title: RAW 264 cells_No pre-treatment_LPS induction 6h_rep1

description: Gene expression data from RAW264 cells, maintained in culture medium for 24 h and then LPS-induced for 6h

source_name: RAW264 cells were maintained in culture medium for 24h and then induced with LPS solution (1 ng/mL) for 6 h


title: 11A_M_1464

status: Public on Apr 19 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain

tag: Sex

value: male


title: BaF3_gp130_IL6R_LIFR_IC7_d

city: Düsseldorf

first: Puyan

last: Rafii

state: NRW

address: Universitätsstraß 1

department: Biochemistry & Molecularbiology

country: Germany

institute: Heinrich-Heine-University

library_source: transcriptomic

data_processing:
Illumina DRAGEN FASTQ Generation tool (version 3.8.4) was used for basecalling.
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 22.0.2, QIAGEN, Venlo. NL).
After UMI (Unique Molecular Identifier) filtering, all remaining reads of all probes were adapter trimmed and quality trimmed (Illumina Adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Mapping was done against the Mus musculus (mm39; GRCm39.107) (July 20, 2022) genome sequence.
After grouping of samples (for biological replicates each) according to their respective experimental condition, the statistical differential expression was determined using the Differential Expression for RNA-Seq tool (version 2.7). The Resulting 𝑃 values were corrected for multiple testing by FDR and Bonferroni-correction. A 𝑃 value of ≤0.05 was considered significant.
Assembly: mm 39 (107)
Supplementary files format and content: xlsx file matrix with raw counts; gene IDs as lines and samples as columns

molecule: total RNA

growth_protocol: All cells were grown at 37°C with 5% CO2 in a water-saturated atmosphere in Dulbecco`s modified Eagle`s medium (DMEM) high-glucose culture medium (GIBCO®, Life Technologies, Darmstadt, Germany) with 10% fetal calf serum (GIBCO®, Life Technologies) and 60 mg/l penicillin and 100 mg/l streptomycin (Genaxxon Bioscience GmbH, Ulm, Germany). Murine Ba/F3-gp130 cells were obtained from Immunex (Seattle, WA, USA) and grown in the presence of HIL-6. 0.2% (10ng/ml) conditioned medium from a stable clone of CHO-K1 cells secreting HIL-6 in the supernatant

extract_protocol:
mRNA was isolated with NucleoSpin RNA (Macherey-Nagel, Düren, Germany; cat. no. 740955.250) according to vendor’s manual. DNase digested total RNA samples used for 3´-RNA Seq analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA standard Sensitivity Assay’ (Agilent Technologies, Inc. Santa Clara, USA). All samples in this study showed very high quality RNA Quality Numbers (RQN; mean = 10.0).
The library preparation was performed according to the manufacturer’s protocol using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Lexogen®. Input mount was 200 ng totalRNA. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, USA) with a read setup of SR 1x100 bp.

treatment_protocol: Ba/F3 cells expressing the appropriate receptors were stimulated with synthetic and control cytokines for 40 min at 37°C.

tag: cell type

tag: condition


title: BaF3_gp130_IL11R_LIFR_GIL11_d


title: RAW 264 cells_No pre-treatment_LPS induction 6h_rep2

type: RNA

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, mouse; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).

label: biotin

organism: Mus

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: RAW264 cells derived from a murine macrophage cell line (Resource No. RCB0535) were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). RAW264 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Bio West, Nuaillé, France) and 1penicillin-streptomycin solution (Merck KGaA) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Lyophilized powder of Botryococcus terribilis TEPMO-26 (100 mg) was extracted with 70% Ethanol (1 mL) at room temperature under the dark for 2 weeks. After the extraction was completed, it was centrifuged at 1000 xg for 10 minutes and collected the supernatant. The supernatant of the extracted sample was filtered by using a 0.22 µm filter unit and stored at -20 ºC in the dark until use. Lipopolysaccharide (LPS; E. coli O111:B4) was purchased from EMD Millipore Co. (Billerica, MA USA). 5 mg of LPS was dissolved in 2 ml of PBS (-), and stored at -80 ℃ under the dark until use. RAW264 cells were seeded into a 96-well plate at density of 2.0×105 cells/mL and incubated at 37 °C for 24 h. The cells were treated with or without BTEE at 37 °C for 24 h. After the BTEE treatment, the LPS solution (1 ng/ml) was added to each well and incubated for 6h and 17 h at 37 °C.

