title: EP000004A06_3_0.149731CF_TC00284663_P18

description:
EP000004A06_3_0.149731CF
TC00284663_P18

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_6

tag: chemical concentration

tag: dose level

value: Drinking Water


title: EP000004A06_1_0.014967CF_TC00284663_P14

status: Public on Mar 05 2024

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
EP000004A06_1_0.014967CF
TC00284663_P14

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 Cells

growth_protocol: Experiments were performed using MCF7 breast adenocarcinoma cells (ATCC® HTB-22) cultured in Dulbecco’s Modified Eagle Medium (DMEM) + 10% heat-inactivated fetal bovine serum (FBS) containing 1× Gibco® penicillin-streptomycin-glutamine (PSG). For each independent culture, a single vial of MCF7 cells was thawed, subject to a uniform expansion and passaging schedule to generate enough cells for seeding in 384-well plates and to ensure that cells were tested at a consistent passage number across all replicate cultures. At the time of seeding into assay plates (Corning 3985BC), cell suspensions were volumetrically adjusted with growth media to a concentration of 2.5x10^2 cells / µL. Forty microliters of cell suspension was then dispensed into each assay well using a MultiFlo FX multi-mode dispenser equipped with a 10 µL dispensing cassette (BioTek, Winooski, VT) in order to achieve an initial seeding density of 10,000 live cells / well. Cells were dispensed into all wells of the HTTr assay plates except column 1 to allow for addition of transcriptomic reference samples to be added to each HTTr assay plate following lysate preparation. After seeding, assay plates were placed in a humidified incubator (37°C) with 5% CO2 atmosphere for 24 h prior to treatment.

extract_protocol:
Six hours after water extract treatment, HTTr assay plates were removed from the incubator and media in each assay well drained to a residual volume of 10 µL. A 10 µL volume of 2× BioSpyder lysis buffer was dispensed into each assay well. Then, 20 µL volumes of Universal Human Reference RNA (UHRR), Human Brain Reference RNA (HBRR), bulk lysates from MCF7 cells treated with 0.5% DMSO (BL DMSO) or 1 µM trichostatin A (BL TSA), and lysis buffer blans were dispensed into the first column of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 min. 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. 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 water extracts collected from each sampling site were shipped frozen to US EPA and stored at  80°C prior to dose plate preparation. Eight-point dilution series (1/2 log10 spacing) of each stock sample was prepared in a LabCyte Echo-qualified 384-well low dead volume (384LDV) plate. Transcriptomics reference chemicals for MCF7 cells (genistein, trichostatin A, sirolimus) were solubilized as 200× dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the reference chemicals were added to the dose plates along with quadruplicate wells of pure DMSO as a vehicle control. The dose plate was then sealed with a Nunc aluminum adhesive plate cover and stored at -80°C until use. On the first day of dosing, the dose plate was thawed to room temperature inside a desiccator, centrifuged briefly to ensure even distribution of the dose solution in each well and unsealed. A LabCyte Echo 550 acoustic dispenser was then used to transfer 200 nL of dosing solutions to the assay plates containing 40 uL of culture media. The final DMSO concentration was 0.5% for all treatment, reference treatment and vehicle control wells. Well coordinates were uniquely randomized on each assay plate with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

tag: treatment

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_6

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: PanSci, mouse liver, part 4

city: New York

first: Zehao

last: Zhang

state: NY

address: 1230 York Ave, The Rockefeller University

institute: The Rockefeller University

description:
EXP101_EXP121_Liver
PanSci_liver_genecount.mtx
PanSci_liver_df_cell.csv
PanSci_liver_df_gene.csv

library_source: transcriptomic single cell

data_processing:
Demultiplex - bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) < 2)
Trim - trim_galore/v0.4.1 with default settings
Alignment - STAR/v2.5.2b with default settings
SAM spilt and gene count generation - customized scripts (https://github.com/JunyueCaoLab/EasySci)
Assembly: mm39
Supplementary files format and content: genecount.mtx - gene count sparse matrix file for each organ
Supplementary files format and content: df_cell.csv - cell annotation csv file for each organ
Supplementary files format and content: df_gene.csv - gene annotation csv file for each organ

molecule: nuclear RNA

organism: Mus musculus

source_name: liver

extract_protocol:
The 10X PBS-hypotonic stock solution was prepared as per the method outlined in [doi: 10.1038/s41596-022-00752-0]. On the day of nuclei extraction, fresh working lysis solution was prepared by diluting 1X hypotonic lysis buffer with RNase-free water (Corning, #46-000-CM), supplementing with 3mM MgCl2, 1% Diethyl pyrocarbonate (Sigma Aldrich, #40718) and specifically optimized detergent for each organ/tissue type: 0.025% IGEPAL CA-630 (VWR, #IC0219859650) for kidney, lung, liver, brown adipose tissue, inguinal adipose tissue, and perigonadal adipose tissue; 0.01% Digitonin (Thermo Fisher, #BN2006) for heart, muscle, duodenum, jejunum, ileum, and colon;  0.49% CHAPS (Sigma Aldrich, #220201) for the stomach. Additionally, 0.33M sucrose (Sigma Aldrich, #S0389) was included in the working lysis buffer for the stomach and intestinal tissues (duodenum, jejunum, ileum, and colon) to maintain osmotic balance and protect the nuclei.  Dry tissue powder stored in liquid nitrogen was directly transferred into 10 mL of the pre-prepared working lysis solution, and a brief vortexing for 10 seconds is followed to disperse larger powder chunks. The mixture was then incubated at 4 °C for 15 minutes with constant racking, and immediately passed through a 40 μm cell strainers (VWR, #470236-276) with the 5 mL syringe plunger. Filter was then rinsed with an additional 5 mL working lysis solution. Finally the extracted nuclei were collected by centrifugation at 500g for 5 minutes at 4 °C, and resuspended in nuclei suspension buffer [10 mM Tris-HCl pH 7.5 (Thermo Fisher, #15567027), 10 mM NaCl (Thermo Fisher, #AM9760G), 3 mM MgCl2 (Sigma Aldrich, #68475-100ML-F) supplemented with 1% SUPERase⋅In RNase Inhibitor (Thermo Fisher, #AM2696) and 0.2mg/mL BSA or Recombinant Albumin (New England Biolabs, #B9000S or #B9200S)] supplemented with 0.005 mg/mL DAPI (Thermo Fisher, #D1306) for fluorescence-activated cell sorting. Sorting were perform on SH800 Cell Sorter with 100 μm sorting chip (Sony, #LE-C3210). All DAPI positive singlet nuclei were included to unbiased recover global cell population and remove cellular debris and doublet cells. Nuclei were collected into a 1.5mL tube (Eppendorf, #022431021 ) with a 100 μL nuclei suspension buffer as the receiving buffer. Sorted clean nuclei were then collected by centrifugation 500g for 5 minutes at 4 °C.
EasySci-RNA; The sequencing library generation for the sorted nuclei was conducted in accordance with the EasySci protocol [doi: https://doi.org/10.1101/2022.09.28.509825]. Briefly, the sorted nuclei were first distributed into 96-well plates for reverse transcription, where indexed oligo-dT primers and indexed random hexamers were used to add the first index. After this, the nuclei were then pooled, washed, and redistributed into fresh 96-well plates for the attachment of a second index by ligation. Following another pooling and washing step, the nuclei were redistributed into the final plates for second-strand synthesis, purification, tagmentation with Tn5 transposase and finally PCR to add the final indexes. Final PCR product is pooled and purified with 0.8X AMPure XP SPRI Reagent (Beckman coulter, #A63882). Each library's quality was assessed using an Agilent TapeStation and sequencing was performed on an Illumina NovaSeq 6000 System with an S4 Flow Cell. For the current study, in addition to the previously reported mouse brain data, a total of 25 NovaSeq S4 runs were executed to generate the new data.

tag: tissue

value: liver

tag: genotype


title: EpiLC_0h_clone8_2

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
Raw reads were processed with bcl2fastq (v 2.19.1) and STAR (v 2.5.3a) was used to map sequencing reads
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw counts per sample

growth_protocol: CRAFR26 ESCs were differentiated into EpiLCs by plating into N2B27 media supplemented with 12 ng/ml bFGF (Peprotech, 450-33-100µG), 20 ng/ml Activin A (Peprotech, 120-14E-200µG) and 1 µM XAV939 (Sigma, X3004).

extract_protocol:
RNA was extracted using the RNEasy Mini Kit (Qiagen, 74106) following manufacturer’s instructions.
1 µg of RNA per sample was treated for ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (NEB, E6350) and then immediately followed by Library prep using NEBNext Ultra II kit (NEB, E7770)

treatment_protocol: For ERK induction, EpiLCs were cultured for 2h before the experiment in 250 nM of the FGFRi PD17 (PD173074, Sigma, P2499). Then, the c-RAF kinase construct was induced by adding 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904).

tag: cell type

value: EpiLC

tag: clone

value: clone 8

tag: time

value: PD17 2h


title: PanSci, mouse liver, part 3


title: total RNA-seq from sample_261

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
Quality control with FastQC version 0.11.8
Unique Molecular Identifiers extraction with UMI-tools version 1.1.1
Adapter trimming with cutadapt version 2.10
Read aligning to the reference genome with STAR version 2.7.7a
Read deduplication with UMI-tools version 1.1.1
Quantification of gene expression with featureCounts version 1.6.4
Batch correction for the GC content and randomization_batch with ComBat_seq from the sva package version 3.38.0
Normalization with vst from DESeq2 version 1.30.1
Assembly: GRCh38.p12
Supplementary files format and content: raw_counts.tsv contains the output of featureCounts (unfiltered raw counts)
Supplementary files format and content: normalized_data.tsv contains the batch corrected and normalized data with low-count genes and genes that are heavily influenced by the GC content filtered out

source_name: PBMCs

extract_protocol:
Blood was collected in the morning under fasted conditions, peripheral blood mononuclear cells (PBMCs) were extracted and stored at in the gas phase of liquid nitrogen. The RNA was extracted automatically with the chemagic 360 instrument by using the chemagic RNA Kit according to the manufacturer’s instructions and 25µl eluate stored in a PCR plate at -80°C until further processing.
200ng RNA was used for rRNA depletion with the RiboCop rRNA Depletion Kit V1.3. 10µl of the depleted RNA was used for library preparation with the Lexogen CORALL total RNA-Seq Library Prep Kit with UDIs 12 nt Sets A1-A4. The library was sequenced on an NovaSeq 6000 using an S4 200 flow cell with paired-end 100bp reads.

