title: WJL1494_RLF_N019

source_name: vAbl-ProB

value: vAbl-ProB

value: pro-B cells


title: 18 CAMA1 Fulvestrant 1hr

status: Public on Sep 01 2023

type: SRA

city: SAN FRANCISCO

first: Alison

last: Parisian

state: California

address: 780 Brannan St

country: USA

institute: Olema Pharmaceuticals

library_source: transcriptomic

data_processing:
Data was analyzed and visualized using the Arpeggio Biosciences Insights portal
Assembly: hg38
Supplementary files format and content: Counts files
Library strategy: Pro-Seq

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: Prior to experiment MCF7 cells were cultured in Eagle’s MEM supplemented with 0.01 mg/mL human recombinant insulin and CAMA1 cells were cultured in Richter’s IMEM supplemented with nonessential amino acids

extract_protocol:
Run-on and subsequent PRO-seq library preparation experiments were performed on permeabilized cell pellets in a freeze buffer as described, but with modifications, from the Mahat 2016 Protol. Briefly, permeabilized cells were mixed with run-on buffer and incubated at 30°C for 5 minutes. Run-on reaction was stopped and RNA was extracted. RNA was fragmented. RNA was cleaned up using columns and reconstituted to a final volume. Biotinylated RNAs were enriched using the streptavidin beads. Binding and incubation occured. Bound beads were washed with a high salt buffer, twice with binding buffer, and once with low salt buffer. RNA was removed from the streptavidin beads. Extracted RNA was dissolved and subjected to a second round of biotinylated RNA enrichment. After the second round, the isolated RNA was dissolved and immediately proceeded to cDNA synthesis.
The RNA libraries were prepared and sequenced using the Illumina NextSeq500, single read, 1x75 bps

treatment_protocol: MCF7 or CAMA1 cells were plated in estradiol-depleted charcoal dextran stripped serum-containing media for 24 hours prior to dosing with 316 nM compound or 100 pM 17-beta estradiol and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. For estradiol pretreated conditions, cells were treated for 24 hours with 17-beta estradiol prior to compound treatment and harvested after 15 min, 1 hr, 6 hr or 24 hr treatment. Harvested samples were processed for precision run-on sequencing.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: treatment

value: Fulvestrant 1 hr

tag: time point


title: WJL1493_RLF_N019

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS

molecule: genomic DNA

organism: Mus musculus

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. DNA-PKcs inhitors, DPKi #1 (Nu7441, 0.5 µM) and DPKi #2 (Nu7026, 20 µM)were added to some of the samples the same day as STI-571.

tag: genotype


title: Steer #4 infected mid anterior lung

type: RNA

city: Orient Point

first: James

middle: Jiangtao

last: Zhu

state: NY

department: Plum Island Animal Disease Center

institute: USDA-ARS

description: Design Format: IS-45220-4-V1

hyb_protocol: One Cy3 labled sample was cohybrided with the Cy5 labled control in one hybridization chamber (Agilent) containing an Agilent microarray (Array design #:Agilent-019963; 4 X 44k per slide). The chambers were incubated in a incubator at 65 C in a rotating cartridge overnight. After incubation, the arrays were washed with Agilent washing buffers according to amnufacturer's protocol.

scan_protocol: After hybridization and washing, the arrays were scanned at 5 micrometer per pixel with a Cy3 to Cy5 ratio of approximately 1 using a GenPix 4000B scanner (Molecular Devices) and the images were saved as tiff files.

data_processing:
The expression data were extracted from the tiff files using Agilent Genpix 7.0 software and the raw data were saved as gpr files for statisitcal analysis using R with librarys(limma, MASS, statmod, splines). LOESS method was applied to normalize interarray variation with a background subtraction of 15.
The gpr files were named based on the Agilent array serial number, the array number of the slide, such as 251996310039_1, the date of the experiment, and the tissues.  The normalized Cy3 results of each sample were used as gene expression levels (photon per pixel) (provided in the Matrix). Averaged Expression is the mean expression of the probe. Fold Change is the difference in expression level (fold) between compared tissues.  adj.P.Val is false discover rate.

molecule: total RNA

organism: Bos taurus

source_name: tissue total RNA

label_protocol: Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA according to the manufacturer's protocol. Pooled total RNA isolated from all infected or non-infected metacarpal skin was labeled with Cy5 as universal control. All Individual RNA samples were individually labeled with Cy3.

growth_protocol: The animal study including the approved Institutional Animal Care and Use Committee protocol was reported in Zhu JJ, Arzt J, Puckette MC, Smoliga GR, Pacheco JM, Rodriguez LL. Mechanisms of foot-and-mouth disease virus tropism inferred from differential tissue gene expression. PLoS One. 2013 May 28;8(5):e64119.

extract_protocol: Total RNA was extracted from each cell culture well using the RNeasy mini kit (Qiagen) following the manufacturer instructions. RNA quality was assessed using the Agilent 2100 bioanalyzer (Santa Clara, CA, USA) using an RNA nanochip. Quantification of RNA was conducted on a Nanodrop 1000 (Thermo Scientific).

treatment_protocol: The FMDV infection was described in Pacheco JM, Arzt J, Rodriguez LL (2010) Early events in the pathogenesis of foot-and-mouth disease in cattle after controlled aerosol exposure. Vet J 183:46–53.

tag: steer number

tag: tissue

value: mid anterior lung

tag: infection status

value: FMDV infected tissue

source_name: Pooled total RNA of metacarpal skin

value: metacarpal skin


title: M1B26 CD10P biological rep1

city: Lyon

first: Véronique

last: Maguer-Satta

address: 28 Rue Laennec, Bat Cheney D, 4ème étage

country: France

institute: Centre de Recherche en Cancérologie de Lyon

description: Gene expression data from CD10+ sorted M1B26 cells

hyb_protocol: 10 µg of labeled cRNA was fragmented and denaturated in hybridization buffer, then hybridized on chip during 16 hours at 45°C with constant mixing by rotation at 60 rpm in an Genechip hybridization oven 640 (Affymetrix). After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip® Hybridization Wash and Stain Kit) in a fluidic 450 (Affymetrix) according to the manufacturer’s instruction.

scan_protocol: The arrays were read with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing: CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. The obtained data were normalized with Affymetrix Expression Console software using MAS5 statistical algorithm.

label: biotin

source_name: CD10+ sorted M1B26 cells

label_protocol: Total RNA (50 ng) was amplified and biotin-labeled using GeneChip® 3’ IVT PLUS kit. Before amplification, spikes of synthetic mRNA at different concentrations were added to all samples; these positive controls were used to ascertain the quality of the process. Biotinylated antisense cRNA for microarray hybridization was prepared. After final purification using magnetic beads, cRNA quantification was performed with a nanodrop and quality checked with Agilent 2100 Bioanalyzer (Agilent technologies, Inc, Palto Alto, CA, USA).

growth_protocol: All cell lines were grown in phenol red-free Dulbecco’s modified Eagle’s medium (DMEM)/F-12 nutrient mix supplemented with 2% horse serum, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 20 ng/ml EGF and 1% penicillin/streptomycin ). MC26 and M1B26 cells culture media wazs supplemented by BMP2 and IL6 (both at 10 ng/ml).

extract_protocol: Total RNA were extracted using RNeasy-Plus mini columns from Qiagen following manufacturer's recommendations.

treatment_protocol: Cells were trypsinized, washed in PBS and either frozen at -80°C or stained for CD10 membrane expression before flow cytometry sorting (see samples section).

value: M1B26 cells

tag: cell culture medium

value: Standard medium supplemented with 5ng/ml recombinant human BMP2 and 10 ng/ml recombinant human IL-6

tag: cell population

value: CD10+ sorted cells


title: 17 CAMA1 Fulvestrant 1hr


title: MC26 CD10P biological rep2

description: Gene expression data from CD10+ sorted MC26 cells

source_name: CD10+ sorted MC26 cells

value: MC26 cells


title: 16 CAMA1 Estradiol 1hr

value: Estradiol 1 hr


title: MC26 CD10N biological rep2

description: Gene expression data from CD10- sorted MC26 cells

source_name: CD10- sorted MC26 cells

value: CD10- sorted cells


title: M1B26 CD10N biological rep2

description: Gene expression data from CD10- sorted M1B26 cells

source_name: CD10- sorted M1B26 cells


title: Steer #4 infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate


title: M1B26 CD10N biological rep1


title: Steer #4 infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium


title: WJL1492_RLF_N019


title: WJL1491_RLF_N019


title: MC26 CD10P biological rep1


title: Steer #4 infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: dorsal nasal pharynx


title: 15 CAMA1 Estradiol 1hr


title: WJL1490_RLF_N019


title: Steer #4 infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium


title: Steer #3 non-infected metacarpal skin

description: Design Format: IS-45220-4-V1

value: not FMDV infected tissue


title: WJL1489_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: MC26 CD10N biological rep1


