title: TP0001651B03_7_30.000000uM_DMEM_12h_TC00283154_C13

description:
TP0001651B03_7_30.000000uM_DMEM_12h
TC00283154_C13

value: 12h exposure of 30 uM of Reserpine

tag: chemical sample id

value: 30 uM


title: H1_JQE_HBCD

status: Public on Dec 05 2023

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

library_source: transcriptomic

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.

molecule: total RNA

organism: Coturnix japonica

source_name: liver

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

tag: lifestage

value: els

tag: tissue

value: liver

tag: chemical

value: hbcd

tag: concentration

value: HIGH


title: Gla KO mouse naive B cells BCR-seq rep2

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

country: USA

institute: Boston Children's Hospital / Harvard Medical School

library_source: genomic

data_processing:
Rep-SHM-Seq was performed as described previously using our established bioinformatics pipeline (18).
In addition, to minimize the potential cross-contamination due to FACS sorting, we further filtered reads by assigning mutated sequences to GC B cell samples and non-mutated sequences to naive B cell samples.
V segment usage analysis: For each sample, the ratio of each functional V segment was calculated as % usage among total productive and non-productive V(D)J junctions.
Assembly: mm9
Supplementary files format and content: xls (tab-delimited)
Supplementary files format and content: *.db.xls: VDJ annotation for each read (R1 & R2 joined read)
Supplementary files format and content: *.stat.*.xls: V segment usage for each sample
Library strategy: BCR-Seq

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

growth_protocol: WT (C57BL/6), and Gla-KO (B6;129-Glatm1Kul/J) mice were acquired from The Jackson Laboratory. A4galt-deficient mice were generated by Koichi Furukawa (50).

extract_protocol:
Splenic naive and germinal-center (GC) B cells were enriched using a B cell isolation kit followed by FACS-sorting. Mice were immunized with NP-OVA and leukocytes were harvested from spleen by passage through a 40-μm mesh and incubated for 10 min with 1 μg/mL of anti-CD16/32 Fc-block in FACS buffer (PBS supplemented with 1 mM EDTA, 2% heat-inactivated FBS, and 0.02% sodium azide). Cells were further labeled using fluorochrome-coupled antibodies directed against the respective antigens: CD45R, GL-7, CD95, CD38 and CD138.  Cells were surface-stained at 4°C for 30 minutes, and subsequently, GC B cells (CD45R+, GL7+, CD95+) and naïve B cells (IgD+, CD45R+, GL7-, CD38-) were sorted either using a FACS Aria II (Becton Dickinson) or SH-800 cell sorter (Sony).
Libraries for sequencing were prepared as described (17). Briefly, genomic DNA was sonicated and subjected to linear amplification-mediated PCR using biotinylated bait primers. Linear amplification-mediated PCR products were purified using Dynabeads MyOne streptavidin C1 magnetic beads (Thermo Fisher Scientific, MA, USA) and ligated to bridge adaptors. Adaptor-ligated products were amplified by nested PCR with indexed JH1/JH3 primers as well as primers annealed to the adaptor. PCR products were further tagged with Illumina sequencing adaptor sequences and size-selected via gel extraction. Libraries were sequenced by paired-end 300-bp sequencing on MiSeq, an Illumina sequencing platform (San Diego, CA, USA).
Rep-SHM-Seq was performed as described previously using our established bioinformatics pipeline (18). We used bait primers close to the coding ends of JHs to capture full-length V(D)J sequences for SHM analysis and used Illumina MiSeq 2 × 300-bp paired-end sequencing (19, 53). As described before, mixed JH primers were designed based on a highly degenerate region to minimize the amplification bias caused by different primers. 400 ng genomic DNA from FACS-sorted naive or GC B cells was used as starting material to keep the level of PCR amplification comparable among different samples. In addition, to minimize the potential cross-contamination due to FACS sorting, we further filtered reads by assigning mutated sequences to GC B cell samples and non-mutated sequences to naive B cell samples.

value: spleen

tag: cell type

value: naive B cells

tag: genotype

value: Gla KO


title: HePG2 cells,mo3

city: Weifang

first: mengyun

last: dong

state: Shandong Province

address: No. 7166, West Baotong Street

department: Public health

country: China

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain the count number and expression level of the gene in each sample.
Supplementary files format and content: tab-delimited text files contain the FPKM expression of all genes in each sample.

organism: Homo sapiens

source_name: model

growth_protocol: HePG2 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% non-essential amino acids in an incubator at 37 ° C, constant humidity, and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The experiment was divided into control, model, and treat  groups, respectively.After 24 h after cell adhesion, a high-fat cell model was constructed by 400  M oleic acid (Sigma) treatment for 24 h, and the treat group was subjected to 16   M sesamin treatment for another 36 h.

tag: cell line

value: Human hepatocellular carcinoma cells


title: H4_JQE_HBCD


title: TP0001651E05_7_30.000000uM_DMEM_12h_TC00283154_C12

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:
TP0001651E05_7_30.000000uM_DMEM_12h
TC00283154_C12

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 Atrazine

tag: chemical name

value: Atrazine

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: A4galt KO mouse germinal-center B cells BCR-seq rep3

value: germinal-center B cells

value: A4galt KO


title: M3_JQE_HBCD

value: MED


title: A4galt KO mouse germinal-center B cells BCR-seq rep4


title: TP0001651E01_2_0.100000uM_DMEM_12h_TC00283154_C11

description:
TP0001651E01_2_0.100000uM_DMEM_12h
TC00283154_C11

value: 12h exposure of 0.1 uM of Bifenthrin

value: Bifenthrin


title: TP0001651D02_4_1.000000uM_DMEM_12h_TC00283154_C10

description:
TP0001651D02_4_1.000000uM_DMEM_12h
TC00283154_C10

value: 12h exposure of 1 uM of PFOA

value: PFOA

value: 1 uM


title: HePG2 cells,mo1


title: A4galt KO mouse germinal-center B cells BCR-seq rep2


title: M4_JQE_HBCD

value: els

value: liver

value: hbcd


title: HePG2 cells,mo2


title: M2_JQE_HBCD


title: Homo sapiens MDA-MB-453 Cells DMSO sRNA-seq r1

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
sRNA-seq; small RNA mapping in MDA-MB-453 cells; Experiment MS21
homo_sapiens_MDAMB453_DMSO-10.tss.txt
allTSRs.merged_anoRlog.txt

data_processing:
All samples (csRNA and sRNA) were trimmed with “homertools trim” to remove 5’ adapter sequence. Samples were then alinged to the hg38 human genome with STAR before being made into tag directories with homer’s batchMakeTagDirectory.pl.
csRNA-seq and sRNA-seq samples combined into peak files with homer’s findcsRNAtss.pl before being passed to homer’s mergePeaks and annotatePeaks.pl to combine all subsample sets (100nM CFZ, 500nM CFZ, Control, and DMSO) into one file and add read tag counts back in, respectively.
Assembly: homo_sapiens.GRCH38.UCSC.gtf, homo_sapiens.GRCH38.UCSC.fa
Supplementary files format and content: tss.txt files are Homer UCSC peak files containing grouped alignment peak names, chromosomes read positions including start and end points, and various read /associated gene data.
Supplementary files format and content: anoRlog.txt files contain peak information similar to tss.txt but with gene annotations and associated tag counts for each PeakID.

growth_protocol: Parental MDA-MB-453 cells were cultured in L-15 Leibovitz media with 10% fetal bovine serum (FBS) and incubated at 37C with room CO2.

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.

treatment_protocol: Cells were treated with DMSO or 100 or 500 nM MG132 and harvested after 24 hours.

value: DMSO


title: Untrtd_DMEM_12h_TC00283154_C08

description:
Untrtd_DMEM_12h
TC00283154_C08

value: untreated


title: M5_JQE_HBCD


title: Gla KO mouse germinal-center B cells BCR-seq rep3

value: spleen

value: Gla KO


title: Homo sapiens MDA-MB-453 Cells DMSO csRNA-seq r2

description:
CsRNA-seq; nascent TSS mapping in MDA-MB-453 cells; Experiment MS18
homo_sapiens_MDAMB453_DMSO-10.tss.txt
allTSRs.merged_anoRlog.txt

data_processing:
All samples (csRNA and sRNA) were trimmed with “homertools trim” to remove 5’ adapter sequence. Samples were then alinged to the hg38 human genome with STAR before being made into tag directories with homer’s batchMakeTagDirectory.pl.
csRNA-seq and sRNA-seq samples combined into peak files with homer’s findcsRNAtss.pl before being passed to homer’s mergePeaks and annotatePeaks.pl to combine all subsample sets (100nM CFZ, 500nM CFZ, Control, and DMSO) into one file and add read tag counts back in, respectively.
Assembly: homo_sapiens.GRCH38.UCSC.gtf, homo_sapiens.GRCH38.UCSC.fa
Supplementary files format and content: tss.txt files are Homer UCSC peak files containing grouped alignment peak names, chromosomes read positions including start and end points, and various read /associated gene data.
Supplementary files format and content: anoRlog.txt files contain peak information similar to tss.txt but with gene annotations and associated tag counts for each PeakID.
Library strategy: csRNA-seq


title: A4galt KO mouse germinal-center B cells BCR-seq rep1


title: DMSO_DMEM_12h_TC00283154_C09

description:
DMSO_DMEM_12h
TC00283154_C09

value: DMEM + 10% HI-FBS

value: 0.5% DMSO vehicle control

value: 0 uM


title: Gla KO mouse germinal-center B cells BCR-seq rep2

value: germinal-center B cells


title: H5_JQE_HBCD

description:
S473, S474, S475, S476, S477
S1_JQE_HBCD, S2_JQE_HBCD, S3_JQE_HBCD, S4_JQE_HBCD, S5_JQE_HBCD
NS.1100.004.NEBNext_dual_i7_D10---NEBNext_dual_i5_D10.QE7-S1-LT_R1.fastq.gz, NS.1100.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.QE7-S2-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.QE7-S3-LT_R1.fastq.gz, NS.1100.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.QE7-S4-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.QE7-S5-LT_R1.fastq.gz
NS.1100.004.NEBNext_dual_i7_D10---NEBNext_dual_i5_D10.QE7-S1-LT_R2.fastq.gz, NS.1100.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.QE7-S2-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.QE7-S3-LT_R2.fastq.gz, NS.1100.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.QE7-S4-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.QE7-S5-LT_R2.fastq.gz
jq_els_hbcd.txt

