 25Ctrl

description:
Ctrl - treated hippocampal neurons
RNA sequencing
25Ctrl_mm_rna_sr_kauranil_A_6_S22_L006_R1_001

value: d


title: fhm_adult_flx_MD4


title: NK Pt12 Pop2 [CHIP_S089]

value: PBMC

value: CD56bri CD16- NK cells

tag: antibody


title: TP0001651D02_5_3.000000uM_DMEM_12h_TC00283154_J02

description:
TP0001651D02_5_3.000000uM_DMEM_12h
TC00283154_J02

tag: cell line

tag: media

value: 12h exposure of 3 uM of PFOA

value: PFOA

value: 3 uM

tag: assay plate well


title: NK Pt15 Pop4 [CHIP_S088]

value: CD56dim CD16+ NK cells

value: EC

value: IgG


title: fhm_adult_tb_MB123

tag: lifestage

value: tb

tag: concentration


title: Ctrl - treated hippocampal neurons 21Ctrl

description:
Ctrl - treated hippocampal neurons
RNA sequencing
21Ctrl_mm_rna_sr_kauranil_A_5_S18_L005_R1_001

tag: strain

value: NMRI

tag: treatment

value: Cell lysate

tag: batch

value: c


title: fhm_adult_flx_MB4

value: adult

tag: tissue

value: liver

value: flx

value: MED


title: Ctrl - treated hippocampal neurons 17Ctrl

description:
Ctrl - treated hippocampal neurons
RNA sequencing
17Ctrl_mm_rna_sr_kauranil_A_4_S14_L004_R1_001


title: NK Pt15 Pop4 [CHIP_S087]

tag: cell type

tag: participant id

tag: participant phenotype


title: Lysis Buffer_TC00283154_J01

description:
Lysis Buffer
TC00283154_J01

source_name: Lysis Buffer

value: untreated

tag: chemical name

tag: chemical sample id

tag: chemical concentration


title: Ctrl - treated hippocampal neurons 13Ctrl

description:
Ctrl - treated hippocampal neurons
RNA sequencing
13Ctrl_mm_rna_sr_kauranil_A_3_S10_L003_R1_001

value: b


title: fhm_adult_flx_HA4

tag: chemical

value: HIGH


title: TP0001651A04_4_1.000000uM_DMEM_12h_TC00283154_I24

description:
TP0001651A04_4_1.000000uM_DMEM_12h
TC00283154_I24

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Rotenone

value: Rotenone

value: 1 uM

tag: dose level

tag: exposure time

tag: assay plate


title: fhm_adult_flx_HC4


title: TP0001651F01_7_30.000000uM_DMEM_12h_TC00283154_I23

description:
TP0001651F01_7_30.000000uM_DMEM_12h
TC00283154_I23

tag: cell line

tag: media

value: 12h exposure of 30 uM of Tetrac

value: Tetrac

value: 30 uM

tag: assay plate well


title: Ctrl - treated hippocampal neurons 1Ctrl

description:
Ctrl - treated hippocampal neurons
RNA sequencing
1Ctrl_mm_rna_sr_kauranil_A_1_S1_L001_R1_001

tag: strain

value: NMRI

value: a


title: NK Pt15 Pop4 [CHIP_S085]

value: PBMC

value: CD56dim CD16+ NK cells

value: EC

tag: antibody


title: fhm_adult_flx_MA4

tag: lifestage

value: adult

value: liver

value: flx

tag: concentration


title: BDNF - treated hippocampal neurons 26BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
26BDNF_mm_rna_sr_kauranil_B_6_S23_L006_R1_001

tag: treatment

value: Cell lysate

tag: batch

value: d


title: NK Pt15 Pop2 [CHIP_S084]