title: MCF10A-CT CD10N biological rep2

description: Gene expression data from CD10- sorted MCF10A cells

source_name: CD10- sorted MCF10A-CT cells

value: MCF10A-CT cells

value: Standard medium


title: 13 CAMA1 DMSO 1hr

value: breast cancer cell line

value: DMSO 1 hr


title: MCF10A-CT CD10Pbiological  rep2

description: Gene expression data from CD10+ sorted MCF10A cells

source_name: CD10+ sorted MCF10A-CT cells


title: WJL1488_RLF_N019


title: 12 CAMA1 OP-1250 15min

value: 15 min


title: WJL1486_RLF_N019

value: WT + DPKi #1


title: 11 CAMA1 OP-1250 15min


title: WJL1487_RLF_N019


title: 14 CAMA1 DMSO 1hr


title: WJL1485_RLF_N019

value: WT + DPKi #2


title: Steer #3 non-infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band

value: metacarpal skin


title: 10 CAMA1 24 HOUR ESTRADIOL + OP-1250 15min

value: Estradiol + OP-1250 15 min


title: 9 CAMA1 24 HOUR ESTRADIOL + OP-1250 15min


title: MCF10A-CT CD10N biological rep1

value: CD10- sorted cells


title: MCF10A-CT CD10P biological rep1

value: CD10+ sorted cells


title: Steer #3 non-infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: dorsal nasal pharynx


title: 8 CAMA1 Tamoxifen 15min

value: Tamoxifen 15 min


title: WJL1484_RLF_N019

value: WT


title: Steer #3 non-infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium

value: not FMDV infected tissue


title: 7 CAMA1 Tamoxifen 15min


title: Steer #3 non-infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium


title: WJL1483_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: WJL1482_RLF_N019


title: M1B26 biological rep2

description: Gene expression data from unsorted M1B26 cells

source_name: M1B26 cells

value: M1B26 cells

value: Standard medium supplemented with 5ng/ml recombinant human BMP2 and 10 ng/ml recombinant human IL-6

value: unsorted


title: Steer #2 non-infected metacarpal skin

description: Design Format: IS-45220-4-V1


title: MEF Sec24D KO with 150 nM scrambled siRNA [Q.Scr.5]

city: Ames

first: Jinoh

last: Kim

state: IA

address: 515 Morrill Rd

department: Biomedical Sciences

institute: Iowa State University

description:
Q.Scr.5
Q-SCR-5_S151_L004

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10).
Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: RPKMs (log2-transformed with an offset value of 1.0) for each sample.

growth_protocol: MEF cells were grown in high glucose DMEM media containing 10% FBS and supplemented with penicillin (50 units/ml) and streptomycin (100 mg/ml).

extract_protocol:
Total RNA was extracted followed TRIzol RNA extraction protocol. The total RNA was subjected to library synthesis using AccuScript High Fidelity 1st strand cDNA synthesis kit to double-stranded cDNA.
The total RNA was subjected to library synthesis using AccuScript High Fidelity 1st strand cDNA synthesis kit to double stranded cDNA.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before transfected with SEC24s siRNA (50 nM for 48 h) to cell culture medium. SEC24s siRNA and Lipofectamine RNAiMAX were mixed and added to DMEM without FBS at day 0. Media were removed and replaced with complete media in the following morning. RNAs were collected next day (24hr) in TRIzol.

tag: cell source

value: Mouse embryo

value: MEF Sec24D knockout

value: Fibroblast

value: 150 nM siRNA scrambled for 48 hrs


title: MC26 biological rep2

description: Gene expression data from unsorted MC26 cells

source_name: MC26 cells

value: MC26 cells


title: MCF10A-CT biological rep2

description: Gene expression data from unsorted MCF10A cells

source_name: MCF10A-CT cells

value: MCF10A-CT cells

value: Standard medium


title: Steer #2 non-infected interdigital cleft skin

description: Design Format: IS-45220-4-V1

value: interdigital cleft skin

value: metacarpal skin


title: 6 CAMA1 Fulvestrant 15min

value: breast cancer cell line

value: Fulvestrant 15 min

value: 15 min


title: Steer #3 non-infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate

value: not FMDV infected tissue


title: Steer #2 non-infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band


title: M1B26 biological rep1

value: M1B26 cells

value: Standard medium supplemented with 5ng/ml recombinant human BMP2 and 10 ng/ml recombinant human IL-6


title: WJL1481_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: MEF Sec24D KO with 150 nM scrambled siRNA [Q.Scr.3]

description:
Q.Scr.3
Q-SCR-3_S149_L004

value: Mouse embryo

value: MEF Sec24D knockout

value: Fibroblast


title: Steer #3 non-infected mid anterior lung

description: Design Format: IS-45220-4-V1

value: mid anterior lung


title: 5 CAMA1 Fulvestrant 15min


title: WJL1480_RLF_N019


title: 4 CAMA1 Estradiol 15min

value: Estradiol 15 min


title: MEF Sec24D KO with 150 nM scrambled siRNA [Q.Scr.2]

description:
Q.Scr.2
Q-SCR-2_S148_L004

value: 150 nM siRNA scrambled for 48 hrs


title: MCF10A-CT biological rep1

value: MCF10A-CT cells

value: Standard medium

value: unsorted


title: Steer #2 non-infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: dorsal nasal pharynx

value: metacarpal skin


title: MEF Sec24D KO with 150 nM scrambled siRNA [Q.Scr.4]

description:
Q.Scr.4
Q-SCR-4_S150_L004


title: MC26 biological rep1

value: MC26 cells


title: Steer #2 non-infected mid anterior lung

description: Design Format: IS-45220-4-V1

value: not FMDV infected tissue


title: WJL1479_RLF_N019


title: Steer #2 non-infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium


title: 3 CAMA1 Estradiol 15min

value: breast cancer cell line

value: 15 min


title: WJL1478_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: MEF Sec24D KO with 50 nM scrambled siRNA [D.Scr.3]

description:
D.Scr.3
D-SCR-3_S139_L004

value: Mouse embryo

value: MEF Sec24D knockout

value: 50 nM siRNA scrambled for 48 hrs


title: 1 CAMA1 DMSO 15 mins

value: DMSO 15 min


title: Steer #2 non-infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate


title: 2 CAMA1 DMSO 15min


title: MEF Sec24D KO with 50 nM scrambled siRNA [D.Scr.1]

description:
D.Scr.1
D-SCR-1_S137_L004

value: Fibroblast


title: MEF Sec24D KO with 50 nM scrambled siRNA [D.Scr.2]

description:
D.Scr.2
D-SCR-2_S138_L004


title: WJL1475_RLF_N019


title: WJL1476_RLF_N019


title: MEF Sec24D KO treated with siRNA knockdown for Sec24B [BD.5]

description:
BD.5
BD-5_S146_L004

value: siRNA Sec24B for 48 hrs


title: MEF Sec24D KO with 150 nM scrambled siRNA [Q.Scr.1]

description:
Q.Scr.1
Q-SCR-1_S147_L004

value: 150 nM siRNA scrambled for 48 hrs


title: 47 MCF7 OP-1250 24hr

value: 24 hr


title: 46 MCF7 24 HOUR ESTRADIOL + OP-1250 24hr

value: Estradiol + OP-1250 24 hr


title: MEF Sec24D KO with 50 nM scrambled siRNA [D.Scr.4]

description:
D.Scr.4
D-SCR-4_S140_L004


title: Steer #2 non-infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium

value: metacarpal skin


title: MEF Sec24D KO treated with siRNA knockdown for Sec24B [BD.4]

description:
BD.4
BD-4_S145_L004


title: WJL1477_RLF_N019


title: Steer #1 non-infected metacarpal skin

description: Design Format: IS-45220-4-V1

value: not FMDV infected tissue


title: Steer #1 non-infected coronary band

description: Design Format: IS-45220-4-V1

value: coronary band


title: 48 MCF7 OP-1250 24hr

value: breast cancer cell line


title: MEF Sec24D KO treated with siRNA knockdown for Sec24B [BD.3]

description:
BD.3
BD-3_S144_L004


title: WJL1472_RLF_N019

value: vAbl-ProB

value: WT


title: WJL1474_RLF_N019

value: pro-B cells

value: WT + DPKi #1


title: WJL1473_RLF_N019

value: WT + DPKi #2


title: Steer #1 non-infected interdigital cleft skin

description: Design Format: IS-45220-4-V1

value: interdigital cleft skin


title: 44 MCF7 Tamoxifen 24hr

value: Tamoxifen 24 hr


title: 43 MCF7 Tamoxifen 24hr


title: Steer #1 non-infected dorsal nasal pharynx

description: Design Format: IS-45220-4-V1

value: dorsal nasal pharynx


title: WJL1471_RLF_N019


title: MEF Sec24D KO treated with siRNA knockdown for Sec24B [BD.1]

description:
BD.1
BD-1_S142_L004

value: Mouse embryo

value: MEF Sec24D knockout

value: Fibroblast

value: siRNA Sec24B for 48 hrs


title: Steer #1 non-infected mid anterior lung

description: Design Format: IS-45220-4-V1

value: mid anterior lung


title: MEF Sec24D KO treated with siRNA knockdown for Sec24B [BD.2]

description:
BD.2
BD-2_S143_L004


title: WJL1470_RLF_N019


title: Steer #1 non-infected nasal turbinate epithelium

description: Design Format: IS-45220-4-V1

value: nasal turbinate epithelium

value: metacarpal skin


title: MEF Sec24D KO treated with siRNA knockdown for Sec24A, Sec24B, & Sec24C  [ABCD.5]

description:
ABCD.5
ABCD-5_S156_L004

value: siRNA knockdown for Sec24A, Sec24B, & Sec24C for 48 hrs


title: 45 MCF7 24 HOUR ESTRADIOL + OP-1250 24hr

value: breast cancer cell line

value: Estradiol + OP-1250 24 hr

value: 24 hr


title: WJL1469_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: 40 MCF7 Estradiol 24hr

value: Estradiol 24 hr


title: Pyk knockout, replicate 2

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

data_processing:
STAR alignment and quantification with --quantMode GeneCounts option
Assembly: BDGP6.32
Supplementary files format and content: STAR gene counts, tab separated

organism: Drosophila melanogaster

source_name: Pyk mutant

growth_protocol: Fly stocks were maintained on Bloomington Drosophila Stock Center media at 25ºC. Larvae were collected on molasses agar plates.