value: HIGH


title: Homo sapiens MDA-MB-453 Cells DMSO sRNA-seq r2

description:
sRNA-seq; small RNA mapping in MDA-MB-453 cells; Experiment MS23
homo_sapiens_MDAMB453_DMSO-10.tss.txt
allTSRs.merged_anoRlog.txt


title: Homo sapiens MDA-MB-453 Cells DMSO csRNA-seq r1

description:
CsRNA-seq; nascent TSS mapping in MDA-MB-453 cells; Experiment MS16
homo_sapiens_MDAMB453_DMSO-10.tss.txt
allTSRs.merged_anoRlog.txt


title: TP0001651C05_2_0.100000uM_DMEM_12h_TC00283154_C07

description:
TP0001651C05_2_0.100000uM_DMEM_12h
TC00283154_C07

value: 12h exposure of 0.1 uM of Bisphenol B

value: Bisphenol B


title: jq_els_flx_H5

value: flx


title: Gla KO mouse germinal-center B cells BCR-seq rep1


title: TP0001651G03_3_0.300000uM_DMEM_12h_TC00283154_C06

description:
TP0001651G03_3_0.300000uM_DMEM_12h
TC00283154_C06

value: 12h exposure of 0.3 uM of Nilutamide

value: Nilutamide


title: Homo sapiens MDA-MB-453 Cells Control sRNA-seq r1

description:
sRNA-seq; small RNA mapping in MDA-MB-453 cells; Experiment MS24
homo_sapiens_MDAMB453_Ctrl-10.tss.txt
allTSRs.merged_anoRlog.txt


title: WT mouse germinal-center B cells BCR-seq rep3

value: WT


title: jq_els_flx_H3

value: els

value: liver


title: TP0001651E01_5_3.000000uM_DMEM_12h_TC00283154_C05

description:
TP0001651E01_5_3.000000uM_DMEM_12h
TC00283154_C05

value: 12h exposure of 3 uM of Bifenthrin

value: Bifenthrin

value: 3 uM


title: jq_els_flx_M3

value: MED


title: WT mouse germinal-center B cells BCR-seq rep2

value: spleen


title: TP0001651D03_2_0.100000uM_DMEM_12h_TC00283154_C04

description:
TP0001651D03_2_0.100000uM_DMEM_12h
TC00283154_C04

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Cypermethrin

value: Cypermethrin


title: Homo sapiens MDA-MB-453 Cells Control csRNA-seq r1

description:
CsRNA-seq; nascent TSS mapping in MDA-MB-453 cells; Experiment MS19
homo_sapiens_MDAMB453_Ctrl-10.tss.txt
allTSRs.merged_anoRlog.txt


title: jq_els_flx_M5


title: WT mouse germinal-center B cells BCR-seq rep1

value: germinal-center B cells


title: Homo sapiens MDA-MB-453 Cells 500nM CFZ sRNA-seq r1

description:
sRNA-seq; small RNA mapping in MDA-MB-453 cells; Experiment MS25
homo_sapiens_MDAMB453_500nMmgi32-10.tss.txt
allTSRs.merged_anoRlog.txt

value: 500nM CFZ


title: TP0001651C03_6_10.000000uM_DMEM_12h_TC00283154_C03

description:
TP0001651C03_6_10.000000uM_DMEM_12h
TC00283154_C03

value: 12h exposure of 10 uM of Simazine

value: Simazine

value: 10 uM


title: jq_els_flx_M4

value: flx


title: TP0001651E02_7_30.000000uM_DMEM_12h_TC00283154_C02

description:
TP0001651E02_7_30.000000uM_DMEM_12h
TC00283154_C02

value: 12h exposure of 30 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

value: 30 uM


title: Homo sapiens MDA-MB-453 Cells 100nM CFZ sRNA-seq r1

description:
sRNA-seq; small RNA mapping in MDA-MB-453 cells; Experiment MS22
homo_sapiens_MDAMB453_100nMCFZ-10.tss.txt
allTSRs.merged_anoRlog.txt

value: 100nM CFZ


title: Homo sapiens MDA-MB-453 Cells 500nM CFZ csRNA-seq r1

description:
CsRNA-seq; nascent TSS mapping in MDA-MB-453 cells; Experiment MS20
homo_sapiens_MDAMB453_500nMmgi32-10.tss.txt
allTSRs.merged_anoRlog.txt


title: HBRR_TC00283154_C01

description:
HBRR
TC00283154_C01

source_name: Human Brain Reference RNA

value: untreated


title: Homo sapiens MDA-MB-453 Cells 100nM CFZ csRNA-seq r1

description:
CsRNA-seq; nascent TSS mapping in MDA-MB-453 cells; Experiment MS17
homo_sapiens_MDAMB453_100nMCFZ-10.tss.txt
allTSRs.merged_anoRlog.txt


title: TP0001651B05_2_0.100000uM_DMEM_12h_TC00283154_B24

description:
TP0001651B05_2_0.100000uM_DMEM_12h
TC00283154_B24

value: 12h exposure of 0.1 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: GEN_DMEM_12h_TC00283154_B23

description:
GEN_DMEM_12h
TC00283154_B23

value: 6h exposure of 10 uM of Genistein

value: Genistein


title: jq_els_flx_H1

value: els

value: liver

value: HIGH


title: jq_els_flx_H2


title: GEN_DMEM_12h_TC00283154_B22

description:
GEN_DMEM_12h
TC00283154_B22

value: DMEM + 10% HI-FBS


title: jq_els_flx_H4

description:
S458, S459, S460, S461, S462
jq_els_flx_S3, jq_els_flx_S5, jq_els_flx_S1, jq_els_flx_S4, jq_els_flx_S2
NS.1100.003.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.QE4-S3-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QE4-S5-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_G11---NEBNext_dual_i5_G11.QE4-S1-LT_R1.fastq.gz, NS.1100.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.QE4-S4-LT_R1.fastq.gz, NS.1100.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.QE4-S2-LT_R1.fastq.gz
NS.1100.003.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.QE4-S3-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QE4-S5-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_G11---NEBNext_dual_i5_G11.QE4-S1-LT_R2.fastq.gz, NS.1100.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.QE4-S4-LT_R2.fastq.gz, NS.1100.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.QE4-S2-LT_R2.fastq.gz
jq_els_flx.txt


title: parental_Rep3_qPRO_Fig4

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.
Library strategy: PRO-seq

molecule: nuclear RNA

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.

value: colorectal cancer

value: wild type


title: KI1_Rep3_qPRO_Fig4

value: MLL4 knockin


title: TP0001651F02_1_0.030000uM_DMEM_12h_TC00283154_B21

description:
TP0001651F02_1_0.030000uM_DMEM_12h
TC00283154_B21

value: 12h exposure of 0.03 uM of Ziram

value: Ziram


title: KI2_Rep2_qPRO_Fig4


title: TP0001651F01_5_3.000000uM_DMEM_12h_TC00283154_B20

description:
TP0001651F01_5_3.000000uM_DMEM_12h
TC00283154_B20

value: 12h exposure of 3 uM of Tetrac

value: Tetrac

value: 3 uM


title: KI1_Rep2_qPRO_Fig4


title: H3_JQE_BaP

value: bap


title: H5_JQE_BaP


title: TP0001651D03_4_1.000000uM_DMEM_12h_TC00283154_B18

description:
TP0001651D03_4_1.000000uM_DMEM_12h
TC00283154_B18

value: 12h exposure of 1 uM of Cypermethrin

value: Cypermethrin

value: 1 uM


title: TERT-KO IP AT scRNAseq

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger™ Single Cell Software Suite v.7.0.0 was used and The reads were aligned to the human transcriptome reference (cellranger mm10-2020-A) with STAR 2.6
Supplementary files format and content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: Adipose tissue (IP)

extract_protocol:
Cells were dissect from adipose tissue and suspended in the buffer.
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Primary cells (mixed)

value: Adipose tissue (IP)

tag: strain

value: Tie2e-cre; TERTfl/fl; mTmG

tag: age

value: 7 moths


title: TSA_DMEM_12h_TC00283154_B19

description:
TSA_DMEM_12h
TC00283154_B19

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

tag: chemical sample id


title: S4_JQE_BaP

tag: lifestage

value: els

tag: tissue

value: liver

value: dmso

value: CTRL


title: parental_Rep2_qPRO_Fig4

value: colorectal cancer

value: wild type


title: TP0001651A04_3_0.300000uM_DMEM_12h_TC00283154_B17

description:
TP0001651A04_3_0.300000uM_DMEM_12h
TC00283154_B17

value: 12h exposure of 0.3 uM of Rotenone

value: Rotenone


title: jq_els_flx_M2

tag: chemical

value: flx

tag: concentration

value: MED


title: KI2_Rep3_qPRO_Fig4

tag: cell type

tag: genotype

value: MLL4 knockin


title: S3_JQE_BaP


title: EC-TERT-KO SC AT scRNAseq

description: 10x Genomics

source_name: Adipose tissue (SC)

value: Primary cells (mixed)

value: Adipose tissue (SC)


title: jq_els_flx_M1


title: KI1_Rep1_qPRO_Fig4

tag: cell line


title: WT IP AT scRNAseq

description: 10x Genomics

value: Adipose tissue (IP)

value: Tie2e-cre; TERT+/+; mTmG

value: 7 moths


title: H2_JQE_BaP

value: bap

value: HIGH


title: TP0001651B06_5_3.000000uM_DMEM_12h_TC00283154_B15

description:
TP0001651B06_5_3.000000uM_DMEM_12h
TC00283154_B15

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 3 uM of Troglitazone

value: Troglitazone

value: 3 uM


title: KI2_Input_ChIP_Fig4

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.

value: colorectal cancer

tag: antibody


title: TP0001651H03_2_0.100000uM_DMEM_12h_TC00283154_B14

description:
TP0001651H03_2_0.100000uM_DMEM_12h
TC00283154_B14

value: 12h exposure of 0.1 uM of Fomesafen

tag: chemical name

value: Fomesafen

tag: chemical concentration

tag: dose level


title: S1_JQE_BaP

value: els

value: liver

value: dmso

value: CTRL


title: WT SC AT scRNAseq

description: 10x Genomics

value: Primary cells (mixed)

value: Adipose tissue (SC)


title: KI1_Input_ChIP_Fig4

value: MLL4 knockin


title: Sample 1

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were further processed using nf-core/marsseq pipeline. Count matrices per batch were merged to one count matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: mESCs

growth_protocol: Cells were adapted from SL to 2ILIF, KOSR or EPSC. For at least 4 passages. Cells were apadted in EPSCM for 2 weeks as recommended in original paper Yang. et al 2020.

