title: EP000004A10_4_0.497018CF_TC00284663_E15

description:
EP000004A10_4_0.497018CF
TC00284663_E15

tag: cell line

tag: treatment

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_10

tag: media

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: Blank


title: BDL KO 1

status: Public on Mar 05 2024

type: SRA

city: Westmead

first: Ziyan

last: Pan

state: NSW

address: 176 Hawkesbury Rd

department: Storr Liver Centre

country: Australia

institute: Westmead Institute for Medical Resea

description: one bad fastq file

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: liver

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.

tag: tissue

value: liver

tag: genotype

value: Mertk knockout

value: bile duct ligation


title: EP000004A04_1_0.014967CF_TC00284663_E16

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:
EP000004A04_1_0.014967CF
TC00284663_E16

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

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.

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_4

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: water type

value: Drinking Water


title: BDL WT 3

value: Wild type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G05_S173]

city: Boston

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

source_name: trachea

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

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G10_S178]


title: total RNA-seq from sample_151

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: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: H

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_156

value: C


title: EP000004A04_7_12.711864CF_TC00284663_E14

description:
EP000004A04_7_12.711864CF
TC00284663_E14

tag: cell line

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_4

tag: media

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well


title: BDL WT 2

tag: tissue

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G04_S172]

tag: cell type

tag: phenotype


title: BDL WT 1


title: EP000004A08_5_1.473477CF_TC00284663_E12

description:
EP000004A08_5_1.473477CF
TC00284663_E12

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_8

tag: chemical name

tag: chemical sample_id

tag: water type

value: Wastewater


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G03_S171]


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G09_S177]


title: BILE DUCT LIGATION (BDL)+DMSO 1

value: liver

value: bile duct ligation+DMSO injection


title: total RNA-seq from sample_149

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

tag: column

tag: rin

tag: gc content


title: total RNA-seq from sample_146

value: A

tag: randomization batch


title: EP000004B05_1_0.014967CF_TC00284663_E10

description:
EP000004B05_1_0.014967CF
TC00284663_E10

tag: cell line

tag: treatment

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_17

tag: media

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: EP000004B01_5_1.473477CF_TC00284663_E13

description:
EP000004B01_5_1.473477CF
TC00284663_E13

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_13

tag: chemical name

tag: chemical sample_id

tag: water type


title: EP000004A05_4_0.497018CF_TC00284663_E11

description:
EP000004A05_4_0.497018CF
TC00284663_E11

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_5

value: Surface Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G07_S175]

tag: tissue

value: trachea

tag: cell type

value: pseudostratified

tag: genotype

tag: phenotype

value: adjacent pseudostratified basal cells


title: BDL Sham KO 2

value: Mertk knockout

value: sham


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G02_S170]


title: total RNA-seq from sample_148

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: F

tag: column

tag: rin

tag: gc content


title: BDL Sham KO 4

value: liver

tag: treatment


title: BDL Sham KO 1


title: BDL Sham KO 3


title: total RNA-seq from sample_145

value: female

value: C

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-G01_S169]


title: total RNA-seq from sample_147

value: H


title: total RNA-seq from sample_150

value: male

value: D


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F11_S167]


title: total RNA-seq from sample_144

value: A


title: EP000004A02_6_4.716981CF_TC00284663_E08

description:
EP000004A02_6_4.716981CF
TC00284663_E08

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_2

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: Wastewater


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F12_S168]

tag: tissue

value: trachea

tag: cell type

value: pseudostratified

tag: genotype

tag: phenotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F09_S165]

value: adjacent pseudostratified basal cells


title: EP000004A06_6_4.716981CF_TC00284663_E07

description:
EP000004A06_6_4.716981CF
TC00284663_E07

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_6

tag: water type

value: Drinking Water


title: BDL Sham WT 4

description: two bad fastq files

value: Wild type

value: sham


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F10_S166]


title: BL_DMSO_TC00284663_E01

description:
BL_DMSO
TC00284663_E01

value: untreated

value: 0 uM


title: total RNA-seq from sample_143

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

tag: column

tag: rin

tag: gc content


title: BDL Sham WT 3

description: one bad fastq file

value: liver

tag: treatment


title: EP000004A04_5_1.473477CF_TC00284663_D24

description:
EP000004A04_5_1.473477CF
TC00284663_D24

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_4

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate


title: BDL Sham WT 2

tag: tissue

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F08_S164]

tag: cell type

tag: phenotype


title: GEN_TC00284663_D23

description:
GEN
TC00284663_D23

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM

tag: assay plate_well

tag: water type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F06_S162]

value: trachea


title: UUO KO 4

source_name: kidney

value: kidney

value: Mertk knockout

value: unilateral ureteral obstruction


title: EP000004A12_1_0.014967CF_TC00284663_D21

description:
EP000004A12_1_0.014967CF
TC00284663_D21

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_12

value: DMEM + 10% HI-FBS

value: Surface Water


title: total RNA-seq from sample_142

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: C

tag: column

tag: rin

tag: randomization batch


title: total RNA-seq from sample_141

value: PBMCs

tag: gc content


title: BDL Sham WT 1

value: Wild type

tag: treatment

value: sham


title: EP000004A10_8_50.000000CF_TC00284663_D18

description:
EP000004A10_8_50.000000CF
TC00284663_D18

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_10

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate

value: Blank


title: total RNA-seq from sample_140

tag: cell type

tag: age

tag: Sex

tag: bmi

value: affected

value: E


title: total RNA-seq from sample_158

tag: status

tag: plate

tag: row

tag: column


title: EP000004A01_8_50.000000CF_TC00284663_D17

description:
EP000004A01_8_50.000000CF
TC00284663_D17

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_1

tag: assay plate_well

tag: water type

value: Reclaimed Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F05_S161]

tag: tissue

value: trachea

value: pseudostratified

tag: genotype

tag: phenotype

value: adjacent pseudostratified basal cells


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F04_S160]


title: total RNA-seq from sample_138

value: B

tag: rin

tag: gc content

tag: randomization batch


title: EP000004B05_2_0.049970CF_TC00284663_D13

description:
EP000004B05_2_0.049970CF
TC00284663_D13

tag: cell line

value: 6h exposure of 0.04997 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: total RNA-seq from sample_139

tag: cell type

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: A

tag: column


title: UUO KO 2

tag: tissue

value: kidney

tag: genotype

value: Mertk knockout

tag: treatment

value: unilateral ureteral obstruction


title: UUO KO 1


title: EP000004B02_3_0.149731CF_TC00284663_D11

description:
EP000004B02_3_0.149731CF
TC00284663_D11

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_14

tag: media

tag: chemical name

tag: assay plate_well

tag: water type

value: Blank


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F02_S158]

tag: phenotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F03_S159]

tag: cell type


title: total RNA-seq from sample_136

tag: age

value: affected

value: G

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A08_7_12.711864CF_TC00284663_D09

description:
EP000004A08_7_12.711864CF
TC00284663_D09

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_8

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

value: Wastewater


title: UUO WT 3

description: one bad fastq file

tag: tissue

tag: genotype

value: Wild type

tag: treatment


title: total RNA-seq from sample_135

tag: Sex

tag: status

tag: plate

tag: row

value: B

tag: column


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F01_S157]

value: trachea

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: UUO WT 4

description: one bad fastq file


title: EP000004A03_4_0.497018CF_TC00284663_D07

description:
EP000004A03_4_0.497018CF
TC00284663_D07

tag: cell line

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_3

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: assay plate_well

tag: water type

value: Surface Water


title: UUO KO 3

value: kidney


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E12_S156]


