title: miRNA CX_wt_crush_28

description: cortex, nerve-injured, miRNA, biol rep2

value: right sciatic nerve crush


title: EP000004A05_7_12.711864CF_TC00284699_K04

status: Public on Mar 05 2024

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
EP000004A05_7_12.711864CF
TC00284699_K04

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 Cells

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

extract_protocol:
Six hours after water extract treatment, HTTr assay plates were removed from the incubator and media in each assay well drained to a residual volume of 10 µL. A 10 µL volume of 2× BioSpyder lysis buffer was dispensed into each assay well. Then, 20 µL volumes of Universal Human Reference RNA (UHRR), Human Brain Reference RNA (HBRR), bulk lysates from MCF7 cells treated with 0.5% DMSO (BL DMSO) or 1 µM trichostatin A (BL TSA), and lysis buffer blans were dispensed into the first column of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 min. The plates were then stored at -80°C prior to shipment to BioSpyder, Inc.
Samples were analyzed by BioSpyder using a custom-attenuated version of the TempO-Seq human whole transcriptome version 1 (hWTv1) assay, which includes 21,111 probes covering 19,287 genes. In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv1 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 hours. Excess oligos were then removed via nuclease digestion (90 min at 37°C) and hybridized detector oligos were ligated (60 min at 37°) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification (10 min at 37°C, 2 min at 95°C, 6 cycles of 95°C for 30 s, 54°C for 30 s, 72°C for 120 s, 16 cycles of 95°C for 30s and 72°C for 120s, followed by 72°C for 60 s) with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were then pooled into a series of three sequencing libraries (1 for each plate). Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized water extracts collected from each sampling site were shipped frozen to US EPA and stored at  80°C prior to dose plate preparation. Eight-point dilution series (1/2 log10 spacing) of each stock sample was prepared in a LabCyte Echo-qualified 384-well low dead volume (384LDV) plate. Transcriptomics reference chemicals for MCF7 cells (genistein, trichostatin A, sirolimus) were solubilized as 200× dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the reference chemicals were added to the dose plates along with quadruplicate wells of pure DMSO as a vehicle control. The dose plate was then sealed with a Nunc aluminum adhesive plate cover and stored at -80°C until use. On the first day of dosing, the dose plate was thawed to room temperature inside a desiccator, centrifuged briefly to ensure even distribution of the dose solution in each well and unsealed. A LabCyte Echo 550 acoustic dispenser was then used to transfer 200 nL of dosing solutions to the assay plates containing 40 uL of culture media. The final DMSO concentration was 0.5% for all treatment, reference treatment and vehicle control wells. Well coordinates were uniquely randomized on each assay plate with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

tag: treatment

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_5

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type

value: Surface Water


title: DNAse_NC Brgf/f mice hepatocytes Dnase #4 WT Rep.3

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

library_source: genomic

data_processing:
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq: normalized by the library size and using a window size of 200bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: bedgraph files for RNA-seq: normalized by the library size and using a window size of 20bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates; irst column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both KO replicates; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density

molecule: genomic DNA

organism: Mus musculus

source_name: Hepatocytes

extract_protocol:
Briefly, 10,000 cells from each cell type were collected by FACS sorting. 0.3 unit of DNase I (Roche) was added to each cell type and incubated at 37°C for 5 minutes. Reactions were stopped by adding 80 μl of stop buffer (10 mM Tris-HCl, 10 mM NaCl, 0.1% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55°C overnight, and DNAs were purified by using MinElute reaction cleanup kit following the manufacturer's protocol.
Purified DNA was end-repaired using end-repair kit (ER81050, Epicentre), followed by A-addition using Klenow fragment (3’ to 5’ exo minus) and dATP. The Y-shaped adaptors were then ligated to DNA ends using T4 DNA ligase. Libraries were amplified with Illumina primers for 16 cycles and library fragments from 150bp to 300bp were isolated for sequencing on Illumina HiSeq or NovaSeq platforms.

tag: cell type

value: Hepatocytes

tag: genotype

value: WT


title: siNIPBL_ethanol_replicate_2

first: Gordon

last: Hager

address: 41 Center Dr

department: NCI

institute: NIH

description: 2nd replicate

data_processing:
Micro-C datasets were analyzed following the published bioinformatic pipelines. Briefly raw data were analyzed through the distiller-nf (v0.3.3) pipeline, mapping to the mouse reference assembly mm10 using bwa mem with the -SP flags. Pairtools package was then used to parse alignments and classify pairs to generate pairs files compliant with the 4DN and deduplicated pair files with an option -max-mismatch=1 on either side. Pairs classified as uniquely mapped with high mapping quality scores (MAPQ > 30 for both) were used to obtain contact matrices in the coolor format at 500bp and in balanced multiresolution cooler format files.
HiC balanced files were generated by juicer_tools pre (v1.6) and pairtools merge (v0.3.0) functions using pair files obtained from the distiller-nf pipeline.
Assembly: mm10
Supplementary files format and content: fastq, hic, cool files
Library strategy: Micro-C

source_name: cell line derived from mouse mammary epithelial tissues

growth_protocol: Three days in CSS medium

extract_protocol:
After crosslinking, nuclei were isolated and microC was performed
Kapa biosystem

treatment_protocol: To achieve an effective knockdown, 5 million 3134 cells were transfected during log phase growth, by electroporation (140V, 10ms, 3pulses) with 10ug of each siRNA against NIPBL, SMC1 or RAD21. Smartpool siRNAs were purchased by Dharmacon. Cells were treated with vehicle or dexamethasone after 72hrs after electroporation.

tag: tissue

value: 3134 cells

value: siNIPBL

value: EtOH 2hrs


title: siNIPBL_dex_replicate_2

description: 2nd replicate

value: cell line derived from mouse mammary epithelial tissues

value: Dexamethasone 100mM 2 hrs


title: siCTRL_ethanol_replicate_2

description: 2nd replicate

value: siCTRL


title: miRNA CX_wt_naive_160

city: Würzburg

first: Chi Wang

last: Ip

address: Josef-Schneider-Strasse 11

department: Neurology

country: Germany

institute: Neurologische Klinik und poliklinik

description: cortex, naive, miRNA, biol rep6

data_processing:
R version 4.1.0
Sequence reads were annoted, adapter-trimmed and mapped using miRge3.0
Read counts were summarized for each gene using featureCounts version 1.6.4
Assembly: miRge3.0
Supplementary files format and content: tab-delimited text files include raw count and r-log transformed count for each sample, as well as log2Foldchange, pvalue and p.adjust vlaue

source_name: Left cortex

growth_protocol: Mice were housed in the animal facility of the University Hospital of Würzburg and kept in standard condition (21°C, 12-h light/dark cycle)

extract_protocol:
miRNA was harvested using miRneasy mini kit(Qiagen) for the cerebellum and miRNeasy micro kit (Qiagen) for cortex and striatum . 500 ng of total RNA was used for the construction of sequencing libraries.
DNA libraries for miRNA-seq were prepared using QIASeq miRNA UDI Library Kit following manufacturer's protocols.

treatment_protocol: A right sciatic nerve crush injury was performed for 1 minute on isoflurane- anesthetized 12 week-old wt and DYT1KI mice