extract_protocol:
Cells were dissociated in Accutase for 3 minutes at 37°C, and then the enzyme was inactivated by diluting in PBS and spinning 3min at 400rcf. Single cells suspension was obtained by repeatedly washing with 10 volume of ice-cold washing buffer (PBS- 10% FBS).
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq2 protocol (Keren-Shaul et al., 2019)
single cell RNA-seq for gene expression quantitation

value: SGGC (E14JU)


title: TP0001651F05_7_30.000000uM_DMEM_12h_TC00283154_B13

description:
TP0001651F05_7_30.000000uM_DMEM_12h
TC00283154_B13

value: 12h exposure of 30 uM of Fenofibrate

value: Fenofibrate

value: 30 uM

tag: exposure time

tag: assay plate

tag: assay plate well


title: KI2_Rep1_qPRO_Fig4


title: M5_JQE_BaP

value: bap

value: MED


title: S2_JQE_BaP


title: nEnd_B12_IgG_S7

data_processing:
Reads were trimmed to 21bp with Cutadapt 1.18, mapped to the GRCm38/mm10 mouse genome reference with bowtie v2.3.4.1 with options -X 1000 -no mixed -no-discordant.
only unique mapped reads with MAPKQ>10 were kept using samtools v1.9. Bam files were sorted, deduplicated with Picard v2.9.1 and indedxed. For the TF analysis, bam files were subset shorter or equal to 150bp. For chromatin marks, all bam files were used.
bedgraphs were generated using bedtools v2.27.1 and Bigwig files were generated using bamCoverage v3.2.0 from Deeptools and the RPGC option (-bs=1 -mormalize using RPKM)
Peaks were called using SEACR with stringent conditions for histone marks (H3K27ac and H3K4me1) and relaxed conditions for TFs (SOX2 and GATA6)
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

source_name: SGGC B12, IgG, nEnd

extract_protocol:
DNA from Cut&RUN samples were extracted using phenol-chloroform extraction as described in Janssens & Henikoff 2019. DNA concentraction was measured using Qubit (ThermoFisher Scientific, Q32854).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Kit for Illumina Sequencing according to Liu, 2019. 6 ng of total DNA was used for library preparation. Libraries were amplified using 9-12 cycles on the thermocycler. Post amplification libraries were size selected at 150-350bp in length using AMPure XP beads. Libraries were quantified by Qubit and validated at the Agilent Fragment Analyzer 5200.

value: SGGC

value: mouse ESC (E14JU)


title: TP0001651E02_1_0.030000uM_DMEM_12h_TC00283154_B11

description:
TP0001651E02_1_0.030000uM_DMEM_12h
TC00283154_B11

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

tag: chemical sample id


title: KI2_H3K27Ac_ChIP_Fig4

value: colorectal cancer


title: parental_Input_ChIP_Fig4

value: wild type


title: nEnd_B12_H3K27ac_S8

source_name: SGGC B12, H3K27ac, nEnd

value: H3K27ac (Abcam, #ab4729)


title: H1_JQE_BaP

tag: lifestage

value: els

value: liver

value: HIGH


title: TP0001651E04_6_10.000000uM_DMEM_12h_TC00283154_B16

description:
TP0001651E04_6_10.000000uM_DMEM_12h
TC00283154_B16

value: 12h exposure of 10 uM of Farglitazar

value: Farglitazar

value: 10 uM


title: parental_Rep1_qPRO_Fig4


title: nEnd_B12_Gata6_S10

source_name: SGGC B12, GATA6, nEnd

value: GATA6 (Cell Signaling, #5851)


title: S5_JQE_BaP

tag: tissue

value: dmso

value: CTRL


title: M4_JQE_BaP

tag: chemical

value: bap

value: MED


title: TP0001651G01_8_100.000000uM_DMEM_12h_TC00283154_B10

description:
TP0001651G01_8_100.000000uM_DMEM_12h
TC00283154_B10

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Vinclozolin

value: Vinclozolin


title: nEnd_B9_IgG_S1

source_name: SGGC B9, IgG, nEnd

value: SGGC

value: mouse ESC (E14JU)


title: TP0001651A06_6_10.000000uM_DMEM_12h_TC00283154_B09

description:
TP0001651A06_6_10.000000uM_DMEM_12h
TC00283154_B09

value: 12h exposure of 10 uM of Cyproconazole

value: Cyproconazole


title: parental_H3K27Ac_ChIP_Fig4

value: colorectal cancer

value: wild type


title: M2_JQE_BaP

value: els

value: liver

tag: concentration


title: KI2_H3K4me1_ChIP_Fig4

tag: cell type

value: MLL4 knockin


title: nEnd_B9_IgG_r2_S7


title: nEnd_B9_IgG_210701_S19


title: M1_JQE_BaP


title: TP0001651G05_2_0.100000uM_DMEM_12h_TC00283154_B07

description:
TP0001651G05_2_0.100000uM_DMEM_12h
TC00283154_B07

value: 12h exposure of 0.1 uM of Cyproterone acetate

value: Cyproterone acetate


title: TP0001651E01_1_0.030000uM_DMEM_12h_TC00283154_B12

description:
TP0001651E01_1_0.030000uM_DMEM_12h
TC00283154_B12

value: 12h exposure of 0.03 uM of Bifenthrin

value: Bifenthrin


title: parental_H3K4me1_ChIP_Fig4

tag: genotype


title: M3_JQE_BaP

value: bap

value: MED


title: HCT116_MLL4KI_LTX_100_Rep2_RNA_Fig6

tag: cell line

value: 100 nM lometrexol


title: KI1_H3K27Ac_ChIP_Fig4


title: TP0001651E03_1_0.030000uM_DMEM_12h_TC00283154_B05

description:
TP0001651E03_1_0.030000uM_DMEM_12h
TC00283154_B05

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Prochloraz

value: Prochloraz


title: nEnd_B9_H3K27ac_S2

source_name: SGGC B9, H3K27ac, nEnd

value: SGGC

value: mouse ESC (E14JU)

value: H3K27ac (Abcam, #ab4729)


title: TP0001651B05_8_100.000000uM_DMEM_12h_TC00283154_B06

description:
TP0001651B05_8_100.000000uM_DMEM_12h
TC00283154_B06

tag: treatment

value: 12h exposure of 100 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: HCT116_MLL4KI_LTX_100_Rep1_RNA_Fig6

value: colorectal cancer


title: nEnd_B9_Gata6_S4

source_name: SGGC B9, GATA6, nEnd

tag: antibody

value: GATA6 (Cell Signaling, #5851)


title: H1_JQA_TB

value: adult

value: liver

value: tb

value: HIGH


title: HCT116_MLL4KI_LTX_50_Rep2_RNA_Fig6

value: MLL4 knockin

value: 50 nM lometrexol


title: TP0001651C03_8_100.000000uM_DMEM_12h_TC00283154_B04

description:
TP0001651C03_8_100.000000uM_DMEM_12h
TC00283154_B04

value: 12h exposure of 100 uM of Simazine

tag: chemical name

value: Simazine


title: nEnd_B9__H3K4me1_S8

source_name: SGGC B9, H3K4me1, nEnd

value: H3K4me1 (abcam, #ab8895)


title: M5_JQA_TB

value: MED


title: HCT116_MLL4KI_LTX_50_Rep1_RNA_Fig6


title: KI1_H3K4me1_ChIP_Fig4


title: TP0001651B04_3_0.300000uM_DMEM_12h_TC00283154_B08

description:
TP0001651B04_3_0.300000uM_DMEM_12h
TC00283154_B08

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Propiconazole

value: Propiconazole

tag: chemical concentration


title: NACL_B12_Sox2_S34

source_name: SGGC B12, IgG, SOX2

value: SGGC

value: mouse ESC (E14JU)

value: SOX2 (Active Motif, #39843)


title: M4_JQA_TB


title: TP0001651D05_1_0.030000uM_DMEM_12h_TC00283154_B02

description:
TP0001651D05_1_0.030000uM_DMEM_12h
TC00283154_B02

value: 12h exposure of 0.03 uM of Thiram

value: Thiram

tag: dose level


title: HCT116_MLL4KI_LTX_0_Rep2_RNA_Fig6

value: colorectal cancer

value: DMSO


title: UHRR_TC00283154_B01

description:
UHRR
TC00283154_B01

source_name: Universal Human Reference RNA

value: untreated

tag: exposure time


title: H4_JQE_BaP

source_name: liver

value: els

value: liver

value: bap

value: HIGH


title: NACL_B12_IgG_S32

source_name: SGGC B12, IgG, NACL


title: H2_JQA_TB

value: adult

value: tb


title: NACL_B12_IgG_210701_S25


title: HCT116_MLL4KI_LTX_0_Rep1_RNA_Fig6

value: MLL4 knockin


title: HCT116_parental_LTX_100_Rep2_RNA_Fig6

value: wild type

value: 100 nM lometrexol


title: TP0001651C05_8_100.000000uM_DMEM_12h_TC00283154_A23

description:
TP0001651C05_8_100.000000uM_DMEM_12h
TC00283154_A23

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Bisphenol B

value: Bisphenol B

tag: assay plate


title: TP0001651D02_3_0.300000uM_DMEM_12h_TC00283154_B03

description:
TP0001651D02_3_0.300000uM_DMEM_12h
TC00283154_B03

value: 12h exposure of 0.3 uM of PFOA

value: PFOA

tag: assay plate well


title: M2_JQA_TB

value: MED


title: NACL_B12_H3K4me1_210701_S26

source_name: SGGC B12, H3K4me1, NACL

value: SGGC

value: mouse ESC (E14JU)

value: H3K4me1 (abcam, #ab8895)


title: H4_JQA_TB

value: liver


title: TP0001651C06_2_0.100000uM_DMEM_12h_TC00283154_A22

description:
TP0001651C06_2_0.100000uM_DMEM_12h
TC00283154_A22

source_name: MCF7 Cells

value: 12h exposure of 0.1 uM of Cycloheximide

value: Cycloheximide

tag: chemical sample id


title: HCT116_parental_LTX_50_Rep2_RNA_Fig6

value: colorectal cancer

value: 50 nM lometrexol


title: nEnd_B9_H3K4me1_210701_S20


title: NACL_B9_Sox2_S29

source_name: SGGC B9, SOX2, NACL

value: SOX2 (Active Motif, #39843)


