title: UHRR_TC00000652_B01

description: UHRR


title: DMSO_TC00000652_B19

status: Public on Apr 18 2022

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description: DMSO

library_source: transcriptomic

data_processing:
Read alignment:
Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts:
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

molecule: total RNA

organism: Homo sapiens

source_name: U-2 OS

growth_protocol: U-2 OS human osteosarcoma cells (HTB-96®, Lot: 64048673, ATCC) were cultured as described in Nyffeler et al. (2020). Briefly, cells were cultured in media consisting of Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum and penicillin/streptomycin/glutamine, passaged using TrypLE Select and maintained at 37 C in a humidified atmosphere of 5% CO2 in air.   A cryo stock of internal passage number 6 (P6) was generated as described in Nyffeler et al. (2020); experiments were performed using U-2 OS cells from P7 to P10. Cells were counted using a Countess II automated cell counter and seeded into CellCarrier-384 Ultra microplates at 3000 cells/well in 40 ul media per well.

extract_protocol:
Twentyfour hours after chemical treatment, HTTr assay plates were removed from the incubator and media in each assay well was drained to a residual volume of 10 µL using MultiFlo FX microdispenser equipped with a vacuum-driven aspiration manifold. To create cell lysates, 10 µL volumes of 2X BioSpyder lysis buffer were dispensed into each assay well using the same MultiFlo FX instrument equipped with 1 µL peristaltic pump dispensing cassette. Plates were temporarily sealed with an adhesive film, shaken for 30 s on the stage of MultiFlow FX microplate dispenser (BioTek, Winooski, VT) and then placed in a hybridization oven (37°C) for 10 min. The adhesive films were removed, plates were re-sealed with NuncTM aluminum acrylate sealing tape and stored at -80°C. Prior to shipment, the tape was removed and reference samples (reference RNAs, bulk lysates and lysis buffer blank) (Harrill et al., 2021) were added in duplicate to each plate while keeping the plates frozen. The plates were then resealed with new NuncTM aluminum acrylate sealing tape.
384-well plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. Lysates were processed as described in. In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized chemical stock solutions were received frozen from the US EPA ToxCast chemical inventory management contractor (EvoTec, Princeton, NJ) and stored at -80°C prior to dose plate preparation. A seven-point dilution series (1/2 log10 spacing) of test chemicals was prepared in a LabCyte Echo-qualified 384-well polypropylene (384PP) plate at 200x the desired nominal test concentration for screening. Duplicated wells of dosing solutions for each test chemical concentration were arrayed in columns 2 through 24 of the dose plate (Figure 1A). Transcriptomics reference chemicals (genistein, trichostatin A, sirolimus) were solubilized as 200x dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. At 24 h post-plating, 200 nL of 200x dosing solutions were transferred to the assay plates using a LabCyte Echo 550 acoustic dispenser. The final concentration of DMSO in all treatment, reference treatment and vehicle control wells was 0.5%.  Well coordinates on each assay plate were uniquely randomized with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

value: U-2 OS

tag: treatment

value: 0.5% DMSO vehicle control

tag: chemical name

value: DMSO

tag: chemical id

tag: chemical concentration

value: 0 uM

tag: dose level

tag: assay plate

tag: assay plate well


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_7_1.000000uM_TC00000651_O18

value: 1 uM Dexamethasone

value: Dexamethasone

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_2_0.003000uM_TC00000651_O15

value: 0.003 uM Retinoic acid

value: Retinoic acid


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_3_1.000000uM_TC00000651_O16

value: 1 uM Berberine chloride

value: Berberine chloride


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_1_0.000030uM_TC00000651_O14

value: 3e-05 uM Docetaxel

value: Docetaxel


title: DMSO_TC00000651_O10

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_3_0.001000uM_TC00000651_O12

value: 0.001 uM Cucurbitacin I

value: Cucurbitacin I


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_4_0.003000uM_TC00000651_O09

value: 0.003 uM Cucurbitacin I


title: DMSO_TC00000651_O07

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_5_1.000000uM_TC00000651_O13

value: 1 uM Etoposide

value: Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_2_0.030000uM_TC00000651_O08

value: U-2 OS

value: 0.03 uM Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_4_0.003000uM_TC00000651_O11

value: 0.003 uM Actinomycin D

value: Actinomycin D


title: DMSO_TC00000651_O05

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_1_0.003000uM_TC00000651_O06

value: 0.003 uM Trichostatin A

value: Trichostatin A


title: DMSO_TC00000651_O20

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_1_0.000100uM_TC00000651_M23

value: 1e-04 uM Cucurbitacin I


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_2_0.003000uM_TC00000651_M24

value: 0.003 uM Dexamethasone

value: Dexamethasone


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_1_0.003000uM_TC00000651_O17


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_5_1.000000uM_TC00000651_M21

value: 1 uM Cycloheximide

value: Cycloheximide

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_7_0.030000uM_TC00000651_M20

value: 0.03 uM Docetaxel

value: Docetaxel


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_3_0.001000uM_TC00000651_M22

value: U-2 OS

value: 0.001 uM Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_5_0.010000uM_TC00000651_M19

value: 0.01 uM Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_6_3.000000uM_TC00000651_M16

value: 3 uM Cycloheximide

value: 3 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_3_0.000300uM_TC00000651_M17

value: 3e-04 uM Docetaxel


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_3_0.010000uM_TC00000651_M18

value: 0.01 uM Rapamycin

value: Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_5_0.010000uM_TC00000651_M12

value: Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_6_0.030000uM_TC00000651_M13

value: 0.03 uM Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_4_0.030000uM_TC00000651_M14

value: 0.03 uM Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_1_0.010000uM_TC00000651_M10

value: 0.01 uM Cycloheximide


title: DMSO_TC00000651_M11

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_6_0.300000uM_TC00000651_M15

value: 0.3 uM Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_5_0.003000uM_TC00000651_O04

value: 0.003 uM Docetaxel

value: Docetaxel


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_6_0.300000uM_TC00000651_O03

value: U-2 OS

value: 0.3 uM Dexamethasone

value: Dexamethasone


title: DMSO_TC00000651_K24

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_2_0.030000uM_TC00000651_K23

value: 0.03 uM Etoposide

value: Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_3_0.100000uM_TC00000651_M06

value: 0.1 uM Cycloheximide

value: Cycloheximide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_1_0.010000uM_TC00000651_M05

value: 0.01 uM Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_4_0.100000uM_TC00000651_M04


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_6_0.010000uM_TC00000651_M03

value: 0.01 uM Docetaxel


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_1_0.001000uM_TC00000651_M07

value: 0.001 uM Dexamethasone


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_6_1.000000uM_TC00000651_K18

value: 1 uM Ca-074-Me

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_6_3.000000uM_TC00000651_K19

value: 3 uM Etoposide

value: 3 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_7_10.000000uM_TC00000651_K22

value: 10 uM Cycloheximide

value: 10 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_1_0.100000uM_TC00000651_K21

value: 0.1 uM Berberine chloride

value: Berberine chloride


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_4_0.300000uM_TC00000651_K20

value: U-2 OS

value: 0.3 uM Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_2_0.003000uM_TC00000651_K17

value: 0.003 uM Rapamycin

value: Rapamycin


title: DMSO_TC00000651_K16

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_7_10.000000uM_TC00000651_K15

value: 10 uM Etoposide

value: Etoposide


title: DMSO_TC00000651_M09

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_7_3.000000uM_TC00000651_K14

value: 3 uM Ca-074-Me


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_4_0.100000uM_TC00000651_K11

value: 0.1 uM Trichostatin A

value: Trichostatin A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_6_0.300000uM_TC00000651_M08

value: 0.3 uM Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_2_0.010000uM_TC00000651_K10


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_7_3.000000uM_TC00000651_K09

value: 3 uM


title: Control_24h_rep3

city: Vandoeuvre les nancy

first: Romain

last: Larbat

address: 2 avenue de la forêt de Haye

department: INRAE

country: France

institute: LAE

data_processing:
Reads were processed and filtered using the Trimmomatic software
they were mapped on the tomato genome (ITAG2.4) using the BWA-MEM software
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using FeatureCounts software
Assembly: tomato genome (ITAG2.4)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Tomato plants (cv. Better Bush) were grown on a Nutrient Film Technique system set in a growth chamber (16h photoperiod, 23°C/18°C day/night in air and 23°C in nutrient solutions, 60% air humidity)

extract_protocol:
RNA was harvested using EZNA Plant RNA kit mini plus kit (Omega bio-tek, Norcross, GA, USA). Three micrograms of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina HiSeq 2500

treatment_protocol: Six tomato plants were infested with 6 larvae deposited on the three terminal leaflets of the 3rd true leaf and six control plants were subject to mock deposition. Two harvests were conducted after 5 h and 24 h of herbivory. At both harvest time, the infested leaflets from which the larvae have been removed (and the corresponding leaflets of the control plant) were sampled, immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Twelve sequencing libraries were created corresponding to 4 conditions in triplicates (Tuta infested 5h and 24h; control 5h and 24h)

tag: tissue

value: leaf

tag: genotype

value: cv. Better Bush


title: Control_24h_rep2


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_5_0.100000uM_TC00000651_K08

value: 0.1 uM Retinoic acid

value: Retinoic acid


title: Control_5h_rep3


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_3_0.010000uM_TC00000651_K06

value: U-2 OS

value: 0.01 uM Retinoic acid


title: Control_5h_rep1


title: Tuta_infested_24h_rep2

value: Tuta absoluta infested_24h


title: Tuta_infested_24h_rep3


title: Control_5h_rep2


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_5_0.300000uM_TC00000651_K03

value: 0.3 uM Trichostatin A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_1_0.001000uM_TC00000651_K04

value: 0.001 uM Retinoic acid


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_3_0.100000uM_TC00000651_K13

value: 0.1 uM Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_1_0.001000uM_TC00000651_I24

value: 0.001 uM Dexamethasone

value: Dexamethasone


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_2_0.300000uM_TC00000651_I23

value: 0.3 uM Berberine chloride

value: Berberine chloride


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_7_3.000000uM_TC00000651_K07