value: Left cortex

tag: Sex

value: male

value: naive

tag: time

value: 12 weeks post injury


title: EP000004A10_7_12.711864CF_TC00284699_K02

description:
EP000004A10_7_12.711864CF
TC00284699_K02

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_10

value: Blank


title: siNIPBL_dex_replicate_1

description: 1st replicate


title: DNAse_NC Brgf/f mice hepatocytes Dnase  #6 KO Rep.2

value: Brg1f/f, Alb-Cre


title: EP000004A10_5_1.473477CF_TC00284699_K12

description:
EP000004A10_5_1.473477CF
TC00284699_K12

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_10

value: DMEM + 10% HI-FBS


title: siNIPBL_ethanol_replicate_1

description: 1st replicate


title: miRNA CX_wt_naive_159

description: cortex, naive, miRNA, biol rep5


title: miRNA CX_wt_naive_158

description: cortex, naive, miRNA, biol rep4


title: DNAse_NC Brgf/f mice hepatocytes Dnase #6 KO Rep.1

value: Hepatocytes


title: siCTRL_dex_replicate_1

description: 1st replicate


title: EP000004A03_2_0.049970CF_TC00284699_J21

description:
EP000004A03_2_0.049970CF
TC00284699_J21

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_3

value: Surface Water


title: DNAse_NC Brgf/f mice hepatocytes Dnase #4 WT Rep.2

value: WT


title: EP000004A08_8_50.000000CF_TC00284699_J20

description:
EP000004A08_8_50.000000CF
TC00284699_J20

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_8

value: 50 CF

value: Wastewater


title: siCTRL_ethanol_replicate_1

description: 1st replicate

value: cell line derived from mouse mammary epithelial tissues

value: 3134 cells

value: siCTRL

value: EtOH 2hrs


title: miRNA CX_wt_naive_157

description: cortex, naive, miRNA, biol rep3

value: Left cortex

value: male

value: naive

value: 12 weeks post injury


title: DNAse_NC Brgf/f mice hepatocytes Dnase #4 WT Rep.1


title: miRNA CX_wt_naive_138

description: cortex, naive, miRNA, biol rep2


title: siCTRL_dex_replicate_2

description: 2nd replicate

value: Dexamethasone 100mM 2 hrs


title: SIRO_TC00284699_J15

description:
SIRO
TC00284699_J15

value: 6h exposure of 0.1 uM of Sirolimus

value: DMEM + 10% HI-FBS

value: Sirolimus


title: DNAse_Brg1AID mice Hepatocyte KO GFP+ 10h Rep.2

value: Hepatocytes


title: DNAse_Brg1AID mice Hepatocyte KO GFP+ 10h Rep.1


title: Untrtd_TC00284699_J10

description:
Untrtd
TC00284699_J10

value: untreated


title: LV, SRPK3_WT_3

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

country: China

institute: Wuhan university

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: left ventricle

value: WT


title: LV, SRPK3_WT_2


title: miRNA CX_wt_naive_31

description: cortex, naive, miRNA, biol rep1


title: RNA_CB_tg_crush_146

description: cerebellum, nerve-injured, RNA, biol rep6

data_processing:
R version 4.1.0
Sequence reads were trimmed for adaptor sequence using Cutadapt version 4.6
Trimmed sequence reads were mapped to  the mouse genome GRCm38.p6 using STAR version 2.7.2b
Read counts were summarized for each gene using featureCounts version 1.6.4
Count output was used to to calculate differentially expressed genes using DESeq2 package
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw count and r-log transformed count for each sample, as well as log2Foldchange, pvalue and p.adjust vlaue

source_name: Right cerebellum

extract_protocol:
RNA was harvested using miRneasy mini kit(Qiagen) for the cerebellum and miRNeasy micro kit (Qiagen) for cortex and striatum . 500 ng of total RNA was used for the construction of sequencing libraries.
DNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Preparation Kit following manufacturer's protocols.
RNA-seq, Samples were sequenced twice to achieve a higher depth

value: Right cerebellum

value: right sciatic nerve crush


title: EP000004B02_3_0.149731CF_TC00284699_J07

description:
EP000004B02_3_0.149731CF
TC00284699_J07

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_14

value: Blank


title: DNAse_Brg1AID mice Hepatocyte WT GFP+ 10h Rep.2


title: LV, SRPK3_WT_1


title: EP000004A09_2_0.049970CF_TC00284699_J23

description:
EP000004A09_2_0.049970CF
TC00284699_J23

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_9


title: DNAse_Brg1AID mice Hepatocyte WT GFP+ 10h Rep.1


title: TSA_TC00284699_J05

description:
TSA
TC00284699_J05

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: RNA CB_tg_crush_127

description: cerebellum, nerve-injured, RNA, biol rep4

value: male

value: 12 weeks post injury


title: LV, SRPK3_TG_3

source_name: Cardiac SRPK3_cTG

value: SRPK3 cTg


title: EP000004A02_7_12.711864CF_TC00284699_J04

description:
EP000004A02_7_12.711864CF
TC00284699_J04

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_2

value: DMEM + 10% HI-FBS

value: Wastewater


title: RNA CB_tg_crush_37

description: cerebellum, nerve-injured, RNA, biol rep3


title: DNAse_NC Brg1f/f Th1 Day6 WT  Rep.3

source_name: CD4 Th1 cells

value: In vitro cultured mouse primary CD4+ T cells


title: DNAse_NC Brg1f/f Th1 Day6 KO  Rep.3

value: Brg1f/f, Esr x Cre


title: LV, SRPK3_TG_2

value: left ventricle


title: LV, SRPK3_TG_1


title: RNA CB_tg_crush_26

description: cerebellum, nerve-injured, RNA, biol rep2

value: Right cerebellum


title: Lysis Buffer_TC00284699_J01

description:
Lysis Buffer
TC00284699_J01

source_name: Lysis Buffer

value: NA (Universal Human Reference RNA)

value: untreated


title: EP000004B01_3_0.149731CF_TC00284699_J02

description:
EP000004B01_3_0.149731CF
TC00284699_J02

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_13


title: LV, Alox5ko_TAC_3

value: TAC


title: DNAse_NC Brg1f/f Th1 Day6 KO  Rep.2


title: RNA CB_tg_crush_17

description: cerebellum, nerve-injured, RNA, biol rep1

value: right sciatic nerve crush


title: LV, Alox5ko_TAC_2


title: DNAse_NC Brg1f/f Th1 Day6 WT  Rep.2

value: WT


title: DNAse_NC Brg1f/f Th1 Day6 KO  Rep.1


title: EP000004B04_6_4.716981CF_TC00284699_I18

description:
EP000004B04_6_4.716981CF
TC00284699_I18

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: RNA CB_tg_crush_145

description: cerebellum, nerve-injured, RNA, biol rep5

value: male

value: 12 weeks post injury


title: LV, Alox5ko_TAC_1


title: RNA CB_tg_naive_140

description: cerebellum, naive, RNA, biol rep6

value: naive


title: RNA CB_tg_naive_139

description: cerebellum, naive, RNA, biol rep5


title: DNAse_NC Brg1f/f Th1 Day6 WT  Rep.1


title: LV, Alox5ko_NS_3

value: NS


title: RNA CB_tg_naive_133

description: cerebellum, naive, RNA, biol rep4


title: DNAse_KO Brg1-AID 10K T cell GFP+ 10hr, with 293T rep.3


title: LV, Alox5ko_NS_2


title: EP000004B04_3_0.149731CF_TC00284699_I15

description:
EP000004B04_3_0.149731CF
TC00284699_I15

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_16

value: DMEM + 10% HI-FBS


title: RNA CB_tg_naive_60

description: cerebellum, naive, RNA, biol rep3


title: DNAse_WT 10K T cell GFP+ 10hr, with 293T rep.3

value: In vitro cultured mouse primary CD4+ T cells


title: RNA CB_tg_naive_39

description: cerebellum, naive, RNA, biol rep2


title: LV, Alox5ko_NS_1

value: left ventricle


title: RNA CB_tg_naive_27

description: cerebelum, naive, RNA, biol rep1

value: Right cerebellum


title: BRG1-AID mice AID hepatocytes P300.R1

description: ChIC-seq

data_processing:
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Assembly: mm10
Supplementary files format and content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq::
Supplementary files format and content: bedgraph files for RNA-seq:: normlized by the library size and using a window size of 200bp
Supplementary files format and content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: normlized by the library size and using a window size of 20bp
Supplementary files format and content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates

extract_protocol:
cells for ChIC-seq were fixed for 10 minutes with 1% formaldehyde and permeabilized with RIPA buffer (10 mM Tris-Cl, 150 mM NaCl, 0.1% SDS, 0.1% NaDOC, 1% Triton X-100) for 10 minutes at RT. Antibodies (anti-H3K4me3 (17-614, Millipor and protein A-MNase fusion protein were mixed well and incubated at 4°C for 30 minutes. Next, the antibody-pA-Mnase complex was added to the permeabilized cells and incubated at 4°C for 1 hour. Then, the cells were washed with 600 μl RIPA buffer four times and rinsed once with 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM NaCl, 0.1% Triton X-100). The MNase digestion was initiated by re-suspending rinsed cells in 40 μl reaction solution buffer (10 mM Tris-Cl, 10 mM NaCl, 0.1% Triton X-100, 2 mM CaCl2) and incubated at 37°C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer (20 mM Tris-Cl, 10 mM EGTA, 20 mM NaCl, 0.2% SDS) and 1 μl proteinase K, then incubated at 65°C for overnight. DNAs were purified by using MinElute reaction cleanup kit.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. The ligation reaction was performed by adding 2 μM Illumina's adapters to each sample and incubated at RT one hour. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments from 180bp to 300bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Hi-seq3000 following the manufacturer's protocols.