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: control

tag: plate

tag: row

value: F

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_262

value: D


title: EpiLC_2h_clone8_1

tag: cell line

tag: treatment

value: PD17 2h, 4OHT 2h


title: DMSO_TC00284663_P10

description:
DMSO
TC00284663_P10

value: 0.5% DMSO vehicle control

tag: media

tag: chemical name

value: DMSO

tag: chemical sample_id

tag: chemical concentration

value: 0 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: PanSci, mouse liver, part 2

tag: tissue

tag: genotype


title: EP000004B04_4_0.497018CF_TC00284663_O23

description:
EP000004B04_4_0.497018CF
TC00284663_O23

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: total RNA-seq from sample_260

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: A

tag: column


title: PanSci, mouse liver, part 1


title: RSC_rev_clone8_2

growth_protocol: CRAFR26 RSCs were routinely cultured in N2B27 media supplemented with 2 µM IWP2 (Millipore, 681671), 1 µM of the MEKi PD03 (PD0325901, Sigma, PZ0162) and 1000 U/ml of LIF (prepared in house).

treatment_protocol: For ERK induction, RSCs were cultured for 48h before the experiment in 250 nM of the FGFRi PD17 (PD173074, Sigma, P2499) instead of PD03. Then, the c-RAF kinase construct was induced by adding 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904).

tag: cell line

value: RSC

tag: clone

tag: time

value: rev

tag: treatment

value: PD17 48h, 4OHT 4h, MEKi 2h


title: total RNA-seq from sample_259

value: B

tag: rin

tag: gc content

tag: randomization batch


title: PanSci, mouse lung, part 9

description:
EXP100_Lung
PanSci_lung_genecount.mtx
PanSci_lung_df_cell.csv
PanSci_lung_df_gene.csv

source_name: lung

tag: tissue

value: lung


title: EP000004A12_4_0.497018CF_TC00284663_O22

description:
EP000004A12_4_0.497018CF
TC00284663_O22

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_12

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Surface Water


title: total RNA-seq from sample_258

tag: cell type

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

value: control

tag: plate

tag: row

value: C

tag: column


title: EP000004A01_3_0.149731CF_TC00284663_O18

description:
EP000004A01_3_0.149731CF
TC00284663_O18

tag: cell line

tag: treatment

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_1

tag: media


title: RSC_rev_clone8_1

tag: clone

value: clone 8

tag: time


title: EpiLC_2h_clone4_2

value: EpiLC

value: clone 4

value: PD17 2h, 4OHT 2h


title: PanSci, mouse lung, part 8

tag: tissue

tag: genotype


title: RSC_rev_clone4_2

value: RSC


title: total RNA-seq from sample_257

tag: rin

tag: gc content

tag: randomization batch


title: PanSci, mouse lung, part 7


title: EP000004A03_1_0.014967CF_TC00284663_O16

description:
EP000004A03_1_0.014967CF
TC00284663_O16

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_3

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: RSC_rev_clone4_1

tag: cell line

tag: cell type

value: rev

tag: treatment

value: PD17 48h, 4OHT 4h, MEKi 2h


title: EpiLC_0h_clone8_1

tag: clone

tag: time

value: PD17 2h


title: total RNA-seq from sample_255

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: A

tag: column


title: total RNA-seq from sample_256

value: G

tag: rin

tag: gc content

tag: randomization batch


title: PanSci, mouse lung, part 6

tag: tissue

value: lung

tag: genotype


title: RSC_4h_clone8_2

tag: cell line

value: PD17 48h, 4OHT 4h


title: EpiLC_0h_clone4_1

tag: cell type


title: PanSci, mouse lung, part 5


title: EP000004A11_8_50.000000CF_TC00284663_O11

description:
EP000004A11_8_50.000000CF
TC00284663_O11

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_11

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: GEN_TC00284663_O09

description:
GEN
TC00284663_O09

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: RSC_4h_clone8_1

value: RSC

tag: clone

value: clone 8

tag: time


title: PanSci, mouse lung, part 4


title: total RNA-seq from sample_254

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

value: control

tag: plate

tag: row

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: RSC_4h_clone4_2

tag: cell line

tag: cell type

value: clone 4

tag: treatment


title: total RNA-seq from sample_253

value: female

value: D


title: EP000004A02_1_0.014967CF_TC00284663_O08

description:
EP000004A02_1_0.014967CF
TC00284663_O08

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_2

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Wastewater


title: PanSci, mouse lung, part 3

tag: tissue

value: lung

tag: genotype


title: EP000004A05_5_1.473477CF_TC00284663_O03

description:
EP000004A05_5_1.473477CF
TC00284663_O03

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_5

tag: water type

value: Surface Water


title: total RNA-seq from sample_252

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: E

tag: column

tag: rin


title: RSC_4h_clone4_1

tag: cell line

tag: cell type

tag: clone

tag: time

tag: treatment

value: PD17 48h, 4OHT 4h


title: TSA_TC00284663_N23

description:
TSA
TC00284663_N23

value: 6h exposure of 1 uM of Trichostatin A

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well


title: EP000004A09_3_0.149731CF_TC00284663_O17

description:
EP000004A09_3_0.149731CF
TC00284663_O17

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_9

tag: water type

value: Blank


title: PanSci, mouse lung, part 2

tag: tissue

tag: genotype


title: RSC_2h_clone8_2

value: RSC

value: clone 8

value: PD17 48h, 4OHT 2h


title: RSC_2h_clone8_1


title: PanSci, mouse lung, part 1


title: EP000004A08_1_0.014967CF_TC00284663_N21

description:
EP000004A08_1_0.014967CF
TC00284663_N21

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_8


title: PanSci, mouse kidney, part9

description:
EXP096_Kidney
PanSci_kidney_genecount.mtx
PanSci_kidney_df_cell.csv
PanSci_kidney_df_gene.csv

source_name: kidney

value: kidney


title: RSC_2h_clone4_2

value: clone 4


title: EP000004A11_7_12.711864CF_TC00284663_N19

description:
EP000004A11_7_12.711864CF
TC00284663_N19

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_11


title: total RNA-seq from sample_249

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: control

tag: plate

tag: row

value: B

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: PanSci, mouse kidney, part8


title: total RNA-seq from sample_248

tag: cell type


title: EP000004A06_5_1.473477CF_TC00284663_N17

description:
EP000004A06_5_1.473477CF
TC00284663_N17

tag: cell line

tag: treatment

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_6

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

value: Drinking Water


title: PanSci, mouse kidney, part7

tag: tissue

tag: genotype


title: RSC_0h_clone8_2

tag: clone

tag: time


title: total RNA-seq from sample_247

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: C

tag: column


title: Untrtd_TC00284663_N14

description:
Untrtd
TC00284663_N14

tag: cell line

tag: treatment

value: untreated

tag: media

value: DMEM + 10% HI-FBS

tag: assay plate

tag: assay plate_well

tag: water type


title: RSC_0h_clone8_1

tag: cell type

value: RSC


title: total RNA-seq from sample_246

value: F

tag: rin

tag: gc content

tag: randomization batch


title: RSC_0h_clone4_2

tag: clone

tag: time


title: PanSci, mouse kidney, part5

tag: tissue

tag: genotype


title: total RNA-seq from sample_245

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

value: A


title: PanSci, mouse kidney, part4


title: total RNA-seq from sample_250

tag: row

value: D

tag: column


title: total RNA-seq from sample_251


title: TSA_TC00284663_N16

description:
TSA
TC00284663_N16

tag: cell line

tag: treatment

value: 6h exposure of 1 uM of Trichostatin A

tag: media

tag: chemical name

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well


title: RSC_0h_clone4_1

tag: cell type

tag: clone

value: clone 4

tag: time


title: EP000004A07_7_12.711864CF_TC00284663_N07

description:
EP000004A07_7_12.711864CF
TC00284663_N07

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_7

tag: water type

value: Reclaimed Water


title: total RNA-seq from sample_244

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: control

tag: plate

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_243

value: male

tag: row

value: B

tag: column


title: PanSci, mouse kidney, part3

tag: tissue

value: kidney

tag: genotype


title: EP000004B05_5_1.473477CF_TC00284663_N09

description:
EP000004B05_5_1.473477CF
TC00284663_N09

tag: cell line

tag: treatment

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_17

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Drinking Water


title: EP000004B03_5_1.473477CF_TC00284663_N06

description:
EP000004B03_5_1.473477CF
TC00284663_N06

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_15

tag: water type

value: Wastewater


title: PanSci, mouse kidney, part2


title: RSC_2h_clone4_1

tag: cell type

value: RSC

tag: clone

tag: time

value: PD17 48h, 4OHT 2h


title: ESC_rev_clone8_1

growth_protocol: CRAFR26 mESCs were routinely cultured on 0.1% gelatine-coated flasks in 2i/LIF media consisting of N2B27 media supplemented with 3 μM of the GSK3 inhibitor Chir (Axon, CHIR99021), 1 μM of the MEKi PD03 (PD0325901, Sigma PZ0162) and 1000 U/ml of LIF (prepared in house).