value: 3 uM Trichostatin A

value: Trichostatin A


title: Control_24h_rep1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_6_30.000000uM_TC00000651_I22

value: 30 uM Berberine chloride

value: 30 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_7_10.000000uM_TC00000651_K12

value: 10 uM Etoposide

value: Etoposide

value: 10 uM


title: Tuta_infested_5h_rep2

value: leaf

value: cv. Better Bush

value: Tuta absoluta infested_5h


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_4_0.300000uM_TC00000651_I19

value: U-2 OS

value: 0.3 uM Cycloheximide

value: Cycloheximide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_5_0.300000uM_TC00000651_I18


title: Tuta_infested_5h_rep1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_4_0.030000uM_TC00000651_I17

value: 0.03 uM Retinoic acid

value: Retinoic acid


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_5_0.010000uM_TC00000651_I21

value: 0.01 uM Cucurbitacin I

value: Cucurbitacin I


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_7_0.100000uM_TC00000651_K05

value: 0.1 uM Cucurbitacin I


title: Cp36-WT-C

city: Memphis

first: David

last: Rogers

state: TN

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
RNA-seq data were analyzed using CLC Genomics Workbench version 20.0 (Qiagen)
Reads were trimmed using default settings for failed reads and adaptor sequences and then subsequently mapped to the C. parapsilosis genome (GenBank accession: GCA_000182765.2) with paired reads counted as one and expression values set to RPKM
Principal-component analysis was utilized for the assessment the clustering of biological replicates
Whole transcriptome differential gene expression analysis was performed with the prescribed algorithm of CLC Genomics Workbench version 20.0
Mismatch, insertion, and deletion costs were set to default parameters and the Wald test was used for all group pairs against the matched parent control strain
Genome_build: ASM18276v2
Supplementary_files_format_and_content: clc files contain RPKM

organism: Candida parapsilosis

source_name: isolate Cp36

growth_protocol: Isolates and strains were grown in biological triplicate at 30°C overnight in YPD liquid media and subsequently plated onto Sabouraud-Dextrose minimal medium agar for 24h growth at 30°C. Sterile loops were used to transfer cells into 20mL RPMI for final OD600=0.1. Cultures were incubated in a 35°C shaking incubator (110rpm) for 8h, after which the cells were collected by centrifugation at 4000rpm for 5 min. Supernatants were removed, and the pellets were stored at -80°C for a minimum of 24hrs.

extract_protocol:
RNA isolation was performed using the RiboPureTM Yeast (Invitrogen) system per manufacturer’s instructions.
RNA Sequencing performed using Illumina NextSeq for stranded mRNA.  Libraries were prepared with paired-end adapters using Illumina chemistries per manufacturer’s instructions, with read lengths of approximately 150bp with at least 50 million raw reads per sample.

tag: mrr1 genotype

value: wild-type

tag: biological replicate

value: C

tag: azole resistance

value: susceptible


title: DMSO_TC00000651_I15

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Tuta_infested_5h_rep3

value: leaf


title: Cp36B

value: B

value: resistant


title: Cp36C


title: Cp36-WT-B


title: Tuta_infested_24h_rep1

value: cv. Better Bush

value: Tuta absoluta infested_24h


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_3_0.030000uM_TC00000651_I20

value: U-2 OS


title: Cp36A

value: A


title: Cp30-WT-C

source_name: isolate Cp30


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_5_1.000000uM_TC00000651_I14

value: 1 uM Cycloheximide

value: Cycloheximide

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_4_3.000000uM_TC00000651_I13

value: 3 uM Berberine chloride

value: Berberine chloride

value: 3 uM


title: Cp30-WT-B

value: wild-type

value: susceptible


title: Cp30-WT-A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_7_100.000000uM_TC00000651_I11

value: 100 uM Berberine chloride


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_4_0.003000uM_TC00000651_I12

value: 0.003 uM Cucurbitacin I

value: Cucurbitacin I


title: Cp36-WT-A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_7_0.100000uM_TC00000651_I10

value: 0.1 uM Actinomycin D

value: Actinomycin D


title: Cp30A

value: resistant


title: Cp30B

value: B


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_1_0.000100uM_TC00000651_I16

value: U-2 OS

value: 1e-04 uM Actinomycin D


title: Cp30C

value: C


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_2_0.030000uM_TC00000651_I09

value: 0.03 uM Cycloheximide

value: Cycloheximide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_6_0.010000uM_TC00000651_I08

value: 0.01 uM Docetaxel

value: Docetaxel


title: Cp29-WT-C

source_name: isolate Cp29


title: Cp29-WT-B


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_4_0.100000uM_TC00000651_I06

value: 0.1 uM Trichostatin A

value: Trichostatin A


title: Cp29-WT-A

value: wild-type

value: A

value: susceptible


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_6_30.000000uM_TC00000651_I05

value: 30 uM Berberine chloride

value: Berberine chloride

value: 30 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_3_0.100000uM_TC00000651_I03

value: 0.1 uM Cycloheximide


title: Cp29B

value: B

value: resistant


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_2_0.000100uM_TC00000651_I04

value: U-2 OS

value: 1e-04 uM Docetaxel


title: Lysis Buffer_TC00000651_I02

description: Lysis Buffer

source_name: Lysis Buffer


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_2_0.300000uM_TC00000651_G24

value: 0.3 uM Berberine chloride


title: Cp29C

value: C


title: Cp29A


title: Lysis Buffer_TC00000651_I01

description: Lysis Buffer


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_6_0.300000uM_TC00000651_G22

value: 0.3 uM Retinoic acid

value: Retinoic acid


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_4_0.300000uM_TC00000651_G21

value: 0.3 uM Etoposide

value: Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_1_0.003000uM_TC00000651_G20


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_1_0.010000uM_TC00000651_G18

value: 0.01 uM Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_4_0.003000uM_TC00000651_G16

value: 0.003 uM Actinomycin D

value: Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_4_0.030000uM_TC00000651_G17

value: 0.03 uM Rapamycin

value: Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_3_0.010000uM_TC00000651_G19

value: 0.01 uM Dexamethasone

value: Dexamethasone


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_5_10.000000uM_TC00000651_I07

value: 10 uM Berberine chloride

value: Berberine chloride

value: 10 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_2_0.010000uM_TC00000651_G15

value: U-2 OS

value: 0.01 uM Trichostatin A

value: Trichostatin A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_6_0.030000uM_TC00000651_G13

value: 0.03 uM Cucurbitacin I

value: Cucurbitacin I


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_4_0.030000uM_TC00000651_G14

value: 0.03 uM Dexamethasone


title: DMSO_TC00000651_G12

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: T8.D32.Fat2

city: La Jolla

first: John

middle: Tyler

last: Crowl

state: California

address: 5107 Natural Sciences Building 0377, 9500 Gilman Drive

department: Molecular Biology

institute: University of California - San Diego

data_processing:
Trimmomatic v0.38 was used to remove adapters and trim low-quality reads (NexteraPE-PE.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25)
STAR v2.5.2b was then used to align trimmed reads to the mm10 genome using default conditions
featureCounts v1.5.3 was then used to quantify aligned reads per transcript
DESeq2 v1.3.2 was used to normalize raw read counts using the median of ratios method
Genome_build: mm10
Supplementary_files_format_and_content: Raw_gene_counts_matrix.csv contains a matrix with raw gene counts for every sample and gene
Supplementary_files_format_and_content: Normalize_gene_counts_matrix.csv contains a matrix with all gene counts and all samples normalized using the media of ratios method

molecule: polyA RNA

organism: Mus musculus

source_name: CD8+ T cells

extract_protocol:
To identify CD8+ T cells in the vasculature of non-lymphoid tissues (small intestine, kidney, salivary gland, fat, and liver), 3 µg of CD8α (53-6.7) conjugated to APC eFluor780 was injected by i.v. into mice three minutes prior to sacrifice, as has been previously described. Cells labeled with low to no CD8α antibody were considered to be outside of the vasculature. Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. Blood samples were treated with ACK lysis buffer. Small intestine intraepithelial lymphocytes were prepared through the removal of Peyer’s patches and the luminal contents. The small intestine was then cut longitudinally and into 1 cm pieces, then incubated at 37°C for 30 min in HBSS with 2.1 mg/mL sodium bicarbonate, 2.4 mg/mL HEPES, 8% bovine growth serum, and 0.154 mg/mL of dithioetheritol (EMD Millipore). The kidneys, salivary glands, fat, and liver were minced into small pieces and then incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. Lymphocytes from the small intestine, kidney, salivary gland, and liver were separated on a 44%/67% Percoll density gradient. For each replicate, cells from 10-15 mice were pooled and then sorted for bulk RNA-seq. 32 days after initial infection with LCMV, 5e3 P14 cells were sorted from the spleen and blood and 5e3 IV- P14 cells were sorted from the IEL, kidney, salivary gland, fat, and liver into PBS + 5% BSA. To further improve sample purity, 1e3 cells from each sample were resorted into 1x TCL lysis buffer + 1% 2-mercaptoethanol.
Samples were prepared using Immgen's standard protocol for ultra-low input RNA-seq (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf). Excerpt here: 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as  previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was  captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected  using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to  cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5  transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were  then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific  combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing.