tag: cell lines

value: Hepatocytes


title: DNAse_KO Brg1-AID 10K T cell GFP+ 10hr, with 293T rep.2


title: LV, WT_TAC_3


title: DNAse_WT 10K T cell GFP+ 10hr, with 293T rep.2


title: LV, WT_TAC_2


title: EP000004A12_6_4.716981CF_TC00284699_I13

description:
EP000004A12_6_4.716981CF
TC00284699_I13

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_12

value: Surface Water


title: EP000004A12_8_50.000000CF_TC00284699_I10

description:
EP000004A12_8_50.000000CF
TC00284699_I10

tag: treatment

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_12

value: 50 CF


title: GEN_TC00284699_I22

description:
GEN
TC00284699_I22

value: 6h exposure of 10 uM of Genistein

tag: media

value: Genistein

value: 10 uM


title: EP000004B03_8_50.000000CF_TC00284699_I17

description:
EP000004B03_8_50.000000CF
TC00284699_I17

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_15

tag: chemical name

value: Wastewater


title: LV, WT_TAC_1

value: WT

value: TAC


title: EP000004B06_8_50.000000CF_TC00284699_I08

description:
EP000004B06_8_50.000000CF
TC00284699_I08

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_18

tag: chemical sample_id


title: DNAse_KO Brg1-AID 10K T cell GFP+ 10hr, with 293T rep.1


title: RNA CB_wt_crush_154

value: male

value: right sciatic nerve crush

value: 12 weeks post injury


title: DNAse_WT 10K T cell GFP+ 10hr, with 293T rep.1

value: In vitro cultured mouse primary CD4+ T cells


title: LV, WT_NS_3

value: left ventricle

value: NS


title: Lysis Buffer_TC00284699_I01

description:
Lysis Buffer
TC00284699_I01

value: NA (Universal Human Reference RNA)

value: untreated

tag: chemical concentration


title: RNA CB_wt_crush_128

value: Right cerebellum


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs Pol2 rep2

data_processing:
Library strategy: ChIC-seq
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq: normalized by the library size and using a window size of 200bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: bedgraph files for RNA-seq: normalized by the library size and using a window size of 20bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates; irst column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both KO replicates; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density


title: LV, WT_NS_2


title: EP000004B05_5_1.473477CF_TC00284699_H24

description:
EP000004B05_5_1.473477CF
TC00284699_H24

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS

tag: dose level

value: Drinking Water


title: EP000004B01_8_50.000000CF_TC00284699_I14

description:
EP000004B01_8_50.000000CF
TC00284699_I14

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_13

value: 50 CF

tag: exposure time


title: RNA CB_wt_crush_29

value: WT


title: EP000004A06_8_50.000000CF_TC00284699_H22

description:
EP000004A06_8_50.000000CF
TC00284699_H22

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_6

tag: assay plate


title: LV, WT_NS_1


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs Pol2 rep1


title: RNA CB_wt_crush_28


title: RNA CB_wt_crush_156


title: RNA CB_wt_crush_19


title: EP000004A04_4_0.497018CF_TC00284699_H20

description:
EP000004A04_4_0.497018CF
TC00284699_H20

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_4

tag: assay plate_well


title: EP000004B01_2_0.049970CF_TC00284699_H19

description:
EP000004B01_2_0.049970CF
TC00284699_H19

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_13

tag: water type

value: Wastewater


title: EP000004B03_1_0.014967CF_TC00284699_H10

description:
EP000004B03_1_0.014967CF
TC00284699_H10

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_15


title: RNA CB_wt_naive_160

description: cerebellum, naive, RNA, biol rep6

value: male

value: naive

value: 12 weeks post injury


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs Pol2 rep1

tag: cell type

value: In vitro cultured mouse primary CD4+ T cells


title: P6_SVZ_scMultiome-seq

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Division of Neurology

country: Canada

institute: The University of British Columbia

description: 10X Genomics

library_source: other

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome using 10x Genomics Cell Ranger ARC v2 software (cellranger-arc count function) with settings as recommended by the manufacturer.
The data packages include fragment output and filtered digital gene expression files generated by Cell Ranger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Mutiome-Seq

molecule: other

source_name: Brain

extract_protocol:
For single-cell isolation of the early postnatal (P6) cortex, thick coronal sections, spanning the rostral end of the lateral ventricles to the rostral end of the hippocampus, were generated from each brain.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell Multiome ATAC + Gene Expression Library and Bead Kits (single cell multiome).

value: Brain

value: Primary Cells

value: SVZ

tag: genotype


title: P7_SVZ_scRNA-seq

description: 10X Genomics

library_source: transcriptomic single cell

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

molecule: polyA RNA

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

tag: tissue


title: PRO-seq_Brg1-AID CD4+ Th1 cell 10hs  rep2

data_processing:
Library strategy: Pro-seq
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq: normalized by the library size and using a window size of 200bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: bedgraph files for RNA-seq: normalized by the library size and using a window size of 20bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates; irst column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both KO replicates; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density

extract_protocol:
PRO-seq (precision nuclear run-on sequencing) assays were performed as previously reported {Mahat, 2016 #10} with some modifications. Briefly, 500,000 cells were sorted from both Brg1-AID and control mice and permeabilized with ice-cold permeabilization buffer (1x106 cells/ml) on ice for 5 minutes. Then, the nuclear run-on reaction was carried out in the presence of biotin-dATP and unlabeled dCTP, dATP, dGTP, dUTP and sarkosyl. The nascent RNAs were extracted, fragmented, and purified by streptavidin pull-down. Next, 3' adapters were ligated directly to the purified nascent RNA. Following streptavidin purification, 5' ends were repaired using TAP and PNK and then ligated to 5' adapters. The adapter-containing RNA fragments are enriched by streptavidin pull-down, followed by reverse transcription
Reverse transcripted cDNA were PCR amplified with Illumina primers for 18 cycles, The fragments from 150bp to 700bp were isolated from E-gel and sequenced on Illumina NovaSeq.


title: RNA CB_wt_naive_159

description: cerebellum, naive, RNA, biol rep5

value: Right cerebellum

tag: Sex


title: PRO-seq_Brg1-AID CD4+ Th1 cell 10hs rep1


title: P90_control_WM_biol 1_scATAC-seq

description: 10X Genomics

library_source: genomic single cell

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome (mm10) using Cell Ranger ATAC v1 software (cellranger-atac count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages include fragment output files generated by Cell Ranger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For single-cell isolation of the early postnatal (P7) and adult (P60 and P90) cortex, thick coronal sections, spanning the rostral end of the lateral ventricles to the rostral end of the hippocampus, were generated from each brain. For whole cortex datasets (P7 cortex scATAC-seq data) the region dorsal to the lateral ventricles was dissected out. This region contained the ventricular-subventricular zone (V-SVZ), cortical white matter, and cortical grey matter. For grey matter datasets (P60 grey matter scATAC-seq data), coronal sections were taken as described above and the region dorsal to the cortical white matter was dissected out. For white matter datasets (P60 white matter scATAC-seq data, P90 control scATAC-seq data, P90 cuprizone-rapamycin scATAC-seq data), coronal sections were taken as described above and the region immediately dorsal to the lateral ventricles, containing both the corpus callosum and V-SVZ, was dissected out.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell Next GEM Single Cell ATAC Library and Gel Bead Kits.

treatment_protocol: For the induction of global demyelination and the inhibition of remyelination, mice aged P25-35 were fed ad libitum standard powdered chow containing 0.3% cuprizone (Sigma) for six weeks, while also receiving intraperitoneal injections of 10 mg/kg rapamycin dissolved in 5% ethanol, 5% polyethylene glycol 400 (Sigma), and 5% Tween 80 (Sigma) in PBS five days a week. Control mice were fed standard powdered chow and received saline injections five days a week for six weeks. At the end of this period, cuprizone ceased to be added to the feed and all injections were halted. Mice were then collected after recovering for three weeks, which is considered to be approximately the midpoint of recovery

value: White matter

value: Control


title: miRNA CX_wt_crush_19

description: cortex, nerve-injured, miRNA, biol rep1

value: Left cortex

value: right sciatic nerve crush

tag: time


title: P90_control_WM_biol 2_scATAC-seq

description: 10X Genomics


title: RNA CB_wt_naive_158

description: cerebellum, naive, RNA, biol rep4

value: WT


title: DMSO_TC00284699_H06

description:
DMSO
TC00284699_H06

value: 0.5% DMSO vehicle control

value: DMEM + 10% HI-FBS

value: DMSO

value: 0 uM


title: P90_cup-rap_WM_biol 2_scATAC-seq

description: 10X Genomics

value: Cuprizone-Rapamycin


title: PRO-seq_Brg1-WT CD4+ Th1 cell 10hs  rep2


title: RNA CB_wt_naive_157

description: cerebellum, naive, RNA, biol rep3

value: male

value: naive


title: PRO-seq_Brg1-WT CD4+ Th1 cell 10hs  rep1

value: In vitro cultured mouse primary CD4+ T cells


title: P90_cup-rap _WM_biol 1_scATAC-seq

description: 10X Genomics

value: Brain


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs Pol2 rep2


title: EP000004B02_1_0.014967CF_TC00284699_H05

description:
EP000004B02_1_0.014967CF
TC00284699_H05

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_14

value: Blank


title: RNA-seq_Brg1-AID CD4+ Th1 cell 10hs  rep2

extract_protocol:
Briefly, total RNAs from 10,000 sorted cells were extracted using miRNAeasy Micro Kit (Qiagen, Cat#217084), followed by elution with 15 ul RNase-free water. Total RNAs from 2K cells were reverse transcribed and pre-amplified by PCR using KAPA HiFi Hotstart Ready Mix (Roche Cat#KK2602) with IS PCR for 9 cycles. PCR products were purified by Ampure XP beads (Beckman Coulter, Cat#A63881) and eluted with 17.5 ml nuclease-free water as described in Smart-seq2 method {Picelli, 2014 #13}. Amplified cDNAs (40 ul) were sonicated to 200-400 bp by Bioruptor Pico (Diagenode) for 20 cycles (30 seconds on and 30 seconds off).
libraries prepared and sequenced as described for the DNase-seq assays