tag: cell line

value: RAW264 cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: BaF3_gp130_IL6R_LIFR_NC_d

description: untreated control


title: BaF3_gp130_IL6R_LIFR_LIF_d


title: 11A_M_1463


title: 11A_M_1462


title: 11A_M_1461


title: BaF3_gp130_IL11R_LIFR_LIF_c


title: BaF3_gp130_IL11R_LIFR_IL11_c


title: BaF3_gp130_IL11R_LIFR_GIL11_c


title: 11A_M_1460


title: BaF3_gp130_IL11R_LIFR_NC_c

description: untreated control


title: 11A_M_146


title: 11A_M_1456


title: 11A_M_1458


title: 11A_M_1455


title: BaF3_gp130_IL6R_LIFR_LIF_c


title: BaF3_gp130_IL6R_LIFR_GIL6_c


title: BaF3_gp130_IL6R_LIFR_IL6_c


title: 11A_M_1457


title: BaF3_gp130_IL6R_LIFR_IC7_c


title: BaF3_gp130_IL6R_LIFR_NC_c

description: untreated control


title: 11A_M_1452


title: 11A_M_1453


title: BaF3_gp130_IL11R_LIFR_LIF_b


title: 11A_M_1454


title: BaF3_gp130_IL11R_LIFR_IL11_b


title: 11A_M_1451


title: 11A_M_145


title: BaF3_gp130_IL11R_LIFR_GIL11_b


title: BaF3_gp130_IL6R_LIFR_LIF_b


title: 11A_M_1449


title: BaF3_gp130_IL11R_LIFR_NC_b

description: untreated control


title: 11A_M_1448


title: BaF3_gp130_IL6R_LIFR_IL6_b


title: BaF3_gp130_IL6R_LIFR_GIO6_c


title: 11A_M_1446


title: BaF3_gp130_IL6R_LIFR_GIO6_b


title: BaF3_gp130_IL6R_LIFR_GIL6_b


title: 11A_M_1447


title: 11A_M_1445


title: BaF3_gp130_IL6R_LIFR_NC_b

description: untreated control


title: 11A_M_1459


title: BaF3_gp130_IL11R_LIFR_LIF_a


title: 11A_M_1442


title: 11A_M_1444


title: BaF3_gp130_IL11R_LIFR_GIL11_a


title: BaF3_gp130_IL11R_LIFR_IL11_a


title: 11A_M_1441


title: 11A_M_1443


title: BaF3_gp130_IL11R_LIFR_NC_a

description: untreated control


title: 11A_M_144


title: 11A_M_1440


title: 11A_M_1439


title: 11A_M_1438


title: BaF3_gp130_IL6R_LIFR_IL6_a


title: BaF3_gp130_IL6R_LIFR_LIF_a


title: 11A_M_1436


title: BaF3_gp130_IL6R_LIFR_GIO6_a


title: BaF3_gp130_IL6R_LIFR_GIL6_a


title: 11A_M_1437


title: 11A_M_1435


title: BaF3_gp130_IL6R_LIFR_IC7_b


title: BaF3_gp130_IL6R_LIFR_NC_a

description: untreated control


title: 11A_M_1432


title: 11A_M_1433


title: 11A_M_1434


title: 11A_M_1430


title: 11A_M_1431


title: 11A_M_143


title: 11A_M_1429


title: Hu3112_v_1_MyC

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
RNA-seq:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.9a) was used to index the Schizosaccharomyces_pombe (ASM294v2) genome and ERCC spike ins and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Schizosaccharomyces_pombe.ASM294v2.35.gff3).
ChIP-Seq:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.9a) was used to index the Schizosaccharomyces_pombe (ASM294v2) genome and Drosophila melanogaster reference genome (BDGP6) and then map the fastq files.
bedtools (v2.30.0) was used to generate bedgraph files scaled according to the Drosophila spike in counts and bedGraphToBigWig (v4) to convert them to big wig format
Assembly: RNA-seq: Schizosaccharomyces_pombe (ASM294v2)
Assembly: ChIP-seq: Schizosaccharomyces_pombe (ASM294v2) and Drosophila melanogaster reference genome (BDGP6)
Supplementary files format and content: RNA-seq: Tab delimited text files that contain gene or ERCC raw counts, one column for each sample.
Supplementary files format and content: ChIP-seq: bigwig

organism: Schizosaccharomyces pombe

growth_protocol: ChIP-seq: Hu3110 smt0 iec1D::ura4 pht1-myc and the Hu3112 smt0 pht1-myc strains are the cells were used in ChIP-seq assay, they were grown in PMG media.