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-F07_S163]


title: EP000004A05_7_12.711864CF_TC00284663_D06

description:
EP000004A05_7_12.711864CF
TC00284663_D06

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_5

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time


title: total RNA-seq from sample_134

value: PBMCs

tag: age

value: male

tag: bmi

value: F

tag: rin

tag: gc content

tag: randomization batch


title: UUO WT 1

tag: tissue

tag: genotype

tag: treatment

value: unilateral ureteral obstruction


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E11_S155]

tag: cell type

tag: phenotype


title: total RNA-seq from sample_133

tag: Sex

tag: status

value: affected

tag: plate

tag: row

value: H

tag: column


title: UUO Sham KO 4

value: Mertk knockout

value: sham


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E10_S154]


title: EP000004A09_4_0.497018CF_TC00284663_D04

description:
EP000004A09_4_0.497018CF
TC00284663_D04

tag: cell line

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_9

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: total RNA-seq from sample_132

tag: age

tag: bmi

value: A

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_131

tag: cell type

tag: Sex

tag: status

tag: plate


title: total RNA-seq from sample_137

value: female

tag: row

value: G

tag: column


title: UUO Sham KO 3

tag: tissue

tag: genotype

tag: treatment


title: EP000004A09_6_4.716981CF_TC00284663_C22

description:
EP000004A09_6_4.716981CF
TC00284663_C22

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_9

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


title: HBRR_TC00284663_D01

description:
HBRR
TC00284663_D01

source_name: Human Brain Reference RNA

value: NA (Universal Human Reference RNA)

value: untreated

tag: assay plate_well

tag: water type


title: UUO Sham KO 2

description: one bad fastq file

value: kidney


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E08_S152]

value: trachea

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: EP000004A02_8_50.000000CF_TC00284663_C19

description:
EP000004A02_8_50.000000CF
TC00284663_C19

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_2

value: 50 CF

value: Wastewater


title: EP000004B06_6_4.716981CF_TC00284663_C21

description:
EP000004B06_6_4.716981CF
TC00284663_C21

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_18

value: Surface Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E07_S151]


title: UUO Sham KO 1

value: Mertk knockout

value: sham


title: UUO Sham WT 4

description: one bad fastq file

value: Wild type


title: UUO WT 2

value: unilateral ureteral obstruction


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E06_S150]


title: total RNA-seq from sample_128

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: B

tag: rin

tag: gc content

tag: randomization batch


title: EP000004B05_8_50.000000CF_TC00284663_C15

description:
EP000004B05_8_50.000000CF
TC00284663_C15

tag: cell line

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_17

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: Drinking Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E05_S149]

tag: tissue

value: trachea

tag: cell type

value: pseudostratified

tag: genotype

value: adjacent pseudostratified basal cells


title: UUO Sham WT 2

value: kidney


title: total RNA-seq from sample_126

tag: age

tag: Sex

value: F

tag: column


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E04_S148]

tag: phenotype


title: EP000004A08_4_0.497018CF_TC00284663_C12

description:
EP000004A08_4_0.497018CF
TC00284663_C12

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_8

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Wastewater


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E09_S153]


title: total RNA-seq from sample_125

tag: bmi

tag: status

tag: plate

tag: row

value: G

tag: rin

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E02_S146]

tag: tissue

tag: cell type

tag: genotype


title: UUO KO2

description: one fastq file is corrupt

library_source: genomic

data_processing:
Some fastq files became corrupt during transfer and storage. The processed data were derived from the raw data before corruption.
Paired-end 100bp sequencing was performed on an Illumina platform by Novogene, yielding 30-40M paired reads per sample. The ATAC-seq utilises a Nextera transposase sequence.
Read alignment was performed using Bowtie2 version 2.2.5 in end-to-end and very sensitive modes using the hg38 reference sequence. Peak finding was accomplished using MACS2.
Differential peak analysis between samples was performed using Homer (http://homer.ucsd.edu/homer/) program getDifferentialPeaks and annotation & enrichment was performed using the Homer program annotatePeaks.pl. Integrated genomics viewer (IGV; 8) was used to visualise ATACseq data.
Assembly: mm10
Supplementary files format and content: bw; read alignmennt, peak, annotation&enrichment

molecule: genomic DNA

extract_protocol:
Mouse tissue samples were first homegenised to obtain intact nuclei and then treated with a highly active Tn5 transposable mutant capable of simultaneously tagging the target DNA with a sequencing adapter, thus completing the fragmentation of the DNA also called “tagmentation".
Labeling and library preparation were performed using the ATAC-Seq Kit (Catalog No. 53150 Active Motif North America) according to the instructions provided within the kit. The nuclei were first counted and centrifuged at 4°C, 500g speed for 5 min to prepare aliquots containing 50,000 to 100,000 nuclei. The samples were resuscitated with 100 μl ice-cold ATAC Lysis Buffer and to each sample was added 50 μl Tagmentation Master Mix and incubated in a thermomixer at 800 rpm and 37℃ for 30 minutes. The library was then prepared by PCR amplification of the labelled DNA using a unique combination of Illumina's i7/i5 primers based on a Nextera adapter. Finally, the library was purified using SPRI bead washing. Two biological replicates per condition were performed.

value: Mertk knockout

tag: treatment


title: EP000004B04_6_4.716981CF_TC00284663_C06

description:
EP000004B04_6_4.716981CF
TC00284663_C06

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_16

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: Reclaimed Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E03_S147]

tag: phenotype


title: total RNA-seq from sample_124

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

value: C

tag: column


title: total RNA-seq from sample_130

tag: status

value: affected

tag: plate

tag: row

value: H

tag: rin


title: total RNA-seq from sample_129

tag: cell type

value: A

tag: gc content

tag: randomization batch


title: EP000004A10_6_4.716981CF_TC00284663_C05

description:
EP000004A10_6_4.716981CF
TC00284663_C05

tag: cell line

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_10

value: DMEM + 10% HI-FBS

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-E01_S145]

tag: tissue

value: trachea

value: pseudostratified

tag: genotype

tag: phenotype

value: adjacent pseudostratified basal cells


title: UUO WT2

description: one fastq file is corrupt

value: kidney

value: wild type

value: unilateral ureteral obstruction


title: total RNA-seq from sample_123

tag: age

tag: Sex

tag: bmi

tag: status

value: E

tag: column


title: UUO Sham WT 3

description: one bad fastq file

value: Wild type

value: sham


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D12_S144]

tag: cell type


title: total RNA-seq from sample_122

value: PBMCs

value: male

tag: plate

tag: row

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A09_8_50.000000CF_TC00284663_C03

description:
EP000004A09_8_50.000000CF
TC00284663_C03

tag: cell line

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_9

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

value: 50 CF

tag: dose level

tag: exposure time

tag: assay plate


title: UUO WT1

tag: tissue

tag: genotype


title: EP000004A09_7_12.711864CF_TC00284663_C14

description:
EP000004A09_7_12.711864CF
TC00284663_C14

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_9

tag: assay plate_well

tag: water type


title: EP000004A06_2_0.049970CF_TC00284663_C02

description:
EP000004A06_2_0.049970CF
TC00284663_C02

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_6

value: Drinking Water


title: total RNA-seq from sample_127

tag: cell type

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: B

tag: column


title: sham UUO KO2

value: Mertk knockout

tag: treatment


title: total RNA-seq from sample_121

tag: rin

tag: gc content

tag: randomization batch


title: UUO Sham WT 1


title: EP000004A12_7_12.711864CF_TC00284663_C07

description:
EP000004A12_7_12.711864CF
TC00284663_C07

tag: cell line

value: 6h exposure of 12.7118644 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

value: Surface Water


title: sham UUO KO1

tag: tissue

value: kidney

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D10_S142]

value: trachea

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: HBRR_TC00284663_C01

description:
HBRR
TC00284663_C01

value: NA (Universal Human Reference RNA)

value: untreated

tag: assay plate_well

tag: water type


title: total RNA-seq from sample_119

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

tag: column

tag: rin


title: DMSO_TC00284663_B24

description:
DMSO
TC00284663_B24

tag: cell line

tag: treatment

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


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D08_S140]

tag: tissue

tag: cell type

tag: genotype

tag: phenotype


title: sham UUO WT2

value: wild type

value: sham


title: EP000004A03_5_1.473477CF_TC00284663_B22

description:
EP000004A03_5_1.473477CF
TC00284663_B22

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_3

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: total RNA-seq from sample_118

tag: age

tag: Sex

value: male

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: C

tag: column

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D09_S141]

tag: tissue


title: UUO KO1

value: kidney

value: Mertk knockout

tag: treatment

value: unilateral ureteral obstruction


title: sham UUO WT1

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D07_S139]

value: trachea

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: total RNA-seq from sample_117

value: PBMCs

value: D

tag: rin


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D11_S143]


title: BDL KO2

value: liver

value: bile duct ligation


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D06_S138]


title: EP000004B03_1_0.014967CF_TC00284663_B19

description:
EP000004B03_1_0.014967CF
TC00284663_B19

tag: cell line

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_15

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: Wastewater


title: total RNA-seq from sample_116

tag: age

tag: Sex

value: female

tag: bmi

tag: status

tag: plate

tag: row

value: F

tag: column

tag: gc content


title: total RNA-seq from sample_115

tag: cell type

value: affected

value: G

tag: rin

tag: randomization batch


title: BDL KO1

description: one fastq file is corrupt

tag: tissue

tag: genotype

tag: treatment


title: EP000004B02_5_1.473477CF_TC00284663_B14

description:
EP000004B02_5_1.473477CF
TC00284663_B14

tag: cell line

value: 6h exposure of 1.4734774 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: EP000004B04_1_0.014967CF_TC00284663_B20