title: RNA CB_wt_naive_138

description: cerebellum, naive, RNA, biol rep2

value: Right cerebellum

value: 12 weeks post injury


title: EP000004B02_8_50.000000CF_TC00284699_H04

description:
EP000004B02_8_50.000000CF
TC00284699_H04

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_14

value: 50 CF


title: EP000004A04_6_4.716981CF_TC00284699_H03

description:
EP000004A04_6_4.716981CF
TC00284699_H03

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_4

value: Drinking Water


title: RNA-seq_Brg1-AID CD4+ Th1 cell 10hs rep1


title: P60_GM_scATAC-seq

description: 10X Genomics

value: Primary Cells

value: Grey matter


title: RNA STR_tg_crush_146

description: striatum, nerve-injured, RNA, biol rep6

source_name: Left striatum

value: Left striatum

value: right sciatic nerve crush


title: BL_TSA_TC00284699_H01

description:
BL_TSA
TC00284699_H01

value: 6h exposure of 0 uM of Trichostatin A

value: Trichostatin A

value: 0 uM


title: P7_cortex_scATAC-seq

description: 10X Genomics

value: Cortex


title: RNA-seq_Brg1-WT CD4+ Th1 cell 10hs  rep2

value: In vitro cultured mouse primary CD4+ T cells

value: WT


title: RNA CB_wt_naive_31

description: cerebelum, naive, RNA, biol rep1

value: male

value: naive


title: EP000004A11_6_4.716981CF_TC00284699_G24

description:
EP000004A11_6_4.716981CF
TC00284699_G24

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_11

value: DMEM + 10% HI-FBS

value: Blank


title: RNA STR_tg_crush_145

description: striatum, nerve-injured, RNA, biol rep5

value: 12 weeks post injury


title: EP000004A01_7_12.711864CF_TC00284699_H07

description:
EP000004A01_7_12.711864CF
TC00284699_H07

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: RNA-seq_Brg1-WT CD4+ Th1 cell 10hs  rep1


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs Brg1 rep2


title: RNA STR_tg_crush_127

description: striatum, nerve-injured, RNA, biol rep4


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs Brg1 rep2


title: RNA STR_tg_crush_37

description: striatum, nerve-injured, RNA, biol rep3


title: Tumor_1 [5107-MR-46_4]

city: Chapel Hill,

first: Jessica

last: Thaxton

state: NC

address: 5229 Marsico Hall

department: Department of Cell Biology and Physiology

institute: The University of North Carolina at Chapel Hill

data_processing:
Raw reads were aligned to the Mouse GRCM38v100 version of the mouse genome and transcriptome using the STAR alignment tool.
Gene expression was quantified using the Salmon toolkit.
Filtering and normalization was carried out using the DESeq2 Bioconducotr package.
Assembly: GRCm38v100
Supplementary files format and content: Salmon gene expression matrices for each of the two experiments are presented in .TSV format

source_name: MCA205 tumor

growth_protocol: Experiment 1: Whole splenocytes from OT-1 mice were activated with 1 µg/mL OVA 257-264 peptide (InvivoGen) and expanded for 3 days with 200 U/mL rhIL-2 (NCI) ± 100nM ACCi (ND-646, MedChemExpress), then split and expanded into similar conditions for 4 more days. Experiment 2: MCA-205 fibrosarcomas (2.5 x 105) were established via subcutaneous injection into the right flank of C57BL/6 mice. After 14 days of tumor growth, spleens and tumors from groups of mice were harvested and tumors were processed using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi Biotec) according to manufacturer’s protocol. Samples were pre-enriched using the EasySep Mouse CD8+ T Cell Isolation Kit (Stemcell Technologies) according to manufacturer’s protocol and sorted using the FACSAria II cell sorter. CD8+ spleen and pooled TIL samples were washed in PBS and frozen for RNA-seq analysis.

extract_protocol:
Cells were washed in PBS and pellets were flash frozen at -80°C. RNA was extracted with a Promega Maxwell RSC 16 using the Maxwell RSC simplyRNA Cells kit according to the manufacturer’s instructions.
1 mg of total RNA was used for the construction of libraries with the New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.  Dual-indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: MCA205 tumor

value: CD8+ T cells

tag: compound


title: EP000004A02_6_4.716981CF_TC00284699_G17

description:
EP000004A02_6_4.716981CF
TC00284699_G17

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_2

value: Wastewater


title: Spleen_3 [5107-MR-46_3]

description: Dual-indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

source_name: Splenocytes

value: Splenocytes

tag: treatment


title: RNA STR_tg_crush_26

description: striatum, nerve-injured, RNA, biol rep2

value: Left striatum

value: right sciatic nerve crush


title: EP000004A12_3_0.149731CF_TC00284699_G20

description:
EP000004A12_3_0.149731CF
TC00284699_G20

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_12

tag: media

value: Surface Water


title: Spleen_2 [5107-MR-46_2]

value: WT


title: P60_WM_scATAC-seq

description: 10X Genomics

value: Brain

value: Primary Cells

value: White matter


title: EP000004B05_7_12.711864CF_TC00284699_G14

description:
EP000004B05_7_12.711864CF
TC00284699_G14

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS

tag: chemical name

value: Drinking Water


title: EP000004A09_6_4.716981CF_TC00284699_G11

description:
EP000004A09_6_4.716981CF
TC00284699_G11

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_9

tag: chemical sample_id

value: Blank


title: RNA STR_tg_crush_17

description: striatum, nerve-injured, RNA, biol rep1

value: male

value: 12 weeks post injury


title: Tumor_2 [5107-MR-46_5]

value: MCA205 tumor

value: CD8+ T cells


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs Brg1 rep1

value: In vitro cultured mouse primary CD4+ T cells


title: RNA STR_tg_naive_133

description: striatum, naive, RNA, biol rep4

value: Left striatum

value: naive


title: Tumor_3 [5107-MR-46_6]


title: RNA STR_tg_naive_139

description: striatum, naive, RNA, biol rep5


title: Spleen_1 [5107-MR-46_1]

value: Splenocytes


title: RNA STR_tg_naive_140

description: striatum, naive, RNA, biol rep6


title: ND-646_4 [5107-MR-105_8]

value: WT

value: Drug treatment

value: ND-646 (ACCi)


title: EP000004A10_2_0.049970CF_TC00284699_G04

description:
EP000004A10_2_0.049970CF
TC00284699_G04

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_10

tag: chemical concentration


title: EP000004A02_1_0.014967CF_TC00284699_G06

description:
EP000004A02_1_0.014967CF
TC00284699_G06

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_2

tag: dose level

value: Wastewater


title: EP000004A07_1_0.014967CF_TC00284699_G05

description:
EP000004A07_1_0.014967CF
TC00284699_G05

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_7

value: DMEM + 10% HI-FBS

tag: exposure time

value: Reclaimed Water


title: EP000004A01_3_0.149731CF_TC00284699_G08

description:
EP000004A01_3_0.149731CF
TC00284699_G08

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_1

tag: assay plate


title: RNA STR_tg_naive_39

description: striatum, naive, RNA, biol rep2

value: male

value: 12 weeks post injury


title: ND-646_2 [5107-MR-105_6]

value: CD8+ T cells


title: RNA STR_tg_naive_60

description: striatum, naive, RNA, biol rep3


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs Brg1 rep1

value: In vitro cultured mouse primary CD4+ T cells


title: EP000004A01_4_0.497018CF_TC00284699_G02

description:
EP000004A01_4_0.497018CF
TC00284699_G02

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_1

tag: assay plate_well


title: BL_TSA_TC00284699_G01

description:
BL_TSA
TC00284699_G01

value: 6h exposure of 0 uM of Trichostatin A

value: Trichostatin A

value: 0 uM

tag: water type


title: RNA STR_wt_crush_156

description: striatum, nerve-injured, RNA, biol rep6

value: Left striatum

value: WT

value: right sciatic nerve crush


title: ND-646_1 [5107-MR-105_5]

value: Splenocytes

tag: cell type

value: Drug treatment

value: ND-646 (ACCi)


title: EP000004A11_7_12.711864CF_TC00284699_F23

description:
EP000004A11_7_12.711864CF
TC00284699_F23

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_11

value: DMEM + 10% HI-FBS

value: Blank


title: RNA STR_tg_naive_27

description: striatum, naive, RNA, biol rep1

value: male

tag: genotype

value: naive


title: Control_3 [5107-MR-105_3]

tag: tissue

value: CD8+ T cells

value: Vehicle treatment

value: DMSO


title: EP000004A11_3_0.149731CF_TC00284699_F15

description:
EP000004A11_3_0.149731CF
TC00284699_F15

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_11


title: Control_2 [5107-MR-105_2]


title: RNA STR_wt_crush_128

description: striatum, nerve-injured, RNA, biol rep4

tag: Sex

value: 12 weeks post injury


title: ND-646_3 [5107-MR-105_7]


title: Control_1 [5107-MR-105_1]


title: EP000004A08_2_0.049970CF_TC00284699_F14

description:
EP000004A08_2_0.049970CF
TC00284699_F14

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_8

value: Wastewater


title: EP000004B03_7_12.711864CF_TC00284699_F09

description:
EP000004B03_7_12.711864CF
TC00284699_F09

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_15


title: RNA STR_wt_crush_28

description: striatum, nerve-injured, RNA, biol rep2

value: Left striatum

value: WT

value: right sciatic nerve crush

tag: time


title: Hillock-derived basal stem cells, RNA,  rep 2

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

data_processing:
hisat2 was used for mapping reads to the genome
featureCounts was used for quantification
DESeq2 and edgeR were used for differential analysis
Assembly: grcm38_p6_gca_000001635_8
Supplementary files format and content: xls, table of raw counts per sample

source_name: Trachea

growth_protocol: Cells from K13-CreER;LSL-tdTomato;p63gfp/+ tracheas were dissociated and sorted. tdTomato+ GFP+ hillock basal cells and tdTomato- GFP+ pseudostratified basal cells were expanded in vitro for 10 days prior to sample collection for bulk RNA/ATAC sequencing. Total RNA samples were provided to Novogene for processing according to standard protocols. Reads were mapped by Novogene to genome build grcm38_p6_gca_000001635_8.