tag: tissue

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id

tag: participant phenotype

value: IgG


title: TP0001651H01_3_0.300000uM_DMEM_12h_TC00283154_I22

description:
TP0001651H01_3_0.300000uM_DMEM_12h
TC00283154_I22

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Flutamide

tag: chemical name

value: Flutamide

tag: chemical sample id

tag: chemical concentration


title: TP0001651B01_6_10.000000uM_DMEM_12h_TC00283154_I21

description:
TP0001651B01_6_10.000000uM_DMEM_12h
TC00283154_I21

value: 12h exposure of 10 uM of Cyanazine

value: Cyanazine

value: 10 uM

tag: dose level

tag: exposure time

tag: assay plate


title: BDNF - treated hippocampal neurons 22BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
22BDNF_mm_rna_sr_kauranil_B_5_S19_L005_R1_001

value: NMRI

value: c


title: fhm_adult_bap_SE123

tag: chemical

value: dmso

value: CTRL


title: TP0001651D02_2_0.100000uM_DMEM_12h_TC00283154_I20

description:
TP0001651D02_2_0.100000uM_DMEM_12h
TC00283154_I20

tag: cell line

tag: media

value: 12h exposure of 0.1 uM of PFOA

value: PFOA

tag: assay plate well


title: fhm_adult_flx_HD4

tag: lifestage

value: adult

value: liver

value: flx

tag: concentration

value: HIGH


title: BDNF - treated hippocampal neurons 2BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
2BDNF_mm_rna_sr_kauranil_B_1_S3_L001_R1_001

tag: strain

tag: treatment

value: Cell lysate

tag: batch

value: a


title: NK Pt15 Pop2 [CHIP_S082]

tag: tissue

value: PBMC

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id

value: EC

tag: antibody


title: TP0001651C03_2_0.100000uM_DMEM_12h_TC00283154_I19

description:
TP0001651C03_2_0.100000uM_DMEM_12h
TC00283154_I19

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Simazine

tag: chemical name

value: Simazine

tag: chemical sample id

tag: chemical concentration


title: NK Pt15 Pop4 [CHIP_S086]

value: CD56dim CD16+ NK cells

tag: participant phenotype


title: BDNF - treated hippocampal neurons 18BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
18BDNF_mm_rna_sr_kauranil_B_4_S15_L004_R1_001

value: NMRI

value: c


title: NK Pt15 Pop2 [CHIP_S081]


title: fhm_adult_bap_SC123

tag: chemical

value: dmso

value: CTRL


title: TP0001651E04_5_3.000000uM_DMEM_12h_TC00283154_I18

description:
TP0001651E04_5_3.000000uM_DMEM_12h
TC00283154_I18

tag: cell line

value: 12h exposure of 3 uM of Farglitazar

value: Farglitazar

value: 3 uM

tag: dose level

tag: exposure time

tag: assay plate


title: NK Pt12 Pop4 [CHIP_S080]

value: HIVN

value: IgG


title: TP0001651D02_8_100.000000uM_DMEM_12h_TC00283154_I17

description:
TP0001651D02_8_100.000000uM_DMEM_12h
TC00283154_I17

tag: media

value: 12h exposure of 100 uM of PFOA

value: PFOA

tag: assay plate well


title: BDNF - treated hippocampal neurons 14BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
14BDNF_mm_rna_sr_kauranil_B_3_S11_L003_R1_001

tag: strain

tag: treatment

value: Cell lysate

value: b


title: TP0001651D03_3_0.300000uM_DMEM_12h_TC00283154_I16

description:
TP0001651D03_3_0.300000uM_DMEM_12h
TC00283154_I16

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Cypermethrin

value: Cypermethrin


title: fhm_adult_bap_SB123

tag: lifestage

value: adult

tag: tissue

value: liver

tag: concentration


title: NK Pt12 Pop4 [CHIP_S079]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: antibody


title: fhm_adult_bap_SA23

value: dmso

value: CTRL


title: BDNF - treated hippocampal neurons 10BDNF

description:
BDNF - treated hippocampal neurons
RNA sequencing
10BDNF_mm_rna_sr_kauranil_B_2_S7_L002_R1_001

value: NMRI

tag: batch


title: fhm_adult_bap_ME123

value: bap

value: MED


title: BDNF-EV - treated hippocampal neurons 16BDNFEV

description:
BDNF-EV - treated hippocampal neurons
RNA sequencing
16BDNFEV_mm_rna_sr_kauranil_D_3_S9_L003_R1_001