extract_protocol:
TriPure isolation reagent and further purified using a Qiagen RNeasy kit (Catalog #74004)
Standard Illumina TruSeq Stranded mRNA libraries
TrueSeq Stranded mRNA loaded to a target depth of 15-20 million reads each

value: whole animal


title: Pyk knockout, replicate 3


title: MEF Sec24D KO treated with siRNA knockdown for Sec24A, Sec24B, & Sec24C  [ABCD.3]

description:
ABCD.3
ABCD-3_S154_L004


title: 39 MCF7 Estradiol 24hr


title: 42 MCF7 Fulvestrant 24hr

value: Fulvestrant 24 hr


title: MEF Sec24D KO treated with siRNA knockdown for Sec24A, Sec24B, & Sec24C  [ABCD.4]

description:
ABCD.4
ABCD-4_S155_L004


title: MEF Sec24D KO treated with siRNA knockdown for Sec24A, Sec24B, & Sec24C  [ABCD.2]

description:
ABCD.2
ABCD-2_S153_L004


title: WJL1468_RLF_N019


title: Pyk control, replicate 3

source_name: Pyk heterozygous control


title: Steer #1 non-infected dorsal soft palate

description: Design Format: IS-45220-4-V1

value: dorsal soft palate

value: not FMDV infected tissue


title: 41 MCF7 Fulvestrant 24hr


title: WJL1466_RLF_N019


title: WJL1467_RLF_N019


title: Steer #1 non-infected tongue epithelium

description: Design Format: IS-45220-4-V1

value: tongue epithelium


title: 38 MCF7 DMSO 24hr

value: DMSO 24 hr


title: Pyk control, replicate 2


title: MEF Sec24D KO treated with siRNA knockdown for Sec24A, Sec24B, & Sec24C  [ABCD.1]

description:
ABCD.1
ABCD-1_S152_L004

value: Mouse embryo

value: MEF Sec24D knockout

value: Fibroblast


title: 37 MCF7 DMSO 24hr


title: Pyk control, replicate 1


title: WJL1465_RLF_N019


title: WJL1464_RLF_N019


title: Luminal parous KO [830kLu]

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Eightysix-base-pair single-end reads were preprocessed with BBDuk (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) to remove possible traces of rRNA, adapters and polyA tails, as recommended by Lexogen. UMI-tools were used to extract UMIs from sequended reads, which were then aligned to the mouse genome (GRCm39) with Bowtie2. SAMtools were used to create the corresponding  sorted BAM files. UMI-tools were used again for final read deduplication, and the resulting BAM files were converted to FASTQ format with BEDtools. FASTQ files were analysed with the nextpresso pipeline. Sequencing quality was checked with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 10 in at least 25% of the samples (the Gencode vM26 gene annotation for GRCm39 was used). Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered. Bubble plots were built with ggseabubble (https://gitlab.com/bu_cnio/ggseabubble). CellPhoneDB was used to infer combined expression of ligand-receptor pairs.
Assembly: GRCm39
Supplementary files format and content: Normalized counts obtained with DESeq2

source_name: mammary gland

growth_protocol: Animals were maintained in standard anaimal facility conditions

extract_protocol:
Rna was extracted using the mini Rneasy kit from Quiagen
Quantseq 3’UTR; Total RNA samples, 500 ng with an average RIN=6.9 (range: 2.5-8.6) were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) with a UMI Second Strand Synthesis module. Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. While primers from both steps contain Illumina-compatible sequences, random primers additionally feature 6 nt long Unique Molecular Identifier (UMI) tags. Libraries are completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation, i.e., the read1 (the only read in single read format) has the sense orientation.

treatment_protocol: Animal were treated with doxicyclin (1mg/ml in the drinking water) between 3 and 8 weeks of age to induce cre recombination

tag: developmental stage

value: Parous

value: Luminal

tag: genetic model origin

value: K8rta:TETO CRE:RANK fl/fl:mTmG


title: Pg H2O2-3

city: Loma Linda

first: Yuetan

last: Dou

state: CA

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to P. gingivalis W83 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Assembly: Porphyromonas gingivalis W83, Filifactor alocis ATCC 35896
Supplementary files format and content: original process to.csv file, with all genes reads in two files, P. gingivalis and F. alocis respectively.

organism: Porphyromonas gingivalis W83

source_name: culture

growth_protocol: Anaerobic condotions (80% N2, 10% H2, 10%CO2)

extract_protocol:
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).
cDNA in library were taged by specific barcode sequence and exposed to sequencing.

treatment_protocol: Treated by 0.25 mM of hydrogen peroxide

value: culture

value: 0.25 mM H2O2 stress


title: 36 MCF7 OP-1250 6hr

value: breast cancer cell line

value: 6 hr


title: Basal parous KO [830kBa]

value: Basal


title: Pyk knockout, replicate 1

value: whole animal


title: WJL1463_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: WJL1462_RLF_N019

value: WT + DPKi #1


title: Pg H2O2-1


title: Pg H2O2-2


title: 34 MCF7 24 HOUR ESTRADIOL + OP-1250 6hr

value: Estradiol + OP-1250 6 hr


title: Luminal virgin KO [825kLu]

value: Virgin


title: Luminal virgin KO [822kLu]


title: 03-day7

city: guangzhou

first: anning

last: chen

address: 195 West Dongfeng Road

country: China

institute: Guangzhou Medical University Cancer Hospital

library_source: transcriptomic single cell

data_processing:
Single-cell gel bead emulsion generation of blood-derived PBMCs was performed using a chromium controller (10×Genomics), single cell 3' library and gel bead kit V3.1 (10×Genomics).
The resulting GEM libraries were then sequenced on an Illumina Novaseq 6000 using a custom paired-end sequencing mode of 150 bp for the first read and 150 bp for the second read.
The raw data was processed using the Cell Ranger Single-Cell Software Suite (v5.0.0) with default parameters and aligned to the genomic reference.
To maintain data quality, cells were discarded if they had gene counts below 200 or over 5000, or mitochondrial gene expression greater than 15%.
The most variable genes among the single cells were identified, and their log-transformed gene-barcode matrices were subjected to principal component analysis to reduce their dimensionality.
The resulting data was visualized in a t-SNE plot constructed with Seurat (v3.1.1) to differentiate among the PBMC cell types.
Assembly: NOT PROVIDED; REQUESTED
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: PBMC

value: disease state

value: sepsis-ARDS

value: Blood was collected on the 7th day of admission


title: Basal virgin KO [825kBa]

value: K8rta:TETO CRE:RANK fl/fl:mTmG


title: 03-day1

value: Blood collected on the 1st day of admission


title: Basal virgin KO [822kBa]


title: WJL1459_RLF_N019

source_name: vAbl-ProB


title: 31 MCF7 Tamoxifen 6hr

value: Tamoxifen 6 hr


title: 35 MCF7 OP-1250 6hr

value: breast cancer cell line


title: 32 MCF7 Tamoxifen 6hr

value: 6 hr


title: 02-day7


title: Luminal virgin KO [821kLu]

value: Luminal


title: WJL1458_RLF_N019


title: 33 MCF7 24 HOUR ESTRADIOL + OP-1250 6hr


title: WJL1461_RLF_N019

value: WT + DPKi #2


title: 02-day1


title: WJL1460_RLF_N019

value: vAbl-ProB

value: WT


title: WJL1457_RLF_N019

value: pro-B cells


title: 29 MCF7 Fulvestrant 6hr

value: Fulvestrant 6 hr


title: 01-day7


title: Basal virgin KO [820kBa]

value: Virgin

value: Basal


title: WJL1456_RLF_N019


title: 28 MCF7 Estradiol 6hr

value: Estradiol 6 hr


title: Steer #3 non-infected interdigital cleft skin

description: Design Format: IS-45220-4-V1

source_name: tissue total RNA

value: interdigital cleft skin

value: not FMDV infected tissue

value: metacarpal skin


title: WJL1455_RLF_N019


title: Luminal parous KO [798kLu]

value: Parous

value: K8rta:TETO CRE:RANK fl/fl:mTmG


title: 01-day1

value: blood

value: PBMC

value: disease state

value: sepsis-ARDS

value: Blood collected on the 1st day of admission


title: 27 MCF7 Estradiol 6hr

value: breast cancer cell line

value: 6 hr


title: WJL1454_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: Basal parous KO [798kBa]


title: Luminal parous KO [794kLu]

value: Luminal


title: WJL1453_RLF_N019


title: 25 MCF7 DMSO 6hr

value: DMSO 6 hr


title: 26 MCF7 DMSO 6hr


title: Basal parous KO [794kBa]

value: Basal


title: HNEpC_LPS_3

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and RPKM values for each Sample

source_name: HNEpC

growth_protocol: Cells were cultured in an airway epithelial cell basal medium (PromoCell, C-21060) with growth medium kit (PromoCell, C- 21160) in a 5% CO2 incubator at 37℃.