description:
EP000004B04_1_0.014967CF
TC00284663_B20

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_16

tag: assay plate

tag: assay plate_well

value: Reclaimed Water


title: total RNA-seq from sample_120

tag: age

tag: Sex

value: male

tag: bmi

tag: status

tag: plate

tag: row

value: C

tag: column

tag: gc content


title: BDL WT2

tag: tissue

tag: genotype

value: wild type

tag: treatment


title: total RNA-seq from sample_114

tag: cell type

value: PBMCs

value: B

tag: rin

tag: randomization batch


title: total RNA-seq from sample_113

value: H


title: EP000004B01_3_0.149731CF_TC00284663_B13

description:
EP000004B01_3_0.149731CF
TC00284663_B13

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_13

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: water type


title: BDL WT1

description: one fastq file is corrupt

value: liver

value: bile duct ligation


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D03_S135]

value: trachea

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: EP000004A02_5_1.473477CF_TC00284663_B12

description:
EP000004A02_5_1.473477CF
TC00284663_B12

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_2

value: DMEM + 10% HI-FBS

tag: assay plate

tag: assay plate_well

value: Wastewater


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D05_S137]

tag: tissue


title: sham BDL KO2

tag: genotype

value: Mertk knockout

value: sham


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D01_S133]


title: total RNA-seq from sample_111

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

tag: column

tag: gc content


title: sham BDL KO1

tag: treatment


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D04_S136]

tag: cell type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C12_S132]


title: EP000004B05_3_0.149731CF_TC00284663_B08

description:
EP000004B05_3_0.149731CF
TC00284663_B08

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_17

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

value: Drinking Water


title: sham BDL WT2

description: one fastq file is corrupt

tag: tissue

tag: genotype

value: wild type


title: total RNA-seq from sample_110

value: PBMCs

tag: age

tag: Sex

tag: bmi

value: D

tag: rin

tag: randomization batch


title: EP000004B03_7_12.711864CF_TC00284663_B07

description:
EP000004B03_7_12.711864CF
TC00284663_B07

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_15

tag: assay plate

tag: assay plate_well

tag: water type


title: sham BDL WT1

value: liver

tag: treatment


title: total RNA-seq from sample_109

tag: cell type

value: male

tag: status

tag: plate

tag: row

value: A

tag: column

tag: gc content


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C11_S131]

tag: tissue

value: trachea

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: BDL KO2 p-Rpb1

data_processing:
Paired-end 100bp sequencing was performed on an Illumina platform by Novogene, yielding 30-40M paired reads per sample. Cut & Tag utilises a Nextera transposase sequence.
Read alignment was performed using Bowtie2 version 2.2.5 in end-to-end and very sensitive modes using the hg38 reference sequence.
Peak finding was accomplished using MACS2 Differential peak analysis between samples was performed using Homer (http://homer.ucsd.edu/homer/) program getDifferentialPeaks and annotation & enrichment was performed using the Homer program annotatePeaks.pl.
Assembly: mm10
Supplementary files format and content: bedgraph, expression
Supplementary files format and content: bw, peak
Library strategy: CUT&Tag

extract_protocol:
50,000 to 100,000 cells per aliquot were prepared and cleaned with a 1× wash buffer supplemented with a protease inhibitor cocktail.
The cells were combined with concanavalin A beads and incubated overnight with primary antibody at 4℃. After incubation with the antibody, the chromatin was directly clipped, tagentation was performed using protein A-Tn5 (pA-Tn5) transposition, and NGS libraries are prepared. The CUT&Tag-ITTM assay kit (catalog No. 53160Active Motif North America) was used for labelling and library preparation according to the instructions accompanying the kit. Two biological replicates per condition were performed.

tag: genotype


title: UHRR_TC00284663_B01

description:
UHRR
TC00284663_B01

source_name: Universal Human Reference RNA

tag: cell line

value: NA (Universal Human Reference RNA)

value: untreated

tag: media

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time


title: total RNA-seq from sample_108

tag: age

tag: Sex

tag: bmi

tag: rin

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C10_S130]

tag: cell type


title: total RNA-seq from sample_107

tag: status

tag: plate

tag: row

value: H

tag: column

tag: gc content


title: BDL KO2 CTCF

tag: tissue

tag: genotype

value: Mertk knockout

tag: treatment

value: CTCF


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C09_S129]

tag: phenotype


title: EP000004A10_3_0.149731CF_TC00284663_A21

description:
EP000004A10_3_0.149731CF
TC00284663_A21

tag: cell line

value: 6h exposure of 0.1497305 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: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: BDL KO2 H3K27ac


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C08_S128]

tag: cell type


title: total RNA-seq from sample_112

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: C

tag: rin

tag: randomization batch


title: total RNA-seq from sample_106

value: male

value: G

tag: column

tag: gc content


title: BDL KO2 H3K27me3

tag: tissue

value: liver

tag: genotype

tag: treatment


title: EP000004A07_4_0.497018CF_TC00284663_A20

description:
EP000004A07_4_0.497018CF
TC00284663_A20

tag: cell line

value: 6h exposure of 0.4970179 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: assay plate

value: Reclaimed Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C07_S127]

value: trachea

tag: cell type

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: BDL KO2 H3K4me3

value: Mertk knockout


title: EP000004A04_2_0.049970CF_TC00284663_A19

description:
EP000004A04_2_0.049970CF
TC00284663_A19

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_4

tag: assay plate_well

tag: water type

value: Drinking Water


title: total RNA-seq from sample_105

tag: age

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: D

tag: column

tag: rin

tag: randomization batch


title: total RNA-seq from sample_104

tag: gc content


title: EP000004B02_4_0.497018CF_TC00284663_A18

description:
EP000004B02_4_0.497018CF
TC00284663_A18

tag: cell line

tag: treatment

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_14

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

value: Blank


title: BDL KO2 H3K4me1

tag: tissue

tag: genotype


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C06_S126]

tag: cell type

tag: phenotype


title: total RNA-seq from sample_103

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: plate

value: A


title: EP000004A07_2_0.049970CF_TC00284663_A12

description:
EP000004A07_2_0.049970CF
TC00284663_A12

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_7

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: EP000004A10_7_12.711864CF_TC00284663_A23

description:
EP000004A10_7_12.711864CF
TC00284663_A23

tag: cell line

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_10

tag: media

tag: chemical name


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C05_S125]

tag: tissue


title: EP000004B01_7_12.711864CF_TC00284663_A11

description:
EP000004B01_7_12.711864CF
TC00284663_A11

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_13

tag: chemical sample_id

tag: chemical concentration

tag: dose level

value: Wastewater


title: BDL KO1 p-Rpb1

value: liver

tag: genotype


title: total RNA-seq from sample_102

tag: cell type

tag: age

tag: Sex

value: male

tag: row

value: B

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C04_S124]

value: trachea

value: pseudostratified

tag: phenotype

value: adjacent pseudostratified basal cells


title: BDL KO1 CTCF

value: Mertk knockout

tag: treatment

value: CTCF


title: total RNA-seq from sample_101

tag: bmi

tag: status

tag: plate

value: D


title: EP000004A12_2_0.049970CF_TC00284663_A10

description:
EP000004A12_2_0.049970CF
TC00284663_A10

tag: cell line

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_12

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

value: Surface Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C02_S122]

tag: tissue

tag: cell type

tag: genotype


title: BDL KO1 H3K27ac


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C03_S123]


title: EP000004A07_1_0.014967CF_TC00284663_A09

description:
EP000004A07_1_0.014967CF
TC00284663_A09

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_7

tag: chemical concentration

tag: dose level

value: Reclaimed Water


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-C01_S121]

tag: phenotype


title: BDL KO1 H3K27me3

tag: treatment


title: EP000004A05_8_50.000000CF_TC00284663_A06

description:
EP000004A05_8_50.000000CF
TC00284663_A06

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_5

value: 50 CF


title: total RNA-seq from sample_100

value: PBMCs

tag: age

tag: Sex

value: female

tag: bmi

tag: status

value: affected

tag: row

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_098

tag: plate

value: H


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B12_S120]

tag: tissue

value: trachea


title: BDL KO1 H3K4me3

value: liver


title: EP000004A04_8_50.000000CF_TC00284663_A05

description:
EP000004A04_8_50.000000CF
TC00284663_A05

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_4

tag: media

tag: chemical name

tag: chemical sample_id

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Drinking Water


title: total RNA-seq from sample_097

tag: cell type

tag: age

tag: Sex

value: male

tag: bmi


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B11_S119]

value: pseudostratified

tag: genotype

tag: phenotype

value: adjacent pseudostratified basal cells


title: total RNA-seq from sample_096

tag: status

tag: row

value: C

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: EP000004A02_2_0.049970CF_TC00284663_A04