treatment_protocol: For ERK induction, mESCs were cultured for 48h before the experiment in 250 nM of the FGFRi PD17 (PD173074, Sigma, P2499) instead of PD03. Then, the c-RAF kinase construct was induced by adding 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904).

value: ESC

value: clone 8

value: rev

value: PD17 48h, 4OHT 4h, MEKi 2h


title: ESC_rev_clone8_2


title: total RNA-seq from sample_242

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: ESC_rev_clone4_2

tag: cell line

value: clone 4

tag: treatment


title: EP000004B02_8_50.000000CF_TC00284663_N05

description:
EP000004B02_8_50.000000CF
TC00284663_N05

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_14

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Blank


title: PanSci, mouse kidney, part1

tag: tissue

value: kidney

tag: genotype


title: total RNA-seq from sample_241

tag: cell type

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: control

tag: plate

tag: row

value: D


title: EP000004A03_7_12.711864CF_TC00284663_M24

description:
EP000004A03_7_12.711864CF
TC00284663_M24

tag: cell line

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_3

tag: media

value: DMEM + 10% HI-FBS

tag: water type

value: Surface Water


title: ESC_rev_clone4_1

value: ESC

tag: clone

tag: time


title: PanSci, mouse kidney, part6


title: trachea, 24 months, replicate 2, scRNA

city: Boston

first: Gergana

last: Shipkovenska

state: Massachusetts

address: 185 Cambridge Street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, genome alignment and gene counting were performed using Cell Ranger.
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files

source_name: trachea

extract_protocol:
Murine tracheas were dissected from 2 young (2-month) and 2 old (24-month) animals and dissociated to single cells in a two-step protocol. Tracheas were first incubated in papain and DNase  I for 30min at 37℃ with rotation, then triturated to release cells. Cells, debris and undissociated tracheal husks were pelleted and resuspended for a second enzymatic digestion in a mix of collagenase I, hyaluronidase, dispase, papain and DNase I for 20min at 37℃ with rotation. After the second digestion the husks including the cartilaginous scaffold dissociated fully. Single cells were filtered through a 100µm filter and red blood cells were lysed.
Libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v.3.1, according to the manufacturer's instructions.

value: trachea

value: male

value: trachea unsorted single cells

value: 24 months


title: total RNA-seq from sample_240

value: PBMCs

value: E

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: ESC_4h_clone8_2

tag: cell type

value: clone 8

value: PD17 48h, 4OHT 4h


title: EP000004A06_8_50.000000CF_TC00284663_M23

description:
EP000004A06_8_50.000000CF
TC00284663_M23

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_6

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Drinking Water


title: trachea, 2 months, replicate 2, scRNA

description: 10x Genomics

tag: tissue

tag: Sex

tag: genotype

tag: age

value: 2 months


title: EP000004B02_2_0.049970CF_TC00284663_M21

description:
EP000004B02_2_0.049970CF
TC00284663_M21

tag: cell line

tag: treatment

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_14

tag: media

tag: water type

value: Blank


title: trachea, 24 months, replicate 1, scRNA

description: 10x Genomics


title: ESC_4h_clone8_1

tag: clone

tag: time


title: EP000004A12_3_0.149731CF_TC00284663_M20

description:
EP000004A12_3_0.149731CF
TC00284663_M20

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_12

value: DMEM + 10% HI-FBS

tag: chemical name


title: total RNA-seq from sample_238

tag: cell type

tag: bmi

tag: status

value: control

tag: plate

tag: row

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_237

tag: age

tag: Sex

value: female

value: C


title: ESC_4h_clone4_2

tag: cell line

value: ESC

value: clone 4

tag: treatment


title: EP000004B06_4_0.497018CF_TC00284663_M19

description:
EP000004B06_4_0.497018CF
TC00284663_M19

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_18

tag: media

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Surface Water


title: trachea, 2 months, replicate 1, scRNA

description: 10x Genomics

tag: tissue

value: trachea

value: male

tag: cell type

value: trachea unsorted single cells

tag: genotype


title: KO Male Low-calcium diet [KO_M_LC_29]

city: Indianapolis

first: Anika

last: Shimonty

state: Indiana

address: 635 Barnhill Dr

department: Indiana Center for Musculoskeletal Health

institute: Indiana University

data_processing:
The sequencing reads were quality-checked using FastQC (v0.11.5).
The read counts matrix was imported to R Team (2022) and analyzed with DEseq2.
Within DESeq2, read counts data were normalized with median of ratios, and differentially expressed genes (DEGs) were detected after independent filtering.
sequence data were mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v2.7.10a) with the following parameter: “--outSAMmapqUnique60”.
Assembly: mm10
Supplementary files format and content: Normalized read counts for each sample and all genes

source_name: long bone osteocyte

extract_protocol:
Osteocyte RNA was extracted from tibia and femur diaphyses after sequential digestion to remove surface cells including osteoclasts, osteoblasts, and lining cells. Briefly, soft tissue was removed from the bones, the epiphyses were cut off and bone marrow was removed by flushing with PBS. The remaining midshafts were incubated at 37○C with 0.2% type 1 collagenase for 30 minutes, followed by chelation/ digestion in 0.53 mM EDTA/ 0.05% trypsin at 37○C for 30 min followed by a second collagenase digestion. After each step, the bone chips were rinsed with PBS and after the final step, flash-frozen in liquid nitrogen, and pulverized in liquid nitrogen, with Trizol reagent added to the resulting bone powder. Total RNA was isolated with an RNA purification kit (Qiagen miRNeasy mini kit) and DNase treatment to remove DNA contamination.
100 nanograms of total RNA were used for library preparation with the KAPA total RNA Hyperprep Kit (KK8581) (Roche). Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation. Multiple libraries were pooled in equal molarity. The pooled libraries were sequenced on an Illumina NovaSeq 6000 sequencer with the v1.5 reagent kit. 100 bp paired-end reads were generated.

treatment_protocol: 5-month-old male and female WT and FNDC5 global KO mice were fed either a control diet (0.6% calcium, Teklad, TD.97191) or a low calcium (Ca) diet (0.01% calcium, 0.4% phosphorus, Teklad TD.95027) for 2 weeks.

value: long bone osteocyte

tag: strain background

value: Male

value: FNDC5/ irisin KO

value: 2 weeks of low-calcium-diet


title: total RNA-seq from sample_236

value: PBMCs

tag: bmi

tag: status

tag: plate

tag: row

value: F

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: KO Male Low-calcium diet [KO_M_LC_31]

tag: age

tag: Sex

tag: treatment


title: EP000004A07_5_1.473477CF_TC00284663_M18

description:
EP000004A07_5_1.473477CF
TC00284663_M18

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_7

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Reclaimed Water


title: total RNA-seq from sample_235

tag: cell type

value: female

tag: bmi

tag: status

value: control

tag: plate

tag: row

value: E


title: ESC_2h_clone8_2

value: ESC

tag: clone

value: clone 8

tag: time

value: PD17 48h, 4OHT 2h


title: ESC_2h_clone8_1

tag: treatment


title: EP000004B06_2_0.049970CF_TC00284663_M15

description:
EP000004B06_2_0.049970CF
TC00284663_M15

tag: cell line

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_18

tag: water type

value: Surface Water


title: WT Male low-calcium diet [WT_M_LC_26]

tag: tissue

value: long bone osteocyte

tag: age

tag: strain background

tag: Sex

tag: genotype

value: WT


title: EP000004B03_6_4.716981CF_TC00284663_M17

description:
EP000004B03_6_4.716981CF
TC00284663_M17

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_15

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

value: Wastewater


title: EP000004A08_6_4.716981CF_TC00284663_M13

description:
EP000004A08_6_4.716981CF
TC00284663_M13

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_8

tag: assay plate_well


title: ESC_2h_clone4_1

tag: cell type

tag: clone

value: clone 4

tag: time


title: ESC_2h_clone4_2

tag: cell line

tag: treatment


title: total RNA-seq from sample_234

value: PBMCs

tag: age

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: C

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_239

tag: Sex

value: A


title: WT Male low-calcium diet [WT_M_LC_9]

tag: tissue

tag: strain background

value: Male

tag: genotype

value: 2 weeks of low-calcium-diet


title: total RNA-seq from sample_232

tag: cell type

value: female

value: control


title: EP000004A07_8_50.000000CF_TC00284663_M11

description:
EP000004A07_8_50.000000CF
TC00284663_M11

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_7

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Reclaimed Water


title: WT Male low-calcium diet [WT_M_LC_8]

value: long bone osteocyte

tag: age

value: WT

tag: treatment


title: total RNA-seq from sample_233

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_231

tag: cell type

tag: Sex

value: F


title: ESC_0h_clone8_2

tag: cell line

value: ESC

tag: clone

value: clone 8

tag: time


title: EP000004B06_3_0.149731CF_TC00284663_M06

description:
EP000004B06_3_0.149731CF
TC00284663_M06

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_18

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Surface Water


title: ESC_4h_clone4_1

value: clone 4

tag: treatment

value: PD17 48h, 4OHT 4h


title: total RNA-seq from sample_230

value: PBMCs

tag: age

tag: bmi

tag: status

tag: plate

tag: row

tag: column

tag: rin


title: EP000004A08_3_0.149731CF_TC00284663_M05

description:
EP000004A08_3_0.149731CF
TC00284663_M05

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_8

tag: water type

value: Wastewater


title: ESC_0h_clone8_1

tag: cell type

tag: clone

tag: time


title: KO Female Low-calcium diet [KO_F_LC_5]