value: Gonadal adipose tissue

tag: iv label

value: IV-

tag: days post infection with lcmv-arm


title: T8.D32.Liv1

value: Liver


title: T8.D32.SG3

value: Salivary Gland


title: T8.D32.Fat1


title: T8.D32.Liv2


title: T8.D32.SG2


title: T8.D32.SG1


title: T8.D32.Kid3

value: Kidney


title: T8.D32.Kid2


title: DMSO_TC00000651_G07

description: DMSO


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_3_0.100000uM_TC00000651_G06

value: 0.1 uM Etoposide

value: Etoposide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_6_1.000000uM_TC00000651_G09

value: 1 uM Trichostatin A

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_7_3.000000uM_TC00000651_G10

value: U-2 OS

value: 3 uM Trichostatin A

value: 3 uM


title: T8.D32.Kid1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_6_0.300000uM_TC00000651_G23

value: 0.3 uM Retinoic acid

value: Retinoic acid


title: T8.D32.IEL3

value: IEL


title: T8.D32.IEL2


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_6_3.000000uM_TC00000651_G05

value: 3 uM Cycloheximide

value: Cycloheximide


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_4_0.300000uM_TC00000651_G04

value: 0.3 uM Cycloheximide


title: T8.D32.Bl4

value: Blood


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_7_10.000000uM_TC00000651_G03

value: 10 uM Cycloheximide

value: 10 uM


title: BL_TSA_TC00000651_G02

value: Trichostatin A

value: TSA


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_3_0.010000uM_TC00000651_G11

value: 0.01 uM Rapamycin

value: Rapamycin


title: T8.D32.Bl3


title: BL_TSA_TC00000651_G01

value: 1 uM Trichostatin A

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_3_0.030000uM_TC00000651_E24

value: U-2 OS

value: 0.03 uM Trichostatin A


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_4_0.001000uM_TC00000651_G08

value: 0.001 uM Docetaxel

value: Docetaxel


title: T8.D32.Bl2


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_2_0.000100uM_TC00000651_E23

value: 1e-04 uM Docetaxel


title: T8.D32.Spl4

value: Spleen


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_2_0.010000uM_TC00000651_E20

value: 0.01 uM Trichostatin A


title: DMSO_TC00000651_E19

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: DMSO_TC00000651_E22

description: DMSO


title: DMSO_TC00000651_E21

description: DMSO


title: T8.D32.Spl5


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_1_0.000030uM_TC00000651_E17

value: 3e-05 uM Docetaxel


title: T8.D32.Spl1


title: pmIA.Hic1_2

extract_protocol:
Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. 5e3 empty vector transduced and 5e3 Hic1-Overexpressing P14 cells were sorted into PBS + 5% BSA. To improve sample purity, 1e3 cells were then resorted into 1x TCL lysis buffer + 1% 2-mercaptoethanol.
Samples were prepared using Immgen's standard protocol for ultra-low input RNA-seq (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf). Excerpt here: 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as  previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was  captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected  using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to  cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5  transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were  then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific  combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing.

tag: cell type

value: CD8+ T cells

tag: overexpression vector


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_3_0.000300uM_TC00000651_E16

tag: cell line

value: 3e-04 uM Docetaxel


title: pMIA.Hic1_1


title: T8.D32.Spl2


title: T8.D32.Spl3


title: pMIA.Ctrl_2

value: Control


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_5_0.100000uM_TC00000651_E15

tag: treatment

value: 0.1 uM Retinoic acid

value: Retinoic acid


title: pMIA.Ctrl_1


title: Kid_CAP_2 [RNA-seq]

extract_protocol:
To identify CD8+ T cells in the vasculature of non-lymphoid tissues (small intestine, kidney, salivary gland, fat, and liver), 3 µg of CD45.1 (47-0453-82) conjugated to APC-eFluor780 was injected by i.v. into mice three minutes prior to sacrifice, as has been previously described. Cells labeled with low to no CD8α antibody were considered to be outside of the vasculature. Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. Splenocytes from 4-6 mice were pooled, and then treated with DTE, collagenase, or a cold active protease as described below. Kidneys were minced into small pieces and then incubated in either collagenase or a cold active protease. Each sample comprises pooled cells from 4-6 mice. For DTE treatment, tissues were incubated at 37°C for 30 min in HBSS with 2.1 mg/mL sodium bicarbonate, 2.4 mg/mL HEPES, 8% bovine growth serum, and 0.154 mg/mL of dithioetheritol. For collagenase treatment, kidneys were minced into small pieces and then both  incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. For digestion with cold active protease, tissues were shaken at 4°C for 30 min in PBS with 10 mg/mL protease from Bacillus Sp (Sigma), 0.5 mM EDTA, and 125 U/mL DNase (Sigma). Cold active protease digestion was quenched with an equal volume of PBS containing 20% bovine growth serum. Lymphocytes from each digestion condition for both splenocytes and kidneys were separated using a 44%/67% Percoll density gradient.
Samples were prepared using Immgen's standard protocol for ultra-low input RNA-seq (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf). Excerpt here: 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as  previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was  captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected  using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to  cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5  transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were  then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific  combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing.

value: Kidney

tag: isolation method

value: Cold Active Protease

value: IV-


title: Kid_CAP_1 [RNA-seq]


title: Kid_coll_3 [RNA-seq]

value: Collagenase


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_5_1.000000uM_TC00000651_E14

value: U-2 OS

value: 1 uM Etoposide

tag: chemical name

value: Etoposide

tag: chemical id

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_2_0.000300uM_TC00000651_E13

value: 3e-04 uM Cucurbitacin I

value: Cucurbitacin I

tag: chemical concentration

tag: dose level


title: Kid_coll_2 [RNA-seq]


title: T8.D32.Bl1

value: Blood


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_1_0.010000uM_TC00000651_E11

value: 0.01 uM Cycloheximide

value: Cycloheximide

tag: assay plate

tag: assay plate well


title: Kid_coll_1 [RNA-seq]

tag: tissue


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_1_0.000100uM_TC00000651_E09

value: 1e-04 uM Actinomycin D

value: Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_7_0.100000uM_TC00000651_E12

value: 0.1 uM Cucurbitacin I


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_2_0.000300uM_TC00000651_E10

value: 3e-04 uM Actinomycin D


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_5_0.010000uM_TC00000651_E18

value: 0.01 uM Cucurbitacin I


title: DMSO_TC00000651_E08

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Spleen_CAP_2 [RNA-seq]

value: Spleen

value: Cold Active Protease


title: Spleen_CAP_3 [RNA-seq]


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_1_0.001000uM_TC00000651_E07

value: U-2 OS

value: 0.001 uM Rapamycin

value: Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_2_0.003000uM_TC00000651_E06

value: 0.003 uM Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_5_0.100000uM_TC00000651_E04

value: 0.1 uM Dexamethasone

value: Dexamethasone


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_2_0.010000uM_TC00000651_E05


title: Spleen_DTE_3 [RNA-seq]

value: DTE


title: Spleen_CAP_1 [RNA-seq]


title: Spleen_DTE_2 [RNA-seq]


title: Spleen_DTE_1 [RNA-seq]


title: Spleen_coll_3 [RNA-seq]

value: Collagenase


title: DMSO_TC00000651_E03

description: DMSO


title: BL_DMSO_TC00000651_E01


title: DMSO_TC00000651_C24

description: DMSO


title: BL_DMSO_TC00000651_E02


title: Spleen_coll_2 [RNA-seq]


title: Spleen_coll_1 [RNA-seq]


title: Spleen_NoTx_3 [RNA-seq]

value: No Digestion


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_7_1.000000uM_TC00000651_C23

value: 1 uM Rapamycin

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_2_0.000300uM_TC00000651_C22

value: 3e-04 uM Cucurbitacin I

value: Cucurbitacin I


title: MSD4

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

department: Plant Science

institute: South Dakota State University

data_processing:
Fastq files were generated and multiplexed with cassava1.8 pipeline.
Raw sequence reads were checked for their quality using FastQC.
Sequence reads were trimmed for adapters, length of 20 nucleotides, quality of 20 nucleotides using Cutadapt, Prinseq and Trimmomatic respectively.
Cleaned sequence reads were aligned to the 12X.V2 genome and VCostV3 annotation using Hisat2 and Gene expression levels in FPKM were quantified using Stringtie.
Differential gene expression analysis was performed using DESeq2.
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each sample

organism: Vitis

source_name: Marquette Skin at 22 degree Brix

growth_protocol: Frontenac and Marquette grapes were grown in a randomized complete block design with six vines per replicate and 1 replicate in each of four blocks as part of the NE-1020 Cold Hardy Wine Grape Cultivar Trial at the NE Hansern research farm in Brookings, South Dakota, USA.

extract_protocol:
A random sampling 25 berries from a pool of berries from 12 clusters/replicate was immediately separated into skins and pulp directly into liquid nitrogen and stored in -80C for RNAseq analysis.  A 50 berry random sample was used for assessing brix and pH.  Samples with soluble solids closest to 18, 20, 22 and 24 °Brix were used for RNAseq analysis.
Two replicates were single end RNAseq libraries were prepared with TruSeq Stranded RNA Sample Prep Kit. Two replicates were paired end libraries prepared with TruSeq strand specific kits.

tag: genotype

value: Marquette

value: Skin


title: MSE4

source_name: Marquette Skin at 24 degree Brix


title: MSE3


title: Spleen_NoTx_2 [RNA-seq]

value: Spleen


title: MSD3


title: MSC4

source_name: Marquette Skin at 20 degree Brix


title: MSC3


title: MSA4

source_name: Marquette Skin at 18 degree Brix


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_5_10.000000uM_TC00000651_C20

value: 10 uM Berberine chloride

value: Berberine chloride

value: 10 uM


title: MSA3


title: Spleen_NoTx_1 [RNA-seq]


title: MPE4

source_name: Marquette Pulp at 24 degree Brix

value: Pulp


title: 20190920_ES013_RNA_primary_844374_4_S13_R1_001

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 44 Binney St

institute: Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes. Spike-in normalization of bigWig files can be incoporated by scaling the bigWig files by the ratio of fly to human reads in the control sample divided by the ratio of fly to human reads in each sample, i.e. (fly / human)_control / (fly / human)_sample. The total number of mapped fly and human reads can be estimated by aligning the fastq files to the hg19 and dm3 genome and then summing the third column (mapped reads) from the samtools idxstats output.

source_name: primary tumor

growth_protocol: MLPS-1765-92 and MLPS-402-91 cells were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), and 1% Penicillin-Streptomycin (Gibco). MLPS-DL221 cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), and 1% Penicillin-Streptomycin (Gibco). hTERT-MSC and AD-MSC lines were cultured in Mesenchymal Stem Cell Basal Medium (ATCC No. PCS-500-030) supplemented with the Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum (ATCC No. PCS-500-040) and 0.1% Penicillin-Streptomycin (Gibco). HEK293T LentiX cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), 1% HEPES (Gibco), 1% MEM NEAA (Gibco), and 1% Penicillin-Streptomycin (Gibco). All cells were maintained in a humidified incubator at 37°C with 5% CO2.     Deidentified myxoid liposarcoma (n=10 for RNA-seq), Ewing sarcoma (n=10 for RNA-seq), cases were identified, with pathology and diagnosis confirmed by two independent pathologists at MD Anderson Cancer Center (MDACC).