extract_protocol:
Total RNA was extracted using a standard Trizol RNA extraction kit prior to shipment to Novogene
poly-T oligo attached magnetic beads were used to purify poly-A RNA prior to standard illumina library construction

value: Trachea

value: hillock basal stem cell


title: EP000004A06_1_0.014967CF_TC00284699_F08

description:
EP000004A06_1_0.014967CF
TC00284699_F08

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_6

value: DMEM + 10% HI-FBS

value: Drinking Water


title: RNA STR_wt_crush_19

description: striatum, nerve-injured, RNA, biol rep1

value: male


title: EP000004A12_5_1.473477CF_TC00284699_F06

description:
EP000004A12_5_1.473477CF
TC00284699_F06

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_12

value: Surface Water


title: Hillock-derived basal stem cells, RNA,  rep 1


title: RNA STR_wt_naive_160

description: striatum, naive, RNA, biol rep6

value: naive


title: Pseudostratified-derived basal stem cells, RNA,  rep 2

value: pseudostratified basal stem cell


title: EP000004A12_7_12.711864CF_TC00284699_F05

description:
EP000004A12_7_12.711864CF
TC00284699_F05

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_12


title: Control_4 [5107-MR-105_4]

value: Splenocytes

value: CD8+ T cells

value: Vehicle treatment

tag: compound

value: DMSO


title: EP000004A03_8_50.000000CF_TC00284699_F04

description:
EP000004A03_8_50.000000CF
TC00284699_F04

tag: cell line

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_3

value: 50 CF


title: RNA STR_wt_naive_159

description: striatum, naive, RNA, biol rep5

value: Left striatum

value: WT

tag: treatment

value: 12 weeks post injury


title: Pseudostratified-derived basal stem cells, RNA,  rep 1

value: Trachea


title: Hillock-derived basal stem cells, rep 1

data_processing:
skewer was used for trimming and filtering
BWA was used for mapping to the reference genome
MACS2 was used for peak calling, with the following parameters: -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all
Assembly: grcm38_p6_gca_000001635_8
Supplementary files format and content: pooled bigwig files for hillock and pseudostratified basal cells

growth_protocol: Cells from K13-CreER;LSL-tdTomato;p63gfp/+ tracheas were dissociated and sorted. tdTomato+ GFP+ hillock basal cells and tdTomato- GFP+ pseudostratified basal cells were expanded in vitro for 10 days prior to sample collection for bulk RNA/ATAC sequencing. Frozen cell pellets were provided to Novogene for processing according to standard protocols. Reads were mapped by Novogene to genome build grcm38_p6_gca_000001635_8.

extract_protocol:
Nuclei were extracted from frozen cell pellets, before transposition and library construction
Nuclei pellets are resuspended in TN5 transposase reaction mix including standard adapters. PCR amplification and AMPure bead purification were performed.

value: hillock basal stem cell


title: RNA STR_wt_naive_157

description: striatum, naive, RNA, biol rep3

value: male


title: RNA STR_wt_crush_154

description: striatum, nerve-injured, RNA, biol rep5

value: right sciatic nerve crush


title: islet CD45+, wild-type, rep3

city: Fitzroy

first: Balasubramanian

last: Krishnamurthy

state: VIC

address: 41 Victoria Parade

department: Department of Endocrinology and Diabetes

country: Australia

institute: St. Vincent’s Hospital Melbourne

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: gzipped TSV files containing filtered feature-barcode matrices (feature and barcode sequences corresponding to row and column indices respectively)

source_name: pancreatic islet

extract_protocol:
Mouse pancreata were perfused with 3 mL of Collagenase P- in,complete Hanks’ balanced salt solution (cHBSS) injected via clamped pancreatic duct. Perfused pancreata were then excised and incubated at 37°C for 15 minutes. Digested pancreata were mechanically disrupted and islets were separated from exocrine tissue on a Histopaque density gradient by centrifugation. Islets were dispersed into single cells using bovine trypsin and stained for immune cell markers. Live CD45+ cells were sorted using FACS Aria Fusion (Beckton Dickinson) and resuspended in complete RPMI medium for further processing.
Library was performed according to the manufacter’s instructions (Single Cell 3’ v3 chemistry, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: pancreatic islet

value: Female

value: CD45+ cells

value: NOD, wildtype


title: BL_DMSO_TC00284699_F01

description:
BL_DMSO
TC00284699_F01

value: untreated

tag: media

value: 0 uM


title: EP000004B02_6_4.716981CF_TC00284699_F03

description:
EP000004B02_6_4.716981CF
TC00284699_F03

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_14

value: DMEM + 10% HI-FBS

tag: chemical name

value: Blank


title: Pseudostratified-derived basal stem cells, rep 1

value: pseudostratified basal stem cell


title: RNA STR_wt_naive_138

description: striatum, naive, RNA, biol rep2

value: Left striatum

value: naive


title: islet CD45+, wild-type, rep2


title: islet CD45+, wild-type, rep1


title: EP000004A05_3_0.149731CF_TC00284699_E22

description:
EP000004A05_3_0.149731CF
TC00284699_E22

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_5

tag: chemical sample_id

value: Surface Water


title: EP000004A02_8_50.000000CF_TC00284699_E24

description:
EP000004A02_8_50.000000CF
TC00284699_E24

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_2

tag: chemical concentration

value: 50 CF

value: Wastewater


title: RNA STR_wt_crush_29

description: striatum, nerve-injured, RNA, biol rep3

value: male

value: WT

value: right sciatic nerve crush

value: 12 weeks post injury


title: RNA CX_tg_crush_146

description: cortex, nerve-injured, RNA, biol rep6

value: Left cortex


title: RNA CX_tg_crush_145

description: cortex, nerve-injured, RNA, biol rep5


title: PanSci, mouse duodenum, part 6

city: New York

first: Zehao

last: Zhang

state: NY

address: 1230 York Ave, The Rockefeller University

institute: The Rockefeller University

description:
EXP119_EXP121_Duodenum
PanSci_duodenum_genecount.mtx
PanSci_duodenum_df_cell.csv
PanSci_duodenum_df_gene.csv

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

molecule: nuclear RNA

source_name: duodenum

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

value: duodenum


title: RNA STR_wt_naive_158

description: striatum, naive, RNA, biol rep4


title: EP000004B06_3_0.149731CF_TC00284699_E21

description:
EP000004B06_3_0.149731CF
TC00284699_E21

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

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).

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_18

tag: dose level


title: EP000004B05_6_4.716981CF_TC00284699_E19

description:
EP000004B05_6_4.716981CF
TC00284699_E19

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS

tag: exposure time

value: Drinking Water


title: PanSci, mouse duodenum, part 5


title: RNA CX_tg_crush_127

description: cortex, nerve-injured, RNA, biol rep4


title: SIRO_TC00284699_E18

description:
SIRO
TC00284699_E18

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus

tag: assay plate


title: EP000004A12_4_0.497018CF_TC00284699_E15

description:
EP000004A12_4_0.497018CF
TC00284699_E15

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_12

tag: assay plate_well


title: PanSci, mouse duodenum, part 3


title: PanSci, mouse duodenum, part 4


title: RNA CX_tg_crush_37

description: cortex, nerve-injured, RNA, biol rep3


title: RNA CX_tg_crush_26

description: cortex, nerve-injured, RNA, biol rep2


title: EP000004A05_6_4.716981CF_TC00284699_E14

description:
EP000004A05_6_4.716981CF
TC00284699_E14

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_5

tag: water type

value: Surface Water


title: PanSci, mouse duodenum, part 2


title: RNA CX_tg_crush_17

description: cortex, nerve-injured, RNA, biol rep1


title: RNA STR_wt_naive_31

description: striatum, naive, RNA, biol rep1

value: Left striatum

value: naive


title: SIRO_TC00284699_E11

description:
SIRO
TC00284699_E11


title: RNA CX_tg_naive_140

description: cortex, naive, RNA, biol rep6

value: male


title: RNA CX_tg_naive_139

description: cortex, naive, RNA, biol rep5


title: PanSci, mouse jejunum, part 7

description:
EXP117_Jejunum
PanSci_jejunum_genecount.mtx
PanSci_jejunum_df_cell.csv
PanSci_jejunum_df_gene.csv