tag: tissue

tag: strain background

tag: Sex

value: Female

tag: genotype

value: FNDC5/ irisin KO

value: 2 weeks of low-calcium-diet


title: KO Female Low-calcium diet [KO_F_LC_6]

tag: treatment


title: KO Male Low-calcium diet [KO_M_LC_12]

tag: age

value: Male


title: total RNA-seq from sample_229

value: female

tag: bmi

value: affected

tag: gc content

tag: randomization batch


title: WT Female Low-calcium diet [WT_F_LC_18]

value: long bone osteocyte

value: WT


title: ESC_0h_clone4_1

value: ESC


title: ESC_0h_clone4_2


title: total RNA-seq from sample_228

value: male

tag: status

tag: plate

tag: row

value: C


title: EP000004B01_4_0.497018CF_TC00284663_M02

description:
EP000004B01_4_0.497018CF
TC00284663_M02

tag: cell line

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_13

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well


title: WT Female Low-calcium diet [WT_F_LC_17]

tag: tissue

tag: strain background

tag: Sex

tag: genotype

tag: treatment


title: total RNA-seq from sample_227

tag: cell type

tag: age

tag: bmi

tag: status

value: E

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A11_5_1.473477CF_TC00284663_L24

description:
EP000004A11_5_1.473477CF
TC00284663_L24

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_11

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: water type

value: Blank


title: WT Female Low-calcium diet [WT_F_LC_16]

tag: tissue

tag: strain background

tag: Sex

tag: genotype


title: mouse ES cells, Uhrf1-/- +K667R/K668R/K670R mutant human UHRF1 rescue

city: Hong Kong

first: Zhongjun

last: Zhou

state: Hong Kong

address: Room 3-53, Laboratory Block,, 21 Sassoon Road,

country: Hong Kong

institute: The University of Hong Kong

library_source: genomic

data_processing:
Adapter sequences (read1: -AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-; read2: -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA-) were trimmed by using cutadapt implemented in Trim Galore. Low-quality bases were trimmed by using the following algorithm: Subtract 22 from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal. Only reads whose length is not less than 30 after above process was retained. The parameters used were “trim_galore --stringency 4 --quality 22 --clip_R1 7 -- clip_R2 7”.
The cleaned reads were mapped back to mouse genome (mm10) using BSMAP software version 2.73 . The parameters used were “bsmap -n 0 -v 0.08 -R -u -z 33”. Methylation ratios were extracted from BSMAP output using a Python script (methratio.py) which is distributed with the BSMAP package. Only unique mapped reads were used to calculate methylation ratios. Only cytosines in a CpG context with sufficient sequencing depth (greater than or equal to 5x coverage) were retained for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include information of all identified CpG cytosines for each Sample. "meth_3KR.diff.txt" file shows CpG methylation in wild-type, Uhrf1-/- and Uhrf1-/- with wild-type or K667R/K668R/K670R mutant human UHRF1 rescue mESCs. "meth_mMofKD.diff.txt" file shows CpG methylation in wild-type and Mof knockdown mESCs.
Supplementary files format and content: In "meth_3KR.diff.txt" and "meth_mMofKD.diff.txt" files, "mWT1" refers to sample "mESCs_WT_1"; "mWT2" refers to sample "mESCs_WT_2"; "UFKO_1" refers to sample "mESCs_Uhrf1KO_1"; "UFKO_2" refers to sample "mESCs_Uhrf1KO_2"; "m3KR" refers to sample "mESCs_Uhrf1KO+3KR"; "mUKOU2" refers to sample "mESCs_Uhrf1KO+hUHRF1"; "mMofKD" refers to sample "mESCs_MofKnockdown"; "mWT" refers to the average of sample "mESCs_WT_1" and "mESCs_WT_2"; "UFKO" refers to the average of sample "mESCs_Uhrf1KO_1"and "mESCs_Uhrf1KO_2".

molecule: genomic DNA

source_name: J1 ESCs

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin (Sigma) coated dishes in DMEM (high glucose, Gibco, 11965), supplemented with 15% ES-fetal bovine serum (Gibco, 16141-079), 100 units/mL Leukemia Inhibitory Factor (Millipore, ESG1107), GlutaMAX Supplement (Life Technologies, 35050), Sodium Pyruvate (Life Technologies, 11360), and 2-Mercaptoethanol (Life Technologies, 31350), maintained in a 37°C incubator with 5% CO2, and passaged every two days.

extract_protocol:
Total genomic DNA was extracted using TIANamp Genomic DNA Kit (TIANGEN, DP304).
The double-enzyme RRBS library was prepared according to a previously published protocol (PMC3570491).
The libraries were sequenced using Illumina NextSeq 500 system according to the manufacturer’s instructions.

value: J1 ESCs

tag: cell type

value: Embryonic stem cells

value: Uhrf1-/- +K667R/K668R/K670R human UHRF1 rescue


title: total RNA-seq from sample_226

value: PBMCs

tag: age

tag: bmi

tag: status

tag: plate

tag: row

value: G


title: mouse ES cells, Uhrf1-/- +wild-type human UHRF1 rescue

tag: cell line

value: Uhrf1-/- +wild-type human UHRF1 rescue


title: EP000004A07_3_0.149731CF_TC00284663_L22

description:
EP000004A07_3_0.149731CF
TC00284663_L22

tag: treatment

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_7

tag: media

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Reclaimed Water


title: KO Male control [KO_M_C_27]

value: long bone osteocyte

value: Male

value: FNDC5/ irisin KO


title: total RNA-seq from sample_225

value: female

value: affected

value: H

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: mouse ES cells, Uhrf1-/-, sample 2

tag: genotype


title: total RNA-seq from sample_224

tag: cell type

tag: Sex

value: B


title: KO Male control [KO_M_C_28]

tag: tissue

tag: age

tag: strain background


title: KO Male control [KO_M_C_10]


title: total RNA-seq from sample_223

value: male

tag: bmi

tag: status

tag: plate

tag: row


title: TSA_TC00284663_L15

description:
TSA
TC00284663_L15

tag: cell line

tag: treatment

value: 6h exposure of 1 uM of Trichostatin A

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time

tag: water type


title: EP000004A12_5_1.473477CF_TC00284663_L19

description:
EP000004A12_5_1.473477CF
TC00284663_L19

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_12

tag: assay plate

tag: assay plate_well

value: Surface Water


title: EP000004B03_3_0.149731CF_TC00284663_L18

description:
EP000004B03_3_0.149731CF
TC00284663_L18

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_15

value: Wastewater


title: mouse ES cells, Uhrf1-/-, sample 1

value: J1 ESCs

tag: cell type

value: Embryonic stem cells

tag: genotype


title: WT Male control [WT_M_C_25]

tag: tissue

value: long bone osteocyte

tag: age

tag: strain background

tag: Sex

value: Male

value: WT


title: mouse ES cells, wild type, sample 2

description:
meth_3KR.diff.txt
meth_mMofKD.diff.txt

tag: cell line

value: wild type


title: EP000004B01_6_4.716981CF_TC00284663_M03

description:
EP000004B01_6_4.716981CF
TC00284663_M03

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_13


title: EP000004A09_2_0.049970CF_TC00284663_L14

description:
EP000004A09_2_0.049970CF
TC00284663_L14

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_9

tag: media

value: Blank


title: total RNA-seq from sample_222

value: PBMCs

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: E

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: mouse ES cells, Mof stable knockdown

tag: cell type

value: Mof knockdown


title: total RNA-seq from sample_221

value: H


title: WT Male control [WT_M_C_24]

tag: genotype


title: EP000004B03_2_0.049970CF_TC00284663_L13

description:
EP000004B03_2_0.049970CF
TC00284663_L13

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_15

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: WT Male control [WT_M_C_7]

tag: tissue

tag: age

tag: strain background

tag: Sex

tag: treatment


title: total RNA-seq from sample_220

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin

tag: gc content


title: KO Female control [KO_F_C_20]

value: long bone osteocyte

value: Female

tag: genotype

value: FNDC5/ irisin KO


title: total RNA-seq from sample_219

tag: cell type

value: D

tag: randomization batch


title: EP000004B06_8_50.000000CF_TC00284663_L08

description:
EP000004B06_8_50.000000CF
TC00284663_L08

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_18

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Surface Water


title: KO Female control [KO_F_C_19]

tag: tissue

tag: age

tag: strain background

tag: Sex

tag: treatment


title: EP000004A01_5_1.473477CF_TC00284663_L07

description:
EP000004A01_5_1.473477CF
TC00284663_L07

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_1

tag: water type

value: Reclaimed Water


title: total RNA-seq from sample_218

tag: cell type

value: PBMCs

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: F

tag: column

tag: rin

tag: gc content


title: KO Female control [KO_F_C_4]

tag: genotype


title: adult brain, per01 control-3

city: Ann Arbor

first: Swathi

last: Yadlapalli

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
Reads were trimmed to remove sequencing adapters (cutadapt 4.1) and aligned against the dm6 genome assembly using Bowtie2 (version 2.4.5) with parameters ‘--very-sensitive --dovetail -X 1000’.
After alignment, mitochondrial reads were removed (samtools 1.15.1) and PCR duplicates were removed using Picard Tools (version 2.27.4).
BAM alignment was converted to BED using Bioconductor (Release 3.14) Rsamtools to split read pairs into single BED rows.
Peak calling (MACS2 2.2.7.1) was performed using parameters '-g dm -q 0.001 --nomodel --shift -37 --extsize 74 --keep-dup all'.
Pile-up of ATAC signal was obtained by R Bioconductor (Release 3.14) GenomicRanges package.
Assembly: dm6
Supplementary files format and content: bigWig, pile-up of ATAC signal
Supplementary files format and content: narrowPeak, MACS2 output of called peaks

organism: Drosophila melanogaster

source_name: adult brain

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study were previously described or obtained from the Bloomington Stock Center: Clk-GAL4 (BDSC#93198), per01 (BDSC#80928).

extract_protocol:
~50 fly brains were dissected and dissociated with collagenase. Single cell suspension was sorted on a BD Aria III sorter to isolate clock neurons (GFP+ DAPI-) and non-clock cells (GFP- DAPI-). Sorted clock neurons were immediately used for ATAC assay.
Transposed DNA was amplified using limited-cycle PCR. Ampliication cycle numbers were determined by qPCR to make sure exponential phase of amplification. Amplified libraries were purified by non-selective SPRI bead purification and size distribution was assessed by gel electrophoresis(Agilent Tapestation, high-sensitivity DNA 5000 assay). If excess adapter dimers were observed, an extra size-selective SPRI purification was performed.