extract_protocol:
Wild type and mutant strains were grown in a 200 ml liquid PMG+N medium using a shaking incubator (200 rpm at 30o C) to reach between 1.0x10^6 and 10x10^6 cells/ml. For each culture 100 ml was removed for the T0 timepoint, and the rest of the culture was washed with pre-warmed PMG-N and incubated for 24 hours in 500 ml of pre-warmed PMG-N using a shaking incubator (200 rpm at 30o C). For RNA extraction, cells were washed with ice-cold PBS and resuspended in 500 ¼l of ice-cold RNA extraction buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2% Triton X-100, 1% SDS, 100 mM NaCl). Then we added 500 µl of Phenol (acidic phenol pH 4.5, Sigma) and 500 µl of glass beads (acid washed, Sigma). The tubes were vortexed vigorously and incubated at 65¡C for 45-60 min. Next, the tube was placed on ice for 5 min. and centrifuged (1300 g, 5 min, 4¡C). The upper aqueous part was collected and transferred to a tube with 500 µl of chloroform (Sigma Aldrich), vortexed and centrifuged (1300 g, 5 min, 4 ¡C). The upper phase was collected and subjected to RNA precipitation at -20o C overnight. The precipitated RNA was washed once with 70% ethanol and dissolved in 30 ¼l H2O.
RNA-seq: To remove rRNA, 3 µg of purified total RNA was treated with Ribominus Eukaryote System v.2 kit (Ambion, Thermo Fisher Scientific). To generate sequencing libraries, a total of 100 ng of rRNA-depleted stocks and Illumina Stranded mRNA Prep Ligation kit (Illumina) were used. To quantify the samples, Qubit (HS dsDNA) was used, and samples were sequenced using an Illumina Nextseq 2000 platform (P3 100 cycle kit, 58 + 58 cycles, paired-end sequencing) at the BEA facility (Huddinge, Swe den) following the manufacturer's instruction.
ChIP-seq: Log phase cells grown in PMG or PMG-N media were harvested and cross-linked by 1% formaldehyde for 30 min, and then 125 mM Glycine was added to quench the crosslinking for 5 min. After three times washing with cold PBS, the cells pellet was resuspended in ChIP lysis buffer with 0.5mm Zirconia/Silica Beads, and then lysed in FastPrep machine for 7 times at max power 6.5. Sonication was done by using Bioruptor® Pico for 10 cycles, and then chromatin concentration was measured with Qubit dsDNA HS assay kit.  Immunoprecipitation was performed with 20 µg sheared chromatin, 40 ng spike-in chromatin (activemotif 53083), 1.6 µl Spike-in antibody (activemotif 61686) and 6 µl anti-c-Myc antibody (Sigma-Aldrich, M4439). After three times washing with low salt wash buffer, high salt wash buffer and LiCl wash buffer successively, ChIP-DNA was extracted by ChIP DNA Clean & Concentrator kit (ZYMO RESEARCH, D5205) and DNA concentration measured by Qubit dsDNA HS assay kit.

treatment_protocol: ChIP-seq: T0 means vegetaive cell, we harvest them when cells entry to log-phase in PMG media; T1D meas quiescent cells which are cells entred to log-phase and were switched to PMG-N media and continue grown for 1 day.

tag: spike-in

value: Drosophila Melanogaster

tag: antibody

value: Anti-c-Myc (Sigma-Aldrich, M4439)

tag: spike-in antibody

value: Activemotif 61698


title: Hu3112_v_1_Input


title: Hu3112_v_2_MyC

value: Activemotif 61699


title: 11A_M_1428


title: Hu3112_G0_2_MyC

value: Activemotif 61695


title: Hu3112_G0_1_MyC

value: Activemotif 61694


title: Hu3112_G0_1_Input


title: Hu3112_G0_3_MyC

value: Activemotif 61696


title: Hu3112_v_3_MyC

value: Activemotif 61700


title: 11A_M_1426


title: 11A_M_1427


title: Hu3110_v_3_MyC

value: Activemotif 61692


title: Hu3110_v_2_MyC

value: Activemotif 61691


title: 11A_M_1425


title: Hu3110_v_1_MyC

value: Activemotif 61690


title: BaF3_gp130_IL6R_LIFR_IC7_a


title: 11A_M_1424


title: Hu3110_G0_3_MyC

value: Activemotif 61688


title: Hu3110_v_1_Input


title: Hu3110_G0_2_MyC

value: Activemotif 61687


title: Hu3110_G0_1_MyC

value: Activemotif 61686


title: 11A_M_1422


title: 11A_M_1421


title: 11A_M_1423


title: 11A_M_1420


title: 11A_M_142


title: 11A_M_1415


title: Hu3110_G0_1_Input


title: IES2_T1W_C

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T1W_B

description:
gene_counts.txt
ercc_counts.txt


title: 11A_M_1414


title: 11A_M_1418


title: 11A_M_1417


title: IES2_T1D_C

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T0_B

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T1D_A

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T1W_A

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T1D_B

description:
gene_counts.txt
ercc_counts.txt


title: IES2_T0_C

description:
gene_counts.txt
ercc_counts.txt


title: 11A_M_1413


title: 11A_M_1410


title: 11A_M_1411


title: IES2_T0_A

description:
gene_counts.txt
ercc_counts.txt


title: 11A_M_1409


title: 11A_M_1408


title: ARP42_T2W_C

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.9a) was used to index the Schizosaccharomyces_pombe (ASM294v2) genome and ERCC spike ins and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Schizosaccharomyces_pombe.ASM294v2.35.gff3).
Assembly: Schizosaccharomyces_pombe (ASM294v2)
Supplementary files format and content: Tab delimited text files that contain gene or ERCC raw counts, one column for each sample.