description:
EP000004A02_2_0.049970CF
TC00284663_A04

tag: cell line

tag: treatment

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_2

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

value: Wastewater


title: BDL WT2  p-Rpb1

tag: tissue

value: wild type


title: BDL WT2 CTCF

value: CTCF


title: EP000004A09_1_0.014967CF_TC00284663_A03

description:
EP000004A09_1_0.014967CF
TC00284663_A03

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_9

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Blank


title: total RNA-seq from sample_095

tag: cell type

value: PBMCs

tag: age

tag: Sex

tag: bmi

tag: status

value: affected

tag: plate

tag: row

value: F


title: UHRR_TC00284663_A01

description:
UHRR
TC00284663_A01

tag: cell line

value: NA (Universal Human Reference RNA)

tag: treatment

value: untreated

tag: media


title: total RNA-seq from sample_099

value: female

value: A

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B07_S115]

tag: tissue

value: trachea

value: pseudostratified

tag: genotype

tag: phenotype


title: BDL WT2 H3K27me3

value: liver


title: total RNA-seq from sample_093

tag: cell type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B08_S116]

value: adjacent pseudostratified basal cells


title: total RNA-seq from sample_094

tag: age

value: H


title: BDL WT2 H3K27ac


title: sample86_crHS2-3

city: Palo Alto

first: Chris

last: Hsiung

state: CA

address: 3181 Porter Dr

institute: Arc Institute

data_processing:
The QuantSeq Pool data was demultiplexed and preprocessed using an implementation of pipeline originally provided by Lexogen (https://github.com/Lexogen-Tools/quantseqpool_analysis). The final outputs of this step are gene level counts for all samples (including samples from multiple projects multiplexed together).
Assembly: hg38
Supplementary files format and content: csv file of read gene-level read counts

extract_protocol:
~200k-1 million cells were harvested, resuspended in 300ul RNA Lysis Buffer (Zymo cat# R1060), and stored at -70deg. C until further processing for RNA isolation using the Quick-RNA Miniprep Kit (Zymo cat #R1055).
3' RNA-seq was batch processed together with samples unrelated to this study using a QuantSeq-Pool Sample-Barcoded 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen cat#139) in accordance with the manufacturer’s instructions. 10 ng of each purified input RNA was used for first strand cDNA synthesis with an oligo(dT) primer containing a sample barcode and a unique molecular identifier. Subsequently, barcoded samples were pooled and used for second strand synthesis and library amplification.


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B06_S114]


title: total RNA-seq from sample_092

tag: Sex

value: male

value: B


title: BDL WT2 H3K4me3

value: wild type


title: BDL KO1 H3K4me1

value: Mertk knockout


title: sample85_crHS2-2


title: BDL WT2 H3K4me1


title: total RNA-seq from sample_091

tag: bmi


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B10_S118]


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B09_S117]


title: sample84_crHS2-1


title: total RNA-seq from sample_090

tag: status

value: G


title: sample83_crHBG-3


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B04_S112]


title: BDL WT1 p-Rpb1


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B03_S111]


title: sample87_no crRNA

description: no crRNA


title: sample82_crHBG-2


title: total RNA-seq from sample_089

value: PBMCs

tag: plate

value: D


title: sample80_nocrRNA

description: no crRNA


title: total RNA-seq from sample_087

value: affected

tag: row


title: BDL WT1 H3K27ac


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B02_S110]


title: BDL WT1 H3K4me1


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B01_S109]


title: CB21day old biol replicate1

city: Chicago

first: Jayasri

last: Nanduri

state: IL

address: 5841 S. Maryland Avenue

institute: University of Chicago

data_processing:
pseudo aligner: salmon v1.5.2
Assembly: Rnor_6.0_r102
Supplementary files format and content: gene counts in csv format

organism: Rattus norvegicus

source_name: Carotid body

extract_protocol:
RNA was extracted using the Direct -ZOL- RNA micro prep kit ( Zyme Research #R2060). 1000ng was used for construction of sequencing libraries
RNA libraries for RNA seq were prepared using Illumina TrueSEQ based following manfacturers protocol.

value: Carotid body

tag: cell line

value: tissue

value: 21day old

value: Sprague Dawley


title: BDL WT1 H3K4me3

tag: treatment


title: total RNA-seq from sample_088

value: female

value: F


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A12_S108]

value: trachea

value: pseudostratified


title: total RNA-seq from sample_085


title: CB21day old biol replicate2


title: BDL WT1 H3K27me3

value: liver


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A10_S106]

value: adjacent pseudostratified basal cells


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-B05_S113]


title: total RNA-seq from sample_086


title: sham KO2 p-Rpb1


title: sham KO2 CTCF

value: CTCF


title: CB5day old biol replicate1

value: 5day old


title: sham KO2 H3K27ac

value: Mertk knockout


title: BDL WT1 CTCF

value: wild type


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A09_S105]


title: total RNA-seq from sample_083

value: PBMCs

value: A


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A08_S104]


title: input,5do,pTAC3,mutant,R3

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were stratified for 48 hours in darkness and then were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1).

extract_protocol:
Fifty 5 days-old seedlings were harvested, crosslinked with 4 % formaldehyde for 4 hours, and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a pestle. The homogenate was filtered through two layers of miracloth, and centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer.
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

value: Seedling

value: Chloroplast


title: input,5do,pTAC3,mutant,R2


title: total RNA-seq from sample_082

value: affected


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A07_S103]


title: CB5day old biol replicate2

value: Carotid body

value: tissue


title: sham KO2 H3K27me3


title: total RNA-seq from sample_080

value: female

value: B


title: input,5do,pTAC3,mutant,R1


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A11_S107]

value: trachea


title: total RNA-seq from sample_079

value: male


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A05_S101]

value: pseudostratified


title: input,5do,pTAC3,Col0,R1


title: total RNA-seq from sample_078

value: D


title: sham KO2 H3K4me3

value: liver


title: input,5do,pTAC3,Col0,R3


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A06_S102]

value: adjacent pseudostratified basal cells


title: sham KO2  H3K4me1

value: Mertk knockout


title: total RNA-seq from sample_077

value: E


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A04_S100]


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A03_S99]


title: input,5do,pTAC3,Col0,R2

value: wild type


title: sham KO1 CTCF

value: CTCF


title: sham KO1 p-Rpb1


title: input,5do,RpoB,mutant,ptac14,R3

value: Seedling


title: total RNA-seq from sample_076

value: PBMCs

value: F


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A02_S98]


title: sham KO1 H3K27me3


title: total RNA-seq from sample_081

value: affected


title: input,5do,RpoB,mutant,ptac14,R2

value: Chloroplast


title: total RNA-seq from sample_075

value: female


title: input,5do,RpoB,mutant,ptac14,R1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H12_S384]

value: hillock

value: hillock structure


title: sham KO1  H3K4me3


title: EP000004B04_5_1.473477CF_TC00284663_B09

description:
EP000004B04_5_1.473477CF
TC00284663_B09

value: 6h exposure of 1.4734774 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

tag: water type

value: Reclaimed Water


title: total RNA-seq from sample_074

tag: cell type

tag: age

value: H

tag: column

tag: rin

tag: gc content

tag: randomization batch


title: total RNA-seq from sample_073

tag: Sex

tag: bmi

tag: status

tag: plate

tag: row

value: A


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H11_S383]

tag: tissue

value: trachea

tag: genotype

tag: phenotype


title: sham KO1 H3K4me1

value: liver

value: Mertk knockout

tag: treatment


title: input,5do,RpoB,Col0,ptac14,R2

tag: cell line

value: wild type


title: input,5do,RpoB,Col0,ptac14,R3

value: Seedling


title: input,5do,RpoB,Col0,ptac14,R1


title: sham WT2 p-Rpb1


title: sham KO1 H3K27ac


title: sham WT2 CTCF

value: CTCF


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H09_S381]


title: input,5do,RpoB,mutant,ptac3,R3


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H07_S379]