extract_protocol:
RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells were treated with 2mL 1μg/ml LPS or same amount of normal culture medium for 6h.

value: HNEpC

value: nasal epithelial cell

value: LPS


title: WJL1452_RLF_N019


title: 30 MCF7 Fulvestrant 6hr

value: Fulvestrant 6 hr


title: Basal virgin KO [821kBa]

value: Virgin

value: K8rta:TETO CRE:RANK fl/fl:mTmG


title: 24 MCF7 OP-1250 1hr

value: 1 hr


title: Luminal parous KO [787kLu]

value: Parous


title: 23 MCF7 OP-1250 1hr


title: WJL1450_RLF_N019

value: WT + DPKi #1


title: HNEpC_Control_2

value: Control


title: HNEpC_Control_1


title: HNEpC_Control_3


title: Basal virgin [568Ba]

value: K8rta:TETO CRE:mTmG


title: Basal parous KO [787kBa]


title: 21 MCF7 24 HOUR ESTRADIOL + OP-1250 1hr

value: breast cancer cell line

value: Estradiol + OP-1250


title: WJL1449_RLF_N019

value: vAbl-ProB

value: pro-B cells

value: WT + DPKi #2


title: WJL1448_RLF_N019

value: WT


title: HNEpC_LPS_2

value: HNEpC


title: HNEpC_LPS_1

value: nasal epithelial cell


title: Luminal parous [558Lu]

value: Luminal


title: 20 MCF7 Tamoxifen 1hr

value: Tamoxifen


title: Basal Parous [558Ba]

value: Basal


title: celltag2_ispinesib_day139_GEX

city: New York

first: Peter

middle: A.

last: Sims

address: 3960 Broadway

institute: Columbia University Medical Center

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-715

data_processing:
GEX: Raw data obtained from NovaSeq was corrected for index swapping according to Griffiths et al. Nat Commun (2018). Raw reads were processed as described in Yuan et al. Genome Med (2018), with a brief description follows.  Raw reads were trimmed of polyA tail and aligned with STAR. We constructed an address comprised of cell-barcode, UMI, and gene identifier for each read with a unique, strand-specific alignment to exonic sequence. Reads with same address were collapsed and sequencing errors in cell-barcodes and UMI were corrected. Cell-barcodes of empty microwell or poor quality cells were removed. Empty cell-barcodes were identified with EmptyDrops algorithm (Lun et al Genome Biol (2019)). Cells are poor quality if they meet any of the following criteria: 1) fractional alignment to the mitochondrial genome per cell-barcode is greater than 10%; 2) a ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons is greater than 1.96 standard deviations above the mean; 3) average number of reads per molecule or average number of molecules per gene is greater than 2.5 standard deviations above the mean; or 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4. .
CellTag: CellTag binary count matrices were generated with the CellTagWorkflow algorithm (https://github.com/morris-lab/CellTagWorkflow), with an additional preprocessing step of removing UMI with less than three raw reads.
Assembly: GRCh38 GRCm38
Supplementary files format and content: GEX counts matrix file is a tab-delimited text file with rows being genes, columns being cell-barcodes and values being counts, with the first two columns being the gene IDs and gene symbols.   CellTag binary matrix file is a tab-delimited text file with rows being cell-barcode_sampleIDs, columns being celltags, and values being 0 or 1 for the absence and presence of the celltag in a given cell-barcode respectively.

growth_protocol: TS543 were cultured with NeuroCultTM NS-A Proliferation Kit Human from STEMCELL Technologies.

extract_protocol:
TS543 neurospheres were dissociated to single cells by mechanical pipetting. Mouse brain tumor resections were dissociated to single cells using Adult Brain Dissociation kit on gentleMACSTM Octo Dissociator with Heater (Miltenyi Biotec).
Microwell 3' scRNA-seq were performed as described in Yuan et al. Sci Rep (2016). Briefly, individual single cell was compartmentalized with a barcoded-mRNA-capture-bead (MACOSKO-2011-10, ChemGenes) and lysed in microwell-based platform, mRNA were captured and reverse transcribed on the bead, and cDNA-beads were pooled for PCR amplification and illumina Nextera library construction for each sample.   To sequence the CellTag library separately from the GEX library at greater sequencing depth, CellTag libraries were constructed with custom P5_TSO_hybrid primer and custom P7_TruSeq-Unique-Index_EGFP primer.
3' single-cell RNA-seq

treatment_protocol: TS543 were treated with 75 nM ispinesib or with vehicle DMSO.

value: ispinesib


title: celltag2_DMSO_day139_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-714

value: DMSO


title: 19 MCF7 Tamoxifen 1hr

value: 1 hr


title: celltag2_ispinesib_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-712


title: celltag2_ispinesib_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-710


title: WJL1447_RLF_N019


title: Basal parous [557Ba]

value: Parous


title: WJL1446_RLF_N019


title: WJL1451_RLF_N019


title: 17 MCF7 Fulvestrant 1hr

value: Fulvestrant


title: WJL1445_RLF_N019


title: 22 MCF7 24 HOUR ESTRADIOL + OP-1250 1hr


title: 18 MCF7 Fulvestrant 1hr


title: 16 MCF7 Estradiol 1hr

value: Estradiol

value: 15 min


title: Luminal virgin [538Lu]

value: Virgin

value: K8rta:TETO CRE:mTmG


title: WJL1443_RLF_N019

value: vAbl-ProB

value: pro-B cells


title: celltag2_ispinesib_day42_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-707


title: celltag2_DMSO_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY052-709


title: 15 MCF7 Estradiol 1hr

value: breast cancer cell line


title: Basal virgin [538Ba]


title: celltag2_DMSO_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-711


title: Luminal parous [534Lu]


title: WJL1442_RLF_N019


title: 14 MCF7 DMSO 1hr


title: WJL1441_RLF_N019


title: Luminal virgin [533Lu]


title: celltag2_ispinesib_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-706


title: Luminal parous [557Lu]


title: Basal parous [534Ba]


title: 13 MCF7 DMSO 1hr


title: celltag2_ispinesib_day21_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-708


title: WJL1440_RLF_N019


title: celltag2_DMSO_day21_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-704


title: WJL1439_RLF_N019


title: celltag2_DMSO_day42_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-705


title: Basal parous [532Ba]


title: WJL1438_RLF_N019

value: WT + DPKi #1


title: Luminal parous [532Lu]


title: WJL1444_RLF_N019


title: celltag2_ispinesib_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-703


title: 10 MCF7 24 HOUR ESTRADIOL + OP-1250 15min

value: Estradiol + OP-1250


title: 9 MCF7 24 HOUR ESTRADIOL + OP-1250 15min


title: Basal virgin [531Ba]


title: celltag2_DMSO_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-701


title: celltag2_DMSO_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY051-702


title: Luminal parous [494Lu]

value: Luminal


title: AgaPCg-6, scRNAseq

city: Los Angeles

first: Jennifer

last: Zieba

address: 615 Charles E. Young Dr.

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Femoral and tibial growth plate cartilage

extract_protocol:
Proximal tibia and distal femur epiphyses from postnatal day 5 mouse pups were collected and digested with Collagenase I tissue removal solution (1% Collagenase I, 2.5% trypsin w/o EDTA, 30mM Cacl2, in HBSS) at 37ºC for 45 minutes to remove muscle tissue that remained following dissection. Cartilage samples were then incubated at 37ºC in Collagenase II single cell isolation solution (1% Collagenase II, 2.5% trypsin w/o EDTA, 30mM Cacl2, in HBSS) for 2-3 hours with brief vortexing every 10-15 minutes. Single cells were passed through a 40um cell strainer in PBS containing 0.04% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 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.