source_name: ARP42 mutant

extract_protocol:
Wild type and mutant strains were grown in a 200 ml liquid PMG+N medium using a shaking incubator (200 rpm at 30o C) to reach between 1.0x106 and 10x106 cells/ml. For each culture 100 ml was removed for the T0 timepoint, and the rest of the culture was washed with pre-warmed PMG-N and incubated for 24 hours in 500 ml of pre-warmed PMG-N using a shaking incubator (200 rpm at 30o C). For RNA extraction, cells were washed with ice-cold PBS and resuspended in 500 ¼l of ice-cold RNA extraction buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2% Triton X-100, 1% SDS, 100 mM NaCl). Then we added 500 µl of Phenol (acidic phenol pH 4.5, Sigma) and 500 µl of glass beads (acid washed, Sigma). The tubes were vortexed vigorously and incubated at 65¡C for 45-60 min. Next, the tube was placed on ice for 5 min. and centrifuged (1300 g, 5 min, 4¡C). The upper aqueous part was collected and transferred to a tube with 500 µl of chloroform (Sigma Aldrich), vortexed and centrifuged (1300 g, 5 min, 4 ¡C). The upper phase was collected and subjected to RNA precipitation at -20o C overnight. The precipitated RNA was washed once with 70% ethanol and dissolved in 30 ¼l H2O.
To remove rRNA, 3 µg of purified total RNA was treated with Ribominus Eukaryote System v.2 kit (Ambion, Thermo Fisher Scientific). To generate sequencing libraries, a total of 100 ng of rRNA-depleted stocks and Illumina Stranded mRNA Prep Ligation kit (Illumina) were used. To quantify the samples, Qubit (HS dsDNA) was used, and samples were sequenced using an Illumina Nextseq 2000 platform (P3 100 cycle kit, 58 + 58 cycles, paired-end sequencing) at the BEA facility (Huddinge, Swe den) following the manufacturer's instruction.