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-A01_S97]

value: pseudostratified

value: adjacent pseudostratified basal cells


title: Mouse normal pseudostratified basal cells, TdTomato+ [Mouse-td2-5-D02_S134]


title: sham WT2 H3K27ac


title: sham WT2 H3K27me3


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H08_S380]


title: input,5do,RpoB,mutant,ptac3,R1

value: Chloroplast


title: total RNA-seq from sample_070

value: PBMCs

value: female

value: affected

value: F


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H10_S382]

value: hillock

value: hillock structure


title: input,5do,RpoB,mutant,ptac3,R2


title: total RNA-seq from sample_071

value: male

value: H


title: sham WT2 H3K4me3


title: total RNA-seq from sample_069

value: E


title: total RNA-seq from sample_084

value: D


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H06_S378]

value: trachea


title: total RNA-seq from sample_068


title: total RNA-seq from sample_067


title: total RNA-seq from sample_072

value: G


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H05_S377]


title: sham WT2 H3K4me1

value: liver

value: wild type


title: sham WT1 p-Rpb1


title: input,5do,RpoB,Col0,ptac3,R1

value: Seedling


title: total RNA-seq from sample_066

value: A


title: input,5do,RpoB,Col0,ptac3,R2

value: Chloroplast


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H04_S376]


title: total RNA-seq from sample_065

value: PBMCs


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H03_S375]


title: sham WT1 CTCF

value: CTCF


title: ChIP,5do,pTAC3,mutant,R3


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H02_S374]


title: sham WT1 H3K27ac


title: total RNA-seq from sample_064

value: female

value: affected

value: C


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-H01_S373]

value: hillock

value: hillock structure


title: sham WT1 H3K27me3


title: ChIP,5do,pTAC3,mutant,R2


title: total RNA-seq from sample_063


title: input,5do,RpoB,Col0,ptac3,R3


title: ChIP,5do,pTAC3,mutant,R1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G12_S372]


title: ChIP,5do,pTAC3,Col0,R3


title: total RNA-seq from sample_062


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G11_S371]


title: ChIP,5do,pTAC3,Col0,R2


title: total RNA-seq from sample_061


title: total RNA-seq from sample_060

value: male


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G10_S370]


title: BDL KO GEX

description: Active Motif

data_processing:
Track for visualization of observed transposition sites across the genome
Count and barcode information for every ATAC fragment
Annotation of peaks based on gene proximity; these annotations are not based off linkage to gene expression
BED formatted file containing the location of called peaks
Position sorted BAM file of ATAC reads
Index for ATAC read BAM file
Loupe Browser input file
Filtered expression and peak data for cellular barcodes in H5 format
Contains information on the gene expression data including reads, barcodes, features, and library details
Position sorted BAM file of gene expression reads
Index for the gene expression BAM file
Read count summaries for every observed barcode
Expression and peak data for all barcodes in H5 format
Assembly: mm10

extract_protocol:
Nuclei were isolated from frozen liver using the Omni-ATAC protocol (https://doi.org/10.17504/protocols.io.6t8herw). Briefly, tissues were Dounce homogenized in cold homogenization buffer containing 0.3% IGEPAL CA-630 in the presence of protease and RNase inhibitors to release nuclei from frozen cells. Nuclei were subsequently purified via iodixanol gradient centrifugation and washed with ATAC resuspension buffer containing RNase inhibitor and 0.1% Tween-20 before permeabilization following the 10x Genomics demonstrated protocol for complex tissues (CG000375, Rev. B). After resuspension in diluted nuclei buffer, nuclei were counted using a manual hemocytometer to achieve a targeted nuclei recovery of 10,000 nuclei per sample.
Joint scRNA- and scATAC-seq libraries were prepared by Active Motif, Inc using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions by. Libraries were sequenced with paired-end 150-bp reads on an Illumina NovaSeq 6000 to a target depth of 250 million read pairs per sample.

value: Mertk knockout

value: bile duct ligation


title: ChIP,5do,pTAC3,Col0,R1


title: BDL WT GEX

description: Active Motif


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G09_S369]

value: trachea


title: total RNA-seq from sample_059

value: F


title: ChIP,5do,RpoB,mutant,ptac14,R3


title: total RNA-seq from sample_058

value: H


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G08_S368]


title: ChIP,5do,RpoB,mutant,ptac14,R2

value: wild type


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G06_S366]


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G07_S367]


title: total RNA-seq from sample_057


title: sham WT1 H3K4me3

value: liver


title: Mono_Prf1_Ruxo_3 2511432_15

city: Memphis

first: Kim

last: Nichols

state: TN

address: 262 Danny Thomas Pl

department: Oncology

institute: St. Jude Children's Research Hospital

description:
Mono_Prf1_Ruxo_3
Mono_Prf1_Ruxo_3

data_processing:
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (mm10) (STAR v2.7). The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (M22 [mm10]).
Assembly: GRCm38
Supplementary files format and content: coutns matrix, RSEM counts

source_name: Blood

extract_protocol:
RNA was extracted from sorted cell populations using the RNeasy Micro Kit (Qiagen, Germantown, Maryland). The quality and quantity of the initial RNA was determined by using the Agilent 2100 Bioanalyzer with the Eukaryote Total RNA Pico kit.
For each good quality sample, 2.5-25 nanograms of total RNA was used in the Tecan Ovation RNA sequencing system v2 protocol as written to create SPIA (single primer isothermal amplification)-cDNA. Once the cDNA was purified, five hundred nanograms of each sample was sheared using the Covaris LE220 focused ultra sonicator. The shearing plate used was the 96 microtube-50 AFA fiber plate and the target base pair size was 300. The settings for the shearing were the following: Peak incident Power (W) of 450, duty factor of 15%, cycles per burst 1000 with a 100 second treatment time. Once the cDNA was sheared, libraries were created using the KAPA Hyper-Prep kit from Roche.
Based on the starting cDNA input amount, the Kapa Hyper protocol recommended four pcr cycles for the amplification step while the rest of the protocol was followed as described. The indexes used were the UDI DNA indexes from Illumina. Eukaryote Total RNA Pico kit (catalog: 5067-1513) Tecan (formally NuGen) Ovation RNA sequencing system v2 (catalog: 7102-32) Covaris 96 tube plate (catalog:520168) KAPA Hyper-Prep (catalog: KK8504) UDI DNA Indexes from Illumina (catalog: 20022370)

treatment_protocol: CD8 T cells and CD11b+  Ly6C+Ly6G- monocytes were sort-purified from the spleens of mice collected on day 9 post-infection, 1 hour after receiving an 11th dose of JAK inhibitor or vehicle via oral gavage (3 mice per treatment group)

tag: strain

value: C57BL/6 Prftm1Sdz/J

value: Blood

value: Monocytes

value: LCMV + Ruxolitinib

tag: time

value: Day 9


title: total RNA-seq from sample_055

tag: cell type

value: PBMCs

tag: age

value: affected

value: A


title: BDL WT ATAC

description: Active Motif


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G05_S365]

value: hillock

value: hillock structure


title: sham WT1  H3K4me1


title: ChIP,5do,RpoB,mutant,ptac14,R1

value: Seedling

value: Chloroplast


title: total RNA-seq from sample_056

value: female

value: E

tag: column

tag: rin


title: Mono_Prf1_Ruxo_2 2511431_14

description:
Mono_Prf1_Ruxo_2
Mono_Prf1_Ruxo_2


title: total RNA-seq from sample_053

value: H

tag: gc content

tag: randomization batch


title: ChIP,5do,RpoB,Col0,ptac14,R3

value: wild type


title: ChIP,5do,RpoB,mutant,ptac3,R3


title: ChIP,5do,RpoB,Col0,ptac14,R2


title: total RNA-seq from sample_054

tag: Sex

tag: bmi

value: D


title: Mono_Prf1_Ruxo_1 2511430_13

description:
Mono_Prf1_Ruxo_1
Mono_Prf1_Ruxo_1

value: C57BL/6 Prftm1Sdz/J


title: ChIP,5do,RpoB,Col0,ptac14,R1


title: total RNA-seq from sample_052

value: male

tag: status

tag: plate


title: Mono_Prf1_Fedra_3 2511429_12

description:
Mono_Prf1_Fedra_3
Mono_Prf1_Fedra_3

tag: tissue

value: Blood

value: Monocytes

value: LCMV + Fedratinib


title: Mono_Prf1_Fedra_1 2511427_10

description:
Mono_Prf1_Fedra_1
Mono_Prf1_Fedra_1

tag: genotype

value: Day 9


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F12_S360]

value: trachea

tag: phenotype


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G01_S361]


title: Mono_Prf1_Fedra_2 2511428_11

description:
Mono_Prf1_Fedra_2
Mono_Prf1_Fedra_2

tag: treatment


title: total RNA-seq from sample_051

value: PBMCs

value: affected

tag: row

value: B


title: BDL KO ATAC

description: Active Motif

value: liver

value: Mertk knockout

value: bile duct ligation


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F10_S358]

value: hillock

value: hillock structure


title: total RNA-seq from sample_050

value: E


title: ChIP,5do,RpoB,Col0,ptac3,R3

value: Seedling

tag: cell line

value: Chloroplast

value: wild type


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-G02_S362]