tag: strain

value: Chondrocytes

tag: age

value: Postnatal day 5


title: 12 MCF7 OP-1250 15min


title: AgaPCg-4, scRNAseq

description: 10x Genomics

value: Femoral and tibial growth plate cartilage


title: 7 MCF7 Tamoxifen 15min

value: Tamoxifen


title: 11 MCF7 OP-1250 15min


title: control2_ispinesib_day139_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-715

value: ispinesib


title: 6 MCF7 Fulvestrant 15min


title: WT_7dLight7dDark_3

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

data_processing:
Basecalling was done by using RTA software version 1.18.54.0
Files were generated by bcl2fastq tool version 2.17.1 and bam files were generated by fastq2bam tool version 0.7.
The sequence libraries were processed using Trimmomatic with options “ILLUMINACLIP:adaptors:2:20:8, SLIDINGWINDOW:4:15, TRAILING:15, HEADCROP:12, MINLENGTH:20”
Trimmed and filtered reads were mapped against the Aethionema arabicum genome version 3.0, using Bowtie2 version 2.3.5.1 with the options "--no-unal and --very-sensitive-local" and uniquely mapped reads were kept.
Mapped reads per feature were counted using HTSeq-count version 0.11.2 with the options “-f bam -s no -t gene -i ID -m intersection-nonempty”.
Assembly: Aethionema arabicum genome version 3.0 (id59426) https://genomevolution.org/coge/OrganismView.pl?gid=36061
Supplementary files format and content: xls matrix table file includes Aethionema gene model IDs (v3.1 annotation; id37218), gene length, TAIR10IDs, TAIR10 description, Raw Counts and RPKM values for each sample.

molecule: polyA RNA

organism: Aethionema arabicum

source_name: imbibed seeds

extract_protocol:
Intact, non-germinating seeds were collected into liquid nitrogen. RNA was extracted as described at Chang et. al. 1993 (http://dx.doi.org/10.1007/BF02670468) followed by additional purification using columns (QIAGEN RNeasy Kit, Cat. No. 74104).
Libraries were constructed from 600 ng RNA using Lexogen SENSE mRNA seq library Prep Kit (Cat. No. 009) including  Poly(A) RNA Selection Kit (Cat. No. 039).

treatment_protocol: All samples are seed material, treated on wet filter paper at 14°C. The light conditions are indicated separately.

value: imbibed seeds

value: Cyprus accession

value: 7 days kept under 100µmol m-2s-1 white light and 7 following days kept in darkness


title: AgaPCg-1, scRNAseq

description: 10x Genomics


title: 5 MCF7 Fulvestrant 15min

value: Fulvestrant

value: 15 min


title: Luminal virgin [531Lu]

value: Virgin

value: K8rta:TETO CRE:mTmG


title: AgaCg26-3, scRNAseq

description: 10x Genomics


title: 4 MCF7 Estradiol 15min

value: Estradiol


title: WT_7dLight7dDark_1


title: control2_DMSO_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-711

value: DMSO


title: WJL1437_RLF_N019

value: vAbl-ProB

value: pro-B cells

value: WT + DPKi #2


title: WT_14dLight_2

value: 14 days kept under 100µmol m-2s-1 white light


title: WT_14dLight_3


title: AGA2, scRNAseq

description: 10x Genomics

value: Chondrocytes

value: Postnatal day 5


title: WJL1436_RLF_N019

value: WT


title: 3 MCF7 Estradiol 15min

value: breast cancer cell line


title: 8 MCF7 Tamoxifen 15min

value: Tamoxifen


title: control2_DMSO_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-709


title: control2_ispinesib_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-710

value: ispinesib


title: WT_7dLight7dDark_2

value: imbibed seeds

value: Cyprus accession

value: 7 days kept under 100µmol m-2s-1 white light and 7 following days kept in darkness


title: 2 MCF7 DMSO 15min

value: 15 min


title: control2_ispinesib_day42_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-708


title: mouse 5, scRNAseq

description: 10x Genomics

value: Femoral and tibial growth plate cartilage

value: Wild type


title: control2_DMSO_day139_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY050-714

value: DMSO


title: WT_14dLight_1


title: 1 MCF7 DMSO 15 mins


title: control2_ispinesib_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-712


title: WT_7dLight_3

value: 7 days kept under 100µmol m-2s-1 white light


title: mouse 3, scRNAseq

description: 10x Genomics


title: iPSC-EC_flow_01

city: Los Angeles,

first: Arun

last: Sharma

address: 127 S San Vicente Blvd,

department: Regenerative Medicine Institute

institute: Cedars Sinai Medical Center

data_processing:
Illumina bcl2fastq software was used to assess sequence quality
Reads were aligned to the GRCh38 genome assembly (GENCODE 28) using Salmon version 0.11.3.
Gene-level read counts were quantified with Salmon, and differential gene expression and normalization was subsequently performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample.

growth_protocol: iPC-CMs and iPSC-ECs were both maintained with Heart media (RPMI / insulin / VEGF / FBS / PSA), either under a continuous flow of medium using the chips, or in static conditions. Both conditions were maintained in a humidified incubator of 37C and 5% CO2.

extract_protocol:
An Rneasy Mini Kit (Qiagen) was used with on-column DNA digestion to extract the RNA samples from the cells on chips. 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a SMART-Seq v4 Ultra Low Input RNA Kit (Takara) following the manufacturers' protocol.

treatment_protocol: Cells were under flow and stretch, or flow only, or in static conditions (no flow or stretch). Flow of 30uL/hr and stretch of 10% with 0.4 Hz frequency were applied to the cells on emulate S1 chips.

tag: time

value: mesenchymal stem cells

tag: cell type (differentiated)

value: ECs

value: Flow only applied culture on Emulate Chips


title: control2_ispinesib_day21_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-707

tag: cell line


title: mouse 2, scRNAseq

description: 10x Genomics

tag: cell type

value: Chondrocytes


title: iPSC-EC_flowandstretch_03

tag: treatment

value: Flow and stretch applied culture on Emulate Chips


title: WT_7dLight_2


title: mouse 1, scRNAseq

description: 10x Genomics

value: Postnatal day 5


title: WT_7dLight_1


title: WT_1dLight_3

value: 23 hours kept under 100µmol m-2s-1 white light


title: iPSC-EC_flowandstretch_02

value: WT


title: K101R-3

city: Hang zhou

first: guangyuan

last: Song

address: No. 17 Shilongshan Street

institute: westlake university

description: 11 dpi

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size(RPKM) were calculated using a protocol from Chepelev et al.,Nucleic Acids Research, 2009. In short,exons from all isoforms.
Assembly: mm8
Supplementary files format and content: table-delimited text files inclide RPKM values for each Sample ......

source_name: brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: K101R infected


title: control2_DMSO_day21_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-704


title: control2_ispinesib_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-705

value: ispinesib


title: WT_1dLight_2

value: imbibed seeds

value: Cyprus accession


title: control2_DMSO_day42_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-706


title: WT_1dLight_1


title: iPSC-CM_flow_02

source_name: gCaMP-iPSC-CMs

value: gCaMP-iPSC-CMs

value: CMs


title: mouse 4, scRNAseq

description: 10x Genomics

value: Femoral and tibial growth plate cartilage

value: Wild type


title: iPSC-CM_flow_03

value: mesenchymal stem cells


title: K101R-2

description: 11 dpi


title: WT-3

description: 11 dpi

value: WT infected


title: iPSC-EC_flowandstretch_01

value: ECs


title: Mini-pig-4

city: Rodovre

first: Farideh

last: Moharrek

address: Hvidovrevej 22B

country: Denmark

institute: Novo Nordisk Foundation Center for Basic Metabolic Research

data_processing:
1) Reads were trimmed using Trim Galore! v0.4.3 with the --rrbs flag and using a stringency of 3.
2) Trimmed reads were mapped to susScr11 and methylation levels estimated using Bismark aligner v0.18.1 on default settings.
3) Uniquely mapped reads were deduplicated using the deduplicate_bismark tool with the --barcode flag.
4) The SNPs (dbSNP, build 150) overlapping with CpGs were filtered out.
5) CpGs with coverage larger than 10 times the 95-percentile of coverage in each sample were filtered out.
6) Orthologous CpGs were assigned using the liftOver tool available through the UCSC Genome Browser.
7) CpGs with a minimum of 6 counts were considered for differential methylation analysis.
8) Differential methylation analysis was performed by GeneDMRs.
Assembly: susScr11
Supplementary files format and content: Coverage (cov) files contain the coverage per sample (data processing step 3)

organism: Sus scrofa

source_name: Sperm

extract_protocol:
AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Germany, cat no.: 802224) according to the instructions of the manufacturer
RRBS libraries were constructed from 100ng genomic input DNA using the Ovation® RRBS Methyl-Seq library preparation kit (Tecan, cat no.: 0553-32). Briefly, genomic DNA was digested with MspI enzyme, followed by adaptor ligation to Ovation RRBS Methyl-seq adaptors, containing unique molecular barcodes (UMIs), followed by a final end-repair. Ligated DNA was subjected to bisulfite conversion and left in the thermal cycler overnight at room temperature. The following day, bisulfite-converted DNA was amplified by PCR followed by a final clean-up. Sequencing of RRBS libraries was performed on a NovaSeq 6000 platform (Illumina) as 101 bp single-end reads.