extract_protocol:
ChIP-seq protocol Cells were harvested following 72-hr exposure to specified lentivirus and 4 day selection with 2 μg/ml of puromycin. ChIP experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, cells were cross-linked for 10 min with 1% formaldehyde at 37 °C. This reaction was subsequently quenched with 125 mM glycine for 5 min and 10 million fixed cells were used per ChIP experiment. Chromatin from fixed cells was fragmented by sonication with a Covaris E220 and the solubilized chromatin was incubated with the indicated antibody listed overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein G-Dynabeads (Thermo Scientific) for 2 hours at 4°C, washed, and eluted. The samples then underwent crosslink reversal, RNase A (Roche) treatment, and proteinase K (Thermo Scientific) treatment before the captured DNA was extracted with AMPure XP beads (Beckman Coulter). ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.
ATAC-seq protocol Cells were harvested following 72-hr exposure to lentivirus and 4 days of selection with 2 μg/ml of puromycin. ATAC-seq experiments were performed as previously described. Samples for ATAC-seq prepared using the Nextera DNA sample Prep Kit (Illumina). Briefly, 50K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 12 cycles of amplification. ATAC-seq samples were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing parameters.
RNA-seq protocol Cells were harvested following 72-hr exposure to the specified lentivirus and either 4 day (day 7 post-transduction) or 11 day (day 14 post-transduction) selection with 2 μg/ml of puromycin for RNA-seq experiments. All RNA was collected using the RNeasy Mini Kit (Qiagen). RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 (Illumina) using 75 bp single-end sequencing parameters.    Snap-frozen tumor tissue samples were obtained from the MD Anderson Institutional Tissue Bank (ITB) using an IRB-approved protocol. Frozen samples were embedded in O.C.T. (Tissue-Tek), sectioned in a Cryostat (Leica CM1680 UV) and underwent hematoxylin and eosin staining for pathologist review to confirm the presence of viable tumor tissue. Tissues were then excised from O.C.T. using scalpel and forceps and 30 mg samples were placed in RNAlater-ICE (Invitrogen) pre-chilled to -80°C. Samples were thawed overnight at -20°C, then disrupted using a TissueLyser LT (Qiagen) for 5 minutes at 50 Hz. RNA was isolated using the RNeasy Mini Kit (Qiagen), following the manufacturer protocol with on-column DNase I (Qiagen) digestion.
Cut & Run protocol Cells were harvested following 24-hr exposure to DMSO or 10uM of CMP12 (generous gift of Jun Qi) followed by 24-hr exposure to DMSO plus base media or StemPro Adipogenesis media (ThermoFisher) or 10uM CMP12 plus base media or StemPro Adipogenesis media. CUT&RUN experiments were performed according to established protocols with minor modifications. Briefly, 500K cells per sample were incubated with Concanavalin A-coated beads (Polysciences) for 10 min and then permeabilized with Triton X-100. Cell-bead complexes were then incubated with the indicated antibody for 2 hr at 4°C. Cell-bead complexes were washed and then incubated with pA-MNase for 1 hr at 4°C. Cell-bead complexes were washed and then cooled to ~0°C. pA-MNase was activated by the addition of calcium chloride and incubated for 30 min at ~0°C. The cleavage reaction was quenched with a solution containing spike-in DNA and RNAase A. Cleaved DNA fragments released into solution were then collected and treated with sodium dodecyl sulfate (SDS) and proteinase K (Thermo Scientific). DNA was then isolated using phenol-chloroform. CUT&RUN libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit with modifications that aim to preserve short fragments.
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.    CUT&RUN libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit with modifications that aim to preserve short fragments.    ATAC-seq samples were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing parameters.    RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 (Illumina) using 75 bp single-end sequencing parameters.

treatment_protocol: Constitutive expression of short-hairpin RNA (shRNA) constructs targeting either the C-terminal end of the FUS-DDIT3 fusion (shDDIT3: 5’-CGGCTCAAGCAGGAAATCG-3’), SMARCA4/BRG1 (shBRG1: 5’-AGCCTCAACGACCTAGAGA-3’), or a scrambled, non-silencing sequence (shSCR: 5’-TCTCGCTTGGGCGAGAGTAAG-3’) was achieved using lentiviral infection of the GIPZ vector selected with puromycin (2 μg/ml).    Lentivirus was produced by PEI (Polysciences) transfection of HEK293T LentiX cells (Clontech) with gene delivery vector co-transfected with packaging vectors pspax2 and pMD2.G. Viral supernatants were harvested 72 hr post-transfection and concentrated by ultracentrifugation at 20,000 rpm for 2.5 hr at 4°C. Virus containing pellets were resuspended in PBS and added dropwise to cells in the presence of 10 μg/mL polybrene. Selection of lentivirally-infected cells was achieved with puromycin used at 2 μg/ml. Knockdown efficiency and overexpression was measured by western blot analysis.    The SMARCB1 locus was targeted by the Ini1 (h) CRISPR/Cas9 KO Plasmid (Santa Cruz Biotechnology sc-423027) in MLPS-1765-92 cells following the manufacturer’s protocol with the Lipofectamine 3000 transfection reagent (Invitrogen). Cells were expanded for 72-96 hours and GFP+ cells expressing the KO plasmids were single-cell sorted using FACS (fluorescence-activated cell sorting). Single-cell clones were expanded and screened using immunoblot detection for identification of successful knockouts.

value: ES Primary Tumor

tag: experimental condition

value: genotype:EWS-FLI1 fusion primary tumor

tag: chip antibody


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_4_0.001000uM_TC00000651_C19

value: U-2 OS

value: 0.001 uM Docetaxel

value: Docetaxel


title: MPD3

source_name: Marquette Pulp at 22 degree Brix


title: MPD4


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_5_0.100000uM_TC00000651_C17

value: 0.1 uM Dexamethasone

value: Dexamethasone


title: 20190920_ES011_RNA_primary_360114_2_S11_R1_001


title: 20190920_ES008_RNA_primary_664714_1_3_S8_R1_001


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_6_0.030000uM_TC00000651_C18

value: 0.03 uM Actinomycin D

value: Actinomycin D


title: MPC2

source_name: Marquette Pulp at 20 degree Brix


title: 20190920_ES012_RNA_primary_807460_3_S12_R1_001


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_1_0.001000uM_TC00000651_C16

value: 0.001 uM Rapamycin

value: Rapamycin


title: MPC4

value: Marquette


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_4_0.030000uM_TC00000651_C21

value: 0.03 uM Dexamethasone


title: 20190920_ES007_RNA_primary_530104_6_S7_R1_001


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_6_1.000000uM_TC00000651_C15

value: 1 uM Ca-074-Me

value: 1 uM


title: MPA4

source_name: Marquette Pulp at 18 degree Brix


title: 20190920_ES006_RNA_primary_340291_1_S6_R1_001


title: FSE2

source_name: Frontenac Skin at 24 degree Brix

value: Frontenac

value: Skin


title: MPA3

value: Pulp


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_1_0.000100uM_TC00000651_C14

source_name: U-2 OS

value: 1e-04 uM Cucurbitacin I

value: Cucurbitacin I


title: FSE3


title: FSC3

source_name: Frontenac Skin at 22 degree Brix


title: MPE3


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_1_0.001000uM_TC00000651_C13

value: U-2 OS

value: 0.001 uM Retinoic acid

value: Retinoic acid


title: 20190920_ES005_RNA_primary_289110_3_S5_R1_001

value: ES Primary Tumor

value: genotype:EWS-FLI1 fusion primary tumor


title: FSB2

source_name: Frontenac Skin at 20 degree Brix


title: FSB3


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_4_0.030000uM_TC00000651_C12

value: 0.03 uM Retinoic acid


title: 20190920_ES004_RNA_primary_249497_6_S4_R1_001


title: FSA3

source_name: Frontenac Skin at 18 degree Brix


title: 20190920_ES003_RNA_primary_170347_10_S3_R1_001


title: 20190920_ES002_RNA_primary_164216_3_S2_R1_001


title: FPE2

source_name: Frontenac Pulp at 24 degree Brix


title: FSA2


title: FPC3

source_name: Frontenac Pulp at 22 degree Brix


title: 20210309_HJZCR108_CandR_AD_MSC_CMP12_StemProAdipogenesis_24hr_H3K27ac_S22_aligned_reads

library_source: genomic

data_processing:
Library strategy: Cut&Run
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes. Spike-in normalization of bigWig files can be incoporated by scaling the bigWig files by the ratio of fly to human reads in the control sample divided by the ratio of fly to human reads in each sample, i.e. (fly / human)_control / (fly / human)_sample. The total number of mapped fly and human reads can be estimated by aligning the fastq files to the hg19 and dm3 genome and then summing the third column (mapped reads) from the samtools idxstats output.