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F09_S357]


title: total RNA-seq from sample_049

value: male

value: F


title: Mono_Prf1_Ita_1 2511424_07

description:
Mono_Prf1_Ita_1
Mono_Prf1_Ita_1

tag: strain

value: C57BL/6 Prftm1Sdz/J

value: Blood

value: Monocytes

value: LCMV + Itacitinib

tag: time


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F08_S356]

value: trachea

tag: cell type


title: ChIP,5do,RpoB,Col0,ptac3,R2


title: total RNA-seq from sample_048

value: PBMCs

tag: age

value: female

value: affected

tag: column


title: Mono_Prf1_UnRx_3 2511423_06

description:
Mono_Prf1_UnRx_3
Mono_Prf1_UnRx_3

value: LCMV untreated

value: Day 9


title: total RNA-seq from sample_047

value: A

tag: rin

tag: gc content


title: ChIP,5do,RpoB,Col0,ptac3,R1+B34:B69


title: ChIP,5do,RpoB,mutant,ptac3,R2


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F11_S359]

value: hillock

value: hillock structure


title: total RNA-seq from sample_046

tag: Sex

value: H

tag: randomization batch


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F06_S354]


title: AcH2A.Z ChIP 3

city: Mississauga

first: Iva

last: Zovkic

state: Ontario

address: 3359 Mississauga Rd

department: Department of Psychology

country: Canada

institute: University of Toronto

data_processing:
Bowtie2 (v2.2.5), Picard (v2.5.0), Deeptools (v3.5.1), Macs2 (v2.2.6), R (v4.3.2), Bedtools (v2.30.0), IGV (v2.8.9)
Bowtie2 was used to align raw fastq files to the mm10 geonome
Picard was used to de-duplicate aligned reads
Deeptools was used for sample normalization, bigwig file generation, heatmap generation, coorelation plots, bigwig summary.
Macs2 was used to call peaks from aligned reads
R was used for statistcs and quantile plot generation
Bedtools was used to generate random regions 1kb in length, calculating odds ratios and two-tailed hypergeomtetry testing
IGV was used to visualize ChIP-seq tracks
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Primary neuron culture

growth_protocol: Hippocampal neurons were prepared from E17 mice floxed for both H2A.Z.1 (H2afz) and H2A.Z.2 (H2afv), as previously described. Hippocampi were washed with Hank’s Balanced Salt Solution (1x HBSS Gibco#14175-095) and trypsinated for 30 s (0.25% Trypsin, Life Technologies#15050065), then washed with HBSS. Trypsin was inhibited with dissecting medium (10% normal horse serum, Life Technologies#26050070) in DMEM (Life Technologies#11995065). Neurons were dissociated by triturating and diluted in Neurobasal Medium (L-Glutamine) (Gibco#21103-049) with 20 mM L-glutamine (Gibco 25030-081), 1x Penicillin-Streptomycin (Sigma P4333-100ML) and 1xB27 (Gibco 17504-044) and plated in 6-well plates. Neurons were infected with Syn-Cre on 1 day in vitro (DIV) and harvested on DIV8.

extract_protocol:
Primary hippocampal neurons, cultures were fixed on the plates and then scraped and resuspended in buffer B (50mM NaCl, 10mM Pipes pH6.8, 5mM MgCl 2 , 1mM CaCl 2 ), incubated for 5 min at 37_x000E_C and digested using 100U of MNase (Cell Signaling, 1011S) for 15 min at 37_x000E_C. MNase digestion was halted by adding EDTA to a final concentration of 5mM. SDS was added to a final concen- tration of 1% and samples were aliquoted and diluted with ChIP dilution buffer. Hippocampal samples were treated with 20ul of Protein G magnetic beads (Millipore, 16-662) and 1ul of H2A.Z (Millipore, ABE1348) antibody overnight at 4_x000E_C. The next day, samples were washed sequentially with low-salt (20mM Tris pH7.4, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl), high-salt (20mM Tris pH7.4, 0.1%SDS, 1% Triton X-100, 1mM EDTA, 500mM NaCl), LiCl (Millipore, 20-156) and TE (10mM Tris pH7.4, 1mM EDTA) buffers, and incubated while rotating for 5 min between washes. Immune complexes were extracted using TE Buffer and proteinase K (Roche, 3115828001) for both ChIP and Input samples, and heated at 65_x000E_C for 2 h, followed by 95_x000E_C for 10 min with QIAquick PCR Purification Kit (QIAGEN, 28104) for sequencing samples
Purifed DNA was sent to Genome Quebec in Montreal, Canada where the library was constructed and sequenced on an Illumina HiSeq 4000

value: Primary neuron culture

value: Hippocampal Neuron

tag: chip antibody

value: anti-AcH2A.Z (Millipore #ABE1363)


title: total RNA-seq from sample_045

value: male

tag: bmi

tag: status

tag: plate

value: C


title: Mono_Prf1_UnRx_1 2511421_04

description:
Mono_Prf1_UnRx_1
Mono_Prf1_UnRx_1

value: C57BL/6 Prftm1Sdz/J

tag: tissue

value: Blood

value: Monocytes

tag: genotype


title: AcH2A.Z ChIP 2


title: ChIP,5do,RpoB,mutant,ptac3,R1

value: Seedling

value: Chloroplast

value: wild type

tag: treatment


title: Mono_Prf1_Ita_3 2511426_09

description:
Mono_Prf1_Ita_3
Mono_Prf1_Ita_3

value: LCMV + Itacitinib


title: Mono_Prf1_Naive_3 2511420_03

description:
Mono_Prf1_Naive_3
Mono_Prf1_Naive_3

value: Naive

value: Day 9


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F04_S352]

value: trachea

value: hillock

tag: phenotype


title: Mono_Prf1_Ita_2 2511425_08

description:
Mono_Prf1_Ita_2
Mono_Prf1_Ita_2

tag: strain


title: total RNA-seq from sample_044

value: PBMCs

value: female

value: affected

tag: row

value: F


title: AcH2A.Z ChIP 1

tag: cell line

value: Primary neuron culture

tag: cell type

value: Hippocampal Neuron

value: anti-AcH2A.Z (Millipore #ABE1363)


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F03_S351]

value: hillock structure


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F07_S355]


title: Mono_Prf1_Naive_1 2511418_01

description:
Mono_Prf1_Naive_1
Mono_Prf1_Naive_1

value: C57BL/6 Prftm1Sdz/J

value: Blood

value: Monocytes

tag: time


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F02_S350]


title: Input 1


title: total RNA-seq from sample_042

tag: age

value: C

tag: column

tag: rin


title: Mono_Prf1_UnRx_2 2511422_05

description:
Mono_Prf1_UnRx_2
Mono_Prf1_UnRx_2

value: LCMV untreated


title: CD8_Prf1_Ruxo_3 2511416_15

description:
CD8_Prf1_Ruxo_3
CD8_Prf1_Ruxo_3

value: CD8+ T cells

value: LCMV + Ruxolitinib


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F05_S353]

value: trachea


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-F01_S349]

value: hillock


title: CD8_Prf1_Ruxo_2 2511415_14

description:
CD8_Prf1_Ruxo_2
CD8_Prf1_Ruxo_2

value: Day 9


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E12_S348]


title: KAL-LN2-E1, Tumor derived Inflammatory monocytes, LN4, rep4

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Workflow based on BBDuk/BBMap v 37.99
Sequence reads were trimmed for adaptor sequence and applying a length filtering, using BBDuk, with parameters: ktrim=r k=23 hdist=1 minlen=50
Trimmed sequence reads were mapped to GRCm38/mm10 using BBMap, with parameters: maxindel=100000 intronlen=10 ambig=random qin=33 sam=1.3
The bam files were sorted using samtools v 1.8
The read count was perforned using Subread/featureCounts v 1.5.2, with parameters: -T 8 -g gene_id -p -s 0
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: LN4K1 cells were cultured using MEM media and KAL-LN2-E1 cells cultured with DMEM media and supplemented with 10% FBS and Penicillin-Streptomycin.

extract_protocol:
RNA was harvested using Rneasy micro kit.
RNA libraries for RNAseq were prepared with SMARtr Ultra low RNA amp+ NexteraXT/ NON Stranded library kit following manufactuer's protocols.

treatment_protocol: LN4K1 cells (3x10^5 cells/mouse) were intravenously injected in 100uL in DBA2 mice. KAL-LN2-E1 cells (5x10^5 cells/mouse) were orthotopically injected into the lung of FVB mice. After tumor development, inflammatory monocytes were isolated from lungs, lung tumors and LN metastases using the EasyStep Mouse Monocyte Isolation Kit (StemCell) and sorted using CD45, CD11b, Ly6C, Ly6G, live/dead antibodies. The sorted IM populations were further used for RNA isolation.