value: ARP42 mutant


title: ARP42_T2W_B


title: 11A_M_1407

value: male


title: ASP1_T2W_C

source_name: ASP1 mutant

value: ASP1 mutant


title: ARP42_T2W_A


title: ASP1_T2W_B


title: 11A_M_1412


title: 11A_M_1405


title: 11A_M_1406


title: ASP1_T2W_A


title: 11A_M_1403


title: 11A_M_1404


title: 11A_M_1401


title: 11A_M_1400


title: PHT1_T2W_C

source_name: PHT1 mutant

value: PHT1 mutant


title: PHT1_T2W_A


title: IEC1_T2W_A

source_name: IEC1 mutant

value: IEC1 mutant


title: 11A_M_140


title: IEC1_T2W_C


title: 11A_M_14


title: 11A_M_141


title: PHT1_T2W_B


title: HHT2_T2W_B

source_name: HHT2 mutant

value: HHT2 mutant


title: 11A_M_1398


title: HHT2_T2W_A


title: 11A_M_1397


title: SMT0_T2W_C

source_name: SMT0 wild type

value: SMT0 wild type


title: 11A_M_1396


title: SMT0_T2W_B


title: 11A_M_1395


title: SMT0_T2W_A


title: IEC1_T2W_B


title: ARP42_T1W_C


title: 11A_M_1393


title: 11A_M_1402


title: 11A_M_1394


title: ARP42_T1W_B


title: 11A_M_1391


title: 11A_M_1390


title: HHT2_T2W_C


title: ARP42_T1W_A


title: 11A_M_1399


title: 11A_M_1389


title: IEC1_T1W_C


title: IEC1_T1W_B


title: ASP1_T1W_C


title: 11A_M_139


title: IEC1_T1W_A


title: 11A_M_1387


title: 11A_M_1386


title: PHT1_T1W_C


title: 11A_M_1385


title: PHT1_T1W_B


title: HHT2_T1W_C


title: 11A_M_1383


title: 11A_M_1384


title: PHT1_T1W_A


title: ASP1_T1W_B


title: HHT2_T1W_B


title: 11A_M_1382


title: 11A_M_1380


title: HHT2_T1W_A


title: 11A_M_1392


title: 11A_M_1388


title: SMT0_T1W_B


title: ASP1_T1W_A


title: SMT0_T1W_A


title: 11A_M_1381


title: 11A_M_1379


title: SMT0_T1W_C


title: ARP42_T1D_C


title: ARP42_T1D_B


title: 11A_M_1377


title: 11A_M_1378


title: 11A_M_1375


title: 11A_M_1376


title: ASP1_T1D_C


title: ASP1_T1D_B


title: 11A_M_1374


title: 11A_M_1373


title: ASP1_T1D_A


title: 11A_M_1371


title: 11A_M_1372


title: IEC1_T1D_C


title: IEC1_T1D_B


title: 11A_M_138


title: 11A_M_1370


title: IEC1_T1D_A


title: ARP42_T1D_A


title: 11A_M_1367


title: 11A_M_1369


title: 11A_M_1368


title: PHT1_T1D_B


title: PHT1_T1D_A


title: HHT2_T1D_C


title: 11A_M_137


title: SMT0_T1D_C


title: HHT2_T1D_A


title: HHT2_T1D_B


title: 11A_M_1364


title: 11A_M_1366


title: 11A_M_1363


title: 11A_M_1361


title: 11A_M_1360


title: SMT0_T1D_A


title: ARP42_T0_B


title: ARP42_T0_C


title: 11A_M_136


title: PHT1_T1D_C


title: ASP1_T0_B


title: ASP1_T0_C


title: 11A_M_1365


title: 11A_M_1357


title: 11A_M_1358


title: ASP1_T0_A


title: 11A_M_1355


title: IEC1_T0_C


title: 11A_M_1356


title: IEC1_T0_B


title: SMT0_T1D_B


title: 11A_M_1354


title: 11A_M_1353


title: 11A_M_1362


title: 11A_M_1350


title: IEC1_T0_A


title: PHT1_T0_C


title: 11A_M_1352


title: 11A_M_135


title: HHT2_T0_C


title: PHT1_T0_A


title: 11A_M_1351


title: PHT1_T0_B


title: 11A_M_1349


title: 11A_M_1359


title: ARP42_T0_A


title: SMT0_T0_C


title: 11A_M_1348


title: 11A_M_1347


title: 11A_M_1346


title: SMT0_T0_A


title: 11A_M_1345


title: S8 hiPSC-neurons + 2µg/mL poly dA:dT

city: Antwerp

first: Pieter

last: Meysman

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: University of Antwerp

data_processing:
Sequencing reads from fastq files were checked for quality using FastQC, trimmed for polyA-tails and further read processing using Trimmomatic v0.36. The reads were then aligned against the human reference genome (GRCh38 from Ensembl) using HISAT2 v2.0.4, and the read count table was assembled using HTSeq. Subsequent expression analysis was performed using the DESeq2 v1.32.0 R package. Principal component analysis (PCA) and heatmap plots were assembled using the ggplot2 and pheatmap R packages. For the PCA of the hiPSC-macrophages, data of primary and iPSC-derived myeloid subtypes available from a public dataset were used [34]. For the heatmap analysis, the gene expression of the different conditions of hiPSC-macrophages and hiPSC-neurons relative to their unstimulated counterparts, was determined for the genes implicated in different host response pathways, retrieved from the Host Response Panel of Nanostring (https://nanostring.com/products/ncounter-assays-panels/immunology/host-response/). Further pathway and gene set enrichment analysis was performed using the topGO and clusterProfiler R packages.
Assembly: GRCh38 from Ensembl

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC - ATCCCRL2522 C10

extract_protocol:
RNA extraction of samples stored in DNA/RNA shield were performed as described previously [9]. In brief, samples were thawed at RT and resuspended in an equal volume of lysis buffer (Zymo Research) before starting the Quick-DNA/RNA miniprep (Zymo Research) protocol following the manufacturer’s instructions. After a TURBOTMDNase (Thermo Fisher Scientific) treatment step, purity of RNA samples was checked using a NanoDropTM2000 spectrophotometer (Thermo Scientific)
RNA quality was verified using the TapestationTM (Agilent, RNA screentape analysis). RNA sequencing was performed as described in Bartholomeus et al. [33]. In brief, RNA samples were prepared with the QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH) following the standard protocol for long fragments. Obtained cDNA libraries were equimolarly pooled, up to 40 samples for one NextSeq 500 sequencing run (high output v2 kit, 150 cycles, single read, Illumina).