molecule: genomic DNA

source_name: stem cell line

value: MSCs-AD


title: FPC2


title: FPB3

source_name: Frontenac Pulp at 20 degree Brix


title: FPA3

source_name: Frontenac Pulp at 18 degree Brix


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_3_1.000000uM_TC00000651_C09

value: 1 uM Berberine chloride

value: Berberine chloride


title: 20210309_HJZCR107_CandR_AD_MSC_CMP12_StemProAdipogenesis_24hr_CEBPB_S21_aligned_reads


title: DMSO_TC00000651_C08

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: 20210309_HJZCR105_CandR_AD_MSC_CMP12_base_H3K27ac_S2_aligned_reads


title: 20210309_HJZCR106_CandR_AD_MSC_CMP12_StemProAdipogenesis_24hr_BRG1_S20_aligned_reads


title: MSE2

source_name: Marquette Skin at 24 degree Brix

value: Marquette


title: FSC2

value: Frontenac

value: Skin


title: FPA2

value: Pulp


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_4_0.100000uM_TC00000651_C11


title: MSE1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_5_0.300000uM_TC00000651_C07


title: FPE3


title: MSC2

source_name: Marquette Skin at 20 degree Brix


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_5_0.100000uM_TC00000651_C06

value: 0.1 uM Rapamycin

value: Rapamycin


title: MSD1

source_name: Marquette Skin at 22 degree Brix


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_3_0.010000uM_TC00000651_C05

value: U-2 OS

value: 0.01 uM Retinoic acid


title: 20210309_HJZCR103_CandR_AD_MSC_CMP12_base_BRG1_S18_aligned_reads


title: 20210309_HJZCR104_CandR_AD_MSC_CMP12_base_CEBPB_S19_aligned_reads


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_1_0.100000uM_TC00000651_C10

value: 0.1 uM Berberine chloride


title: MSC1


title: 20210309_HJZCR102_CandR_AD_MSC_DMSO_StemProAdipogenesis_24hr_H3K27ac_S17_aligned_reads


title: MSA2

source_name: Marquette Skin at 18 degree Brix


title: MSD2


title: FPB2


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_1_0.003000uM_TC00000651_C03

value: 0.003 uM Trichostatin A

value: Trichostatin A


title: MPE2

source_name: Marquette Pulp at 24 degree Brix


title: HBRR_TC00000651_C02

description: HBRR

source_name: vendor-provided reference RNA mixtures


title: MSA1


title: MPD2

source_name: Marquette Pulp at 22 degree Brix


title: 20210309_HJZCR101_CandR_AD_MSC_DMSO_StemProAdipogenesis_24hr_CEBPB_S16_aligned_reads

value: MSCs-AD


title: MPE1


title: 20210309_HJZCR100_CandR_AD_MSC_DMSO_StemProAdipogenesis_24hr_BRG1_S15_aligned_reads


title: MPD1


title: MPC1

source_name: Marquette Pulp at 20 degree Brix


title: 20210309_HJZCR099_CandR_AD_MSC_DMSO_base_H3K27ac_S14_aligned_reads


title: MPA2

source_name: Marquette Pulp at 18 degree Brix


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_6_1.000000uM_TC00000651_A24

source_name: U-2 OS

value: 1 uM Trichostatin A

value: 1 uM


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A02_6_3.000000uM_TC00000651_C04

value: 3 uM Etoposide

value: Etoposide

value: 3 uM


title: 20210309_HJZCR098_CandR_AD_MSC_DMSO_base_CEBPB_S13_aligned_reads

value: DMSO


title: HBRR_TC00000651_C01

description: HBRR


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_3_0.001000uM_TC00000651_A23

value: 0.001 uM Actinomycin D

value: Actinomycin D


title: MPC3

value: Marquette

value: Pulp


title: 20210309_HJZCR097_CandR_AD_MSC_DMSO_base_BRG1_S12_aligned_reads


title: T8.D32.IEL1

source_name: CD8+ T cells

value: IEL

tag: iv label

value: IV-


title: DMSO_TC00000651_A22

description: DMSO

value: U-2 OS

value: 0.5% DMSO vehicle control

value: 0 uM


title: FSE1

source_name: Frontenac Skin at 24 degree Brix

value: Frontenac

value: Skin


title: FSE4


title: FSC4

source_name: Frontenac Skin at 22 degree Brix


title: 20210309_HJZCR096_CandR_hTERT_MSC_CMP12_StemProAdipogenesis_24hr_H3K27ac_S11_aligned_reads

value: MSCs-hTERT


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A04_3_0.030000uM_TC00000651_A21


title: FSB4

source_name: Frontenac Skin at 20 degree Brix


title: 20210309_HJZCR095_CandR_hTERT_MSC_CMP12_StemProAdipogenesis_24hr_CEBPB_S10_aligned_reads

source_name: stem cell line


title: FSB1


title: FSA4

source_name: Frontenac Skin at 18 degree Brix


title: 20210309_HJZCR094_CandR_hTERT_MSC_CMP12_StemProAdipogenesis_24hr_BRG1_S9_aligned_reads


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_4_3.000000uM_TC00000651_A20

value: 3 uM Berberine chloride

value: Berberine chloride


title: FSA1


title: FPE4

source_name: Frontenac Pulp at 24 degree Brix


title: 20210309_HJZCR093_CandR_hTERT_MSC_CMP12_base_H3K27ac_S8_aligned_reads


title: MPA1


title: FPE1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_5_0.300000uM_TC00000651_A18

value: 0.3 uM Trichostatin A

value: Trichostatin A


title: FPC4

source_name: Frontenac Pulp at 22 degree Brix


title: FPB4

source_name: Frontenac Pulp at 20 degree Brix


title: FSC1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_7_1.000000uM_TC00000651_A17

value: 1 uM Dexamethasone

value: Dexamethasone

value: 1 uM


title: FPB1


title: 20210309_HJZCR092_CandR_hTERT_MSC_CMP12_base_CEBPB_S7_aligned_reads


title: FPC1


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A03_2_0.030000uM_TC00000651_A16

value: 0.03 uM Cycloheximide

value: Cycloheximide


title: 20210309_HJZCR091_CandR_hTERT_MSC_CMP12_base_BRG1_S6_aligned_reads


title: FPA4

source_name: Frontenac Pulp at 18 degree Brix

value: Pulp


title: 20210309_HJZCR090_CandR_hTERT_MSC_DMSO_StemProAdipogenesis_24hr_H3K27ac_S5_aligned_reads

value: DMSO


title: 20210309_HJZCR089_CandR_hTERT_MSC_DMSO_StemProAdipogenesis_24hr_CEBPB_S1_aligned_reads


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_7_1.000000uM_TC00000651_A14

value: U-2 OS

value: 1 uM Rapamycin

value: Rapamycin


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_2_0.003000uM_TC00000651_A15

value: 0.003 uM Dexamethasone


title: 5C_B29_88.12

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

data_processing:
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Assembly: mm9 / NCBIm37
Supplementary files format and content: Raw contact maps at the primer resolution reporting the contact frequencies for each pair of forward/reverse primers.
Library strategy: 5C

source_name: mouse ESC (E14)

growth_protocol: Male mouse ESC (E14) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged when needed. Medium was changed daily. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
Cells were fixed in culture plates or flasks and scraped off. Please find more details in the methods section of the manuscript.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017).  Please find more details in the methods section of the manuscript.

tag: strain

value: XY, 129/Ola

tag: differentiation stage

value: day 0 (undifferentiated)

tag: capture-c viewpoint


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A09_3_0.001000uM_TC00000651_A19

tag: cell line

value: 0.001 uM Cucurbitacin I

value: Cucurbitacin I


title: 20210309_HJZCR088_CandR_hTERT_MSC_DMSO_StemProAdipogenesis_24hr_BRG1_S4_aligned_reads

value: MSCs-hTERT

tag: treatment


title: Ri, 150mM, shoot, sample 3

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

data_processing:
The quality control of raw reads was evaluated using FastQC software v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The low-quality reads (Q-value < 20) and adaptors were removed using the sequence preprocessing tool Trimmomatic v0.39 (Bolger et al., 2014). After low-quality reads and adaptors were removed, all cleaned reads were assembled into contigs using Trinity (Grabherr et al., 2011).
To get a more specific gene list, we used CD-HIT-EST version CD-HIT4 to cluster the redundancy of transcripts and removed the shorter redundant transcripts (Li and Godzik, 2006;Fu et al., 2012).
In this analysis, Bowtie2 version V2.3.2 and RSEM version v1.2.31 software were used to map short reads to the Trinity de novo assembly and quantify the read counts that matched to each contig (Li and Dewey, 2011;Langmead and Salzberg, 2012). Then, Transdecoder was used to identify candidate coding regions for gene prediction.
Next, to distinguish the de novo assembled sequences between those of the rice and fungal species, the Basic Local Alignment Search Tool (BLAST) searches against the Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis), was performed for annotation, respectively (Altschul et al., 1990;Droc et al., 2006;Coordinators, 2016).
Assembly: Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis)
Supplementary files format and content: tab-delimited excel files include raw count values for each Sample

organism: Oryza sativa

source_name: shoot

extract_protocol:
Total RNA was extracted from 100 mg shoot or root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 4 μg) per sample were used for transcriptome sequencing.
Strand-specific sequencing libraries were obtained following the handbook for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: shoot

value: wild type

tag: inoculation treatment

value: Rhizophagus irregularis

tag: salt treatment

value: 150mM NaCl

tag: time

value: 8 weeks post inoculation


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_5_0.003000uM_TC00000651_A13

value: 0.003 uM Docetaxel

tag: chemical name

value: Docetaxel

tag: chemical id

tag: chemical concentration


title: 20210309_HJZCR086_CandR_hTERT_MSC_DMSO_base_CEBPB_S2_aligned_reads

value: DMSO


title: 20210309_HJZCR087_CandR_hTERT_MSC_DMSO_base_H3K27ac_S3_aligned_reads


title: Ri, 150mM, shoot, sample 2


title: 5C_B29_51.13


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A11_7_0.030000uM_TC00000651_A11

value: U-2 OS

value: 0.03 uM Docetaxel

tag: dose level

tag: assay plate

tag: assay plate well


title: 20210309_HJZCR085_CandR_hTERT_MSC_DMSO_base_BRG1_S1_aligned_reads

tag: experimental condition


title: Ri, 150mM, root, sample 1

source_name: root

tag: tissue

value: root

tag: genotype


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A07_5_0.100000uM_TC00000651_A09

value: 0.1 uM Rapamycin

value: Rapamycin


title: 5C_B28_RGE4

data_processing:
library strategy: 5C
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls and analysis were performed using the HiTC BioConductor package.
Genome_build: mm9 / NCBIm37
Supplementary_files_format_and_content: Raw contact maps at the primer resolution reporting the contact frequencies for each pair of forward/reverse primers.