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5-7 days, followed by a shift to complete darkness (DD) for another 6-7 days. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period. When referencing the times in the continuous darkness phase, we use Circadian Time (CT) - with CT0 (subjective dawn) marking the time when lights would have been turned on and CT12 (subjective dusk) the time when lights would have been turned off.

value: adult brain

value: non-clock cells

value: per01 (per01/Y;ClkGAL4, UAS-GFP-NLS/+;)

value: constant condition (CT)


title: total RNA-seq from sample_216

value: B

tag: randomization batch


title: adult brain, per01 control-4


title: adult brain, per01 CT24 repeat-4

value: clock neurons ClkGAL4


title: adult brain, per01 CT36 repeat-3


title: adult brain, per01 CT36 repeat-4


title: total RNA-seq from sample_217

value: female


title: EP000004B04_7_12.711864CF_TC00284663_L04

description:
EP000004B04_7_12.711864CF
TC00284663_L04

tag: cell line

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_16

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well


title: EP000004A02_4_0.497018CF_TC00284663_L06

description:
EP000004A02_4_0.497018CF
TC00284663_L06

tag: treatment

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_2

tag: water type

value: Wastewater


title: WT Female control [WT_F_C_14]

tag: tissue

value: long bone osteocyte

tag: age

tag: strain background

tag: Sex

value: Female

value: WT


title: WT Female control [WT_F_C_32]

tag: genotype


title: adult brain, per01 CT24 repeat-3

tag: cell type


title: EP000004B03_4_0.497018CF_TC00284663_L03

description:
EP000004B03_4_0.497018CF
TC00284663_L03

tag: cell line

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_15


title: total RNA-seq from sample_215

value: PBMCs

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: mouse ES cells, wild type, sample 1

description:
meth_3KR.diff.txt
meth_mMofKD.diff.txt

value: J1 ESCs

value: Embryonic stem cells

value: wild type


title: WT Female control [WT_F_C_1]

tag: treatment


title: total RNA-seq from sample_214

value: G


title: Untrtd_TC00284663_K20

description:
Untrtd
TC00284663_K20

value: untreated

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: Tracer TLS Explant Multiseq 3- scRNAseq

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: Single-cell RNA-sequencing of 3 pooled Tracer TLS and 3 TLSCL after explant 2

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
Reads were aligned against the mouse genome (mm10 with additional chromosomes for GFP and mCherry), and barcodes and unique molecular identifiers were counted using ‘cellranger count’.
Assembly: mm10
Supplementary_files_format_and_content:  For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix. 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.
Library strategy: Amplicon-seq

molecule: polyA RNA

source_name: Tracer TLS Explant Multiseq 3- scRNAseq

growth_protocol: For the explant experiments, Tracer TLS and TLSCL have been derived as previously described. To this end, 500 cells per well have been seeded for these experiments. At day 5 TLS and TLSCL have been imaged using the Zeiss Celldiscoverer 7 with incubator chamber temperature set at 37°C and CO2 content at 5%. Next, the most posterior ends from eight TLS and eight TLSCL have been manually dissected using microdissection forceps under a stereomicroscope and each explant transferred in a well of an Ibidi 8-well glass-bottom plates (Ibidi 80827) using a p10 pipette with minimal transferring volume. The anterior portion of each structure has been subjected to single cell RNA sequencing. The dissection was carried out to include most of the posterior end, paying attention not to include any somite. Pre-incubated NDiff227 medium (see “Generation of Tracer Trunk-Like Structures” section) was then put on ice for 5 minutes, after which MG was added to a concentration of 5%. Medium was then put at room temperature for 5 minutes. MG-supplemented medium (200µl) was then added in each well containing an explant, and each of the explant was repositioned in the center of each well and imaged using the Zeiss Celldiscoverer 7 with incubator chamber temperature set at 37°C and CO2 content at 5%. Explant cultures were then returned to the incubator and further cultured at 37°C and 5% or 7.5% CO2 for 24h. The following day, outgrowths from the explants were imaged and used for single cell RNA sequencing.

extract_protocol:
Single-cell RNAseq (scRNA-seq) experiments have been performed as previously described (Veenvliet, Bolondi et al 2020). Briefly, Tracer TLS were generated as described above. Two individual 120h TLS (Tracer TLS 1 and 2) were selected based on the presence of one axis of elongation, clear formation of a neural tube domain and segmentation. Individual structures were picked with a p200 with the pipette tip cut-off at the 50µl mark, and serially washed through pipette transferring (cut 200µl tip) in wells filled with 200µl of 1xPBS/0.4%BSA (5 transfers) to get rid of the Matrigel. Each structure was then dissociated in 200µl TrypLE Express (Gibco) for 25 minutes at 37ºC, with pipetting every 5 minutes intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40µm. Cells were washed twice with 1ml 1xPBS/0.4%BSA with centrifugation steps performed for 5 minutes at 1200rpm in low DNAbind Eppendorf tubes. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3.1; one structure per reaction). Single-cell libraries were generated according to the manual, with one modification: fewer PCR cycles (n=8) were ran than recommended during cDNA amplification or library generation/sample indexing to increase library complexity. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were sequenced with a minimum of 400 million paired end fragments according to parameters described in the manual.
Lineage tracing barcodes (intBCs) libraries were prepared for all samples via PCR amplification from the double stranded 10x cDNA. Briefly, 100ng of 10x cDNA was used to prepare 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 68ºC 30sec – 72ºC 40sec (10 cycles)/ 72ºC 2 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.45X/0.7X) was performed to purify the intBCs libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using asymmetric end sequencing (150 cycles kit; 28/91 FC-410-1002) on a Novaseq platform at a minimum of 100 million fragments per sample.

tag: strain

tag: cell type

value: mESC

tag: genotype

value: LSL-Cas9-GFP-Tracer BC library


title: EP000004B06_5_1.473477CF_TC00284663_L09

description:
EP000004B06_5_1.473477CF
TC00284663_L09

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_18

value: DMEM + 10% HI-FBS

value: Surface Water


title: adult brain, per01 CT36 repeat-2

tag: tissue

value: adult brain

value: clock neurons ClkGAL4

value: per01 (per01/Y;ClkGAL4, UAS-GFP-NLS/+;)

value: constant condition (CT)


title: EP000004A06_4_0.497018CF_TC00284663_K19

description:
EP000004A06_4_0.497018CF
TC00284663_K19

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_6

value: Drinking Water


title: Tracer TLS Explant Multiseq 2- scRNAseq

description: Single-cell RNA-sequencing of 3 pooled Tracer TLS and 3 TLSCL after explant 1

source_name: Tracer TLS Explant Multiseq 2- scRNAseq


title: total RNA-seq from sample_212

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

tag: column

tag: rin

tag: gc content


title: total RNA-seq from sample_211

value: C

tag: randomization batch


title: Tracer TLS Explant Multiseq 1 - scRNAseq

description: Single-cell RNA-sequencing of 3 pooled Tracer TLS and 3 TLSCL before explant


title: EP000004B02_7_12.711864CF_TC00284663_K14

description:
EP000004B02_7_12.711864CF
TC00284663_K14

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_14

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Blank


title: adult brain, per01 CT24 repeat-2

tag: tissue

tag: cell type

tag: genotype


title: total RNA-seq from sample_210

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: H


title: EP000004A09_5_1.473477CF_TC00284663_K17

description:
EP000004A09_5_1.473477CF
TC00284663_K17

tag: cell line

tag: treatment

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_9

tag: media

tag: water type


title: EP000004A12_6_4.716981CF_TC00284663_K12

description:
EP000004A12_6_4.716981CF
TC00284663_K12

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_12

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level


title: total RNA-seq from sample_209

value: A

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: adult brain, per01 control-2

tag: tissue

value: adult brain

tag: cell type

value: non-clock cells

tag: genotype


title: BLEOMYCIN+ DMSO 5

city: Westmead

first: Ziyan

last: Pan

state: NSW

address: 176 Hawkesbury Rd

department: Storr Liver Centre

country: Australia

institute: Westmead Institute for Medical Resea

data_processing:
Some fastq files were found to be corrupt after transfer and storage. All processed data files were derived from uncorrupted fastq files.
Library sequencing quality was determined using FastQC (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/). Illumina adaptor sequence and low quality read trimming(read pair removed if < 20 base pairs) was performed using Trim Galore! (BabrahamBioinformatics). STAR was used to align reads to human genome hg38 using ENSEMBL gene annotations as a guide. Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts.
All analyses were performed in the R Statistical Environment with tidyverse Briefly, counts data were background corrected and normalized for library size using edgeR DGE was determined using the QLFtest (BH MTC p <0.05 or uncorrected p value 0.01). Gene lists were functionally annotated with GO pathways (adjusted p value <0.05) using the clusterProfiler package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated from mouse tissue using an RNA mini kit (Qiagen). RNA purity and integrity were confirmed by Agilent Bioanalyzer.
Sequencing libraries were prepared from 100-500ng total RNA using TrueSeq RNA sample preparation kit v2 (Illumina). Broadly speaking, mRNA is purified, fragmented, and used for first and second strand cDNA synthesis, followed by adenylation of the 3 '-end. The samples were connected to a unique adapter and amplified by PCR. The libraries were validated, standardized, and sequenced using the 2100 BioAnalyzer(Agilent). Three bioreplicated RNA-seq libraries were sequenced on Illumina HiSeq 2000 using barcode multiplexing and a read length of 100 bp for each condition, four bioreplicates were performed for each condition.