value: hiPSC - ATCCCRL2522 C10

value: hiPSC-neurons

tag: treatment

value: 2µg/mL poly dA:dT


title: S9 hiPSC-neurons + 2µg/mL poly dA:dT


title: S7 hiPSC-neurons + 2µg/mL poly dA:dT


title: 11A_M_1342


title: 11A_M_1344


title: 11A_M_1341


title: 11A_M_1343


title: S6 hiPSC-neurons unstimulated

value: unstimulated


title: 11A_M_1340


title: S4 hiPSC-neurons unstimulated


title: S5 hiPSC-neurons unstimulated


title: S40 hiPSC-neurons + IFNA2 + ARPE19-VZV_ORF23 cell lysate batch 3


title: HHT2_T0_B


title: 11A_M_134


title: HHT2_T0_A


title: S39 hiPSC-neurons + IFNA2 + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1337


title: 11A_M_1339


title: 11A_M_1335


title: S37 hiPSC-neurons + IFNA2 + ARPE19-VZV_ORF23 cell lysate batch 3


title: SMT0_T0_B


title: S35 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3

value: ARPE19 control cell lysate batch 3


title: 11A_M_1334


title: S38 hiPSC-neurons + IFNA2 + ARPE19-VZV_ORF23 cell lysate batch 3


title: S3 hiPSC-neurons unstimulated


title: 11A_M_1338


title: 11A_M_1336


title: S34 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: S36 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: 11A_M_1330


title: 11A_M_1329


title: 11A_M_133


title: 11A_M_1332


title: 11A_M_1331


title: 11A_M_1328


title: 11A_M_1333


title: 11A_M_1327


title: S33 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3

value: ARPE19-VZV ORF23 cell lysate batch 3


title: 11A_M_1326


title: S28 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: S32 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: S29 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: S31 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1325


title: S27 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: 11A_M_1324


title: S25 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: 11A_M_1323


title: S24 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1322


title: S23 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1320


title: S21 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: S2 hiPSC-neurons unstimulated


title: S30 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: S1 hiPSC-neurons unstimulated


title: S20 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1319


title: S19 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1318


title: 11A_M_1317


title: S18 hiPSC-neurons + lipofectamine control

value: lipofectamine control


title: 11A_M_1316


title: S26 hiPSC-neurons + ARPE19 ctrl cell lysate batch 3


title: S17 hiPSC-neurons + lipofectamine control


title: 11A_M_1315


title: S15 hiPSC-neurons + lipofectamine control


title: S16 hiPSC-neurons + lipofectamine control


title: 11A_M_1313


title: 11A_M_1314


title: 11A_M_1312


title: S13 hiPSC-neurons + lipofectamine control


title: S14 hiPSC-neurons + lipofectamine control


title: S12hiPSC-neurons + 2µg/mL poly dA:dT


title: S22 hiPSC-neurons + ARPE19-VZV_ORF23 cell lysate batch 3


title: 11A_M_1321


title: 11A_M_1311


title: 11A_M_132


title: 11A_M_1310


title: S11 hiPSC-neurons + 2µg/mL poly dA:dT


title: S10 hiPSC-neurons + 2µg/mL poly dA:dT


title: 11A_M_131


title: 11A_M_1309


title: 11A_M_1308


title: S9 hiPSC-macrophages + 0,25µg/mL poly dA:dT

value: hiPSC-macrophages

value: 0,25µg/mL poly dA:dT


title: 11A_M_1307


title: S8 hiPSC-macrophages + 0,25µg/mL poly dA:dT


title: S6 hiPSC-macrophages unstimulated


title: 11A_M_1306


title: S7 hiPSC-macrophages + 0,25µg/mL poly dA:dT


title: 11A_M_1305


title: S5 hiPSC-macrophages unstimulated


title: 11A_M_1304


title: 11A_M_1303


title: 11A_M_1300


title: S39 ARPE19 control cell lysate batch 3 alone


title: S4 hiPSC-macrophages unstimulated


title: S38 ARPE19 control cell lysate batch 3 alone


title: 11A_M_13


title: S40 ARPE19 control cell lysate batch 3 alone


title: 11A_M_130


title: 11A_M_1299


title: S36 ARPE19-VZV ORF23 cell lysate batch 3 alone


title: 11A_M_1298


title: S37 ARPE19-VZV ORF23 cell lysate batch 3 alone


title: 11A_M_1297


title: S34 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: 11A_M_1296


title: S35 ARPE19-VZV ORF23 cell lysate batch 3 alone


title: S32 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: 11A_M_1294


title: S33 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: S31 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: 11A_M_1295


title: 11A_M_1292


title: S2 hiPSC-macrophages unstimulated


title: S30 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: 11A_M_1302


title: 11A_M_1291


title: 11A_M_1293


title: S3 hiPSC-macrophages unstimulated


title: 11A_M_1290


title: S29 hiPSC-macrophages + ARPE19 control cell lysate batch 3


title: S28 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: 11A_M_129


title: 11A_M_1289


title: 11A_M_1288


title: 11A_M_1286


title: S24 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: 11A_M_1287


title: S25 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: S26 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: S27 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: 11A_M_1285