tag: strain

value: XY, 129/Ola

value: day 0 (undifferentiated)

tag: cell type

value: mouse ESC (E14)


title: Ri, 150mM, root, sample 2


title: 5C_B27_RGE3

tag: differentiation stage


title: FPA1

value: Frontenac

value: Pulp


title: 20190408_MLPS001_RNA_primary_134580-8

source_name: primary tumor

tag: cell line

value: MLPS Primary Tumor

value: genotype:FUS-DDIT3 fusion primary tumor

tag: chip antibody


title: Ri, 150mM, shoot, sample 1

value: shoot

value: wild type

tag: inoculation treatment

value: Rhizophagus irregularis

value: 150mM NaCl


title: 5C_B29_18.24

tag: capture-c viewpoint


title: Ri, 150mM, root, sample 3

tag: salt treatment

tag: time

value: 8 weeks post inoculation


title: 20190408_MLPS020_RNA_primary_950405-11_S12_R1_001


title: 5C_B102_B10


title: 5C_B29_I13


title: DMSO_TC00000651_A12

description: DMSO

value: U-2 OS

tag: treatment

value: 0.5% DMSO vehicle control

tag: chemical name

value: DMSO

tag: chemical id

value: 0 uM


title: mock, 150mM, shoot, sample 2

value: mock


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_2_0.003000uM_TC00000651_A06

value: 0.003 uM Retinoic acid

value: Retinoic acid

tag: chemical concentration

tag: dose level

tag: assay plate


title: 20190408_MLPS017_RNA_primary_1002476-4_S10_R1_001

tag: experimental condition


title: 20190408_MLPS008_RNA_primary_532293-3


title: PBMC day 59 post-symptom onset

city: Newark

first: Natalie

last: Bruiners

state: NJ

address: 225 Warren street

institute: Rutgers University

description: Sample 4 (NB1307)

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the CellRanger software (version 3.1.0). Reads were aligned to a custom reference genome created with the reference human genome (GRCh38)
The resulting unique molecular identifier (UMI) count matrices were imported into R (version 4.0.2) and processed with the R package Seurat (version 4.0.0)
The data was normalized using SCTransform and then dimensionality reduced by finding the top 50 principal components and then using these principal components to run UMAP
Assembly: GRCh38
Supplementary files format and content: h5 format for the count matrices and Rdata for the processed Seurat object.

source_name: peripheral blood cells

extract_protocol:
Cells were washed in complete RPMI medium (supplemented with 10% FBS, 2mM L-glutamine, and 1% penicillin/streptomycin), counted, and assessed for viability using a Countess II automated cell counter (Invitrogen, Waltham, MA, USA). Cells were then suspended to 1 × 106/ml in complete RPMI for single-cell emulsion preparation.
scRNA-seq GEX libraries were prepared according to 10X Genomics specifications. . Cell suspensions were loaded for droplet-encapsulation by the Chromium Controller (10X Genomics). Single-cell cDNA synthesis, amplification, and sequencing libraries were generated using the Single Cell 5′ Reagent kit (10X Genomics, Pleasanton, CA, USA) following the manufacturer’s instructions. The libraries were sequenced with the Illumina NovaSeq 6000 platform (200 M, 150 bp paired-end reads).

tag: post-symptom onset

value: day 59 post-symptom onset

value: peripheral blood cells

tag: molecule

value: single-cell RNA


title: PBMC day 57 post-symptom onset

description: Sample 3 (NB1305)

value: day 57 post-symptom onset

tag: cell type


title: 5C_B101_B10

tag: strain

value: XY, 129/Ola

tag: genotype

tag: differentiation stage

value: day 0 (undifferentiated)


title: PBMC day 56 post-symptom onset

description: Sample 2 (NB1304)

value: day 56 post-symptom onset


title: mock, 150mM, shoot, sample 3

tag: tissue

value: shoot

value: wild type

tag: inoculation treatment


title: 20190408_MLPS016_RNA_primary_863419-8_S9_R1_001

tag: cell line

value: MLPS Primary Tumor

value: genotype:FUS-DDIT3 fusion primary tumor

tag: chip antibody


title: PBMC day 61 post-symptom onset

description: Sample 5 (NB1311)

value: day 61 post-symptom onset


title: 20190408_MLPS015_RNA_primary_644582-2_S8_R1_001


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A06_3_0.010000uM_TC00000651_A10

value: U-2 OS

tag: treatment

value: 0.01 uM Dexamethasone

value: Dexamethasone

tag: assay plate well


title: PBMC day 54 post-symptom onset

description: Sample 1 (NB1302)

value: day 54 post-symptom onset


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A08_3_0.030000uM_TC00000651_A07

value: 0.03 uM Trichostatin A

tag: chemical name

value: Trichostatin A

tag: chemical id


title: Ri, 0mM, shoot, sample 3

value: Rhizophagus irregularis

tag: salt treatment

value: 0mM NaCl

tag: time

value: 8 weeks post inoculation


title: Ri, 0mM, shoot, sample 2


title: 20190408_MLPS012_RNA_primary_768695-1_S6_R1_001

tag: experimental condition


title: 20190408_MLPS018_RNA_primary_1171931-13_S11_R1_001


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A01_7_100.000000uM_TC00000651_A08

value: 100 uM Berberine chloride

value: Berberine chloride

tag: chemical concentration

tag: dose level

tag: assay plate


title: DMSO_TC00000651_A05

description: DMSO

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Ri, 0mM, shoot, sample 1

value: shoot

value: wild type


title: mock, 150mM, shoot, sample 1

value: mock

value: 150mM NaCl


title: 20190408_MLPS009_RNA_primary_947186-4_S5_R1_001

value: MLPS Primary Tumor

value: genotype:FUS-DDIT3 fusion primary tumor


title: mock, 150mM, root, sample 1

value: root


title: mock, 150mM, root, sample 2


title: 20190408_MLPS014_RNA_primary_641607-4_S7_R1_001


title: Replicate 3; MS275 treated Day 5 differentiated hiPSCs

city: Brisbane

first: Nathan

middle: J.

last: Palpant

state: QLD

address: 306 Carmody Rd

country: Australia

institute: University of Queensland

data_processing:
ATAC-seq data processing and alignment was completed using the Harvard pipeline (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). All fastq files initial quality was assessed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) was used to aligned reads to the GRC38_no_alt genome bowtie 2 index for alignment (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), using “-p 8, –very-sensitive” options.  Picard tools (http://broadinstitute.githyb.io/picard/) was used to mark and remove duplicates using the MarkDuplicates tool with default options.  Samtools (Li et al., 2009) was used to sort and obtain uniquely mapped reads suing “-b -q 10” options ato remove reads from the mitochondrial chromosome. This resulted in the final aligned, deduplicated BAM files that were used for downstream analysis.
Peak calling was performed to ensure high quality fixed-width peaks in accordance with Corces et al.(Corces et al., 2018). For each sample, peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” (Feng et al., 2012; Zhang et al., 2008). Then, peak summits were extended by 250 bp on both sides to a final width of 501 bp. Peaks were filtered for GRC38 blacklisted regions (Amemiya et al., 2019) (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
As in Corces et al. (Corces et al., 2018) per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample. Due to samples with higher sequencing depth and quality yield a higher number of MACS2 original number of peaks we normalized their significance peak scores “(-log10(p-value))” to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million (Corces et al., 2018). Thus, scores per million allow the direct comparison of peaks across biological replicates. Next, we complied a peak set across conditions. For that we generated a cumulative peak set across samples and performed the same iterative approach as mentioned above. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered. This resulted in a set of fixed-width, reproducible, high-quality peaks across conditions of 83,554 peaks, each with 501 bp in width.
To assess differential accessibility between conditions the across-conditions ATAC-seq peaks was converted to gtf format. The number of reads falling within these regions per sample were calculated using the featurecounts function within the Subread package (version2.0.1) (Liao et al., 2014). Next, a count matrix containing the samples of interest was inputted into the DESeq2 package (Love et al., 2014), where only peaks with at least 5 counts per million in at least 2 samples were further processed to identify differentially accessible regions between conditions.
Assembly: hg38
Supplementary files format and content: tab-delimited text files

source_name: WTC CRISPRi GCaMP hiPSC (RRID CVCL_VM38)

growth_protocol: WTC CRISPRi GCaMP hiPSCs were maintained on 5μg/mL Vitronectin XF (Stem Cell Technologies, 07180) coated plates in mTESR1 media (Stem Cell Technologies, 05850) treated with  1% penicillin/streptomycin at 37°C with a 5% CO2 incubator

extract_protocol:
Omni-ATACseq sequencing libraries were generated from Day 5 cells undergoing hiPSC cardiac-directed differentiation using an adapted published workflow (Corces et al., 2017). Briefly day 5 cells were harvested and 15,000 cells were pelleted at 500 x g for 5 min at 4oC and washed once in 50 µl cold PBS. The cell suspension was then pelleted again at 500 g for 5 min at 4oC. For cell lysis, the pellets were resuspended in 50 µl cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.4 (Thermo Scientific, 10 mM NaCl (Sigma), and 3 mM MgCl2 (Sigma) in nuclease-free water (Thermo Scientific) containing 0.1% (v/v) NP40 (Sigma), 0.1% (v/v) Tween-20 (Sigma), and 0.01% (v/v) Digitonin (Promega) by gently pipetting up and down three times. After cell lysis, 1 ml of cold ATAC-Resuspension Buffer was added and mixed by inverting the tubes. The samples were then centrifuged at 500 g for 10 min at 4oC and supernatant is carefully removed away from the pellets. For the transposition reaction, each pellet was resuspended in 12.5 µl of transposition mix (6.25 µl 2x TD buffer (Illumina), 0.625 µl Tn5 (Illumina), 4.125 µl PBS, 0.125 µl 1% (v/v) Digitonin (Promega), 0.125 µl 10% (v/v) Tween-20 (Sigma), 1.25 µl nuclease-free water (Thermo Scientific) by gently pipetting up and down six times. The samples were then incubated at 37oC for 30 min in a thermomixer shaking at 300 rpm, followed by immediate purification using a DNA Clean & Concentrator-5 Kit (Zymo, Cat.# D4013) according to the manufacturer’s specification, except for the final elution volume, which was 21 µl. A PCR reaction volume of 50 µl was then set up using 20 µl of the purified DNA, 25 µl of the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) and 1.25 mM of the ATACseq oligos published previously (Buenrostro et al., 2013). The DNA samples were amplified with the following parameters:  72oC for 5 min, 98oC for 30 s and 11 cycles of 98oC for 10 s, 63oC for 30 s and 72oC for 30 s.
The omni-ATAC libraries were then purified using the DNA Clean & Concentrator-5 Kit (Zymo) according to the manufacturer’s specification and eluted in 20 µl nuclease-free water (Thermo Scientific). The libraries were quantified with Qubit dsDNA HS Assay Kit (Invitrogen) and assessed for library size distribution using an Agilent Bioanalyzer.The libraries were then pooled and sequenced in 2x100 cycle paired-end mode on an Illumina Novaseq instrument.