value: lung

value: Wild type

value: bleomycin+DMSO injection


title: EP000004A05_3_0.149731CF_TC00284663_K09

description:
EP000004A05_3_0.149731CF
TC00284663_K09

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_5

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Surface Water


title: adult brain, per01 CT36 repeat-1

value: clock neurons ClkGAL4

value: per01 (per01/Y;ClkGAL4, UAS-GFP-NLS/+;)

tag: treatment

value: constant condition (CT)


title: adult brain, wildtype CT control-3

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)


title: BLEOMYCIN+MERTK inhibitor(UNC569) 6

value: bleomycin+UNC569 injection


title: SHAM (NORMAL)+DMSO 6

value: sham+DMSO injection


title: total RNA-seq from sample_207

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: B


title: adult brain, wildtype CT36-repeat-3

value: adult brain


title: BLEOMYCIN+ DMSO 6


title: EP000004A11_3_0.149731CF_TC00284663_K04

description:
EP000004A11_3_0.149731CF
TC00284663_K04

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_11

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: water type

value: Blank


title: total RNA-seq from sample_206

tag: cell type

value: C

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: adult brain, wildtype CT24 repeat-3

tag: tissue

tag: genotype

tag: treatment


title: total RNA-seq from sample_213

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate


title: BLEOMYCIN+MERTK inhibitor(UNC569) 5

value: lung

value: Wild type


title: adult brain, per01 control-1

value: non-clock cells

value: per01 (per01/Y;ClkGAL4, UAS-GFP-NLS/+;)


title: adult brain, wildtype CT36-repeat-2

value: clock neurons ClkGAL4

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: constant condition (CT)


title: SHAM (NORMAL)+DMSO 5

value: sham+DMSO injection


title: total RNA-seq from sample_203

value: PBMCs

tag: row


title: total RNA-seq from sample_208

value: female

value: affected

value: F


title: adult brain, per01 CT24 repeat-1

value: adult brain


title: EP000004A05_1_0.014967CF_TC00284663_J21

description:
EP000004A05_1_0.014967CF
TC00284663_J21

tag: cell line

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_5

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Surface Water


title: adult brain, wildtype CT24 repeat-2

tag: tissue

tag: cell type


title: GEN_TC00284663_J19

description:
GEN
TC00284663_J19

tag: treatment

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM

tag: dose level

tag: water type


title: adult brain, wildtype CT control-2

value: non-clock cells

tag: genotype


title: SHAM (NORMAL)+DMSO 4

value: lung

value: Wild type


title: BLEOMYCIN+ DMSO 4

value: bleomycin+DMSO injection


title: total RNA-seq from sample_201

tag: age

tag: Sex

tag: bmi

tag: status

value: E

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: BLEOMYCIN+ DMSO 3


title: total RNA-seq from sample_202

tag: plate

tag: row

value: G


title: adult brain, wildtype CT24 repeat-1

value: clock neurons ClkGAL4

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: constant condition (CT)


title: EP000004A06_7_12.711864CF_TC00284663_J17

description:
EP000004A06_7_12.711864CF
TC00284663_J17

tag: cell line

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_6

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Drinking Water


title: SIRO_TC00284663_J18

description:
SIRO
TC00284663_J18

tag: treatment

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus

tag: dose level

tag: water type


title: adult brain, wildtype CT control-1

tag: tissue

value: adult brain

tag: cell type

tag: genotype


title: EP000004B06_7_12.711864CF_TC00284663_K02

description:
EP000004B06_7_12.711864CF
TC00284663_K02

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_18

value: DMEM + 10% HI-FBS

value: Surface Water


title: EP000004B04_2_0.049970CF_TC00284663_J16

description:
EP000004B04_2_0.049970CF
TC00284663_J16

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: total RNA-seq from sample_200

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

value: affected

value: F

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: BLEOMYCIN+MERTK inhibitor(UNC569) 3

value: lung

value: Wild type

value: bleomycin+UNC569 injection


title: adult brain, wildtype ZT control-4

value: non-clock cells

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: cycling condition (ZT)


title: adult brain, wildtype CT36-repeat-1

value: clock neurons ClkGAL4

value: constant condition (CT)


title: total RNA-seq from sample_205

value: female

tag: plate

tag: row

value: C


title: EP000004B05_7_12.711864CF_TC00284663_J22

description:
EP000004B05_7_12.711864CF
TC00284663_J22

tag: cell line

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_17

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Drinking Water


title: BLEOMYCIN+MERTK inhibitor(UNC569) 4

tag: tissue

tag: genotype

tag: treatment


title: total RNA-seq from sample_204

tag: cell type

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

value: A

tag: column


title: total RNA-seq from sample_199

value: affected

tag: plate

tag: row

value: D

tag: rin

tag: gc content

tag: randomization batch


title: BLEOMYCIN+MERTK inhibitor(UNC569) 2

value: lung


title: EP000004B02_6_4.716981CF_TC00284663_J03

description:
EP000004B02_6_4.716981CF
TC00284663_J03

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_14

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: water type

value: Blank


title: Lysis Buffer_TC00284663_J01

description:
Lysis Buffer
TC00284663_J01

source_name: Lysis Buffer

value: NA (Universal Human Reference RNA)

tag: treatment

value: untreated

tag: assay plate

tag: assay plate_well


title: adult brain, wildtype ZT0 repeat-4

tag: tissue

value: adult brain

tag: cell type

tag: genotype

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: cycling condition (ZT)


title: EP000004A10_1_0.014967CF_TC00284663_J04

description:
EP000004A10_1_0.014967CF
TC00284663_J04

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_10


title: total RNA-seq from sample_198

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin


title: BLEOMYCIN+DMSO 1

value: Wild type

value: bleomycin+DMSO injection


title: BLEOMYCIN+ DMSO 2


title: adult brain, wildtype ZT12 repeat-4

value: clock neurons ClkGAL4


title: BLEOMYCIN+MERTK inhibitor(UNC569) 1

value: bleomycin+UNC569 injection


title: total RNA-seq from sample_196

value: PBMCs

value: male

value: affected

value: H

tag: gc content

tag: randomization batch


title: UUO(Unilateral ureter obligation)+  DMSO 4

value: kidney

value: unilateral ureteral obstruction+DMSO injection


title: EP000004A10_5_1.473477CF_TC00284663_I24

description:
EP000004A10_5_1.473477CF
TC00284663_I24

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_10

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: water type

value: Blank


title: EP000004A02_3_0.149731CF_TC00284663_I21

description:
EP000004A02_3_0.149731CF
TC00284663_I21

tag: treatment

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_2

tag: assay plate

tag: assay plate_well

value: Wastewater


title: adult brain, wildtype ZT control-3

tag: tissue

value: adult brain

tag: cell type

value: non-clock cells

tag: genotype

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: cycling condition (ZT)


title: SHAM(normal)+DMSO KIDNEY 3

value: Wild type

value: sham+DMSO injection


title: adult brain, wildtype ZT12 repeat-3

value: clock neurons ClkGAL4


title: total RNA-seq from sample_195

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin


title: adult brain, wildtype ZT0 repeat-3


title: total RNA-seq from sample_194

value: affected

value: E

tag: gc content

tag: randomization batch


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 6

value: kidney

value: unilateral ureteral obstruction+UNC569 injection


title: adult brain, wildtype ZT control-2


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 5


title: EP000004B05_6_4.716981CF_TC00284663_I11

description:
EP000004B05_6_4.716981CF
TC00284663_I11

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_17

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: water type

value: Drinking Water


title: EP000004A05_2_0.049970CF_TC00284663_I17

description:
EP000004A05_2_0.049970CF
TC00284663_I17

tag: treatment

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_5

tag: assay plate

tag: assay plate_well

value: Surface Water


title: total RNA-seq from sample_193

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

value: A


title: adult brain, wildtype ZT12 repeat-2

tag: tissue

value: adult brain

tag: genotype

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: cycling condition (ZT)


title: total RNA-seq from sample_197

value: female

tag: row

value: C

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_192

value: PBMCs

value: male

value: H


title: EP000004A07_6_4.716981CF_TC00284663_I08

description:
EP000004A07_6_4.716981CF
TC00284663_I08

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_7

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: water type

value: Reclaimed Water


title: UUO(Unilateral ureter obligation)+  DMSO 3

value: kidney

value: Wild type

tag: treatment

value: unilateral ureteral obstruction+DMSO injection


title: total RNA-seq from sample_191

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate


title: total RNA-seq from sample_190

tag: row

value: F

tag: column

tag: rin

tag: gc content


title: UUO(Unilateral ureter obligation)+  DMSO 2

tag: tissue

tag: genotype


title: adult brain, wildtype ZT control-1

value: non-clock cells


title: adult brain, wildtype ZT0 repeat-2

value: clock neurons ClkGAL4


title: SHAM(normal)+DMSO KIDNEY 2

value: sham+DMSO injection


title: adult brain, wildtype ZT12 repeat-1

value: adult brain

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)