value: adult


title: control2_ispinesib_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-703


title: K101R-1

description: 11 dpi


title: iPSC-CM_flow_01

value: Flow only applied culture on Emulate Chips


title: Mini-pig-3


title: WT-2

description: 11 dpi


title: control2_DMSO_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-702

value: DMSO


title: control2_DMSO_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY049-701


title: iPSC-CM_flowandstretch_03

value: Flow and stretch applied culture on Emulate Chips


title: Mini-pig-2


title: celltag2_none_day0_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-715


title: WT-1

description: 11 dpi


title: iPSC-CM_flowandstretch_02

value: WT


title: celltag1_ispinesib_day125_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-714


title: Mock-3

description: 11 dpi

value: brain

value: PBS injected


title: iPSC-CM_flowandstretch_01


title: Mock-2

description: 11 dpi


title: celltag1_ispinesib_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-711

value: ispinesib


title: celltag1_ispinesib_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-709


title: iPSC-EC Static_02

description:
EC2
Raw_Counts_CM_EC_Static.csv

value: Static culture on Emulate Chips (No flow, no Stretch)


title: iPSC-EC Static_03

description:
EC3
Raw_Counts_CM_EC_Static.csv


title: celltag1_ispinesib_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-702


title: iPSC-EC Static_01

description:
EC1
Raw_Counts_CM_EC_Static.csv


title: celltag1_DMSO_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-708


title: Tam 66 WT-F p.15 replicate 2 : 39 µL 7/1/2020

city: Denver

first: Susan

last: Majka

email: majkas@njhealth.org, susanmajka@mac.com

state: co

address: 1400 Jackson St, Goodman Bldg K810a

department: Medicine

institute: NJH

data_processing: Sample counts were generated by the sequencing center at National Jewish Health. BBDuk was used for read trimming. Adapter sequences and the first 12 bases at the 5’ end were removed, retaining reads that were greater than 50 bp. Trimmed reads were aligned and raw counts generated with STAR using mouse mg38.p6 (ENSEMBL release 96) as the reference. The raw counts were further processed and analyzed using R (v 4.0.2) and Bioconductor (v 3.11). The count data were first filtered for low counts by removing all rows, whose averages were less than or equal to 10. Next, the MGI symbols were annotated for gene biotype using the Bioconductor package, biomaRt. Only genes/transcripts with the biotype “protein-coding” were retained for further analyses. In order to control for GC content and gene length variation that can influence downstream results, normalization using the Bioconductor package, CQN (conditional quantile normalization) was used. Differential expression (DE) statistics were generated using the Bioconductor package, limma. Genes with an average expression value above 2 across mutant and wild type samples and adjusted p-values below 0.05 were used for further analyses. To explore the large DE lists and compare the changes in female and male knockouts, we employed multiple approaches. First, two STRING networks of functional interactions of all DE genes in the two lists were generated using Cytoscape App (v 3.8.2). These networks were clustered using the MCODE algorithm to identify densely functionally connected subnetworks. To get a comparative visual representation of affected Reactome categories in the two gene lists, we employed the CompareCluster function from the Bioconductor package, clusterProfiler. We, then, employed the self-contained gene set test available via the mROAST function of the limma package to test all mSigDb curated mouse Reactome gene sets. This enabled the identification of Reactome categories that were statistically significantly changed. Thus, we employed functional interaction information from STRING database, visual comparison with clusterProfiler and statistical testing with mROAST in limma to bioinformatically investigate the functional themes of TSC2 knockdown and the differences between mTOR activated versus mTOR regulated MVPC lines.

source_name: Lung

growth_protocol: MVPC isolation and culture published by Majka lab

extract_protocol: 10-500ng of RNA; Nugen library kit to make cDNA library

treatment_protocol: For each replicate: Plate same number of cells to a specific density 24 hours before collection in a T75. (Optimal should be 80% confluent or less at time of collection).

value: Lung

value: MVPC

value: female

value: C57Bl6/B129 mix


title: E. coli promoter activity, FACS, rep2 bin14, glycerol

city: Saint Louis

first: Yichao

last: Han

state: MO

address: 1 Brookings Dr

department: Department of Energy, Environmental & Chemical Engineering

institute: Washington University in St Louis

description: amplicon

library_source: other

data_processing:
align read1 to sgRNA library and read2 to E. coli MG1655 genome using bowtie2, santools, and bedtools
calculate read counts for each promoter-sgRNA pair in each bin
fit the binned distribution of each promoter-sgRNA pair to a log-normal distribution
Supplementary files format and content: GSE213624_PPTP_Ecoli_summary_updated.csv

molecule: other

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli

growth_protocol: For each replicate, 100 μL glycerol stocks of the combinatorial library were thawed and inoculated in 250 mL of LB medium. When an OD600 of 0.5 was reached, 1 mL of cells was diluted into 25 mL of a target medium (either M9 glucose, M9 glycerol, or LB medium). After a few hours of adaptation, 500 μL of the cultures were added to 50 mL of the target medium containing 1 μM aTc as inducer. The induced cells were grown at 37°C until OD600 reached 0.1-0.2. At this point, the cell cultures were supplemented with 250 μg/mL chloramphenicol to halt protein production and were kept on ice until sorting.

extract_protocol:
Reporter plasmids were purified from 3 mL aliquots of overnight cell cultures from each bin using miniprep kits.
50 ng purified plasmids for each bin were amplified by the KAPA HiFi PCR Kit (Kapa Biosystems) for 20 cycles using primers prYH071 and prYH087. The PCR products were purified using the DNA Clean & Concentrator kit, and then were ligated with Illumina sequencing adapters via Golden Gate assembly. The ligation products were gel-purified to select DNA size between 400 bp and 1.5 kb and were subjected to another PCR with primers prYH128 and prYH129 for 8 cycles by the KAPA HiFi to enrich ligated products. The samples from each binned population were mixed at an estimated ratio to ensure that the number of reads sequenced is approximately proportional to the number of cells sorted for each bin in each replicate experiment.
Other: PPTP-seq (pooled promoter responses to transcription factor perturbations sequencing)

tag: replicate

value: replicate 2

tag: facs gate

value: cell sorting according to log(GFP)

value: E. coli


title: E. coli promoter activity, FACS, rep2 bin16, glycerol

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin13, glycerol

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin12, glycerol

description: amplicon


title: Tam 66 WT-F p.18 replicate 1 : 39 µL 6/17/2020

value: male

tag: genotype


title: TAM 65 WT-M p.12 replicate 3: 39 uL 8/19/2020

tag: tissue


title: celltag1_none_day0_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY048-701


title: E. coli promoter activity, FACS, rep2 bin11, glycerol

description: amplicon


title: iPSC-CM Static_04

description:
CM4
Raw_Counts_CM_EC_Static.csv

value: mesenchymal stem cells

value: CMs


title: celltag1_DMSO_day125_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-712

value: DMSO


title: E. coli promoter activity, FACS, rep2 bin15, glycerol

description: amplicon


title: Mini-pig-1

value: adult


title: celltag1_DMSO_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-710


title: TAM 65 WT-M p.10 replicate 2: 39 µL 8/14/2020

value: WT


title: E. coli promoter activity, FACS, rep2 bin9, glycerol

description: amplicon


title: celltag1_DMSO_day31_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-707


title: TAM 65 WT-M p.9 replicate 1: 39 µL 8/05/2020


title: iPSC-CM Static_01

description:
CM1
Raw_Counts_CM_EC_Static.csv


title: celltag1_DMSO_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-705


title: E. coli promoter activity, FACS, rep2 bin7, glycerol

description: amplicon


title: celltag2_DMSO_day139_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI27


title: E. coli promoter activity, FACS, rep2 bin8, glycerol

description: amplicon


title: celltag2_ispinesib_day139_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI28


title: TAM63 TSC2 KO-M p.17 replicate 2: 39 µL 7/1/2020

value: Tsc2 KO -/-


title: TAM63 TSC2 KO-M p. 20 replicate 3: 39 uL 7/9/20


title: iPSC-CM Static_03

description:
CM3
Raw_Counts_CM_EC_Static.csv


title: E. coli promoter activity, FACS, rep2 bin5, glycerol

description: amplicon


title: celltag2_ispinesib_day98_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI26


title: celltag1_DMSO_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-703


title: Tam 60 TSC2 KO-F p.9 replicate 3: 39 µL 7/1/2020


title: E. coli promoter activity, FACS, rep2 bin10, glycerol

description: amplicon


title: celltag2_DMSO_day98_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI25


title: celltag1_ispinesib_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-706


title: TAM63 TSC2 KO-M p.18 replicate 1: 39 µL 6/19/2020


title: E. coli promoter activity, FACS, rep2 bin4, glycerol

description: amplicon


title: iPSC-CM Static_02

description:
CM2
Raw_Counts_CM_EC_Static.csv


title: TAM 66 WT-F WT-F Replicate 3 : 39 uL 7/9/2020


title: TAM 60 TSC2 KO-F p.10 replicate 2: 39 µL 6/19/2020


title: E. coli promoter activity, FACS, rep2 bin6, glycerol

description: amplicon


title: control1_ispinesib_day125_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-714


title: E. coli promoter activity, FACS, rep2 bin3, glycerol

description: amplicon


title: control1_DMSO_day125_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-712


title: TAM60 TSC2 KO-F p.9 replicate 1: 39 µL 6/17/2020


title: celltag1_ispinesib_day31_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY047-704


title: celltag2_DMSO_day69_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI23


title: E. coli promoter activity, FACS, rep2 bin2, glycerol

description: amplicon


title: anti-PD-1 antibody-responsive-3 (group3-3)

city: Wuhan

first: Zhaohan

last: Wei

address: Luoyu Road 1037

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 genome.
The software packages of Bowtie2 (version 2.2.4) and TopHat (version 2.1.1) were used to generate the BAM files, wheareas Cufflinkes (version 2.2.1) was employed to assemble the reads and calculate the expression levels of individual mRNAs based on FPKM values.
Assembly: mm8
Supplementary files format and content: Expressionprofile.txt

source_name: tumor

growth_protocol: The orthotopic Hepa1-6 tumor-bearing mice were intraperitoneally injected with anti-PD-1 antibody or PBS every four days for five times, then the tumor were romoved to further analysis.