title: HCT116_parental_LTX_50_Rep1_RNA_Fig6

value: wild type


title: M1_JQA_TB

tag: lifestage

value: adult

value: tb


title: H5_JQA_TB

tag: tissue

value: HIGH


title: TP0001651G04_5_3.000000uM_DMEM_12h_TC00283154_A20

description:
TP0001651G04_5_3.000000uM_DMEM_12h
TC00283154_A20

value: DMEM + 10% HI-FBS

value: 12h exposure of 3 uM of Cladribine

value: Cladribine

value: 3 uM


title: H3_JQA_TB

description:
S397, S398, S399, S400, S401, S402
S1_JQA_TB, S2_JQA_TB, S3_JQA_TB, S4_JQA_TB, S5_JQA_TB, S6_JQA_TB
NS.1119.001.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.QA1-S1-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.QA1-S2-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.QA1-S3-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.QA1-S4-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QA1-S5-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.QA1-S6-LLT_RNA-seq_R1.fastq.gz
NS.1119.001.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.QA1-S1-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.QA1-S2-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.QA1-S3-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.QA1-S4-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QA1-S5-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.QA1-S6-LLT_RNA-seq_R2.fastq.gz
jq_adult_tb.txt

tag: chemical


title: M3_JQA_TB

tag: concentration

value: MED


title: NACL_B12_H3K27ac

source_name: SGGC B12, H3K27ac, NACL

value: SGGC

tag: cell type

value: mouse ESC (E14JU)

value: H3K27ac (Abcam, #ab4729)


title: NACL_B9_IgG_S27

source_name: SGGC B9, IgG, NACL


title: HCT116_parental_LTX_0_Rep2_RNA_Fig6

tag: genotype

value: DMSO


title: NACL_B9_IgG_210701_S24

tag: cell line


title: NACL_B9_H3K27ac

source_name: SGGC B9, H3K27ac, NACL


title: TP0001651D01_4_1.000000uM_DMEM_12h_TC00283154_A19

description:
TP0001651D01_4_1.000000uM_DMEM_12h
TC00283154_A19

tag: media

value: 12h exposure of 1 uM of Lactofen

value: Lactofen

value: 1 uM


title: TP0001651D04_3_0.300000uM_DMEM_12h_TC00283154_A24

description:
TP0001651D04_3_0.300000uM_DMEM_12h
TC00283154_A24

tag: treatment

value: 12h exposure of 0.3 uM of Clofibrate

value: Clofibrate


title: HCT116_parental_LTX_0_Rep1_RNA_Fig6

value: colorectal cancer

value: wild type


title: HCT116_parental_LTX_100_Rep1_RNA_Fig6

value: 100 nM lometrexol


title: jq_adult_seme_H1

value: adult

value: liver

value: seme

value: HIGH


title: TP0001651H03_8_100.000000uM_DMEM_12h_TC00283154_A18

description:
TP0001651H03_8_100.000000uM_DMEM_12h
TC00283154_A18

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Fomesafen

value: Fomesafen


title: TP0001651H02_2_0.100000uM_DMEM_12h_TC00283154_A21

description:
TP0001651H02_2_0.100000uM_DMEM_12h
TC00283154_A21

value: 12h exposure of 0.1 uM of Maneb

value: Maneb


title: TP0001651B05_6_10.000000uM_DMEM_12h_TC00283154_A17

description:
TP0001651B05_6_10.000000uM_DMEM_12h
TC00283154_A17

value: 12h exposure of 10 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

value: 10 uM


title: HCT116_MLL4KO3_Rep2_RNA_Fig3

value: MLL4 knockout


title: jq_adult_seme_M5

value: MED


title: jq_adult_seme_M4


title: NACL_B9__H3K4me1_210701_S23

source_name: SGGC B9, H3K4me1, NACL

value: SGGC

value: mouse ESC (E14JU)

tag: antibody

value: H3K4me1 (abcam, #ab8895)


title: B_SP_Sox2_S17

source_name: SGGC B12, SOX2, KOSR SOX2+

value: SOX2 (Active Motif, #39843)


title: B_SP_IgG_S14

source_name: SGGC B12, IgG, KOSR SOX2+


title: TP0001651B03_4_1.000000uM_DMEM_12h_TC00283154_A15

description:
TP0001651B03_4_1.000000uM_DMEM_12h
TC00283154_A15

value: 12h exposure of 1 uM of Reserpine

tag: chemical name

value: Reserpine

value: 1 uM


title: HCT116_MLL4KO2_Rep3_RNA_Fig3

value: colorectal cancer


title: HCT116_MLL4KO3_Rep1_RNA_Fig3


title: TP0001651A03_8_100.000000uM_DMEM_12h_TC00283154_A16

description:
TP0001651A03_8_100.000000uM_DMEM_12h
TC00283154_A16

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Butafenacil

value: Butafenacil

tag: chemical concentration


title: jq_adult_seme_M3

value: adult

value: liver

value: seme


title: TP0001651E03_3_0.300000uM_DMEM_12h_TC00283154_A14

description:
TP0001651E03_3_0.300000uM_DMEM_12h
TC00283154_A14

value: 12h exposure of 0.3 uM of Prochloraz

value: Prochloraz

tag: dose level


title: jq_adult_seme_H5

value: HIGH


title: jq_adult_seme_H2


title: HCT116_MLL4KO2_Rep2_RNA_Fig3

value: MLL4 knockout


title: B_SP_H3K4me1_S16

source_name: SGGC B12, H3K4me1, KOSR SOX2+

value: SGGC

value: mouse ESC (E14JU)


title: jq_adult_seme_M2

value: MED


title: HCT116_MLL4KO2_Rep1_RNA_Fig3


title: B_SP_H3K27ac_S15

source_name: SGGC B12, H3K27ac, KOSR SOX2+

value: H3K27ac (Abcam, #ab4729)


title: jq_adult_seme_H4


title: HCT116_MLL4KO3_Rep3_RNA_Fig3


title: B_DP_Sox2_S23

source_name: SGGC B12, SOX2, KOSR DP

value: SOX2 (Active Motif, #39843)


title: HCT116_MLL4KO1_Rep3_RNA_Fig3


title: TP0001651F04_4_1.000000uM_DMEM_12h_TC00283154_A13

description:
TP0001651F04_4_1.000000uM_DMEM_12h
TC00283154_A13

value: 12h exposure of 1 uM of Fulvestrant

value: Fulvestrant

value: 1 uM

tag: exposure time


title: jq_adult_seme_M1


title: TP0001651E01_8_100.000000uM_DMEM_12h_TC00283154_A12

description:
TP0001651E01_8_100.000000uM_DMEM_12h
TC00283154_A12

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Bifenthrin

value: Bifenthrin

tag: assay plate


title: B_DP_IgG_S20

source_name: SGGC B12, IgG, KOSR DP


title: HCT116_MLL4KO1_Rep2_RNA_Fig3

value: colorectal cancer


title: TP0001651D03_5_3.000000uM_DMEM_12h_TC00283154_A11

description:
TP0001651D03_5_3.000000uM_DMEM_12h
TC00283154_A11

value: 12h exposure of 3 uM of Cypermethrin

value: Cypermethrin

value: 3 uM

tag: assay plate well


title: B_DP_H3K27ac_S21


title: TP0001651A03_5_3.000000uM_DMEM_12h_TC00283154_A10

description:
TP0001651A03_5_3.000000uM_DMEM_12h
TC00283154_A10

value: 12h exposure of 3 uM of Butafenacil

value: Butafenacil

tag: chemical sample id


title: jq.adult.pb.S5

tag: lifestage

value: adult

value: liver

value: dmso

value: CTRL


title: B_DP_H3K4me1_S22

value: SGGC

value: mouse ESC (E14JU)

value: H3K4me1 (abcam, #ab8895)


title: HCT116_MLL4KO1_Rep1_RNA_Fig3

value: MLL4 knockout


title: TP0001651C02_3_0.300000uM_DMEM_12h_TC00283154_A09

description:
TP0001651C02_3_0.300000uM_DMEM_12h
TC00283154_A09

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of 4-Hydroxytamoxifen


title: jq.adult.pb.S4

tag: tissue


title: TP0001651G02_7_30.000000uM_DMEM_12h_TC00283154_A08

description:
TP0001651G02_7_30.000000uM_DMEM_12h
TC00283154_A08

value: 12h exposure of 30 uM of Lovastatin

value: Lovastatin

value: 30 uM


title: B_DP_Gata6_S24

source_name: SGGC B12, GATA6, KOSR DP

value: GATA6 (Cell Signaling, #5851)


title: HCT116_MLL4KI3_Rep3_RNA_Fig3

value: colorectal cancer

value: MLL4 knockin


title: HCT116_MLL4KI3_Rep2_RNA_Fig3


title: jq.adult.pb.H3

tag: chemical

value: pb

value: HIGH


title: A1_B12_GFP_Sox2_S11

value: SOX2 (Active Motif, #39843)


title: A1_B12_GFP_IgG_S10


title: TP0001651G04_3_0.300000uM_DMEM_12h_TC00283154_A07

description:
TP0001651G04_3_0.300000uM_DMEM_12h
TC00283154_A07

value: 12h exposure of 0.3 uM of Cladribine

value: Cladribine


title: HCT116_MLL4KI3_Rep1_RNA_Fig3


title: jq.adult.pb.S3

value: adult

value: liver

value: dmso

tag: concentration

value: CTRL


title: jq_adult_seme_H3

description:
S382, S383, S384, S385, S386
jq_adult_seme_S1, jq_adult_seme_S2, jq_adult_seme_S3, jq_adult_seme_S4, jq_adult_seme_S5
NS.1119.001.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.QA2-S1-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.QA2-S2-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.QA2-S3-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.QA2-S4-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.QA2-S5-LLT_RNA-seq_R1.fastq.gz
NS.1119.001.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.QA2-S1-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.QA2-S2-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.QA2-S3-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.QA2-S4-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.QA2-S5-LLT_RNA-seq_R2.fastq.gz
jq_adult_seme.txt

value: seme


title: TP0001651A03_3_0.300000uM_DMEM_12h_TC00283154_A04

description:
TP0001651A03_3_0.300000uM_DMEM_12h
TC00283154_A04

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Butafenacil

value: Butafenacil


title: HCT116_MLL4KI2_Rep1_RNA_Fig3

tag: cell type


title: jq.adult.pb.H1


title: jq.adult.pb.H5


title: A1_B12_DoublePos_Sox2_S13

value: SGGC

value: mouse ESC (E14JU)