title: total RNA-seq from sample_189

value: A

tag: randomization batch


title: EP000004A08_8_50.000000CF_TC00284663_I04

description:
EP000004A08_8_50.000000CF
TC00284663_I04

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_8

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: assay plate

tag: assay plate_well

value: Wastewater


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 4

tag: treatment

value: unilateral ureteral obstruction+UNC569 injection


title: Lysis Buffer_TC00284663_I01

description:
Lysis Buffer
TC00284663_I01

value: NA (Universal Human Reference RNA)

value: untreated

tag: exposure time

tag: water type


title: total RNA-seq from sample_188

tag: cell type

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: H

tag: column


title: adult brain, wildtype ZT0 repeat-1

tag: tissue

tag: genotype

value: cycling condition (ZT)


title: EP000004A04_3_0.149731CF_TC00284663_H23

description:
EP000004A04_3_0.149731CF
TC00284663_H23

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_4

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: Drinking Water


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 3

value: kidney

value: Wild type

tag: treatment


title: EP000004A11_4_0.497018CF_TC00284663_H21

description:
EP000004A11_4_0.497018CF
TC00284663_H21

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_11

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: total RNA-seq from sample_187

tag: cell type

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

value: A

tag: rin

tag: gc content

tag: randomization batch


title: UUO(Unilateral ureter obligation)+  DMSO 1

tag: tissue

tag: genotype

value: unilateral ureteral obstruction+DMSO injection


title: aorta, HFD+TUDCA, rep4

city: 杭州

first: 张

last: 越晟

address: 浙江大学

country: China

institute: 浙江大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 simiality fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm 10
Supplementary files format and content: file includes raw counts for each Sample  and FPKM values for each Sample

source_name: aorta

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.
NEBNext Ultra RNA Library Prep Kit
RNA-seq Principal component analysis (PCA) was performed with R package gmodels in this experiment. RNAs differential expression analysis were performed by DESeq2 software between two groups. The genes/transcripts with parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed gene/transcripts.

value: aorta

value: APOE-/-

value: high fat diet+TUDCA


title: aorta, HFD+TUDCA, rep3


title: aorta, HFD+TUDCA, rep2


title: total RNA-seq from sample_186

value: PBMCs

tag: plate

tag: row

tag: column


title: EP000004A11_2_0.049970CF_TC00284663_I07

description:
EP000004A11_2_0.049970CF
TC00284663_I07

tag: cell line

tag: treatment

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_11

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time


title: SHAM(normal)+DMSO KIDNEY 1

value: sham+DMSO injection


title: total RNA-seq from sample_185

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

value: B


title: aorta, HFD+TUDCA, rep1

tag: tissue

tag: genotype


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 1

value: unilateral ureteral obstruction+UNC569 injection


title: EP000004B03_8_50.000000CF_TC00284663_H13

description:
EP000004B03_8_50.000000CF
TC00284663_H13

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_15

value: 50 CF

tag: assay plate

tag: assay plate_well

tag: water type

value: Wastewater


title: total RNA-seq from sample_183

value: male

tag: plate

tag: row

value: G

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: UUO(Unilateral ureter obligation)+  MERTK inhibitor(unc569) 2

value: kidney

value: Wild type

tag: treatment


title: UUO(Unilateral ureter obligation)+ unc569 2


title: EP000004A03_6_4.716981CF_TC00284663_H05

description:
EP000004A03_6_4.716981CF
TC00284663_H05

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_3

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

value: Surface Water


title: aorta, HFD, rep3

tag: tissue

value: aorta

tag: genotype

value: APOE-/-

value: high fat diet


title: EP000004A03_2_0.049970CF_TC00284663_H07

description:
EP000004A03_2_0.049970CF
TC00284663_H07

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_3

tag: assay plate

tag: assay plate_well

tag: water type


title: total RNA-seq from sample_182

tag: cell type

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: D

tag: column


title: total RNA-seq from sample_184

value: female

value: F

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_181

value: H


title: BL_TSA_TC00284663_H01

description:
BL_TSA
TC00284663_H01

tag: cell line

tag: treatment

value: 6h exposure of 0 uM of Trichostatin A

tag: media

tag: chemical name

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 0 uM

tag: dose level

tag: exposure time


title: UUO(Unilateral ureter obligation)+ unc569 1

tag: tissue

value: kidney

tag: genotype

value: unilateral ureteral obstruction+UNC569 injection


title: aorta, HFD, rep2


title: SHAM(normal)+MERTK inhibitor( UNC569) lung 3

value: lung

value: Wild type

value: sham+UNC569 injection


title: EP000004A10_2_0.049970CF_TC00284663_H16

description:
EP000004A10_2_0.049970CF
TC00284663_H16

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_10

value: DMEM + 10% HI-FBS

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: aorta, HFD, rep1

value: aorta

value: APOE-/-

value: high fat diet


title: aorta, NFD, rep4

value: normal fat diet


title: SHAM(NORMAL)+ DMSO 3

value: liver

value: sham+DMSO injection


title: total RNA-seq from sample_180

tag: cell type

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: E

tag: column


title: total RNA-seq from sample_179

value: G

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A02_7_12.711864CF_TC00284663_G22

description:
EP000004A02_7_12.711864CF
TC00284663_G22

tag: cell line

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_2

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

value: Wastewater


title: EP000004A01_1_0.014967CF_TC00284663_G20

description:
EP000004A01_1_0.014967CF
TC00284663_G20

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_1

tag: assay plate

tag: assay plate_well

tag: water type

value: Reclaimed Water


title: aorta, HFD, rep4

tag: tissue

tag: genotype


title: aorta, NFD, rep3


title: NORMAL (SHAM)+MERTK INHIBITOR(UNC569) LIVER 3

value: Wild type

value: sham+UNC569 injection


title: EP000004A12_8_50.000000CF_TC00284663_G18

description:
EP000004A12_8_50.000000CF
TC00284663_G18

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_12

value: DMEM + 10% HI-FBS

value: 50 CF

value: Surface Water


title: SHAM(NORMAL)+ DMSO 2

value: liver


title: total RNA-seq from sample_177

tag: cell type

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: H

tag: column


title: aorta, NFD, rep2

value: aorta

value: APOE-/-

tag: treatment

value: normal fat diet


title: DMSO_TC00284663_H03

description:
DMSO
TC00284663_H03

tag: cell line

value: 0.5% DMSO vehicle control

tag: media

tag: chemical name

value: DMSO

tag: chemical sample_id

tag: chemical concentration

value: 0 uM


title: total RNA-seq from sample_176

value: PBMCs

value: affected

value: D

tag: rin

tag: gc content

tag: randomization batch


title: SHAM(NORMAL)+ DMSO 1

tag: tissue

tag: genotype

value: Wild type

value: sham+DMSO injection


title: SIRO_TC00284663_G15

description:
SIRO
TC00284663_G15

value: 6h exposure of 0.1 uM of Sirolimus

value: DMEM + 10% HI-FBS

value: Sirolimus

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: total RNA-seq from sample_178

tag: cell type

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: B

tag: column


title: NORMAL (SHAM)+MERTK INHIBITOR(UNC569) LIVER 2

value: liver

tag: treatment

value: sham+UNC569 injection


title: EP000004A01_4_0.497018CF_TC00284663_G16

description:
EP000004A01_4_0.497018CF
TC00284663_G16

tag: cell line

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_1

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: Reclaimed Water


title: aorta, NFD, rep1

tag: tissue

value: aorta

tag: genotype

value: APOE-/-

value: normal fat diet


title: NORMAL (SHAM)+MERTK INHIBITOR(UNC569) LIVER 1


title: total RNA-seq from sample_175

value: PBMCs

value: female

value: E

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_174

tag: cell type

tag: age

tag: Sex

value: affected

value: H


title: P60_GM_scRNA-seq

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Division of Neurology

country: Canada

institute: The University of British Columbia

description: 10X Genomics

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome (mm10) using Cell Ranger v3 software (cellranger count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
For single-cell isolation of the early postnatal (P2, P7, and P15) and adult (P60) cortex, thick coronal sections, spanning the rostral end of the lateral ventricles to the rostral end of the hippocampus, were generated from each brain. For whole cortex datasets (P2 cortex scRNA-seq data, P7 cortex scRNA-seq data, P15 cortex scRNA-seq data, P60 cortex scRNA-seq data) the region dorsal to the lateral ventricles was dissected out. This region contained the ventricular-subventricular zone (V-SVZ), cortical white matter, and cortical grey matter. For grey matter datasets (P60 grey matter scRNA-seq data), coronal sections were taken as described above and the region dorsal to the cortical white matter was dissected out. For white matter datasets (P60 white matter scRNA-seq data), coronal sections were taken as described above and the region immediately dorsal to the lateral ventricles, containing both the corpus callosum and V-SVZ, was dissected out. For single cell isolation of the early postnatal V-SVZ (P7 SVZ scRNA-seq) the dorsal and lateral V-SVZ were microdissected out.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