extract_protocol:
Tumor were romoved, flash frozen on dry ice, and RNA were harvested using Trizol reagent. TruSeq Illumina RNA sample prep kit was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protpcols.

treatment_protocol: The whole tumors were collected and the surrounding tissue was removed. The tumors that had an intermediate response were excluded, and three largest tumors (the nonresponsive tumors) and three smallest tumors (the responsive tumors) compared with PBS-treated group were frozen in liquid nitrogen immediately. The RNA extraction, library preparation and sequencing were performed by Novogene

value: tumor

value: anti-PD-1 antibody

tag: phenotype

value: anti-PD-1 antibody-responsive


title: celltag2_ispinesib_day42_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI22

value: ispinesib


title: control1_DMSO_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-710


title: E. coli promoter activity, FACS, rep2 bin1, glycerol

description: amplicon


title: control1_ispinesib_day98_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-711


title: celltag2_DMSO_day42_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI21


title: iPSC-EC Static_04

description:
EC4
Raw_Counts_CM_EC_Static.csv

value: ECs

value: Static culture on Emulate Chips (No flow, no Stretch)


title: anti-PD-1 antibody-responsive-2 (group3-2)


title: E. coli promoter activity, FACS, rep1 bin16, glycerol

description: amplicon

value: replicate 1


title: control1_ispinesib_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-709


title: anti-PD-1 antibody-nonresponsive-3 (group2-3)

value: anti-PD-1 antibody-nonresponsive


title: control1_DMSO_day69_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY046-708


title: celltag2_ispinesib_day69_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI24


title: control2_none_day0_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-715


title: celltag2_DMSO_day21_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI19


title: anti-PD-1 antibody-responsive-1 (group3-1)


title: E. coli promoter activity, FACS, rep1 bin15, glycerol

description: amplicon

value: cell sorting according to log(GFP)


title: E. coli promoter activity, FACS, rep1 bin13, glycerol

description: amplicon

value: E. coli


title: E. coli promoter activity, FACS, rep1 bin14, glycerol

description: amplicon


title: anti-PD-1 antibody-nonresponsive-2 (group2-2)


title: control1_ispinesib_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-706


title: celltag2_ispinesib_day6_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI18


title: celltag2_DMSO_day6_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI17


title: anti-PD-1 antibody-nonresponsive-1 (group2-1)


title: celltag2_ispinesib_day3_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI16


title: control1_DMSO_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-704


title: control-3 (group1-3)

value: PBS

value: control


title: E. coli promoter activity, FACS, rep1 bin9, glycerol

description: amplicon


title: E. coli promoter activity, FACS, rep1 bin12, glycerol

description: amplicon


title: control1_ispinesib_day31_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-703


title: control-2 (group1-2)


title: control1_DMSO_day6_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-705


title: control1_none_day0_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-702


title: E. coli promoter activity, FACS, rep1 bin10, glycerol

description: amplicon


title: CD4+ FOXP3- Tcon, venetoclax, biol rep 4 [ABT4_TC]

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

data_processing:
Pair end reads were aligned using HISAT2
Sam files were convereed to bam using Samtools
Counts generated using Rsubread
Assembly: mm10
Supplementary files format and content: Tcon_results.csv
Supplementary files format and content: Tregs_results.csv

source_name: Spleen and lymph node

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Barcoded RNA were sequenced using Illumina NovaSeq special

treatment_protocol: FOXP3-IRES-GFP mice were treated for 14 days with vehicle or 50mg/kg venetoclax

value: Spleen and lymph node

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)

value: Venetoclax


title: celltag2_DMSO_day3_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI15

value: DMSO


title: celltag2_ispinesib_day21_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI20


title: CD4+ FOXP3+ Treg, venetoclax, biol rep 4 [ABT4_TR]

value: WT


title: control1_DMSO_day31_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-707


title: control-1 (group1-1)

value: tumor


title: CD4+ FOXP3+ Treg, venetoclax, biol rep 3 [ABT3_TR]


title: control1_ispinesib_day3_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY045-701


title: CMI5 CLL PBMC

city: Boston

first: Salma

last: Parvin

state: MA

address: 440 Brookline ave

institute: Dana Farber Cancer institute

data_processing:
Sequenced reads were aligned to the UCSC hg19 reference genome assembly
gene counts were quantified using STAR (v2.7.3a)
Differential gene expression testing was performed by DESeq2 (v1.22.1).
RNAseq analysis was performed using the VIPER snakemake pipeline
Supplementary files format and content: tab file includes raw count for each sample

source_name: CLL PBMC

extract_protocol:
RNA was harvested using the Zymo Direct-zol RNA Microprep kit
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA

value: CLL PBMC

value: Leukemic cells

value: Leukemia

value: Patient sample

value: CM-independent (CMI)


title: celltag1_ispinesib_day125_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI13

value: ispinesib


title: E. coli promoter activity, FACS, rep1 bin7, glycerol

description: amplicon

value: replicate 1


title: E. coli promoter activity, FACS, rep1 bin8, glycerol

description: amplicon

value: cell sorting according to log(GFP)


title: E. coli promoter activity, FACS, rep1 bin11, glycerol

description: amplicon

value: E. coli


title: E. coli promoter activity, FACS, rep1 bin6, glycerol

description: amplicon


title: CD4+ FOXP3- Tcon, venetoclax, biol rep 3 [ABT3_TC]


title: celltag1_ispinesib_day98_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI11


title: celltag1_DMSO_day98_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI10


title: E. coli promoter activity, FACS, rep1 bin5, glycerol

description: amplicon


title: celltag1_DMSO_day125_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI12


title: celltag2_none_day0_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag2 samples
PY054-RPI14


title: CMI4 CLL PBMC


title: CD4+ FOXP3+ Treg, venetoclax, biol rep 2 [ABT2_TR]


title: celltag1_ispinesib_day69_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI09


title: CMI3 CLL PBMC


title: E. coli promoter activity, FACS, rep1 bin4, glycerol

description: amplicon


title: CD4+ FOXP3- Tcon, venetoclax, biol rep 2 [ABT2_TC]


title: CMI2 CLL PBMC


title: E. coli promoter activity, FACS, rep1 bin3, glycerol

description: amplicon


title: CD4+ FOXP3+ Treg, venetoclax, biol rep 1 [ABT1_TR]


title: CD4+ FOXP3- Tcon, venetoclax, biol rep 1 [ABT1_TC]


title: celltag1_ispinesib_day31_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI07


title: E. coli promoter activity, FACS, rep1 bin2, glycerol

description: amplicon


title: CMI1 CLL PBMC


title: E. coli promoter activity, FACS, rep1 bin1, glycerol

description: amplicon


title: celltag1_DMSO_day31_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI06


title: celltag1_ispinesib_day6_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI05


title: CMD5 CLL PBMC

value: CM-dependent (CMD)


title: CMD3 CLL PBMC


title: CD4+ FOXP3+ Treg, vehicle, biol rep 4 [VEH4_TR]

value: Vehicle


title: E. coli promoter activity, FACS, rep2 bin16, LB

description: amplicon

value: replicate 2


title: CMD4 CLL PBMC


title: celltag1_DMSO_day69_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI08


title: CD4+ FOXP3+ Treg, vehicle, biol rep 3 [VEH3_TR]

value: Spleen and lymph node

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)


title: CD4+ FOXP3- Tcon, vehicle, biol rep 4 [VEH4_TC]


title: celltag1_ispinesib_day3_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI03


title: E. coli promoter activity, FACS, rep2 bin14, LB

description: amplicon


title: celltag1_DMSO_day6_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI04

value: DMSO


title: CMD2 CLL PBMC


title: CMD1 CLL PBMC


title: E. coli promoter activity, FACS, rep2 bin13, LB

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin12, LB

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin11, LB

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin15, LB

description: amplicon


title: Mock-1

description: 11 dpi

value: brain

value: PBS injected


title: E. coli promoter activity, FACS, rep2 bin10, LB

description: amplicon


title: APP/PS1; TERF2DN

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

data_processing:
Cell Ranger Single Cell Software (v 6.0.1) by 10X Genomics against the mm10 murine reference genome with default parameter
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Microglia and ECs were isolated from the brain of indicated mice using PE-conjugated anti-CD11b antibody (#130-113-803 or #130113-235, Miltenyi Biotec) by magnetic-activated cell sorting (MACS) according to the manufactures’ instructions.
10X

value: Brain

value: APP/PS1; TERF2DN

value: Microglia


title: E. coli promoter activity, FACS, rep2 bin9, LB

description: amplicon


title: APP/PS1

description: 10x Genomics


title: TERF2DN-Tg

description: 10x Genomics


title: siADAR1-1.input

city: Tianjin

first: Chunyong

last: Zhang

state: Tianjin

address: Tianjin Medical University HepingNo.22, Qixiangtai Road

institute: TMU

data_processing:
The 150-bp Illumina paired-end reads were trimmed using to Trim Galore(version 0.6.4) to remove adapter and low quality sequences from DRIP-seq sequencing data
Trimmed reads subsequently were checked for quality using FastQC(version 0.11.9).
The cleaned reads were mapped to the human genome(UCSC hg19) using the Bowtie2 aligner (version 2.4.5).
Picard (version 2.26.11) was used to remove PCR duplications.
The profile plots were generated by deepTools (version 3.4.3) bamCoverage and plotProfile programs with “–normalizeUsing RPKM” settings.
Assembly: UCSC hg19
Supplementary files format and content: bw
Library strategy: DRIP-seq

source_name: HeLa

extract_protocol:
Fragmented DNA is extracted through a classic salt/ethanol precipitation and rehydrated in TE buffer.
The DRIP-seq libraries were prepared with a VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the manufacturer's instructions (ND607，Vazyme), and sequenced with PE150 on NovaSeq platform.