value: FVB

value: Inflammatory monocytes

tag: disease state

value: LN metastases


title: KAL-LN2-E1, Tumor derived Inflammatory monocytes, LN5, rep5


title: KAL-LN2-E1, Tumor derived Inflammatory monocytes, LN3, rep3


title: total RNA-seq from sample_041

value: PBMCs

tag: Sex

value: male

value: affected

value: H

tag: gc content

tag: randomization batch


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E11_S347]

value: hillock structure


title: KAL-LN2-E1, Tumor derived Inflammatory monocytes, LN2, rep2


title: CD8_Prf1_Ruxo_1 2511414_13

description:
CD8_Prf1_Ruxo_1
CD8_Prf1_Ruxo_1

value: C57BL/6 Prftm1Sdz/J

value: Blood


title: KAL-LN2-E1, Tumor derived Inflammatory monocytes, LN1, rep1


title: Mono_Prf1_Naive_2 2511419_02

description:
Mono_Prf1_Naive_2
Mono_Prf1_Naive_2

value: Monocytes

value: Naive


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E10_S346]


title: total RNA-seq from sample_043

tag: bmi

tag: status

tag: plate

value: C


title: KAL-LN2-E1, Primary Tumor derived Inflammatory monocytes, Primary5, rep5

value: primary lung tumor


title: total RNA-seq from sample_039

value: female

value: G


title: CD8_Prf1_Fedra_3 2511413_12

description:
CD8_Prf1_Fedra_3
CD8_Prf1_Fedra_3

tag: tissue

value: CD8+ T cells

tag: genotype

tag: treatment

value: LCMV + Fedratinib

value: Day 9


title: total RNA-seq from sample_038

tag: row


title: CD8_Prf1_Fedra_1 2511411_10

description:
CD8_Prf1_Fedra_1
CD8_Prf1_Fedra_1

tag: strain


title: total RNA-seq from sample_037

tag: cell type


title: CD8_Prf1_Fedra_2 2511412_11

description:
CD8_Prf1_Fedra_2
CD8_Prf1_Fedra_2

tag: time


title: KAL-LN2-E1, Primary Tumor derived Inflammatory monocytes, Primary3, rep3

value: FVB

tag: cell line

value: Inflammatory monocytes


title: total RNA-seq from sample_036

value: PBMCs

tag: age

tag: column


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E09_S345]

value: trachea

value: hillock

tag: phenotype


title: KAL-LN2-E1, Primary Tumor derived Inflammatory monocytes, Primary4, rep4

tag: disease state


title: CD8_Prf1_Ita_3 2511410_09

description:
CD8_Prf1_Ita_3
CD8_Prf1_Ita_3

value: LCMV + Itacitinib


title: CD8_Prf1_Ita_2 2511409_08

description:
CD8_Prf1_Ita_2
CD8_Prf1_Ita_2

value: C57BL/6 Prftm1Sdz/J


title: total RNA-seq from sample_034

tag: Sex

value: male

value: affected

value: E

tag: rin

tag: gc content


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E08_S344]

value: hillock structure


title: KAL-LN2-E1, Primary Tumor derived Inflammatory monocytes, Primary2, rep2

value: primary lung tumor


title: KAL-LN2-E1, Primary Tumor derived Inflammatory monocytes, Primary1, rep1


title: DBA2 LN4K1, Lung derived Inflammatory monocytes, L5, rep5

value: lung tumors


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E07_S343]


title: CD8_Prf1_UnRx_2 2511406_05

description:
CD8_Prf1_UnRx_2
CD8_Prf1_UnRx_2

value: Blood

value: LCMV untreated


title: total RNA-seq from sample_040

value: female

tag: bmi

tag: status

tag: randomization batch


title: DBA2 LN4K1, Lung derived Inflammatory monocytes, L4, rep4


title: total RNA-seq from sample_035

tag: plate

value: G


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E06_S342]

tag: tissue

tag: genotype


title: CD8_Prf1_Ita_1 2511408_07

description:
CD8_Prf1_Ita_1
CD8_Prf1_Ita_1

tag: strain

value: CD8+ T cells

tag: treatment

value: Day 9


title: CD8_Prf1_UnRx_3 2511407_06

description:
CD8_Prf1_UnRx_3
CD8_Prf1_UnRx_3

tag: cell type

tag: time


title: total RNA-seq from sample_031

value: PBMCs

tag: age

tag: row

value: B


title: CD8_Prf1_Naive_3 2511404_03

description:
CD8_Prf1_Naive_3
CD8_Prf1_Naive_3

value: Naive


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E04_S340]

value: trachea

value: hillock

tag: phenotype


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E01_S337]


title: total RNA-seq from sample_032

value: male

tag: column


title: DBA2 LN4K1, Lung derived Inflammatory monocytes, L3, rep3

tag: cell line

value: Inflammatory monocytes

tag: disease state


title: total RNA-seq from sample_029

tag: Sex

value: affected

value: E

tag: rin

tag: gc content


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E03_S339]

value: hillock structure


title: total RNA-seq from sample_033

tag: bmi

tag: status

value: F

tag: randomization batch


title: total RNA-seq from sample_028

tag: plate


title: CD8_Prf1_UnRx_1 2511405_04

description:
CD8_Prf1_UnRx_1
CD8_Prf1_UnRx_1

tag: strain

value: C57BL/6 Prftm1Sdz/J

tag: tissue

value: Blood

tag: genotype


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E02_S338]

tag: cell type


title: total RNA-seq from sample_030

tag: age


title: DBA2 LN4K1, Lung derived Inflammatory monocytes, L2, rep2

value: lung tumors


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-E05_S341]


title: CD8_Prf1_Naive_2 2511403_02

description:
CD8_Prf1_Naive_2
CD8_Prf1_Naive_2

tag: treatment

tag: time


title: DBA2 LN4K1, Lung derived Inflammatory monocytes, L1, rep1


title: total RNA-seq from sample_025

value: female

tag: row

value: G

tag: column


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D12_S336]

tag: phenotype


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D09_S333]


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D11_S335]


title: CD8_Prf1_Naive_1 2511402_01

description:
CD8_Prf1_Naive_1
CD8_Prf1_Naive_1

value: CD8+ T cells

value: Day 9


title: total RNA-seq from sample_023

value: PBMCs

tag: Sex

value: D


title: total RNA-seq from sample_027

value: B

tag: rin


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D06_S330]

value: trachea

value: hillock


title: total RNA-seq from sample_022

tag: gc content


title: DBA2 naïve, Bone marrow-derived Inflammatory monocytes, D2, rep2

source_name: Inflammatory monocytes

value: Inflammatory monocytes

tag: disease state

value: healthy


title: Tracer TLS Multiseq - 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 24 pooled Tracer TLS and TLSCL

library_source: transcriptomic single cell

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’.
genome build: mm10
processed data 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.

molecule: polyA RNA

growth_protocol:
All cell lines used are male and derived from an F1G4 genetic background (Nagy et al). Mouse embryonic stem cells (mESCs) have been cultured as previously described (Veenvliet, Bolondi et al 2020; Bolondi et al 2021). Briefly, mESCs were routinely maintained on 6cm plates (Corning 430166) gelatinized with 0.1% gelatin (1:20 dilution of 2% gelatin (Sigma G1393) in tissue-culture grade H2O) and coated with mitotically inactive primary mouse embryo fibroblasts (3-4x104cells/cm²) with standard mESC medium containing 15% FCS and 1000 U/ml leukemia inhibitory factor (LIF, Chemicon ESG1107) at 37°C and 5% or 7.5%  CO2. mESCs were split every second day with a dilution suitable to the proliferation velocity (between 1:5 and 1:9). ES+LIF medium was refreshed daily. For splitting, media was aspirated and cells were washed once with PBS and trypsinized (Tryspin-EDTA (0.05%) (Gibco 25300054)) for 5-10 minutes at 37°C. Trypsin was neutralized by 3ml ES+LIF and cells centrifuged for 5 minutes at 1000 rpm, after which the pellet was resuspended in ES+LIF. For freezing of mESCs, cell pellets were resuspended in ES medium with 20% FCS, and mixed in a 1:1 ratio with ES freezing medium. Cells were frozen down o/n in the –80 °C and transferred to liquid nitrogen the next day.
Trunk-Like Structures (TLS) have been generated as previously described (Veenvliet, Bolondi et al 2020; Bolondi et al 2021) with some modifications to induce Cas9-based molecular recording. Briefly, mESCs were trypsinized on the feeder plate as described above and washed with ES+LIF. Cells were pelleted by centrifugation at 1000rpm for 5 minutes at room temperature and resuspended in 2ml ES+LIF. On three gelatinized (0.1% gelatin) wells of a 6-well plate, cells were sequentially plated for 25 minutes, 20 minutes and 15 minutes during which cells were kept in the incubator at 37°C and 5% or 7.5% CO2. With each transfer, cells were triturated to maintain a single cell suspension. Feeder-freed mESCs were then washed once in 5ml pre-heated (37°C) PBS containing MgCl2 and CaCl2 (Sigma D8662) and once in pre-incubated (37°C, 5% or 7.5% CO2) 5ml NDiff227 (Takara Y40002). mESCs were then pelleted by centrifugation for 5 minutes at 1000rpm and resuspended in 500µl of NDiff227. 10µl of the cell suspension was mixed with 10µl of Trypanblue (Bio-Rad 1450021) for automated cell counting with Luna Automated Cell Counter. 1x106 live cells were then used for nucleofection using the Amaxa 4D-Nucleofector X Kit for mESCs (Lonza V4XP-3012) in combination with 10µg of Cre-expressing plasmid DNA (Addgene #13775) using the manufacturer instruction and the CG-104 program. Nucleofected cells were then washed with 10ml pre-warmed N2Diff227, resuspended in 1ml N2Diff227 and counted again using the automated cell counting with Luna Automated Cell Counter. 500 cells were then plated in a volume of 30 to 40µl NDiff227 into each well of a 96-well round bottom, low attachment plate (Costar 7007 ultra-low attachment 96 well plate (7007)). Cells were then allowed to aggregate for 48 h. After these 48h cells were pulsed with 3µM CHIR99021 (CHIR, Merck Millipore) in 150µl NDiff227. After 72h, medium was refreshed by removing 150µl of the old media and adding the same volume of new, pre-incubated (37°C and 5% or 7.5% CO2) NDiff227. At 96h, structures were then embedded in 5% Growth-Factor-Reduced Matrigel (MG) (Corning 356231). To this end, fresh NDiff227 medium was pre-incubated for at least 20 minutes at 37°C and 5% or 7.5% CO2. Pre-incubated medium was then put on ice for 5 minutes, after which MG was added to achieve a final concentration of 5% in the culture wells. Medium was then put at room temperature for 5 minutes, during which 150µl of old medium was removed from the aggregates. New medium with MG (150µl) was then added, and the cultures were returned to the incubator and further cultured at 37°C and 5% or 7.5% CO2. Tracer TLS cultures were allowed to settle for at least 30 minutes before proceeding to further experimentation. For Tracer TLS treated with CHIR+LDN (Tracer TLSCL), 5µM CHIR together with 600nM LDN was added prior to MG and left from 96h to 120h.