source_name: jejunum

value: jejunum


title: RNA CX_tg_naive_133

description: cortex, naive, RNA, biol rep4


title: RNA CX_tg_naive_60

description: cortex, naive, RNA, biol rep3


title: PanSci, mouse jejunum, part 9


title: EP000004B06_5_1.473477CF_TC00284699_E09

description:
EP000004B06_5_1.473477CF
TC00284699_E09

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_18


title: EP000004A08_5_1.473477CF_TC00284699_E04

description:
EP000004A08_5_1.473477CF
TC00284699_E04

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_8

value: Wastewater


title: PanSci, mouse duodenum, part 1

value: duodenum


title: PanSci, mouse jejunum, part 6


title: PanSci, mouse jejunum, part 5


title: EP000004A07_3_0.149731CF_TC00284699_E07

description:
EP000004A07_3_0.149731CF
TC00284699_E07

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_7

value: Reclaimed Water


title: RNA CX_tg_naive_39

description: cortex, naive, RNA, biol rep2

value: Left cortex

value: 12 weeks post injury


title: Untrtd_TC00284699_E05

description:
Untrtd
TC00284699_E05

value: untreated

value: DMEM + 10% HI-FBS


title: RNA CX_tg_naive_27

description: cortex, naive, RNA, biol rep1


title: PanSci, mouse jejunum, part 8


title: BL_DMSO_TC00284699_E01

description:
BL_DMSO
TC00284699_E01

value: 0 uM


title: RNA CX_wt_crush_154

description: cortex, nerve-injured, RNA, biol rep5

value: WT

value: right sciatic nerve crush


title: RNA CX_wt_crush_128

description: cortex, nerve-injured, RNA, biol rep4


title: PanSci, mouse jejunum, part 1


title: EP000004A11_8_50.000000CF_TC00284699_D23

description:
EP000004A11_8_50.000000CF
TC00284699_D23

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_11

value: 50 CF

value: Blank


title: RNA CX_wt_crush_156

description: cortex, nerve-injured, RNA, biol rep6

value: male


title: PanSci, mouse jejunum, part 4

value: jejunum


title: PanSci, mouse jejunum, part 3


title: TSA_TC00284699_D20

description:
TSA
TC00284699_D20

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: RNA CX_wt_crush_29

description: cortex, nerve-injured, RNA, biol rep3


title: PanSci, mouse colon, part 8

description:
EXP116_EXP121_Colon
PanSci_colon_genecount.mtx
PanSci_colon_df_cell.csv
PanSci_colon_df_gene.csv

source_name: colon

value: colon


title: EP000004A04_5_1.473477CF_TC00284699_D19

description:
EP000004A04_5_1.473477CF
TC00284699_D19

source_name: MCF7 Cells

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_4

value: Drinking Water


title: EP000004A01_1_0.014967CF_TC00284699_D18

description:
EP000004A01_1_0.014967CF
TC00284699_D18

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: RNA CX_wt_crush_28

description: cortex, nerve-injured, RNA, biol rep2

value: Left cortex

value: 12 weeks post injury


title: PanSci, mouse colon, part 7


title: EP000004B03_3_0.149731CF_TC00284699_E02

description:
EP000004B03_3_0.149731CF
TC00284699_E02

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_15

value: DMEM + 10% HI-FBS

value: Wastewater


title: PanSci, mouse colon, part 6


title: RNA CX_wt_crush_19

description: cortex, nerve-injured, RNA, biol rep1

value: WT

value: right sciatic nerve crush


title: EP000004A06_7_12.711864CF_TC00284699_D15

description:
EP000004A06_7_12.711864CF
TC00284699_D15

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_6


title: RNA CX_wt_naive_160

description: cortex, naive, RNA, biol rep6

value: male

value: naive


title: EP000004A09_8_50.000000CF_TC00284699_D13

description:
EP000004A09_8_50.000000CF
TC00284699_D13

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_9

value: 50 CF

value: Blank


title: RNA CX_wt_naive_159

description: cortex, naive, RNA, biol rep5


title: EP000004A07_8_50.000000CF_TC00284699_D11

description:
EP000004A07_8_50.000000CF
TC00284699_D11

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_7


title: PanSci, mouse colon, part 3

value: colon


title: RNA CX_wt_naive_158

description: cortex, naive, RNA, biol rep4


title: EP000004B04_4_0.497018CF_TC00284699_D21

description:
EP000004B04_4_0.497018CF
TC00284699_D21

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_16


title: PanSci, mouse colon, part 4


title: PanSci, mouse colon, part 5


title: PanSci, mouse jejunum, part 2

value: jejunum


title: RNA CX_wt_naive_157

description: cortex, naive, RNA, biol rep3

value: Left cortex


title: EP000004A07_7_12.711864CF_TC00284699_D09

description:
EP000004A07_7_12.711864CF
TC00284699_D09

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_7

value: Reclaimed Water


title: PanSci, mouse colon, part 2


title: EP000004A10_1_0.014967CF_TC00284699_D07

description:
EP000004A10_1_0.014967CF
TC00284699_D07

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_10

value: DMEM + 10% HI-FBS


title: RNA CX_wt_naive_138

description: cortex, naive, RNA, biol rep2

value: WT

value: 12 weeks post injury


title: EP000004A09_7_12.711864CF_TC00284699_D08

description:
EP000004A09_7_12.711864CF
TC00284699_D08

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_9


title: RNA CX_wt_naive_31

description: cortex, naive, RNA, biol rep1

value: male


title: PanSci, mouse colon, part 1


title: PanSci, mouse ileum, part 6

description:
EXP115_Ileum
PanSci_ileum_genecount.mtx
PanSci_ileum_df_cell.csv
PanSci_ileum_df_gene.csv

source_name: ileum

value: ileum


title: H3K4me1_WT_GC_R3

city: New York City

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
The split reads were aligned using bwa mem to mm10. Duplicate marking and removal was done by Picard.
Peaking calling were preformed using two methods. The H3K4me1/H3K4me3 peaks were called against H3 total as input uisng Homer package with following command: findPeaks <H3K4Tag> -style histone 1000 -C 0 -o auto -i <H3_Tag>.
A consensus peaks were called using Genrich packages. All H3K4me1 and H3K4me3 aligned files are provided as sample and previously published H3 aligned files were provided as input to creat a concensus peak file.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Normalized and scaled bigwigs and broadpeak or narrowpeak file

source_name: Spleen

extract_protocol:
Mint-ChIP was performed using H3K27Ac antibody (Cat#39133, lot 31814008) from Active Motif following the protocol from the Berstein lab. Briefly, 50,000 FACS sorted centrocytes, in triplicates, were processed with MNase to fragment native chromatin.
Barcoded adapters were ligated to every sample and samples were multiplexed for chromatin immunoprecipitation (ChIP). After ChIP, material was linearly amplified by RNA in vitro transcription in the presence of RNAse inhibitor RNAseOUT (Invitrogen 10777019). Fragments were reverse-transcribed and amplified as a library

treatment_protocol: Mice were immunized with sheep red blood cells (SRBC) 8 days before extraction of spleens

value: Spleen

tag: cell type

value: GC Centrocytes

value: Ab:Abcam ab8895


title: PanSci, mouse ileum, part 5

tag: genotype


title: H3K4me1_WT_GC_R2

tag: tissue


title: PanSci, mouse ileum, part 4


title: EP000004B05_1_0.014967CF_TC00284699_C23

description:
EP000004B05_1_0.014967CF
TC00284699_C23

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_17

value: Drinking Water


title: H3K4me1_WT_GC_R1


title: GEN_TC00284699_C22

description:
GEN
TC00284699_C22

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: EP000004A09_4_0.497018CF_TC00284699_D10

description:
EP000004A09_4_0.497018CF
TC00284699_D10

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_9

value: Blank


title: PanSci, mouse ileum, part 2


title: H3K4me3_WT_GC_R2

value: Ab:Abcam ab8580


title: H3K4me3_WT_GC_R1


title: PanSci, mouse perigonadal adipose tissue, part 6

description:
EXP114_gWAT
PanSci_gWAT_genecount.mtx
PanSci_gWAT_df_cell.csv
PanSci_gWAT_df_gene.csv

source_name: perigonadal adipose tissue

value: perigonadal adipose tissue


title: E5.5_4h_clone8_2

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

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

growth_protocol: E5.5 embryos were dissected from the uterus of timely pregnant females.

extract_protocol:
A group of 10 Epiblasts were placed into a 1.5 ml tube with 350 µl of lysis buffer of the Micro RNEasy Kit (Qiagen, 74004), used for RNA extraction according to manufacturer’s instructions.
Libraries were prepared from 7 ng of RNA per sample using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420).

treatment_protocol: E5.5 Sox2Cre; CRAFR26 embryos were cultured in IVC2 media (Bedzhov et al. 2014) supplemented with 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904) to induce ERK. To collect the Epiblast, the extraembryonic layers were removed by microdissection.