title: HCT116_MLL4KI2_Rep2_RNA_Fig3

value: colorectal cancer

tag: genotype


title: A1_B12_DoublePos_IgG_S12

tag: cell line


title: jq.adult.pb.S2


title: TP0001651E05_3_0.300000uM_DMEM_12h_TC00283154_A03

description:
TP0001651E05_3_0.300000uM_DMEM_12h
TC00283154_A03

tag: media

value: 12h exposure of 0.3 uM of Atrazine

value: Atrazine


title: HCT116_MLL4KI1_Rep3_RNA_Fig3

value: MLL4 knockin

tag: treatment


title: A1_B12_DoublePos_Gata6_S14

tag: antibody

value: GATA6 (Cell Signaling, #5851)


title: A_SP_IgG_S1


title: TP0001651F01_4_1.000000uM_DMEM_12h_TC00283154_A06

description:
TP0001651F01_4_1.000000uM_DMEM_12h
TC00283154_A06

value: 12h exposure of 1 uM of Tetrac

tag: chemical name

value: Tetrac

value: 1 uM


title: jq.adult.pb.H4

value: adult

value: liver

value: pb

value: HIGH


title: HCT116_MLL4KI2_Rep3_RNA_Fig3


title: TP0001651F04_1_0.030000uM_DMEM_12h_TC00283154_A02

description:
TP0001651F04_1_0.030000uM_DMEM_12h
TC00283154_A02

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Fulvestrant

value: Fulvestrant

tag: chemical concentration


title: UHRR_TC00283154_A01

description:
UHRR
TC00283154_A01

source_name: Universal Human Reference RNA

value: untreated

tag: dose level


title: jq.adult.pb.S1

source_name: liver

value: dmso

value: CTRL


title: HCT116_MLL4KI1_Rep1_RNA_Fig3

value: colorectal cancer


title: jq.adult.pb.M4

value: MED


title: jq.adult.pb.H2


title: HCT116_MLL4KI1_Rep2_RNA_Fig3

value: MLL4 knockin


title: A_SP_H3K27ac_S2

value: SGGC

value: mouse ESC (E14JU)

value: H3K27ac (Abcam, #ab4729)


title: Patient CIII (12B_S47)

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

description: Mutant 6

data_processing:
Transcripts reads were aligned to the hg18 human reference genome using Salmon v0.8.2 (Patro et al. 2017)
raw counts were normalized with the DESeq2 R package (Love et al., 2014)
Assembly: hg18
Supplementary files format and content: normalized_counts

source_name: heart tissue

growth_protocol: We used PBMC of the patient CIII who was diagnosed with desmin-related myofibrillar myopathy (MFM1) with cardiac manifestation at the age of 36 years and carries the DESE439K variant present in his family. PBMC of CIII patient were reprogrammed into induced pluripotent stem cells (iPSCs) using a non-integrative method (Epi5™ Episomal iPSC Reprogramming Kit, Thermo Fisher Scientific). The clone c15 was isolated and used in transcriptome analysis.  Gibco Human Episomal iPSC clone (Control 1, Thermo Fisher Scientific) derived from healthy individuals without any cardiac pathology, was used as control. Frozen iPSC-CM (cardiomyocytes derived from induced pluripotent stem cells) from Clone c15 and Gibco Human Episomal iPSC clone (Control 1), Thermo Fisher Scientific) were thawed, centrifuged at 200xg to remove freezing medium and directly seeded on Matrigel-coated 12 well plates. They were then cultured 20 days in maturation medium, detached using TrypLE Select 1X, pelleted and flash frozen in liquid nitrogen. The cells were afterwards submitted to mRNA sequencing.

extract_protocol:
Total RNA was purified from cells using  RNeasy Plus Micro Kit (Qiagen)
mRNA libraries were prepared with the NEBNext single cell/low input RNA library prep kit for Illumina. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500

tag: subject

value: Patient CIII

value: heart tissue

value: iPSC (clone 15) from PBMC of Patient CIII

value: Cardiomyocytes derived from iPSC


title: TP0001651B04_2_0.100000uM_DMEM_12h_TC00283154_A05

description:
TP0001651B04_2_0.100000uM_DMEM_12h
TC00283154_A05

value: 12h exposure of 0.1 uM of Propiconazole

value: Propiconazole

tag: exposure time

tag: assay plate


title: A_SP_H3K4me1_S3

value: H3K4me1 (abcam, #ab8895)


title: HCT116_parental_Rep3_RNA_Fig3

value: wild type


title: jq.adult.pb.M3

value: adult

value: liver

value: pb


title: A_DP_IgG_S7


title: Patient CIII (11B_S46)

description: Mutant 5


title: Patient CIII (10B_S45)

description: Mutant 4


title: A_SP_Sox2_S4

value: SOX2 (Active Motif, #39843)


title: Patient CIII (9B_S44)

description: Mutant 3


title: HCT116_parental_Rep2_RNA_Fig3

value: colorectal cancer


title: KYSE410 cells, U-2

city: Beijing

first: Jiahui

last: Cai

address: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
After library construction, Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer (Agilent).
Sequencing was performed using an Illumina Novaseq 6000 following Illumina-provided protocols for 2x150 paired-end sequencing in Mingma Technologies Co., Ltd at Shanghai.
Assembly: hg19
Supplementary files format and content: DEG_Case_vs_Control_all_anno.txt

source_name: Human esophagus

extract_protocol:
mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly. The first strand of cDNA and the second strand are then synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end.
RNA purification, reverse transcription, library construction and sequencing were performed in Mingma Technologies Co., Ltd at Shanghai according to the manufacturer's instructions (Illumina). The mRNA-focused sequencing libraries from total RNA were prepared using VAHTS mRNA-seq v3 Library Prep Kit (Vazyme). PolyA mRNA was purified from total RNA using oligo-dT-attached magnetic beads and then fragmented by fragmentation buffer. Taking these short fragments as templates, first strand cDNA was synthesized using reverse transcriptase and random primers, followed by second strand cDNA synthesis. Then the synthesized cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. Then Illumina sequencing adapters were added to both size of the cDNA fragments. After PCR amplification for DNA enrichment, the AMPure XP Beads (Beckmen) were used to clean up the target fragments of 200–300 bp.

value: Human esophagus

value: KYSE410 cells

value: Human esophageal cancer cells

value: UGT2B15 overexpression


title: jq.adult.pb.M5

value: MED


title: A_DP_Sox2_S10

value: SGGC

value: mouse ESC (E14JU)


title: A_DP_H3K4me1_S9

source_name: SGGC B12, H3K4me1, KOSR DP


title: A_DP_H3K27ac_S8

source_name: SGGC B12, H3K27ac, KOSR DP

value: H3K27ac (Abcam, #ab4729)


title: Patient CIII (8B_S43)

description: Mutant 2

value: Patient CIII

value: heart tissue

value: iPSC (clone 15) from PBMC of Patient CIII

value: Cardiomyocytes derived from iPSC


title: jq.adult.pb.M2

value: adult


title: KYSE410 cells, U-1

institute: Cancer Hospital Chinese Academy of Medical Sciences


title: Patient CIII (7B_S42)

description: Mutant  1


title: jq.adult.pb.M1

value: liver


title: H5_JQA_HBCD

value: hbcd

value: HIGH


title: 2iLIF_B12_IgG_S16

source_name: SGGC B12, IgG, 2iLIF


title: HCT116_parental_Rep1_RNA_Fig3

value: colorectal cancer

value: wild type


title: A_DP_Gata6_S11_sub02

value: GATA6 (Cell Signaling, #5851)


title: KYSE410 cells, control-1

value: Human esophagus

value: KYSE410 cells

value: Human esophageal cancer cells

value: WT


title: KYSE410 cells, control-2


title: M2_JQA_HBCD

value: MED


title: Control 1 (6B_S41)

description: Control 6

value: Control 1

value: Gibco Human Episomal iPSC


title: H4_JQA_HBCD


title: 2iLIF_B12_H3K4me1_S17

source_name: SGGC B12, H3K4me1, 2iLIF

value: SGGC

value: mouse ESC (E14JU)

value: H3K4me1 (abcam, #ab8895)


title: WT, spherois, exp16

city: Badalona

first: Lucia

last: Gutierrez-Chamorro

address: Ctra/ del Canyet

country: Spain

institute: IrsiCaixa

description:
In title file exp16 refers to replicate 4
esfWT16

data_processing:
Mapping was performed with HISAT2 against GRCh38
Transcript was assembled with StringTie
Assembly: GRCh38_NCBI_109.20200522
Supplementary files format and content: Counts.txt (raw counts)

source_name: T47D cell line

extract_protocol:
Maxwell® HT simplyRNA Kit
TruSeq Stranded mRNA LT Sample Prep Kit

tag: culture model

value: Spheroid

tag: samhd1 status


title: Control 1 (4B_S39)

description: Control 4

tag: tissue

value: heart tissue

value: Cardiomyocytes derived from iPSC


title: Control 1 (5B_S40)

description: Control 5


title: 2iLIF_B9_IgG_S13

source_name: SGGC B9, IgG, 2iLIF


title: WT, spheroid, exp15

description:
In title file exp15 refers to replicate 3
esfWT15


title: M1_JQA_HBCD

tag: lifestage

value: adult

value: liver

tag: chemical

value: hbcd


title: WT, spheroid, exp10

description:
In title file exp10 refers to replicate 1
esfWT10

value: wild type


title: Control 1 (3B_S38)

description: Control 3

tag: cell type


title: 2i_B12_Sox2_S24

source_name: SGGC B12, SOX2, 2iLIF

value: SOX2 (Active Motif, #39843)


title: 2iLIF_B9_H3K4me1_S14

source_name: SGGC B9, H3K4me1, 2iLIF


title: H3_JQA_HBCD

tag: concentration

value: HIGH


title: WT, spheroid, exp11

description:
In title file exp11 refers to replicate 2
esfWT11


title: H2_JQA_HBCD


title: SAMHD1  KO, spheroids, clone A2, exp16

description:
In title file exp16 refers to replicate 2
esfA2_16

value: knock-out


title: Control 1 (1B_S36)

description: Control 1

tag: cell line

tag: genotype

value: WT


title: Control 1 (2B_S37)

description: Control 2


title: MCF7, ActCas9-VGLL1-FULVR-2_biol rep 3

city: London

first: Carolina

last: Gemma

state: Greater London

address: Du Cane Road, Hammersmith Campus

department: Department of Surgery and Cancer

country: United Kingdom

institute: Imperial College London

data_processing:
Raw reads were aligned to the human reference genome hg19 version using TopHat
Redundant reads were removed using SAMtools
HTSeq was used to count reads at UCSC annotated genes
Normalization and differential expression analysis were carried out using DESeq2 package
Assembly: hg19
Supplementary files format and content: tab-delimited text file including DESeq2 normalised gene read counts for each sample

source_name: MCF7 ActCas9-VGLL1-FULVR

growth_protocol: MCF7-ActCas9-Vector and MCF7-ActCas9-VGLL1 cells were maintained in media containing 0.2 mg/ml hygromycin, 10 µg/ml blasticidin and 1µg/ml puromycin. MCF7-ActCas9-VGLL1-FULVR-1 and MCF7-ActCas9-VGLL1-FULVR-2 cells were cultured in the same media with the addition of 100nM and 1000nM of fulvestrant respectively