title: S21 CD14+ primary monocytes D4 unstimulated

value: CD14+ primary monocytes


title: S22 CD14+ primary monocytes D4 unstimulated


title: 11A_M_1284


title: S20 CD14+ primary monocytes D4 unstimulated


title: 11A_M_1282


title: 11A_M_1283


title: 11A_M_1281


title: S19 CD14+ primary monocytes D4 unstimulated


title: 11A_M_1280


title: S18 CD14+ primary monocytes D4 unstimulated


title: S17 hiPSC-macrophages + lipofectamine control


title: 11A_M_128


title: 11A_M_1279


title: 11A_M_1278


title: S16 hiPSC-macrophages + lipofectamine control


title: 11A_M_1276


title: S15 hiPSC-macrophages + lipofectamine control


title: 11A_M_1275


title: S14 hiPSC-macrophages + lipofectamine control


title: S23 hiPSC-macrophages + ARPE19-VZV ORF23 cell lysate batch 3


title: 11A_M_1274


title: S13 hiPSC-macrophages + lipofectamine control


title: 11A_M_1272


title: S10 hiPSC-macrophages + 0,25µg/mL poly dA:dT


title: S11 hiPSC-macrophages + 0,25µg/mL poly dA:dT


title: 11A_M_1271


title: 11A_M_1273


title: S12 hiPSC-macrophages + 0,25µg/mL poly dA:dT


title: 11A_M_1270


title: OCI-AML3 500 nM VTP2

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

growth_protocol: Cultured and patient-derived AML cells were cultured in 20% FBS containing RPMI media (MOLM13, OCI-AML3, DF68555) or 20% FBS containing IMDM media (MV4-11).

extract_protocol:
Bulk ATAC-Seq analysis was performed following the protocol of Buenrostro et al 2015. Tn5 transposase-tagmented genomic DNA was utilized to make libraries for next generation sequencing.
Bulk ATAC Sequencing Libraries were constructed following standard Illumina protocols for paired-end sample indexing with I7 and I5 sequencing indices.

treatment_protocol: AML cells were treated with VTP50469 for 16 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.


title: OCI-AML3 Control2

value: Control


title: S1 hiPSC-macrophages unstimulated


title: OCI-AML3 500 nM VTP1


title: OCI-AML3 Control1


title: 11A_M_127

value: male


title: 11A_M_1268


title: 11A_M_1269


title: MV4-11 500 nM VTP2


title: 11A_M_1267


title: MV4-11 500 nM VTP1


title: 11A_M_1266


title: MV4-11 Control1


title: 11A_M_1265


title: 11A_M_1264


title: MV4-11 Control2


title: 11A_M_1263


title: 11A_M_1262


title: MOLM13 500 nM VTP1


title: 11A_M_1261


title: MOLM13 Control1


title: MOLM13, 500 nM SNDX + OTX015, input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak

growth_protocol: Human AML MOLM13 cells were cultured in 20% FBS containing RPMI-1640 media.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing. DNA fragments were PCR amplified for 12 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: 1 x 10^7 Human AML MOLM13 cells were treated for 16 hours with DMSO, 500 nM of SNDX-50469, 500 nM of OTX015 or SNDX-50469 plus 500 nM of OTX015. Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analysis.

value: Acute myeloid leukemia

tag: chip antibody

value: 500 nM of Menin inhibitor SNDX-50469 + 500 nM of OTX015, 16 hours


title: 11A_M_1260


title: MOLM13 Control2


title: MOLM13, 500 nM OTX015, input

value: 500 nM of BET inhibitor OTX015, 16 hours


title: 11A_M_1258


title: 11A_M_1256


title: 11A_M_1255


title: MOLM13, 500 nM SNDX + OTX015, H2K27Ac

value: H3K27Ac Active Motif RRID:AB_2793305


title: 11A_M_1253


title: MOLM13, 500 nM OTX015, H2K27Ac


title: 11A_M_1254


title: OCI-AML3 500 nM VTP 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified , pooled and sequenced.

treatment_protocol: AML cells were treated with VTP50469, OTX015, or the combination for 16 hours at 37°C and harvested into RNA lysis buffer.