value: E5.5 Epiblast

tag: clone

value: clone 8

value: 4OHT 4h


title: PanSci, mouse ileum, part 1


title: EP000004B05_4_0.497018CF_TC00284699_C20

description:
EP000004B05_4_0.497018CF
TC00284699_C20

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS


title: EP000004A07_4_0.497018CF_TC00284699_C18

description:
EP000004A07_4_0.497018CF
TC00284699_C18

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_7

value: Reclaimed Water


title: EP000004B04_8_50.000000CF_TC00284699_C17

description:
EP000004B04_8_50.000000CF
TC00284699_C17

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_16

value: 50 CF


title: PanSci, mouse perigonadal adipose tissue, part 4


title: EP000004B01_4_0.497018CF_TC00284699_C09

description:
EP000004B01_4_0.497018CF
TC00284699_C09

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_13

value: Wastewater


title: E5.5_4h_clone4_2

value: clone 4

tag: time


title: HBRR_TC00284699_D01

description:
HBRR
TC00284699_D01

source_name: Human Brain Reference RNA

value: NA (Universal Human Reference RNA)

value: untreated


title: PanSci, mouse perigonadal adipose tissue, part 3


title: EP000004A05_4_0.497018CF_TC00284699_C05

description:
EP000004A05_4_0.497018CF
TC00284699_C05

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_5

value: Surface Water


title: EP000004A09_3_0.149731CF_TC00284699_C03

description:
EP000004A09_3_0.149731CF
TC00284699_C03

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_9

value: Blank


title: PanSci, mouse perigonadal adipose tissue, part 2

value: perigonadal adipose tissue


title: HBRR_TC00284699_C01

description:
HBRR
TC00284699_C01


title: H3K4me3_WT_GC_R3

value: Spleen

value: GC Centrocytes

value: WT

value: Ab:Abcam ab8580


title: E5.5_0h_clone8_1

value: E5.5 Epiblast

value: clone 8

value: Vehicle (ethanol) 4h


title: PanSci, mouse perigonadal adipose tissue, part 1


title: EP000004A11_4_0.497018CF_TC00284699_C21

description:
EP000004A11_4_0.497018CF
TC00284699_C21

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_11

value: DMEM + 10% HI-FBS


title: PanSci, mouse inguinal adipose tissue, part 3

description:
EXP113_iWAT
PanSci_iWAT_genecount.mtx
PanSci_iWAT_df_cell.csv
PanSci_iWAT_df_gene.csv

source_name: inguinal adipose tissue

value: inguinal adipose tissue


title: PanSci, mouse inguinal adipose tissue, part 2


title: E5.5_0h_clone4_2

value: clone 4


title: EP000004A02_2_0.049970CF_TC00284699_B24

description:
EP000004A02_2_0.049970CF
TC00284699_B24

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_2

value: Wastewater


title: PanSci, mouse perigonadal adipose tissue, part 5


title: EP000004A12_1_0.014967CF_TC00284699_C10

description:
EP000004A12_1_0.014967CF
TC00284699_C10

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_12

value: Surface Water


title: EP000004B02_5_1.473477CF_TC00284699_B16

description:
EP000004B02_5_1.473477CF
TC00284699_B16

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_14

value: Blank


title: PanSci, mouse inguinal adipose tissue, part 1


title: PanSci, mouse brown adipose tissue, part 3

description:
EXP111_EXP121_BAT
PanSci_BAT_genecount.mtx
PanSci_BAT_df_cell.csv
PanSci_BAT_df_gene.csv

source_name: brown adipose tissue

value: brown adipose tissue


title: E3.5_4h_clone8_2

growth_protocol: E2.5 embryos were flushed from the oviducts using M2 medium (Sigma, M7167).

extract_protocol:
A group of 10 ICMs were placed into a 1.5ml tube with lysis buffer from the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems, KIT0204), and followed with RNA extraction according to manufacturer’s instructions.
Libraries were prepared from 2 ng of RNA per sample using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420).

treatment_protocol: E2.5 Sox2Cre; CRAFR26 embryos were cultured in KSOM supplemented with 250 nM PD17 (PD173074, Sigma, P2499) for 24h. To induce ERK, the media was supplemented with 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904). To collect the ICM, the trophectoderm layer was removed by blastocyst immunosurgery.

value: E3.5 Epiblast

value: 4OHT 4h


title: E5.5_4h_clone8_1


title: E5.5_0h_clone4_1


title: E3.5_4h_clone8_1


title: EP000004A05_5_1.473477CF_TC00284699_B15

description:
EP000004A05_5_1.473477CF
TC00284699_B15

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_5


title: PanSci, mouse brown adipose tissue, part 2


title: RH4_JQ1_6h_Pol2_HiChIP

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and 1% Pen/Strep/Glut.

extract_protocol:
To isolate RNA, RH4 or RH5 cells were washed with PBS, then lysed on ice with RLT using the RNeasy mini kit (Qiagen). PDXs were directly lysed with RLT.  For HiChIP, the Dovetail MNase HiChIP kit (Catalogue #21007) was used. Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-RNA Pol2 antibody (Santa Cruz Biotechnology, Mouse mAb #sc-47701 X). On-bead bridge incorporation and religation was performed, followed by reversal of crosslinks, proteinase K treatment, and DNA purification.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For in vitro RNA-seq and HiChIP experiments, RH4 and RH5 cells were treated with DMSO, ARV771, or JQ1 for six hours at 100nM.


title: E5.5_4h_clone4_1

value: E5.5 Epiblast


title: E3.5_4h_clone4_2


title: EP000004B04_2_0.049970CF_TC00284699_B14

description:
EP000004B04_2_0.049970CF
TC00284699_B14

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: RH4_ARV771_6h_Pol2_HiChIP


title: E5.5_0h_clone8_2

value: clone 8

value: Vehicle (ethanol) 4h


title: PanSci, mouse brown adipose tissue, part 1


title: E3.5_4h_clone4_1


title: Library2_multiAsCas12aKRAB_T14_Rep2

city: Palo Alto

first: Chris

last: Hsiung

state: CA

address: 3181 Porter Dr

institute: Arc Institute

description: 6-plex crRNA screen

data_processing:
Library 1: Reads were mapped to crRNA constructs using sgcount (https://noamteyssier.github.io/sgcount/), requiring perfect match to the reference sequence.
Library 2: First, reference construct sequences were created by interspersing provided spacer and constant regions. Each construct is then given a unique construct id (CID). Each CID is then split into R1 and R2 reference sequences, which are constructed by taking the first three and last three spacer-construct pairs of the reference sequence respectively. The R2 sequence is then reverse complemented for matching against the R2 sequencing reads. Next, two hashmaps are created for the R1 and R2 spacer-construct pairs respectively, which map the R1/R2 sequences to a set of corresponding CIDs. Finally, for each R1/R2 sequencing pair, each k-mer (k = length of R1/R2 respective construct sequence) in the sequence is mapped against their respective R1/R2 hashmap. If both sequencing pairs are able to be mapped to a CID set, then the intersection of their sets is their original construct, and the total count of that CID is incremented. We implemented the above algorithm as the `casmap constructs` command in a package written in Rust, available at https://github.com/noamteyssier/casmap.
Starting from read counts, the cell fitness scores were calculated using custom scripts in R as detailed in the associated publication. For Library 1, data from a single T0 sample was used to calculate the fitness score for both replicates due to an unexpected global loss of sequencing read counts for one of two originally intended T0 replicate samples. For each screen replicate in Library 2, data from two separate sequencing library preps from the same Round 1 PCR material subjected to separate Round 2 PCR’s and sequenced on separate runs were pooled together for analysis.
Assembly: crRNA library reference for each screen
Supplementary files format and content: Lib1_Counts.txt contains counts table for Library 1.
Supplementary files format and content: Lib1_FitnessScore.txt contains the cell fitness scores (gamma) for Library 1.
Supplementary files format and content: Lib2_Counts.txt containsn counts table for Library 2.
Supplementary files format and content: Lib2_FitnessScore.txt contains the cell fitness scores (gamma) for Library 2.
Supplementary files format and content: README_DescriptionScreenProcessedFiles.txt contains detailed description of the contents of all processed data files

growth_protocol: K562 cells were cultured at 37deg. C with 5% CO2 in tissue culture incubators. Culture media consists of RPMI-1640 (Gibco cat# 22400121) containing 25 mM HEPES, 2mM L-glutamine, and supplemented with 10% FBS (VWR), 100 units/mL streptomycin, and 100 mg/mL penicillin. During the screen, K562 cells were cultured in flasks in a shaking incubator and the culture media was supplemented with 0.1% Pluronic F-127 (Thermo Fisher P6866).