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen 74106).
RNA-seq libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7775) following manufacturer's protocol.

value: MCF7 ActCas9-VGLL1-FULVR

value: Human breast cancer cell line (resistant to fulvestrant)

value: wild type MCF7 cells

tag: treatment


title: MCF7, ActCas9-VGLL1-FULVR-2_biol rep 2


title: 2i_B9_Sox2_S19

source_name: SGGC B9, SOX2, 2iLIF

value: SGGC

tag: antibody


title: M4_JQA_HBCD

value: MED


title: 2i_B12_IgG_S22

value: mouse ESC (E14JU)


title: SAMHD1  KO, spheroids, clone A1, exp15

description:
In title file exp15 refers to replicate 3
esfA1_15

value: Spheroid


title: 2i_B9_IgG_S17


title: H1_JQA_HBCD


title: M5_JQA_HBCD


title: 2i_B9_H3K27ac

source_name: SGGC B9, H3K27ac, 2iLIF

value: H3K27ac (Abcam, #ab4729)


title: SAMHD1  KO, spheroids, clone A1, exp16

description:
In title file exp16 refers to replicate 4
esfA1_16


title: MCF7, ActCas9-VGLL1-FULVR-2_biol rep 1


title: M3_JQA_HBCD

description:
S352, S353, S354, S355, S356
S1_JQA_HBCD, S2_JQA_HBCD, S3_JQA_HBCD, S4_JQA_HBCD, S5_JQA_HBCD
NS.1119.001.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QA3-S1-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.QA3-S2-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.QA3-S3-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.QA3-S4-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.QA3-S5-LLT_RNA-seq_R1.fastq.gz
NS.1119.001.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QA3-S1-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.QA3-S2-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.QA3-S3-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.QA3-S4-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.QA3-S5-LLT_RNA-seq_R2.fastq.gz
jq_adult_hbcd.txt


title: MCF7, ActCas9-VGLL1-FULVR-1_biol rep 3


title: SAMHD1  KO, spheroids, clone A1, exp10

description:
In title file exp10 refers to replicate 1
esfA1_10


title: FB 18C, Rep 1, Day 2, ZT10

city: Evanston

first: William

last: Kath

address: 2145 Sheridan Rd

department: Engineering Sciences and Applied Mathematics

institute: Northwestern University

data_processing:
Basic quality checking of sequence files was performed with FastQC.   Paired-end reads were trimmed using Atropos version 1.1.31 using the options atropos trim --aligner insert -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 50
Reads were aligned using STAR (2.7.10a_alpha_220818) with options --outFilterType BySJout --alignIntronMax 1000000 --outSAMmultNmax 1 --outSAMtype BAM to produce only uniquely mapped reads
Duplicate paired-end reads were removed using bamUtil with the options bam dedup --rmDups --excludeFlags 0xB04 --oneChrom
The resulting reads were then re-aligned with STAR to produce a BAM file with reads aligned to the transcriptome (--quantMode TranscriptomeSAM)
RSEM was then used with options --paired-end --strandedness none to produce tags-per-million (TPM) counts for each gene from transcriptome alignments.
Assembly: Ensembl Drosophila melanogaster BDGP6.32 reference (release 107)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Drosophila melanogaster

source_name: fat body (FB)

growth_protocol: Age-matched female Iso31 flies (an isogenic w1118 strain) were collected and aged for 3 days with males before being transferred to an entrainment incubator for 3 days.

extract_protocol:
RNA was isolated from the abdominal fat bodies using Trizol LS (hermoFisher #10296028)
Non-stranded library preparation was carried out using the NEBNext Ultra II RNA Library Prep kit for Illumina according to manufacturer protocol.

treatment_protocol: The experimental group was shifted to 18 degrees C at seven days old while the control group was kept at 25 degrees C.

value: fat body (FB)


title: SAMHD1  KO, spheroids, clone A1, exp11

description:
In title file exp11 refers to replicate 2
esfA1_11


title: FB 18C, Rep 1, Day 2, ZT08


title: MCF7, ActCas9-VGLL1, rep 2

source_name: MCF7 ActCas9-VGLL1

value: MCF7 ActCas9-VGLL1

value: Human breast cancer cell line


title: MCF7, ActCas9-VGLL1-FULVR-1_biol rep 2


title: FB 18C, Rep 1, Day 2, ZT12


title: SAMHD1  KO, spheroids, clone A2, exp15

description:
In title file exp15 refers to replicate 1
esfA2_15


title: MCF7, ActCas9-VGLL1, rep 3


title: FB 18C, Rep 1, Day 2, ZT06


title: S5_SH_high

first: Allan

last: Goldstein

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

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

source_name: SH-SY5Y cells – RNAseq

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

value: Neuroblastoma

tag: strain


title: MCF7, ActCas9-VGLL1-FULVR-1_biol rep 1


title: S2_SH_low


title: MCF7, ActCas9-Vector, rep 3


title: S4_SH_high


title: MCF7, ActCas9-VGLL1, rep 1


title: S3_SH_low


title: 2i_B12_H3K27ac

source_name: SGGC B12, H3K27ac, 2iLIF


title: FB 18C, Rep 1, Day 2, ZT02


title: FB 18C, Rep 1, Day 2, ZT04


title: Female Hippocampus_GRMREmx1-cre_rep2

type: RNA

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from female hippocampus, GRMREmx1-cre

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.0), using the 1-color defaults for all parameters.

source_name: hippocampus, GRMREmx1-cre

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA for microarray analysis was isolated from the whole hippocampus of adult male and female dflox control and GREmx1-cre, MREmx1-cre, and GRMREmx1-cre mice using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Kit (Qiagen).

tag: gender

value: female

value: hippocampus


title: MCF7, ActCas9-Vector, rep 1


title: FB 18C, Rep 1, Day 1, ZT22


title: S1_SH_low


title: S6_SH_high


title: Female Hippocampus_GRMREmx1-cre_rep3


title: Female Hippocampus_GRMREmx1-cre_rep1


title: Female Hippocampus_MREmx1-cre_rep4

description: Gene expression from female hippocampus, MREmx1-cre

source_name: hippocampus, MREmx1-cre


title: MCF7, ActCas9-Vector, rep 2


title: Female Hippocampus_GRMREmx1-cre_rep4


title: nlf_els_flx_HAP1

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: Lithobates pipiens

source_name: embryo

value: els

value: embryo

value: flx

value: HIGH


title: FB 18C, Rep 1, Day 2, ZT00


title: Female Hippocampus_MREmx1-cre_rep2


title: FULVR, siVGLL1#3, rep 3

source_name: FULVR

value: FULVR

value: Human breast cancer cell line (resistant to fulvestrant)

value: VGLL1 siRNA


title: nlf_els_flx_CCP3

value: dmso

value: CTRL


title: FB 18C, Rep 1, Day 1, ZT20


title: Female Hippocampus_MREmx1-cre_rep1


title: nlf_els_flx_MEP5

value: MED


title: FULVR, siVGLL1#3, rep 2

value: wild type MCF7 cells


title: FULVR, siVGLL1#3, rep 1


title: FB 18C, Rep 1, Day 1, ZT16

value: fat body (FB)


title: Female Hippocampus_GREmx1-cre_rep4

description: Gene expression from female hippocampus, GREmx1-cre

source_name: hippocampus, GREmx1-cre


title: FB 18C, Rep 1, Day 1, ZT14


title: FULVR, siVGLL1#2, rep 3


title: nlf_els_flx_CBP2


title: Female Hippocampus_GREmx1-cre_rep3


title: FULVR, siVGLL1#2, rep 1


title: FB 18C, Rep 1, Day 1, ZT12


title: nlf_els_flx_MDP4


title: Female Hippocampus_MREmx1-cre_rep3


title: nlf_els_flx_CAP1


title: FULVR, siVGLL1#2, rep 2


title: nlf_els_flx_MCP3


title: nlf_els_flx_HEP5


title: Female Hippocampus_GREmx1-cre_rep2


title: FB 18C, Rep 1, Day 1, ZT08


title: Female Hippocampus_GREmx1-cre_rep1


title: FULVR, siVGLL1#1, rep 3


title: Female Hippocampus_dflox control_rep3

description: Gene expression from female hippocampus, dflox control

source_name: hippocampus, dflox control

value: dflox control


title: nlf_els_flx_MBP2


title: FB 18C, Rep 1, Day 1, ZT10


title: FB 18C, Rep 1, Day 1, ZT06


title: Female Hippocampus_dflox control_rep4


title: FB 18C, Rep 1, Day 1, ZT04


title: FULVR, siVGLL1#1, rep 2


title: FULVR, siVGLL1#1, rep 1


title: nlf_els_flx_HDP4


title: FB 18C, Rep 1, Day 1, ZT02


title: FB 18C, Rep 1, Day 1, ZT00


title: nlf_els_flx_MAP1


title: nlf_els_flx_HCP3


title: FULVR, siControl, rep 2

value: Control siRNA


title: Female Hippocampus_dflox control_rep2


title: FULVR, siControl, rep 1


title: FB 25C, Rep 1, Day 2, ZT00


title: FULVR, vehicle, rep 4

value: Vehicle (DMSO), 24 h


title: Male Hippocampus_GRMREmx1-cre_rep3

description: Gene expression from male hippocampus, GRMREmx1-cre

value: male


title: Female Hippocampus_dflox control_rep1

value: female

value: hippocampus


title: FULVR, siControl, rep 3


title: nlf_els_flx_HBP2

value: els

value: embryo


title: nlf_els_flx_CEP5


title: FB 25C, Rep 1, Day 1, ZT12


title: FULVR, vehicle, rep 3


title: Male Hippocampus_GRMREmx1-cre_rep1


title: FB 25C, Rep 1, Day 1, ZT06


title: nlf_els_flx_CDP4


title: Male Hippocampus_GRMREmx1-cre_rep2


title: Male Hippocampus_MREmx1-cre_rep4

description: Gene expression from male hippocampus, MREmx1-cre


title: Male Hippocampus_MREmx1-cre_rep3


title: FULVR, vehicle, rep 2


title: nlf_els_ee2_SEP5


title: FB 25C, Rep 1, Day 1, ZT00


title: FULVR, vehicle, rep 1


title: Male Hippocampus_MREmx1-cre_rep1


title: Male Hippocampus_MREmx1-cre_rep2


title: FB 25C, Rep 1, Day 1, ZT18


title: FULVR, VP, rep 4

value: Verteporfin (VP), 2µM, 24 h


title: nlf_els_ee2_MAP1


title: FB 25C, Rep 2, Day 5, ZT12


title: FULVR, VP, rep 3

value: FULVR


title: nlf_els_ee2_SCP3


title: FULVR, VP, rep 2

value: Human breast cancer cell line (resistant to fulvestrant)