value: Brain

value: Primary Cells

value: Grey matter


title: BILE DUCT LIGATION (BDL)+DMSO 6

value: Wild type

value: bile duct ligation+DMSO injection


title: P60_cortex_scRNA-seq

description: 10X Genomics

value: Cortex


title: total RNA-seq from sample_173

value: male

tag: bmi

tag: status

tag: plate

value: B


title: EP000004B04_8_50.000000CF_TC00284663_G12

description:
EP000004B04_8_50.000000CF
TC00284663_G12

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_16

value: DMEM + 10% HI-FBS

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Reclaimed Water


title: total RNA-seq from sample_172

value: PBMCs

tag: row

value: F

tag: column


title: BILE DUCT LIGATION (BDL)+DMSO 5

tag: tissue

value: liver

tag: genotype


title: EP000004A11_6_4.716981CF_TC00284663_G11

description:
EP000004A11_6_4.716981CF
TC00284663_G11

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_11

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: Blank


title: P15_cortex_scRNA-seq

description: 10X Genomics

value: Brain

tag: cell type


title: EP000004B04_3_0.149731CF_TC00284663_G10

description:
EP000004B04_3_0.149731CF
TC00284663_G10

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_16


title: BILE DUCT LIGATION (BDL)+DMSO 4


title: P7_cortex_scRNA-seq

description: 10X Genomics

value: Primary Cells


title: EP000004A01_7_12.711864CF_TC00284663_G09

description:
EP000004A01_7_12.711864CF
TC00284663_G09

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_1


title: total RNA-seq from sample_170

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

value: C

tag: rin

tag: gc content

tag: randomization batch


title: SHAM(normal)+MERTK inhibitor( UNC569) kidney 3

value: kidney

value: Wild type

tag: treatment

value: sham+UNC569 injection


title: P2_cortex_scRNA-seq

description: 10X Genomics

tag: tissue

value: Cortex


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H12_S192]

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

description:
hillockCounts.csv
sc_manju_hillock_newest_Seurat.rds

data_processing:
FASTQ files were aligned using STAR to MM10 annotation
Aligned reads were then processed using Cufflinks
Downstream analysis was performed using Seurat v4.0
Assembly: mm10
Supplementary files format and content: a concatenated count file of all single cells, and a processed Rdata, Seurat object

extract_protocol:
Cells were FACS plated into lysis buffer in 96 well plates, according to the SMART-Seq2 protocol
RNA libraries were made according to SMART-Seq2 protocols

value: trachea

value: pseudostratified

tag: genotype

tag: phenotype

value: adjacent pseudostratified basal cells


title: SHAM(normal)+MERTK inhibitor( UNC569) lung 2

value: lung


title: EP000004B02_1_0.014967CF_TC00284663_G13

description:
EP000004B02_1_0.014967CF
TC00284663_G13

tag: cell line

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_14

tag: media

value: DMEM + 10% HI-FBS

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: P60_WM_scRNA-seq

description: 10X Genomics

tag: cell type

value: White matter


title: total RNA-seq from sample_169

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: row

value: B

tag: column


title: EP000004B01_8_50.000000CF_TC00284663_G03

description:
EP000004B01_8_50.000000CF
TC00284663_G03

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_13

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

value: Wastewater


title: SHAM(normal)+MERTK inhibitor( UNC569) kidney 2

tag: tissue

value: kidney

tag: genotype


title: SIRO_TC00284663_G02

description:
SIRO
TC00284663_G02

tag: cell line

value: 6h exposure of 0.1 uM of Sirolimus

tag: media

value: Sirolimus

tag: dose level

tag: exposure time


title: total RNA-seq from sample_167

tag: cell type

value: female

value: affected

tag: plate

value: A

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A04_4_0.497018CF_TC00284663_K10

description:
EP000004A04_4_0.497018CF
TC00284663_K10

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_4

tag: assay plate

tag: assay plate_well

tag: water type

value: Drinking Water


title: SHAM(normal)+MERTK inhibitor( UNC569) lung 1

value: lung

value: Wild type

tag: treatment

value: sham+UNC569 injection


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H10_S190]

value: trachea

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: BL_TSA_TC00284663_G01

description:
BL_TSA
TC00284663_G01

value: 6h exposure of 0 uM of Trichostatin A

tag: chemical name

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 0 uM


title: SHAM(normal)+MERTK inhibitor( UNC569) kidney 1

tag: tissue

value: kidney

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H08_S188]


title: total RNA-seq from sample_166

value: PBMCs

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: row

tag: column


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 6

value: liver

value: bile duct ligation+UNC569 injection


title: total RNA-seq from sample_165

tag: cell type

value: female

value: affected

tag: plate

value: H

tag: rin

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H07_S187]

tag: phenotype


title: total RNA-seq from sample_171

value: B


title: EP000004A05_6_4.716981CF_TC00284663_F24

description:
EP000004A05_6_4.716981CF
TC00284663_F24

tag: cell line

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_5

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Surface Water


title: EP000004A11_1_0.014967CF_TC00284663_F22

description:
EP000004A11_1_0.014967CF
TC00284663_F22

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_11

tag: chemical sample_id

tag: chemical concentration

value: Blank


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 5

tag: tissue

tag: genotype

value: Wild type


title: total RNA-seq from sample_164

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: column

tag: rin


title: DMSO_TC00284663_G06

description:
DMSO
TC00284663_G06

tag: cell line

tag: treatment

value: 0.5% DMSO vehicle control

tag: media

tag: chemical name

value: DMSO

value: 0 uM

tag: dose level

tag: exposure time


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H06_S186]

tag: tissue

value: trachea

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: EP000004A01_2_0.049970CF_TC00284663_F19

description:
EP000004A01_2_0.049970CF
TC00284663_F19

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_1

tag: chemical sample_id

tag: chemical concentration

tag: assay plate

tag: assay plate_well

tag: water type

value: Reclaimed Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H05_S185]

tag: cell type

tag: genotype


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 4

value: liver

value: bile duct ligation+UNC569 injection


title: total RNA-seq from sample_163

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: H

tag: column

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_168

value: male

value: F

tag: rin


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H04_S184]

tag: tissue

tag: phenotype


title: EP000004B05_4_0.497018CF_TC00284663_F15

description:
EP000004B05_4_0.497018CF
TC00284663_F15

tag: cell line

tag: treatment

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_17

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

value: Drinking Water


title: EP000004A01_6_4.716981CF_TC00284663_F17

description:
EP000004A01_6_4.716981CF
TC00284663_F17

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_1

tag: assay plate_well

tag: water type


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 3

tag: genotype

value: Wild type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H03_S183]

value: trachea

tag: cell type

value: pseudostratified


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 1


title: total RNA-seq from sample_162

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: A

tag: column

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_161

tag: rin


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H02_S182]

tag: tissue

tag: phenotype

value: adjacent pseudostratified basal cells


title: BILE DUCT LIGATION (BDL)+ MERTK INHIBITOR(UNC569) 2

value: liver

tag: treatment


title: EP000004A03_8_50.000000CF_TC00284663_F14

description:
EP000004A03_8_50.000000CF
TC00284663_F14

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_3

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Surface Water


title: total RNA-seq from sample_160

tag: cell type

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row


title: BILE DUCT LIGATION (BDL)+DMSO 3

tag: tissue

tag: genotype

tag: treatment

value: bile duct ligation+DMSO injection


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H11_S191]

tag: phenotype


title: EP000004B06_1_0.014967CF_TC00284663_F07

description:
EP000004B06_1_0.014967CF
TC00284663_F07

tag: cell line

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_18

tag: media

tag: chemical name

tag: chemical sample_id

tag: water type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G12_S180]


title: BILE DUCT LIGATION (BDL)+DMSO 2


title: total RNA-seq from sample_159

value: F

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-H01_S181]

tag: cell type


title: EP000004A04_6_4.716981CF_TC00284663_F08

description:
EP000004A04_6_4.716981CF
TC00284663_F08

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_4

value: DMEM + 10% HI-FBS

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Drinking Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G11_S179]

tag: tissue

value: trachea

tag: genotype


title: total RNA-seq from sample_157

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: E


title: EP000004A03_3_0.149731CF_TC00284663_F02

description:
EP000004A03_3_0.149731CF
TC00284663_F02

tag: cell line

tag: treatment

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_3

tag: media

tag: chemical name

tag: chemical sample_id

tag: water type


title: BDL KO 4

value: Mertk knockout

value: bile duct ligation


title: EP000004B01_1_0.014967CF_TC00284663_F04

description:
EP000004B01_1_0.014967CF
TC00284663_F04

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_13

tag: chemical concentration

tag: dose level

tag: exposure time

value: Wastewater


title: BL_DMSO_TC00284663_F01

description:
BL_DMSO
TC00284663_F01

value: untreated

value: 0 uM

tag: assay plate

tag: assay plate_well


title: total RNA-seq from sample_155

tag: cell type

value: PBMCs

tag: age

value: female

value: H

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: EP000004B01_2_0.049970CF_TC00284663_E24

description:
EP000004B01_2_0.049970CF
TC00284663_E24

tag: cell line

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_13


title: BDL KO 3

description: one bad fastq file

tag: tissue

value: liver

tag: genotype

tag: treatment


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G08_S176]

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: BDL KO 2


title: EP000004A08_2_0.049970CF_TC00284663_E23

description:
EP000004A08_2_0.049970CF
TC00284663_E23

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_8

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: water type


title: total RNA-seq from sample_153

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: C


title: total RNA-seq from sample_154

tag: cell type

tag: age

value: male

value: E

tag: column

tag: rin


title: BDL WT 4

tag: tissue

value: Wild type

value: bile duct ligation


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G06_S174]

value: trachea

tag: genotype


title: total RNA-seq from sample_152

value: B

tag: gc content

tag: randomization batch