title: BDNF-EV - treated hippocampal neurons 12BDNFEV

description:
BDNF-EV - treated hippocampal neurons
RNA sequencing
12BDNFEV_mm_rna_sr_kauranil_D_2_S8_L002_R1_001


title: NK Pt12 Pop4 [CHIP_S078]

tag: participant phenotype

value: HIVN


title: TP0001651C04_2_0.100000uM_DMEM_12h_TC00283154_I15

description:
TP0001651C04_2_0.100000uM_DMEM_12h
TC00283154_I15

value: 12h exposure of 0.1 uM of Simvastatin

tag: chemical name

value: Simvastatin

tag: chemical sample id

tag: chemical concentration


title: NK Pt12 Pop4 [CHIP_S077]


title: Sample_6_IP-CON2

value: Brain

tag: genotype

value: WT

tag: stress

value: control

tag: fraction

value: IP


title: TP0001651G04_7_30.000000uM_DMEM_12h_TC00283154_I14

description:
TP0001651G04_7_30.000000uM_DMEM_12h
TC00283154_I14

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 30 uM of Cladribine

value: Cladribine

value: 30 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: fhm_adult_bap_SD123

tag: lifestage

value: adult

tag: tissue

value: liver

tag: chemical

tag: concentration


title: NK Pt15 Pop2 [CHIP_S083]

value: PBMC

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id

tag: participant phenotype

value: EC

tag: antibody


title: BDNF-EV - treated hippocampal neurons 4BDNFEV

description:
BDNF-EV - treated hippocampal neurons
RNA sequencing
4BDNFEV_mm_rna_sr_kauranil_D_1_S4_L001_R1_001

tag: strain

value: NMRI

tag: treatment

value: Cell lysate

tag: batch

value: a


title: fhm_adult_bap_MC123

value: bap

value: MED


title: NK Pt12 Pop2 [CHIP_S076]

value: HIVN

value: IgG


title: TP0001651A02_5_3.000000uM_DMEM_12h_TC00283154_I13

description:
TP0001651A02_5_3.000000uM_DMEM_12h
TC00283154_I13

tag: cell line

value: 12h exposure of 3 uM of Imazalil

tag: chemical name

value: Imazalil

tag: chemical sample id

tag: chemical concentration

value: 3 uM


title: Ctrl-EV - treated hippocampal neurons 15CtrlEV

description:
Ctrl-EV - treated hippocampal neurons
RNA sequencing
15CtrlEV_mm_rna_sr_kauranil_C_3_S12_L003_R1_001

value: b


title: fhm_adult_bap_MB12


title: NK Pt12 Pop2 [CHIP_S074]


title: Ctrl-EV - treated hippocampal neurons 11CtrlEV

description:
Ctrl-EV - treated hippocampal neurons
RNA sequencing
11CtrlEV_mm_rna_sr_kauranil_C_2_S6_L002_R1_001


title: TP0001651F03_7_30.000000uM_DMEM_12h_TC00283154_I12

description:
TP0001651F03_7_30.000000uM_DMEM_12h
TC00283154_I12

tag: media

value: DMEM + 10% HI-FBS

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

value: 30 uM

tag: dose level

tag: exposure time

tag: assay plate


title: fhm_adult_bap_MA123

tag: lifestage

value: adult

tag: tissue

value: liver

tag: chemical


title: small EV from Ctrl-treated cortical neurons 9 9CExo

description:
small EV from Ctrl-treated cortical neurons 9
smallRNA sequencing
9CExo_mm_smallrnaneb_sr_kauranil_A_11_S69_L005_R1_001

source_name: Primary cortical neurons

value: small EV

value: z


title: fhm_adult_bap_HE123

tag: concentration

value: HIGH


title: TP0001651C06_8_100.000000uM_DMEM_12h_TC00283154_I11

description:
TP0001651C06_8_100.000000uM_DMEM_12h
TC00283154_I11

value: 12h exposure of 100 uM of Cycloheximide

value: Cycloheximide

tag: assay plate well


title: Ctrl-EV - treated hippocampal neurons 3CtrlEV

description:
Ctrl-EV - treated hippocampal neurons
RNA sequencing
3CtrlEV_mm_rna_sr_kauranil_C_1_S2_L001_R1_001