title: FB 25C, Rep 2, Day 5, ZT06


title: Male Hippocampus_GREmx1-cre_rep4

description: Gene expression from male hippocampus, GREmx1-cre


title: FB 25C, Rep 2, Day 5, ZT00


title: FULVR, VP, rep 1


title: FB 25C, Rep 2, Day 4, ZT18


title: nlf_els_ee2_MEP5


title: nlf_els_ee2_SDP4


title: Male Hippocampus_GREmx1-cre_rep2


title: FB 25C, Rep 2, Day 5, ZT18


title: FULVR, Input

data_processing:
Raw reads were aligned to the human reference genome hg19 version using Bowtie2
Redundant reads were removed using SAMtools
Peaks were called using MACS2 with default parameters, using the input sample as control and with the significance cut-off q-value <0.01
Assembly: hg19
Supplementary files format and content: BED format (peaks common to all the biological replicates)

growth_protocol: MCF7 cells were cultured in DMEM with 10% of fetal bovine serum (FBS) plus 10nM estradiol. FULVR cells were cultured in DMEM with 10% FBS with the addition of 100nM fulvestrant

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonication device (Diagenode, B01060001)
Libraries for ChIP-seq were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, E7370S) according to the manufacturer’s instructions.

tag: chip antibody


title: FB 25C, Rep 2, Day 4, ZT12


title: nlf_els_ee2_HCP3

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.

value: HIGH


title: MCF7, Input

value: Human breast cancer cell line


title: FB 25C, Rep 2, Day 4, ZT06


title: nlf_els_ee2_MCP3


title: FB 18C, Rep 2, Day 5, ZT12


title: MCF7, TEAD4, rep 2

value: TEAD4 (Abcam, #ab58310)


title: MCF7, TEAD4, rep 1


title: nlf_els_ee2_HBP2


title: nlf_els_ee2_MBP2

value: MED


title: FULVR, TEAD4, rep 2

value: wild type MCF7 cells


title: nlf_els_ee2_SAP1

value: dmso

value: CTRL


title: Male Hippocampus_dflox control_rep3

description: Gene expression from male hippocampus, dflox control

value: dflox control


title: FB 18C, Rep 2, Day 5, ZT06

value: fat body (FB)


title: WT: Wild-type mouse digit

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 16 digits in 8 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

value: Ihh+/+; Lgr5GFP/+

tag: tissues

value: Digit III M/P1 interzones

tag: number of cells captured

tag: median number of genes per cell


title: Male Hippocampus_dflox control_rep2

value: male

value: hippocampus


title: Male Hippocampus_dflox control_rep4


title: Male Hippocampus_GREmx1-cre_rep3


title: FB 18C, Rep 2, Day 4, ZT18


title: nlf_els_ee2_HAP1

value: els

value: embryo


title: nlf_els_ee2_SBP2


title: FULVR, TEAD4, rep 1

value: FULVR


title: Male Hippocampus_GREmx1-cre_rep1


title: Male Hippocampus_dflox control_rep1


title: FB 18C, Rep 2, Day 4, ZT12


title: PVH, hM3D expressed, VPA exposed and PND2 CNO treated, snRNA-seq, rep2

city: Kobe

first: Masafumi

last: Tsurutani

state: Hyogo

address: 2-2-3 Minatojima minami, Chuo-ku

country: Japan

institute: RIKEN

description: 10X Genomics

data_processing:
To conduct the analysis, we aligned the fastq files from each library to the mm10 reference transcriptome (mm10, gencode version vm23) using the Cell Ranger pipeline (cellranger v7.0.1, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: paraventricular hypothalamic nucleus

growth_protocol: OT-Cre mice (JAX #024234) were purchased from the Jackson Laboratory. Rosa26tm9(CAG-tdTomato)Hze mice (also known as Ai9 mice) (JAX #007909) were kindly provided by Takeshi Imai, who purchased them from the Jackson Laboratory. Rosa26dreaddm3 mice (also known as stop-hM3 mice) were kindly provided by Takeshi Sakurai. All mice were maintained on a C57BL6 background. Animals were housed at the animal facility of the RIKEN Center for Biosystems Dynamics Research (BDR) under ambient temperature (18–23 C) and a 12-h light, 12-h dark cycle schedule. The mice were allowed free access to the laboratory diet (MFG; Oriental Yeast, Shiga, Japan; 3.57 kcal/g) and water unless otherwise mentioned.

extract_protocol:
Male OT-Cre; Ai9 mice at 5 weeks of age were deeply anesthetized by isoflurane (Fujifilm, #099-06571), perfused by cold phosphate-buffered saline (PBS) to remove blood cells, and euthanized by decapitation. Brains were sectioned into 1000-μm coronal slices under microscopy and the sections were floated in 1% BSA-PBS (Nacalai Tesque, #0128197 and Takara, #T9181). The PVH was dissected based on the fluorescence of tdTomato in OT-Cre; Ai9 male mice, and homogenized sufficiently in ice-cold Nuclei EZ Lysis Buffer (Millipore Sigma, N-3408). The resulting suspension was incubated on ice for 5 min and filtered through a 70-μm strainer. The nuclei were pelletized by centrifugation at 500xg and 4 ℃ for 5 min, and the supernatant was removed. The nuclei were resuspended in Nuclei EZ Lysis Buffer and pelletized again by centrifugation at 500xg and 4 ℃ for 5 min. They were then resuspended in 1% BSA-PBS containing 0.2 U/μL RNase Inhibitor (Roche, 3335399001) (Resuspension Buffer). We utilized 2–4 male mice for each condition, pooled the isolated nuclei, and centrifuged again at 500xg and 4 ℃ for 5 min to pellet the nuclei. The nuclei were then resuspended in resuspension buffer and 10 μg/mL DAPI, and filtered through a 40-μm strainer. The nuclei were sorted from the suspension using a cell sorter (SH800Z; Sony) at 5 ℃. The gate was set first to identify a single nucleus population based on the DAPI signal and then to select larger nuclei preferentially, inferring neurons while simultaneously excluding multiplets. Immediately after sorting was completed, the nuclei stained with DAPI were counted using a hemocytometer to verify the yield of intact nuclei.  For the recovery experiments, we utilized male OT-Cre; stop-hM3 mice at 5–7 weeks of age that had been exposed to VPA prenatally and CNO or saline as a control at PND 2. We followed the above protocols with slight modifications. Briefly, OT-Cre; stop-hM3 mice were injected with AAV in the PVH and the supraoptic nucleus regions at three weeks of age to facilitate visualization of OT neurons during the dissection process. To optimize the yield in collecting neural cell nuclei, the FACS gating was adjusted to accommodate larger nuclei.
Utilizing the 10X Genomics Chromium platform, we crafted single-nucleus RNA libraries targeting a total of 8,000 nuclei per condition for OT-Cre; Ai9 batches. The library preparation was accomplished using the 10X Genomics RNA 3' v3.1 kit (#1000269). Subsequently, the completed libraries were subjected to sequencing to a depth of 110 gigabases using the HiSeqX platform (performed by Novogene, Inc.). For OT-Cre; stop-hM3 mice batches, the aim was to isolate 5,000 nuclei using the Chromium system.

treatment_protocol: To generate a group of mice treated with VPA, we administrated sodium valproate (Sigma, #P4543) at a dosage of 500 mg/kg to pregnant female mice on gestation day 12.5, based on the identification of the mating day through the formation of a vaginal plug. For the control group of mice treated with saline, we injected 10 mL/kg saline to pregnant female mice at the same stage.

value: paraventricular hypothalamic nucleus

value: C57BL6 background

value: OT-Cre; Rosa26dreaddm3

value: Neurons, astrocytes, microglia, oligodendrocytes, oligodendrocyte progenitor cells

value: exposed to valproic acid at prenatal day 12.5 and CNO treatment administered two days postnatal


title: FULVR, VGLL1, rep 3

value: Human breast cancer cell line (resistant to fulvestrant)

value: wild type MCF7 cells

value: VGLL1 (Proteintech, #10124-2-AP)


title: nlf_els_ee2_MDP4

first: Niladri

last: Basu

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

value: MED


title: BDA1-tech-rep1: IhhE95K/E95K/Lgr5DTR-GFP/+ technical replicate 1

description: 10X Genomics single-cell RNA-seq

source_name: pool of 14 digits in 7 embryos


title: nlf_els_ee2_HEP5

value: HIGH


title: FB 18C, Rep 1, Day 5, ZT18

value: fat body (FB)


title: PVH, hM3D expressed and VPA exposed, snRNA-seq

department: Center for Biosystems Dynamics Research (BDR)

description: 10X Genomics

value: exposed to valproic acid at prenatal day 12.5 and saline treatment administered two days postnatal


title: FULVR, VGLL1, rep 2


title: nlf_els_ee2_HDP4


title: PVH, VPA exposed, snRNA-seq

description: 10X Genomics

value: OT-Cre; Rosa26tm9(CAG-tdTomato)Hze

value: male

value: exposed to valproic acid at prenatal day 12.5


title: PVH, typical, snRNA-seq

description: 10X Genomics

value: exposed to saline at prenatal day 12.5


title: FB 18C, Rep 1, Day 5, ZT16


title: nlf_els_cpf_MCP3

value: els

value: embryo

value: cpf


title: FB 18C, Rep 1, Day 5, ZT12


title: BEA-Treated3

city: Guelph

first: Umesh

middle: K.