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.

value: LSL-Cas9-GFP-Tracer BC library + LentiBC

value: mESC


title: cDNA - Tracer mESC - Day3

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 3

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).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference: "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomics.
The reads that did not align to the reference were further processed using the reference and algorithms from the Cassiopeia tool. First, the reads were aligned to the reference (“PCT48”) using the Smith-Waterman algorithm with parameters -gapopen 20 and -gapextend. Next, the intBC cut site information per barcode was determined using the callAlleles-PCT48.pl script. intBC patterns were classified based on the code from the indel table into Deletion&Insertion (I and D), Deletion (D), Insertion (I) or uncut. Barcodes that did appear in the known barcode list were assigned to the closest barcode if the edit distance was less than 4 and otherwise remove.
genome build: mm10
processed data files format and content: Matrix with cutsite label, frequency (coverage), cellBC and cut information for the three target sites.
Library strategy: Amplicon-seq

extract_protocol:
RNA was extracted from isolated Cas9-GFP+ Tracer mESCs at different days after Cas9-GFP activation or from individual Tracer TLS at day 5 post aggregation for downstream intBCs library preparation. Briefly, RNA was extracted from 1x105 isolated Cas9-GFP+ Tracer mESCs or individual Tracer TLS using RNeasy Plus Micro Kit (Qiagen) and RNA concentration and quality was measured using Qubit™ RNA HS (Thermo, Q32852). cDNA synthesis was performed using 1μg total RNA (for Tracer mESCs) or all extraced RNA (for individual Tracer TLS) using the RevertAid First Strand cDNA Synthesis Kit (Thermo, K1622), following the manufacturer’s instructions. OligoT were used as primers first strand cDNA synthesis.
Isolated gDNA from Tracer mESCs and prepared cDNA from Tracer mESCs and individual Tracer TLS were used for Amplicon-seq intBCs library preparation. 200ng gDNA and 100ng cDNA were used as input material. Two subsequent PCR reactions were carried on to prepare the NGS library: (i) in the first step the input material was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.55x-0.8x) was performed and purified intBCs amplicons were eluted in 30µl EB buffer; (ii) in the second step, the whole eluate from the previous PCR reaction was used for 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 65ºC 30sec – 72ºC 45sec (12 cycles)/ 72ºC 5 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a AMPure XP beads (Beckman, A63881) cleanup (0.8x) was performed to purify amplicons 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 paired end sequencing (500 cycles kit; 250/250) on a Miseq platform at a minimum of 50 million fragments per sample.

value: LSL-Cas9-GFP-Tracer BC library


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D10_S334]

description:
hillockCounts.csv
sc_manju_hillock_newest_Seurat.rds

value: hillock structure


title: total RNA-seq from sample_026

value: male

tag: bmi

tag: status

value: affected

value: E


title: mouse liver, GW4064, RNA-Seq,rep2

city: HOUSTON

first: Ruoyu

last: Wang

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
GRO-Seq and RNA-Seq raw data were de-multiplexed by bcl2fastq, and quality-controlled with fastqc
Reads were mapped to mouse reference genome mm10 by STAR v2.7.3a.
For gene/mRNA quantification, mm10 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the RPKM value
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse liver

extract_protocol:
The RNAs from livers of fasted mice (n = 2/group, each group contains RNAs pooled from 2 mice) were prepared using the RNeasy mini prep kit (Qiagen). RNA quality was tested using an Agilent bioanalyzer by the Functional Genomics Core at the Roy J. Carver Biotechnology Center, UIUC.
Ribosomal RNA was removed with the Ribozero Human/Mouse/Ratkit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq

treatment_protocol: C57BL/6 mice were fasted overnight and treated with 30 mg/kg GW4064 or vehicle for 1 h.

value: mouse liver

value: WT

value: 1 hour


title: DBA2 naïve, Bone marrow-derived Inflammatory monocytes, D1, rep1


title: Tracer TLS #2 - scRNAseq

description: Single-cell RNA-sequencing of one Tracer TLS


title: FvBn naïve, Bone marrow-derived Inflammatory monocytes, F3, rep3

value: FVB


title: Tracer TLS #1 - scRNAseq


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D01_S325]


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D08_S332]


title: total RNA-seq from sample_018

value: PBMCs

tag: plate

tag: randomization batch


title: total RNA-seq from sample_024

value: female

value: D


title: FvBn naïve, Bone marrow-derived Inflammatory monocytes, F2, rep2

tag: strain


title: total RNA-seq from sample_017

value: A


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D07_S331]

tag: tissue

value: trachea

value: hillock

tag: genotype


title: FvBn naïve, Bone marrow-derived Inflammatory monocytes, F1, rep1

tag: cell type

value: Inflammatory monocytes

value: healthy


title: cDNA - Tracer mESC - Day5

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 5

value: LSL-Cas9-GFP-Tracer BC library

value: mESC


title: cDNA - Tracer mESC - Day4

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 4


title: total RNA-seq from sample_016

tag: age


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C10_S322]

value: hillock structure


title: total RNA-seq from sample_015

value: male

value: affected


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D05_S329]


title: total RNA-seq from sample_021

value: G


title: LEC Tie1 WT Replicate1

first: Yalu

last: Zhou

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
RNA sequencing reads were mapped to mouse genome mm10 using TopHat.
Reads were counted on the exons of mm10 genes using htseq.
Differential gene expression analysis was performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Dermal lymphatic endothelial cells

growth_protocol: Cells were FACS sorted from fresh E18.5 embryonic skin samples

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were sorted directed to lysis buffer

value: Dermal lymphatic endothelial cells

value: WT

tag: treatment

value: 0.5% Doxycycline water


title: mouse liver, DMSO, RNA-Seq,rep2

value: mouse liver

value: DMSO

tag: time

value: 1 hour


title: cDNA - Tracer mESC - Day2

description: Tracing BCs AmpliconSeq from Tracer mESCs cDNA at day 2


title: total RNA-seq from sample_014

value: PBMCs

value: female

tag: row

value: C

tag: column


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D04_S328]

value: trachea

value: hillock

tag: phenotype


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-C08_S320]


title: total RNA-seq from sample_020

tag: Sex

value: D

tag: rin


title: LEC Tie1 WT Replicate2


title: mouse liver, GW4064, RNA-Seq,rep1


title: Mouse hillock cells, TdTomato+ [Mouse-sq2-D02_S326]


title: mouse liver, DMSO, RNA-Seq,rep1


title: mouse liver, KO,DMSO,GRO-Seq

value: FXR KO

value: Vehicle


title: total RNA-seq from sample_013

value: male

tag: gc content


title: LEC Tie1 KO Replicate2

value: Tie1 knockout