value: NMRI

value: Cell lysate

value: a


title: fhm_adult_bap_HD123

value: bap


title: NK Pt13 Pop4 [CHIP_S072]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: EC

tag: antibody

value: IgG


title: TP0001651E05_2_0.100000uM_DMEM_12h_TC00283154_I09

description:
TP0001651E05_2_0.100000uM_DMEM_12h
TC00283154_I09

tag: cell line

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.1 uM of Atrazine

value: Atrazine


title: fhm_adult_bap_MD123

value: adult

value: liver

value: MED


title: small EV from BDNF-treated cortical neurons 9 9BExo

description:
small EV from BDNF-treated cortical neurons 9
smallRNA sequencing
9BExo_mm_smallrnaneb_sr_kauranil_D_12_S72_L005_R1_001

tag: strain

value: small EV

tag: batch

value: z


title: TP0001651C03_3_0.300000uM_DMEM_12h_TC00283154_I08

description:
TP0001651C03_3_0.300000uM_DMEM_12h
TC00283154_I08

tag: media

value: 12h exposure of 0.3 uM of Simazine

tag: chemical name

value: Simazine

tag: chemical sample id

tag: chemical concentration


title: NK Pt13 Pop4 [CHIP_S070]


title: small EV from Ctrl-treated cortical neurons 8 8CExo

description:
small EV from Ctrl-treated cortical neurons 8
smallRNA sequencing
8CExo_mm_smallrnaneb_sr_kauranil_A_11_S68_L005_R1_001

value: NMRI


title: fhm_adult_bap_HB123

tag: lifestage

value: HIGH


title: TP0001651B03_1_0.030000uM_DMEM_12h_TC00283154_I07

description:
TP0001651B03_1_0.030000uM_DMEM_12h
TC00283154_I07

value: 12h exposure of 0.03 uM of Reserpine

value: Reserpine

tag: dose level

tag: exposure time

tag: assay plate


title: small EV from BDNF-treated cortical neurons 8 8BExo

description:
small EV from BDNF-treated cortical neurons 8
smallRNA sequencing
8BExo_mm_smallrnaneb_sr_kauranil_D_12_S71_L005_R1_001


title: NK Pt12 Pop2 [CHIP_S075]

tag: tissue

value: PBMC

value: CD56bri CD16- NK cells

value: HIVN


title: NK Pt13 Pop2 [CHIP_S068]

tag: cell type

value: EC

value: IgG


title: small EV from Ctrl-treated cortical neurons 7 7CExo

description:
small EV from Ctrl-treated cortical neurons 7
smallRNA sequencing
7CExo_mm_smallrnaneb_sr_kauranil_A_11_S67_L005_R1_001


title: TP0001651F02_2_0.100000uM_DMEM_12h_TC00283154_I10

description:
TP0001651F02_2_0.100000uM_DMEM_12h
TC00283154_I10

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Ziram

value: Ziram

tag: assay plate well


title: NK Pt12 Pop2 [CHIP_S073]

tag: participant id

tag: participant phenotype


title: small EV from BDNF-treated cortical neurons 7 7BExo

description:
small EV from BDNF-treated cortical neurons 7
smallRNA sequencing
7BExo_mm_smallrnaneb_sr_kauranil_D_12_S70_L005_R1_001


title: TP0001651B04_4_1.000000uM_DMEM_12h_TC00283154_I05

description:
TP0001651B04_4_1.000000uM_DMEM_12h
TC00283154_I05

tag: cell line

value: 12h exposure of 1 uM of Propiconazole

value: Propiconazole

value: 1 uM


title: TP0001651G02_1_0.030000uM_DMEM_12h_TC00283154_I04

description:
TP0001651G02_1_0.030000uM_DMEM_12h
TC00283154_I04

tag: treatment

value: 12h exposure of 0.03 uM of Lovastatin

value: Lovastatin


title: NK Pt13 Pop2 [CHIP_S067]