last: Shandilya

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

institute: University of Guelph

description: Sample 15

data_processing:
CLC genomics workbench
Sequence reads were trimmed for adaptor sequences using CLC genomics workbench.
Trimmed sequences were mapped to Bovine genome Bos_Taurus.ARS-UCD1.2.101 using CLC genomics workbench
Read count extraction and normalization were performed using CLC genomics benchwork
Assembly: Bos_Taurus.ARS-UCD1.2.101
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM for each sample

organism: Bos taurus

source_name: Mammary gland

growth_protocol: The bovine epithelial cell line (MAC-T) was cultured in a T25 culture flask (Corning, Tewksbury, MA, USA) according to the previous protocol in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 U/mL; Invitrogen, Waltham, MA, USA; Thermo Fisher Scientific, Inc., Waltham, MA, USA), and maintained in an incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted from the MAC-T cells of the co-culture system 48 h after mycotoxin exposure using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina Seq library preparation kit using the manufacturer instructions

treatment_protocol: The bovine macrophage (BoMac) cell line was cultured in a T25 culture flask (Corning, Tewksbury, MA, USA) using Roswell Park Memorial Institute 1640 medium (RPMI 1640; Invitrogen, Burlington, ON, Canada). The culture medium was supplemented with 2.0 mM L-glutamine, 10% heat-inactivated fetal bovine serum (FBS; Invitrogen), 2.5 mM HEPES buffer (Invitrogen), 1 mM Sodium Pyruvate (Invitrogen), and 1% Antibiotic-Antimycotic (containing 100 units/mL of penicillin, 100 µg/mL of streptomycin, and 0.25 µg/mL of amphotericin B; Invitrogen). The cells were maintained at 37 °C in an atmosphere containing 5% CO2.

value: Mammary gland

value: MAC-T

value: Mammary epithelial cells

value: WT

value: BEA


title: PVH, hM3D expressed, VPA exposed and PND2 CNO treated, snRNA-seq, rep1

description: 10X Genomics

value: paraventricular hypothalamic nucleus

value: C57BL6 background

value: OT-Cre; Rosa26dreaddm3

value: Neurons, astrocytes, microglia, oligodendrocytes, oligodendrocyte progenitor cells

value: exposed to valproic acid at prenatal day 12.5 and CNO treatment administered two days postnatal


title: FB 18C, Rep 1, Day 5, ZT14

value: fat body (FB)


title: nlf_els_cpf_MBP2

value: MED


title: nlf_els_cpf_HDP4

value: HIGH


title: BEA-Treated2

description: Sample 14


title: ENB-Treated3

description: Sample 12

value: ENB


title: FB 18C, Rep 1, Day 5, ZT08


title: BEA-Treated1

description: Sample 13


title: FB 18C, Rep 1, Day 5, ZT10


title: FB 18C, Rep 2, Day 4, ZT06


title: 1000_10_00

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Assembly: NC_000913, NC_002947, L27758
Supplementary files format and content: Excel file includes FPKM values for each sample
Supplementary files format and content: Excel file includes LOG2FC values for each sample

organism: Escherichia coli

source_name: Bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Total RNA was extracted using the Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed the donor (E. coli K-12 LE392) and intrageneric recipient or intergeneric recipient at a 1:1 ratio in PBS, and  incubation in triplicate for 8 h in 0.1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1000 nm PS, 10 mg/L 1000 nm PS, at 25 °C

tag: strain 1

value: E. coli K-12 LE392

tag: strain 2

value: E. coli BL21 (DE3)

value: Bacteria

value: Intrageneric conjugation under the exposure of 10 mg/L 1000 nm PS


title: FULVR, VGLL1, rep 1

value: FULVR

value: Human breast cancer cell line (resistant to fulvestrant)

value: wild type MCF7 cells

value: VGLL1 (Proteintech, #10124-2-AP)


title: FB 18C, Rep 1, Day 5, ZT06

tag: tissue


title: nlf_els_cpf_MAP1

city: Sainte-Anne-de-Bellevue

tag: lifestage

value: els

value: embryo

tag: chemical

value: cpf


title: ENB-Treated2

description: Sample 11

value: Mammary gland

value: MAC-T

tag: cell type

value: Mammary epithelial cells

value: WT


title: 1000_0.1_01

value: Intrageneric conjugation under the exposure of 0.1 mg/L 1000 nm PS with ROS scavenger


title: 120_10_01

value: Intrageneric conjugation under the exposure of 10 mg/L 120 nm PS with ROS scavenger


title: ENB-Treated1

description: Sample 10

tag: cell line

value: ENB


title: FB 18C, Rep 1, Day 5, ZT04

value: fat body (FB)


title: 120_10_00

value: E. coli K-12 LE392

value: E. coli BL21 (DE3)

value: Bacteria

value: Intrageneric conjugation under the exposure of 10 mg/L 120 nm PS


title: nlf_els_cpf_HCP3

tag: concentration

value: HIGH


title: 1000_10_01

tag: treatment

value: Intrageneric conjugation under the exposure of 10 mg/L 1000 nm PS with ROS scavenger


title: nlf_els_cpf_HEP5

value: els


title: DON-Treated3

description: Sample 9

tag: genotype

value: DON


title: FB 18C, Rep 1, Day 5, ZT02


title: 1000_0.1_00

value: Intrageneric conjugation under the exposure of 0.1 mg/L 1000 nm PS


title: DON-Treated1

description: Sample 7

value: Mammary gland


title: FB 18C, Rep 1, Day 5, ZT00


title: DON-Treated2

description: Sample 8

value: MAC-T


title: FB 18C, Rep 1, Day 4, ZT22


title: LPS control 3

description: Sample 6

value: Mammary epithelial cells

value: LPS


title: 20_10_01

value: Intrageneric conjugation under the exposure of 10 mg/L 20 nm PS with ROS scavenger


title: FB 18C, Rep 1, Day 4, ZT20


title: 20_10_00

value: Intrageneric conjugation under the exposure of 10 mg/L 20 nm PS


title: FB 18C, Rep 1, Day 4, ZT18


title: 20_0.1_01

value: Intrageneric conjugation under the exposure of 0.1 mg/L 20 nm PS with ROS scavenger


title: LPS control 1

description: Sample 4

value: WT


title: nlf_els_cpf_MEP5

value: embryo

value: cpf

value: MED


title: 20_0.1_00

value: E. coli K-12 LE392

value: E. coli BL21 (DE3)

value: Bacteria

value: Intrageneric conjugation under the exposure of 0.1 mg/L 20 nm PS


title: nlf_els_cpf_SCP3

value: els

value: dmso

value: CTRL


title: nlf_els_cpf_HAP1

value: HIGH


title: nlf_els_cpf_SBP2


title: FB 18C, Rep 1, Day 4, ZT14

value: fat body (FB)


title: nlf_els_cpf_SEP5


title: 120_0.1_00

value: Intrageneric conjugation under the exposure of 0.1 mg/L 120 nm PS


title: 120_0.1_01

value: Intrageneric conjugation under the exposure of 0.1 mg/L 120 nm PS with ROS scavenger


title: Control 01

value: Intrageneric conjugation with ROS scavenger


title: nlf_els_cpf_MDP4


title: nlf_els_cpf_HBP2


title: FB 18C, Rep 1, Day 4, ZT12


title: LPS control 2

description: Sample 5

value: Mammary gland

value: MAC-T

value: Mammary epithelial cells

value: LPS


title: byMM1736

city: Tianjin

first: Lifang

middle: Li

last: Yu

state: Tianjin

address: Wei Jin road

institute: Tianjin University

data_processing:
Data evaluation and quality control: 1) The quality of the original data of sequencing was evaluated by FastQC. 2) Trimmomatic is used for mass shearing, and relatively accurate and effective data are obtained.
RNAseq sequencing evaluation: 1) Compare the valid data of the sample with the reference genome by using HISAT2, and count the Mapping information. 2) According to the comparison results, RSeQC was used to perform redundant sequence analysis and insert fragment distribution analysis. 3) Using Qualimap to check the homogeneity distribution and analyze the genome structure distribution according to the comparison results. 4) statistical analysis of gene coverage and distribution of sequencing sequences on chromosomes were carried out by BEDTools.
Gene structure analysis: 1) Use BCFtools to find out possible SNP sites according to the Mapping results, and use SnpEff to determine the influence of SNP sites on genes.  2) Assemble the sequence Mapping to the genome with StringTie, and then compare it with the known gene model with GffCompare to find new transcription regions. 3) Perform variable shear analysis with ASprofier. 4) Use EricScript to analyze the fusion gene.
Expression level analysis: 1) Use StringTie and known gene models to evaluate the expression of genes. 2) Using WGCNA to analyze the co-expression of genes. 3) Multi-directional statistical analysis and exploration, such as comparative analysis of samples, are carried out based on the expression matrix of samples.
Analysis of expression differences: 1) Use DESeq2 to analyze gene expression difference, and visualize the results of expression difference analysis. 2) Mapping the differential genes to the STRING protein interaction network database to construct the protein interaction network. 3) Based on the results of difference analysis, Wayne diagram and heat map are drawn and cluster analysis is carried out.
Assembly: Saccharomyces cerevisiae S288C（NCBI）
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1777 and byMM1827), log 2 fold changes, P-value, Q- value, results
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1736 and byMM1832), log 2 fold changes, P-value, Q- value, results

organism: Saccharomyces cerevisiae

source_name: Control strain, wihtout ScRNA expression cassette, for dCas12e:ScRNA activator

extract_protocol:
toal RNA  was ectracted and quality from S. cereviase by using Total RNA Extractor (Trizol) and Qubit2.0 RNA examination kit
Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina®  kit

value: eukaryocyte

value: Control strain: just included dCas12e, MCP-VP64 fusion proteinwithout the ScRNA, no any activation


title: Control 00

value: E. coli K-12 LE392

value: E. coli BL21 (DE3)

value: Intrageneric conjugation


title: byMM1827

source_name: experimental strain contains denAsCas12a:ScRNA activator for HED1 endogenous gene activation

value: Experimental strain included denAsCas12a, MCP-VP64 fusion protein, ScRNA that can target to pHED1, the final result was activate the expression of HED1 endogenous gene.


title: nlf_els_cpf_SDP4

value: els

value: embryo

value: dmso


title: nlf_els_cpf_SAP1

value: CTRL


title: FB 18C, Rep 1, Day 4, ZT10

source_name: fat body (FB)

value: fat body (FB)


title: 1000_10_11

organism:
Pseudomonas putida
Escherichia coli

value: P. putida KT2440

value: Bacteria

value: intergeneric conjugation under the exposure of 10 mg/L 1000 nm PS with ROS scavenger


title: byMM1777

source_name: Control strain, wihtout ScRNA expression cassette, for denAsCas12a:ScRNA activator

value: Control strain: just included denAsCas12a, MCP-VP64 fusion proteinwithout the ScRNA, no any activation


title: nlf_els_bap_SBP2


title: FB 18C, Rep 1, Day 4, ZT08