treatment_protocol:
An established monolayer-based cardiac directed differentiation protocol was modified and used to differentiate WTC CRISPRi GCaMP hiPSCs. On day -1 hiPSCs were dissociated using 0.5% EDTA and plated at a density of 1.8x105 cells/cm2 on Vitronectin XF coated plates and cultured overnight in mTeSR media at 37°C. To initiate differentiation on day 0 cells were washed with PBS, then fed with RPMI media (ThermoFisher, Cat.#11875119) containing 3mM Wnt-agonist CHIR99021 (Stem Cell Technologies, Cat.#72054), 500mg/mL BSA (Sigma Aldrich, Cat.#A9418), and 213mg/mL ascorbic acid (Sigma Aldrich, Cat.#A8960). After 3 days of culture, the media was replaced with RPMI containing 500mg/mL BSA, 213mg/mL ascorbic acid, and 5mM Wnt-antagonist XAV-939 (Stem Cell Technologies, Cat.#72674). On day 5, the media was exchanged for RPMI containing 500mg/mL BSA, and 213mg/mL ascorbic acid without supplemental cytokines.
Cells were treated with 1uM MS275 and 1uM BRD4884 for 48 hours prior to sample collection on Day 5 of differentiation

tag: cell type

value: Day 5 differentiated human induced pluripotent stem cells

value: WT

value: MS275 1uM, cardiac differentiation

value: Day 5


title: 20190408_MLPS003_RNA_primary_45283-8_S2_R1_001


title: UHRR_TC00000651_A02

description: UHRR

source_name: vendor-provided reference RNA mixtures


title: Replicate 2; MS275 treated Day 5 differentiated hiPSCs

value: WTC CRISPRi GCaMP hiPSC (RRID CVCL_VM38)

tag: genotype


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A05_7_1.000000uM_TC00000651_A04

source_name: U-2 OS

value: U-2 OS

value: 1 uM Retinoic acid

value: Retinoic acid

value: 1 uM


title: UHRR_TC00000651_A01

description: UHRR


title: Replicate 1; Control Day 5 differentiated hiPSCs

value: cardiac differentiation


title: mock, 0mM, shoot, sample 3

value: shoot

value: 0mM NaCl

value: 8 weeks post inoculation


title: 20200813_HJZ053_RNA_402_shDDIT3_D7_S10_R1_001

source_name: cancer cell line

value: genotype:FUS-DDIT3 fusion shDDIT3


title: sorted cells from AoLNs, WD, Het samples, scRNAseq

city: Munich

first: Christian

last: Weber

address: Pettenkoferstreet 8a and 9

country: Germany

institute: Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich

description: 10x Gemonics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Further processing was done with Seurat v3.2.3 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: customized reference based on mm10 (GFP was incoperated into the gene CCL17)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: metadata files: comma-separated values files

source_name: lymph nodes

extract_protocol:
For the scRNA-seq experiment of pooled lymph nodes (including mesenteric, paraaortic, inguinal, axillary, brachial and mandibular LNs), eight male Apoe-/-Ccl17wt/e and six Apoe-/-Ccl17e/e mice were fed on normal chow diet. Perfusion was performed with 5 mL PBS. Pooled lymph nodes from either  Apoe-/-Ccl17wt/e or Apoe-/-Ccl17e/e mice were mechanically crushed and passed through a 30 μm cell strainer using Hank’s Medium (HBSS + 0.04% BSA) to obtain single cell suspensions, followed by B cell depletion using CD19 MicroBead. B cell-depleted fractions were stained with Viability Dye, anti-CD45, anti-CD3, anti-CD19 and anti-CD11c at 4°C for 20 minutes. Cells were washed and resuspended in Hank’s Medium and then isolated by fluorescence-activated cell sorting, by gating for Live CD45+CD11c+CD3-CD19- cells. The cell suspension with viability > 80% was ready for subsequent single cell capture and library preparation. For the scRNA-seq experiment of para-aortic LNs, seven male Apoe-/-Ccl17wt/e and ten Apoe-/-Ccl17e/e mice were fed on 6-week HFD. Paraaortic LNs of same genotype were pooled and strained as aforementioned. Cells were resuspended in Hank’s Medium, stained, and isolated by fluorescence-activated cell sorting, by gating for Live CD45+CD19-MHCII+ cells. The cell suspension with viability > 80% was ready for subsequent single cell capture and library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, FACS-sorted cells  were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lymph nodes

value: FACS-sorted CD45+CD19-MHCII+ cells

tag: diet

value: 6-week western diet

tag: strain


title: Replicate 3; Control Day 5 differentiated hiPSCs

value: Day 5 differentiated human induced pluripotent stem cells


title: mock, 0mM, shoot, sample 1

tag: tissue

value: wild type

tag: inoculation treatment

value: mock


title: Replicate 1; BRD4884 treated Day 5 differentiated hiPSCs

tag: cell line

value: WT

value: BRD4884 1uM, cardiac differentiation

value: Day 5


title: Replicate 2; BRD4884 treated Day 5 differentiated hiPSCs

value: WTC CRISPRi GCaMP hiPSC (RRID CVCL_VM38)

tag: treatment


title: Ri, 0mM, root, sample 1

value: root

value: Rhizophagus irregularis


title: Replicate 2; Control Day 5 differentiated hiPSCs

value: cardiac differentiation


title: T8.D32.Kid3 [scRNA-seq]

data_processing:
Cellranger count v4.0.0 was used to align reads to the mm10 genome.
The resulting counts matrices was processed using Seuratv3.1.1. Cells with < 500 or > 2500 detected genes or a mitochondrial read % greater than 10 were discarded. All samples were combined using the merge function, and data was then normalized (normalization.method = "LogNormalize", scale.factor = 10000). The top 2000 features were identified (selection.method = "vst") and the data was scaled. Dimensional reductions were calculated for PCA (npcs = 30) and UMAP (reduction = “pca”, dims = 1:20). Nearest neighbors were calculated (reduction = “pca”, dims = 1:20) and clusters were identified (resolution = 0.35)
Genome_build: mm10
Supplementary_files_format_and_content: seurat_object.rds contains the resulting Seurat object, including the counts matrix, dimensional reductions, and clustering, as described above.

source_name: CD8+ T cells

extract_protocol:
To identify CD8+ T cells in the vasculature of non-lymphoid tissues (small intestine, kidney, salivary gland, fat, and liver), 3 µg of CD8α (53-6.7) conjugated to APC eFluor780 was injected by i.v. into mice three minutes prior to sacrifice, as has been previously described. Cells labeled with low to no CD8α antibody were considered to be outside of the vasculature. Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. Blood samples were treated with ACK lysis buffer. Small intestine intraepithelial lymphocytes were prepared through the removal of Peyer’s patches and the luminal contents. The small intestine was then cut longitudinally and into 1 cm pieces, then incubated at 37°C for 30 min in HBSS with 2.1 mg/mL sodium bicarbonate, 2.4 mg/mL HEPES, 8% bovine growth serum, and 0.154 mg/mL of dithioetheritol (EMD Millipore). The kidneys, salivary glands, fat, and liver were minced into small pieces and then incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. Lymphocytes from the small intestine, kidney, salivary gland, and liver were separated on a 44%/67% Percoll density gradient. For each replicate, cells from 10-15 mice were pooled and then sorted for bulk RNA-seq. 32 days after initial infection with LCMV, 1e4 P14 cells were sorted from the spleen and blood and 1e4 IV- P14 cells were sorted from the IEL, kidney, salivary gland, fat, and liver into T cell media. Cells were then spun down and media removed prior to starting library preparation.
Libraries were prepared using the Chromium Single Cell 3' kit with v3 chemistry according to manufacturer's instructions.

value: Kidney

tag: iv label

value: IV-

tag: days post infection with lcmv-arm


title: 20190408_MLPS007_RNA_primary_904851-7_S3_R1_001

value: MLPS Primary Tumor

value: genotype:FUS-DDIT3 fusion primary tumor

tag: chip antibody


title: 20200813_HJZ058_RNA_1765_shSCR_D14_rep2_S15_R1_001

value: genotype:FUS-DDIT3 fusion shSCR


title: mock, 0mM, shoot, sample 2

value: shoot

tag: salt treatment

value: 0mM NaCl

value: 8 weeks post inoculation


title: Replicate 1; MS275 treated Day 5 differentiated hiPSCs

value: Day 5 differentiated human induced pluripotent stem cells

value: MS275 1uM, cardiac differentiation

tag: time


title: U2OS_HTTR_HTPP_COMBO_Pilot_Source_Plate_A10_7_0.100000uM_TC00000651_A03

value: U-2 OS

value: 0.1 uM Actinomycin D

tag: chemical name

value: Actinomycin D

tag: chemical id

tag: assay plate well


title: T8.D32.IEL3 [scRNA-seq]

value: IEL


title: 20200813_HJZ056_RNA_1765_shSCR_D14_rep1_S13_R1_001

tag: experimental condition


title: Ri, 0mM, root, sample 3

value: root

value: wild type


title: U251 cells, rep3

city: Wuhan

first: Yiqi

last: Wang

state: State...