value: HeLa

tag: drip-antibody


title: siCtrl-1.input

value: siCtrl


title: siADAR1-2-RNH1


title: Wild-type

description: 10x Genomics

value: Wild-type


title: siCtrl-2


title: CD4+ FOXP3+ Treg, vehicle, biol rep 2 [VEH2_TR]

value: WT


title: CD4+ FOXP3- Tcon, vehicle, biol rep 2 [VEH2_TC]


title: CD4+ FOXP3- Tcon, vehicle, biol rep 3 [VEH3_TC]


title: CD4+ FOXP3- Tcon, vehicle, biol rep 1 [VEH1_TC]


title: siADAR1-2


title: CD4+ FOXP3+ Treg, vehicle, biol rep 1 [VEH1_TR]


title: E. coli promoter activity, FACS, rep2 bin7, LB

description: amplicon

value: cell sorting according to log(GFP)


title: E. coli promoter activity, FACS, rep2 bin5, LB

description: amplicon

value: E. coli


title: E. coli promoter activity, FACS, rep2 bin6, LB

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin8, LB

description: amplicon


title: 20mM sodium lactate

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

data_processing:
Sequence Analysis: The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing are mapped to the genome using the BWA algorithm with default settings (“bwa mem”). Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Peak Finding: Genomic regions with high levels of transposition/tagging events are determined using the MACS3 peak calling algorithm (Zhang et al., Genome Biology 2008, 9:R137). Note that we use the generic term “Interval” to describe the genomic regions identified by MACS3. Intervals are defined by the chromosome number and a start and end coordinate.
Determination of Fragment Density: To identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section VI.). BigWig files are also the basis of the peak metrics in the Active Motif analysis program described below.
Normalization: In the default analysis, the tag number of all samples is reduced (by random sampling) to a similar number of tags as in the smallest sample. When samples are not directly comparable or in cases of projects with outlier samples, this strategy is either forgone or can potentially be customized to fit the experimental design.
Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping Intervals (orange bars in diagram on next page) are grouped into “Merged Regions” (green bars), which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Merged Region. The use of Merged Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples. Furthermore, with this approach fragment density values can be obtained even for samples for which no peak was called.
Annotations: After defining the Intervals and Merged Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined and presented in Excel spreadsheets. In addition, average and peak (i.e. at “summit”) fragment densities within Intervals and Merged Regions are compiled.
Assembly: mm10

source_name: prostate

growth_protocol: Organoids were cultured following Drost et al Nature Protocols 2016

extract_protocol: Nextera Library Prep Kit (Illumina)

treatment_protocol: Organoids were treated for seven days with vehicle, 10uM UK5099, or 20mM sodium lactate

value: prostate

value: basal-derived organoid

value: Wildtype

value: 20mM sodium lactate


title: celltag1_DMSO_day3_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI02


title: celltag1_none_day0_CellTag

description:
CellTag (celltag library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains celltag region amplified from the 3' UTR of EGFP, binary matrix file of cell barcodes and celltags of all celltag1 samples
PY054-RPI01


title: siADAR1-1-RNH1


title: siADAR1-1


title: siADAR1-1-RNH1.input


title: siADAR1-2.input


title: siCtrl-2.input


title: siADAR1-2-RNH1.input


title: siCtrl-1


title: RNA-seq, Naive, rep3

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description:
RNAseq1.count_mat.csv.gz
naive_3

data_processing:
Illumina HCS 1.2.0 and RTA 3.7.17 software used for sequencing and basecalling.
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.2.7.1).
RNA-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v2.4.2) and STAR (v2.7.7a), read counts by HTSeq-count (v2.0.1).
Assembly: mm10
Supplementary files format and content: RNA-seq: csv, gene count matrix
Supplementary files format and content: ATAC-seq: bigWig, normalized signal

source_name: CD8+ T

extract_protocol:
P14 CD8+ T cells were FACS-purified from spleens.
ATAC-seq: Nuclei were extracted using the ATAC-Seq Kit (Active Motif). Tagmented DNA was then column-purified and immediately used for PCR amplification and library generation.
RNA-Seq: Library preparation using the  Qiagen RNeasy Mini Kit.

value: GOT1 WT

value: CD8+ T

tag: timepoint

tag: treatment 2


title: Vehicle

value: Vehicle


title: 10uM UK5099


title: RNA-seq, Naive, rep2

description:
RNAseq1.count_mat.csv.gz
naive_2


title: normal, NA, 59, 14

city: Santa Cruz

first: Daniel

last: Kim

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

description:
n32
panc_normal_normalized_counts_20230703.csv
normal_14

data_processing:
RNA sequencing reads (FASTQ) were trimmed with Trimmomatic (v0.39), quality assessed using FASTQC (v0.11.9) and visualized using MultiQC (v1.11). Quantification was performed using Salmon (v1.9.0).
Assembly: Hg38
Supplementary files format and content: csv, normalized gene counts
Supplementary files format and content: tsv, normalized gene counts

source_name: Blood Plasma

extract_protocol:
The ExoRNeasy kit (Qiagen) was used to isolate cell-free RNA from blood plasma of de-identified healthy controls (Discovery Life Sciences, blood collected in K2EDTA tubes) and pancreatic cancer patients (BioIVT, blood collected in K2EDTA tubes). Samples were initially filtered through a 0.8 um filter to remove any contaminants such as buffy coat. Filtered plasma was then processed using the ExoRNeasy kit to isolate cell-free RNA according to manufacturer instructions.
Full-length cDNA was synthesized from cell-free RNA from pancreatic cancer and healthy control samples (Takara SMART-Seq HT kit). Size distribution of cell-free RNA and resulting cDNA were evaluated using an Agilent bioanalyzer. Final libraries were made using the Illumina Nextera XT DNA Prep kit. These libraries were then sequenced (PE150) on an Illumina NextSeq 500.  Nanopore full-length cDNA libraries were prepared as described above, followed by manufacturer instructions for the Oxford Nanopore ligation kit LSK109. Sequencing for each library was performed on an Oxford Nanopore MinION device with R9.4 flowcells.

value: Blood Plasma

tag: subject status

value: normal healthy donor

tag: subject id


title: normal, NA, 55, 12

description:
n26
panc_normal_normalized_counts_20230703.csv
normal_12


title: normal, NA, 74, 11

description:
n25
panc_normal_normalized_counts_20230703.csv
normal_11


title: E. coli promoter activity, FACS, rep2 bin2, LB

description: amplicon

value: replicate 2


title: E. coli promoter activity, FACS, rep1 bin16, LB

description: amplicon

value: replicate 1


title: E. coli promoter activity, FACS, rep2 bin4, LB

description: amplicon


title: E. coli promoter activity, FACS, rep2 bin1, LB

description: amplicon


title: WJL3000_RLF_N026

city: Stanford

first: Jinglong

address: 269 Campus Drive

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

growth_protocol: K562 and its derived cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4). HEK293T and its derived cell lines were cultured at 37 °C and 5% CO2 in DMEM supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1/G0-arrested K562-Bcl2, K562-Bcl2 PKcs-/- and K562-iCas9 cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with pX330-Cas9-sgRNA or pMCB320-sgRNA to generated twined or genome-wide DSBs in different conditions, such as DMSO, 0.5 μM DPKi #1 (Nu7441), 20 μM DPKi #2 (Nu7026) and 10 μM ATMi (Ku60019).

value: lymphoblast cells

value: Pal + Nu7026

tag: dsb induction (bait site)

tag: dsb induction (prey sites)

tag: number of normalized reads


title: normal, NA, 66, 10

description:
n24
panc_normal_normalized_counts_20230703.csv
normal_10

tag: age


title: E. coli promoter activity, FACS, rep2 bin3, LB

description: amplicon


title: normal, NA, 69, 9

description:
n23
panc_normal_normalized_counts_20230703.csv
normal_9


title: E. coli promoter activity, FACS, rep1 bin15, LB

description: amplicon


title: E. coli promoter activity, FACS, rep1 bin13, LB

description: amplicon


title: E. coli promoter activity, FACS, rep1 bin14, LB

description: amplicon