extract_protocol:
Genomic DNA was isolated using the NucleoSpin Blood XL Maxi kit (Machery-Nagel 740950.50)
crRNA inserts were amplified from genomic DNA isolated from screens using 16 cycles of first round PCR using pooled 0-8nt staggered forward and reverse primers, treated with ExoSAP-IT (Thermo Fisher 78201.1.ML), followed by second round of PCR to introduce Illumina unique dual indices and adaptors. Sequencing primer binding sites, unique dual indices, P5 and P7 adaptor sequences are from Illumina Adaptor Sequences Document # 1000000002694 v16. PCR amplicons were subject to size selection by magnetic beads (SPRIselect, Beckman B23318) prior to sequencing on an Illumina NovaSeq6000 using SP100 kit (PE100) for Library 1 or SP500 kit (PE250) for Library 2. Sequencing of plasmid libraries were performed similarly, except 7 cycles of amplification were each used for Round 1 and Round 2 PCR. The size distribution of the final library was measured on an Agilent TapeStation system. We noted that even after magnetic bead selection of Round 2 PCR-amplified Library 2 plasmid library (colonies from which were Sanger sequencing verified) and genomic DNA from screens, smaller sized fragments from non-specific PCR amplification during Illumina sequencing library preparation persisted. This might contribute to the fraction of reads that could not be mapped to our reference 6-plex array. Thus, these unmapped reads do not necessarily reflect recombination of the crRNA library constructs, though the latter could contribute as well.

treatment_protocol: Library 1 screen: K562 cells engineered by piggyBac transposition to constitutively express denAsCas12a-KRAB or multiAsCas12a-KRAB were transduced with lentivirally packaged Library 1 constructs at MOI = ~0.15. Transduced cells were then selected using 1ug/ml puromycin for 2 days, followed by washout of puromycin. On Day 6 after transduction, initial (T0) time point was harvested, and the culture was split into 2 replicates that are separately cultured henceforth. 10 days later (T10), the final time point was harvested (8.6 total doublings for multiAsCas12a-KRAB cells, 9.15 total doublings for denasCas12a-KRAB cells). A cell coverage of >500x was maintained throughout the screen. Library 2 screen: K562 cells engineered by piggyBac transposition to constitutively express multiAsCas12a-KRAB were transduced with lentivirally packaged Library 2 constructs at MOI = ~0.15. The screen was carried out similarly as described for Library 1 screen, except the screen was carried out for 14 days (T14) or 13.5 total doublings and maintained at a cell coverage of >2000x throughout.


title: E3.5_0h_clone8_1


title: Library2_multiAsCas12aKRAB_T14_Rep1

description: 6-plex crRNA screen


title: EP000004B02_2_0.049970CF_TC00284699_B13

description:
EP000004B02_2_0.049970CF
TC00284699_B13

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_14

value: DMEM + 10% HI-FBS


title: PanSci, mouse stomach, part 3

description:
EXP104_Stomach
PanSci_stomach_genecount.mtx
PanSci_stomach_df_cell.csv
PanSci_stomach_df_gene.csv

source_name: stomach

value: stomach


title: EP000004B03_4_0.497018CF_TC00284699_B21

description:
EP000004B03_4_0.497018CF
TC00284699_B21

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_15

value: Wastewater


title: PanSci, mouse stomach, part 2


title: Library2_multiAsCas12aKRAB_T0_Rep2

description: 6-plex crRNA screen


title: E3.5_0h_clone4_2

value: clone 4


title: EP000004A10_8_50.000000CF_TC00284699_B07

description:
EP000004A10_8_50.000000CF
TC00284699_B07

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_10

value: 50 CF


title: Library2_multiAsCas12aKRAB_T0_Rep1

description: 6-plex crRNA screen


title: EP000004B02_7_12.711864CF_TC00284699_B05

description:
EP000004B02_7_12.711864CF
TC00284699_B05

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_14

value: Blank


title: EP000004A04_8_50.000000CF_TC00284699_B04

description:
EP000004A04_8_50.000000CF
TC00284699_B04

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_4

value: Drinking Water


title: PanSci, mouse muscle, part 2

description:
EXP103_Muscle
PanSci_muscle_genecount.mtx
PanSci_muscle_df_cell.csv
PanSci_muscle_df_gene.csv

source_name: muscle

value: muscle


title: EpiLC_rev_clone8_2

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

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

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

value: EpiLC

value: rev

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


title: EpiLC_rev_clone8_1

value: clone 8


title: Library1_denAsCas12aKRAB_T10_Rep1

description: Single-plex crRNA screen


title: PanSci, mouse muscle, part 1


title: PanSci, mouse stomach, part 1


title: EP000004A10_4_0.497018CF_TC00284699_B03

description:
EP000004A10_4_0.497018CF
TC00284699_B03

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_10


title: PanSci, mouse heart, part 6

description:
EXP102_EXP110_Heart
PanSci_heart_genecount.mtx
PanSci_heart_df_cell.csv
PanSci_heart_df_gene.csv

source_name: heart

value: heart


title: Library1_denAsCas12aKRAB_T10_Rep2

description: Single-plex crRNA screen


title: Library1_multiAsCas12aKRAB_T10_Rep2

description: Single-plex crRNA screen


title: E3.5_0h_clone4_1

value: E3.5 Epiblast

value: Vehicle (ethanol) 4h


title: UHRR_TC00284699_B01

description:
UHRR
TC00284699_B01

source_name: Universal Human Reference RNA

value: NA (Universal Human Reference RNA)

value: untreated


title: EP000004A03_7_12.711864CF_TC00284699_B10

description:
EP000004A03_7_12.711864CF
TC00284699_B10

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_3

value: DMEM + 10% HI-FBS

value: Surface Water


title: EpiLC_rev_clone4_1

value: clone 4


title: EP000004A08_3_0.149731CF_TC00284699_A24

description:
EP000004A08_3_0.149731CF
TC00284699_A24

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_8

value: Wastewater


title: PanSci, mouse heart, part 5


title: Library1_multiAsCas12aKRAB_T10_Rep1

description: Single-plex crRNA screen


title: EpiLC_4h_clone8_2

value: PD17 2h, 4OHT 4h


title: PanSci, mouse heart, part 4


title: Library1_denAsCas12aKRAB_T0_Rep2

description: Single-plex crRNA screen


title: EP000004A08_7_12.711864CF_TC00284699_A19

description:
EP000004A08_7_12.711864CF
TC00284699_A19

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_8


title: EpiLC_4h_clone8_1

value: EpiLC


title: Library1_denAsCas12aKRAB_T0_Rep1

description: Single-plex crRNA screen


title: EP000004A08_6_4.716981CF_TC00284699_A18

description:
EP000004A08_6_4.716981CF
TC00284699_A18

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_8


title: PanSci, mouse heart, part 2


title: EpiLC_4h_clone4_2


title: EP000004B04_1_0.014967CF_TC00284699_A15

description:
EP000004B04_1_0.014967CF
TC00284699_A15

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: Library1_multiAsCas12aKRAB_T0_Rep1

description: Single-plex crRNA screen


title: EpiLC_rev_clone4_2

value: rev

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


title: EpiLC_4h_clone4_1


title: EP000004B01_7_12.711864CF_TC00284699_A10

description:
EP000004B01_7_12.711864CF
TC00284699_A10

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_13


title: PanSci, mouse heart, part 1

value: heart


title: PanSci, mouse liver, part 8

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

source_name: liver

value: liver


title: EP000004A12_2_0.049970CF_TC00284699_A06

description:
EP000004A12_2_0.049970CF
TC00284699_A06

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_12


title: EpiLC_2h_clone8_2

value: clone 8

value: PD17 2h, 4OHT 2h


title: KH004_D77_FTY

first: Kam

last: Leong

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

description: Chromium 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: GRCh38
Supplementary files format and content: Expression matrix of each sample.
Supplementary files format and content: For each sample, "features.tsv.gz" corresponded to gene names. "barcodes.tsv.gz" corresponded to cell barcodes. "matrix.mtx.gz" was the expression counts in sparce matrix.

source_name: Midbrain Organoids

growth_protocol: Generation of midbrain organoids was explained in detail in the manuscript Methods session.

extract_protocol:
Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology.
Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD).

value: Midbrain Organoids

value: Day 77

tag: fentanyl treatment

value: Yes

tag: fentanyl treatment_duration

value: 77 Days


title: KH003_D77_UT

description: Chromium 10x Genomics

tag: cell line

value: Untreated


title: KH005_D79_WD

description: Chromium 10x Genomics

value: Day 79


title: PanSci, mouse liver, part 7


title: PanSci, mouse ileum, part 3

value: ileum


title: PanSci, mouse liver, part 6


title: UHRR_TC00284699_A01

description:
UHRR
TC00284699_A01

value: NA (Universal Human Reference RNA)

tag: treatment

value: untreated

tag: media


title: Untrtd_TC00284663_P24

description:
Untrtd
TC00284663_P24

value: DMEM + 10% HI-FBS

tag: chemical name

tag: chemical sample_id


title: KH002_D53_AC_FTY

description: Chromium 10x Genomics

value: Day 53

value: 4 Hours


title: KH001_D53_UT

description: Chromium 10x Genomics


title: PanSci, mouse liver, part 5


title: EpiLC_2h_clone4_1

value: EpiLC

value: clone 4


title: PanSci, mouse heart, part 3

value: heart