address: Shizishan Street

country: China

institute: Huazhong Agricultural University, China

data_processing:
quality control with data trimming, fastp version 0.21.0, default parameters
use hisat2 to align reads to hg38 genome, HISAT2 version 2.1.0, default parameters
use samtools to transfer sam to sorted bam, Version: 1.3.1, default parameters
htcount to bam counts statistiction, Public License v3, htseq-count with default parameters
R library DESeq2 to obtain differential expression genes, R 4.1.2, pvalue<0.05, |log2FC|>1
Assembly: hg38

growth_protocol: U251 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃,DBTRG cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell type

value: glioblastoma cells

value: WT

value: no treatment


title: mock, 0mM, root, sample 3

tag: genotype

value: mock


title: T8.D32.Liv3 [scRNA-seq]

value: Liver

value: IV-


title: 20200813_HJZ059_RNA_1765_shDDIT3_D14_rep2_S16_R1_001

value: genotype:FUS-DDIT3 fusion shDDIT3


title: T8.D32.Bl3 [scRNA-seq]

value: Blood


title: T8.D32.SG3 [scRNA-seq]

value: Salivary Gland


title: sorted cells from AoLNs, WD, Hom samples, scRNAseq

description: 10x Gemonics

value: lymph nodes

value: FACS-sorted CD45+CD19-MHCII+ cells

tag: diet

value: 6-week western diet


title: mock, 0mM, root, sample 1

value: 0mM NaCl

value: 8 weeks post inoculation


title: 20200813_HJZ057_RNA_1765_shDDIT3_D14_rep1_S14_R1_001


title: U251 cells, rep2


title: T8.D32.Spl3 [scRNA-seq]

value: Spleen


title: mock, 0mM, root, sample 2

value: root


title: T8.D32.Fat3 [scRNA-seq]

value: Gonadal adipose tissue


title: EPS-shYy1-ATACseq-rep2

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized by RPKM
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bw

source_name: EPS cells

growth_protocol: Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates.

extract_protocol: For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For 10 × Genomics single cell RNaseq, the cells cultured in F4H medium for 6 days were dissociated with 0.25% TrypLE Express Enzyme at 37°C for 10 min. Single cell populations were resuspended in PBS with 0.04% BSA. Single cell libraries were created using Chromium Single Cell 30 Reagent Kits and sequenced on a Novaseq 6000 sequencer. Approximately 10000 cells were captured for each time point.CUT&Tag experiments were performed as previously described65. In brief, 100,000 cells were harvested washed twice with 200 µL Wash Buffer. 10 µL Concanavalin A beads (Bangs Laboratories) were added per sample and incubated at room time for 15 min. Add 100 µL Dig-wash Buffer containing 2 mM EDTA and 1µg primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Add 200 µL Dig-Wash buffer to remove unbound antibodies. Then incubated with pAG-Tn5 (home-made) at 4 °C for 2 h. Add 200 µL Dig-med Buffer to remove unbound pAG-Tn5 protein. Next, cells were resuspended in 100 µL tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL Proteinase K was added to 50 µL of sample, which was incubated at 55 °C for 30 min, and then at 70 °C for 30 min to inactivate Proteinase K. Then extract the DNA. Antibodies included: H3K27ac (Active Motif, 39133).

tag: strain

tag: tag

value: DNA


title: 20200813_HJZ052_RNA_402_shSCR_D7_S9_R1_001

value: genotype:FUS-DDIT3 fusion shSCR


title: 20210322_HJZ102_RNA_AD_MSC_CMP12_adipo_techrep2_S16_R1_001

source_name: stem cell line

value: MSCs-AD


title: EPS-shYy1-ATACseq-rep1


title: Replicate 3; BRD4884 treated; Day 5 differentiated hiPSCs

value: WTC CRISPRi GCaMP hiPSC (RRID CVCL_VM38)

value: Day 5 differentiated human induced pluripotent stem cells

value: WT

value: BRD4884 1uM, cardiac differentiation

value: Day 5


title: DBTRG cells, rep2

source_name: DBTRG

value: DBTRG

value: glioblastoma cells

value: no treatment


title: EPS-shCtrl-ATACseq-rep2


title: DBTRG cells, rep3


title: 20210322_HJZ101_RNA_AD_MSC_CMP12_adipo_techrep1_S15_R1_001


title: U251 cells, rep1


title: 20210322_HJZ099_RNA_AD_MSC_CMP12_base_techrep1_S13_R1_001


title: T8.D32.Spl2 [scRNA-seq]

tag: tissue


title: T8.D32.IEL2 [scRNA-seq]

value: IEL

value: IV-


title: 20210322_HJZ098_RNA_AD_MSC_DMSO_adipo_techrep2_S12_R1_001

tag: cell line

value: DMSO


title: EPS-shCtrl-ATACseq-rep1


title: DBTRG cells, rep1

tag: treatment


title: 20210322_HJZ100_RNA_AD_MSC_CMP12_base_techrep2_S14_R1_001


title: T8.D32.Bl2 [scRNA-seq]

value: Blood

tag: iv label


title: ES-ChIP-seq-YY1

source_name: ES cells


title: T8.D32.Kid2 [scRNA-seq]

value: Kidney

tag: days post infection with lcmv-arm


title: EPS-ChIP-seq-input


title: T8.D32.Kid1 [scRNA-seq]


title: 20210322_HJZ096_RNA_AD_MSC_DMSO_base_techrep2_S10_R1_001

tag: chip antibody


title: EPS-ChIP-seq-YY1


title: 20210322_HJZ097_RNA_AD_MSC_DMSO_adipo_techrep1_S11_R1_001


title: 20210322_HJZ095_RNA_AD_MSC_DMSO_base_techrep1_S9_R1_001


title: EPS-shYy1-H3K27ac_cut_tag

data_processing:
Library strategy: CUT&TAG
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized by RPKM
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bigwig; counts

extract_protocol:
For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For 10 × Genomics single cell RNaseq, the cells cultured in F4H medium for 6 days were dissociated with 0.25% TrypLE Express Enzyme at 37°C for 10 min. Single cell populations were resuspended in PBS with 0.04% BSA. Single cell libraries were created using Chromium Single Cell 30 Reagent Kits and sequenced on a Novaseq 6000 sequencer. Approximately 10000 cells were captured for each time point.CUT&Tag experiments were performed as previously described65. In brief, 100,000 cells were harvested washed twice with 200 µL Wash Buffer. 10 µL Concanavalin A beads (Bangs Laboratories) were added per sample and incubated at room time for 15 min. Add 100 µL Dig-wash Buffer containing 2 mM EDTA and 1µg primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Add 200 µL Dig-Wash buffer to remove unbound antibodies. Then incubated with pAG-Tn5 (home-made) at 4 °C for 2 h. Add 200 µL Dig-med Buffer to remove unbound pAG-Tn5 protein. Next, cells were resuspended in 100 µL tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL Proteinase K was added to 50 µL of sample, which was incubated at 55 °C for 30 min, and then at 70 °C for 30 min to inactivate Proteinase K. Then extract the DNA. Antibodies included: H3K27ac (Active Motif, 39133).
RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme).

value: EPS cells

tag: genotype/variation

value: H3K27ac (Active Motif, 39133)


title: T8.D32.Bl1 [scRNA-seq]


title: T8.D32.IEL1 [scRNA-seq]


title: 20210322_HJZ094_RNA_hTERT_MSC_CMP12_adipo_techrep1_S8_R1_001

value: MSCs-hTERT


title: EPS-shYy1-F4H-D6-scRNA-seq

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized by RPKM
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bigwig; counts


title: T8.D32.Fat2 [scRNA-seq]

value: Gonadal adipose tissue


title: SP656

city: Beijing

first: Yiming

last: Zhang

address: No.9 Dongdan Santiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Clean read data with adapters removed and low-quality reads filtered out were aligned to the hg19 reference sequence by Tophat2.
Gene annotation and quantification were performed by featureCounts (version 2.0.1)
Batch effect was romved by Combat-seq function in sva packages on R platform.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files were generated by featureCounts.

source_name: White blood cell

extract_protocol:
Whole blood was centrifuged at 2,000 rpm for 5 ~ 10 min at 25℃.  The lower blood cells were mixed with 10ml Red Blood Cell Lysis Buffer (R1010, Solarbio) for 5min on ice, and the mixture was centrifuged at 2,000~3,000 rpm for 5min at 4℃. Then adding 5ml Red Blood Cell Lysis Buffer to the precipitate and centrifuging it at 2,000 ~ 3,000rpm for 5min at 4℃, and discarding the supernatant. Finally, 1.5ml RNA later (76544, Qiagen) was added to the total RNA precipitate for RNA library preparation.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

tag: disease state

value: Severe Community Acquired Pneumonia (SCAP)

tag: batch

value: White blood cell


title: SP666


title: EPS-shCtrl-H3K27ac-cut_tag

value: Ctrl shRNA


title: T8.D32.Spl1 [scRNA-seq]

value: Spleen


title: SP616


title: 20210322_HJZ093_RNA_hTERT_MSC_CMP12_adipo_techrep1_S7_R1_001


title: T8.D32.Liv2 [scRNA-seq]

value: Liver


title: SP607


title: SP625


title: SP693


title: SP621


title: EPS-shCtrl-F4H-D6-scRNA-seq

value: control


title: 20210322_HJZ092_RNA_hTERT_MSC_CMP12_base_techrep2_S6_R1_001


title: 20210322_HJZ091_RNA_hTERT_MSC_CMP12_base_techrep1_S5_R1_001


title: T8.D32.Liv1 [scRNA-seq]


title: SP661


title: ES-oeYy1-F4H-D6-scRNA-seq

value: ES cells


title: SP591


title: SP585


title: T8.D32.Fat1 [scRNA-seq]


title: T8.D32.SG1 [scRNA-seq]

value: Salivary Gland


title: ES-oeYy1-F4H-D6-RNA-seq-rep2


title: 20210322_HJZ089_RNA_hTERT_MSC_DMSO_adipo_techrep1_S3_R1_001


title: ES-oeCtrl-F4H-D6-scRNA-seq


title: ES-oeYy1-F4H-D6-RNA-seq-rep1


title: 20210322_HJZ090_RNA_hTERT_MSC_DMSO_adipo_techrep2_S4_R1_001


title: 20210322_HJZ088_RNA_hTERT_MSC_DMSO_base_techrep2_S2_R1_001