tag: antibody


title: heart, CAST, Ctrl, rep 2

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

data_processing:
HiSat alignment
FeatureCount
DESeq2
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel table: read counts, expression values, DESeq2 output

source_name: heart

extract_protocol:
total RNA isolation, polyA RNA isolation
stranded RNA-seq library

value: heart

tag: genotype

value: TAZ WT/Y

tag: strain

tag: age

value: 2 months


title: fhm_adult_bap_HC123

value: adult

value: liver

tag: chemical

value: bap

tag: concentration

value: HIGH


title: heart, CAST, Ctrl, rep 1


title: small EV from Ctrl-treated cortical neurons 3 3CExo

description:
small EV from Ctrl-treated cortical neurons 3
smallRNA sequencing
3CExo_mm_smallrnaneb_sr_kauranil_A_3_S45_L004_R1_001

value: NMRI

value: small EV

tag: batch

value: x


title: NK Pt13 Pop2 [CHIP_S066]

value: PBMC

value: CD56bri CD16- NK cells

value: EC


title: small EV from BDNF-treated cortical neurons 3 3BExo

description:
small EV from BDNF-treated cortical neurons 3
smallRNA sequencing
3BExo_mm_smallrnaneb_sr_kauranil_D_4_S48_L004_R1_001


title: heart, CAST, Ctrl, rep 3


title: NK Pt13 Pop4 [CHIP_S071]

value: CD56dim CD16+ NK cells


title: heart, CAST, KO, rep 3

value: TAZ KO/Y


title: NK Pt13 Pop2 [CHIP_S065]


title: small EV from Ctrl-treated cortical neurons 2 2CExo

description:
small EV from Ctrl-treated cortical neurons 2
smallRNA sequencing
2CExo_mm_smallrnaneb_sr_kauranil_A_3_S44_L004_R1_001


title: TP0001651A05_3_0.300000uM_DMEM_12h_TC00283154_I02

description:
TP0001651A05_3_0.300000uM_DMEM_12h
TC00283154_I02

source_name: MCF7 Cells

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Clomiphene citrate (1:1)

tag: chemical name

value: Clomiphene citrate (1:1)

tag: chemical sample id

tag: chemical concentration

tag: dose level


title: NK Pt06 Pop4 [CHIP_S064]

tag: tissue

tag: cell type

value: HIVN

value: IgG


title: heart, CAST, KO, rep 2

value: heart

value: 2 months


title: NK Pt13 Pop4 [CHIP_S069]

tag: participant id

tag: participant phenotype


title: fhm_adult_bap_HA123

tag: lifestage

value: adult

value: liver

value: bap


title: TP0001651B02_5_3.000000uM_DMEM_12h_TC00283154_I06

description:
TP0001651B02_5_3.000000uM_DMEM_12h
TC00283154_I06

tag: cell line

tag: treatment

value: 12h exposure of 3 uM of 3,5,3'-Triiodothyronine

value: 3 uM

tag: exposure time

tag: assay plate

tag: assay plate well


title: small EV from BDNF-treated cortical neurons 2 2BExo

description:
small EV from BDNF-treated cortical neurons 2
smallRNA sequencing
2BExo_mm_smallrnaneb_sr_kauranil_D_4_S47_L004_R1_001

tag: strain

value: NMRI

value: small EV

value: x


title: NK Pt06 Pop4 [CHIP_S063]

value: PBMC

value: CD56dim CD16+ NK cells

tag: antibody


title: small EV from Ctrl-treated cortical neurons 1 1CExo

description:
small EV from Ctrl-treated cortical neurons 1
smallRNA sequencing
1CExo_mm_smallrnaneb_sr_kauranil_A_3_S43_L004_R1_001

tag: batch


title: heart, CAST, KO, rep 1

tag: genotype

value: TAZ KO/Y

tag: age


title: NK Pt06 Pop4 [CHIP_S062]


title: heart, BL6J, Ctrl, rep 4

value: TAZ WT/Y