tag: genotype

value: OCI-AML3 500 nM VTP


title: OCI-AML3 500 nM VTP 2


title: OCI-AML3 500 nM VTP 3


title: OCI-AML3 Control 3

value: OCI-AML3 Control


title: 11A_M_1252


title: MOLM13 500 nM VTP2


title: 11A_M_1251


title: MV4-11 1000 nM VTP 2

value: MV4-11000 nM VTP


title: OCI-AML3 Control 1


title: MV4-11 1000 nM VTP 1


title: 11A_M_126


title: MOLM13 500 nM VTP + 500 nM OTX 2

value: MOLM13 500 nM VTP + 500 nM OTX


title: 11A_M_1249


title: MV4-11 Control 1

value: MV4-11 Control


title: MOLM13 500 nM VTP + 500 nM OTX 1


title: IBC_10

city: Boston

first: Aditi

last: Hazra

state: MA

address: 900 Commonwealth Ave

institute: Brigham and Women's Hospital

description: Gene expression data from IBC biopsy sample before systemic treatment.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) default analysis (RMA) settings.

source_name: IBC biopsy

label_protocol: Standard Affymetrix protocol

extract_protocol:
Extraction was performed using the Qiagen AllPrep DNA/RNA FFPE Kit (Qiagen - cat# 80234)  according to the manufacturer's instructions.
SensationPlus FFPE Amplification protocol was used to amplify 50ng of RNA from the biopsies

tag: tissue

value: Formalin-fixed paraffin embedded biopsy

value: Female

tag: age category at diagnosis

value: Greater than or equal to 50

tag: disease

value: Inflammatory breast cancer

tag: Stage

value: III


title: IBC_11


title: IBC cell line

source_name: cell line

value: Cell line SUM149


title: IBC_12

value: Less than 50


title: IBC_13


title: MOLM13 500 nM OTX 2

value: MOLM13 500 nM OTX


title: MOLM13 500 nM VTP 2

value: MOLM13 500 nM VTP


title: MOLM13 500 nM OTX 1


title: OCI-AML3 Control 2

value: Control


title: IBC_6


title: MOLM13 Control 1

value: MOLM13 Control


title: MOLM13 Control 2


title: 11A_M_1247

tag: brain region

value: male


title: 11A_M_1246

tag: age


title: 11A_M_1245

tag: strain


title: 11A_M_1244

tag: Sex


title: IBC_3


title: IBC_5


title: 11A_M_1248


title: 11A_M_1250


title: 11A_M_1243


title: MV4-11 Control 2


title: CSC (Cancer stem cells) 9H_S9

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: CSC (Cancer stem cells)

data_processing:
NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (#20024906; Illumina, San Diego, CA, USA)
The output was >20 million reads in most samples. Trimming was performed on low-quality reads.
STAR v2.7.3a
Partek Flow (Build version  9.0.20.0804) E/M algorithm
Assembly: hg38
Supplementary files format and content: Expression_normalized_Hagar_BenBaruch_30082020.xls

extract_protocol:
RNA extraction kit RNeasy Micro Kit (#74004, Qiagen, Hilden, Germany).
KAPA Stranded RNA-seq Kit with RiboErase (HMR) (#KR1151; Roche, Basel, Switzerland)

value: tumor microenvironment  (TME)-stimulation CD44+/CD24low/-


title: NON-CSC 8H_S8

description: NON-CSC

value: tumor microenvironment  (TME)-stimulation not CD44+/CD24low/-


title: 11A_M_1242


title: control 7H_S7

description: control

value: vehicles


title: NON-CSC 5H_S5

description: NON-CSC


title: CSC (Cancer stem cells) 6H_S6

description: CSC (Cancer stem cells)


title: IBC_7


title: Tas1r3KO-WD_Male_rep2

city: Seoul

first: Woo-Jeong

last: Shon

address: 103 Daehak-ro, Jongno-gu,

department: College of Medicine

country: South Korea

institute: Seoul National University

data_processing:
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
After mapping and aligning, the resulting BAM files were imported into Partek® Genomics Suite software v6.3 (Partek Inc.) (http://www.partek.com/partekgs) and converted into gene transcript levels as reads per kilobase of exon per million mapped reads (RPKM) with the use of a mixed-model approach.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Terminal ileum tissue

extract_protocol:
After the 10-week experimental period, all mice were anesthetized and euthanized through intraperitoneal injection of 20% urethane (U2500, Sigma-Aldrich, St. Louis, MO, USA), and the entire intestine was removed. Ileum were immediately snap frozen (by immersion in liquid nitrogen) after harvest and stored at −80 °C until RNA extraction. Total RNA was isolated using RNAqueous (AM1914, Ambion) according to the manufacturer’s instructions. Isolated RNA 1 ug (1000 ng) was used as input for library generation.
Intact mRNA was isolated from total RNA using the Dynabeads mRNA DIRECT Micro Kit (Ambion). The total mRNA samples were depleted of up to 99.9% of 5S, 5.8S, 18S, and 28S rRNA using the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA, USA). Barcoded cDNA libraries were prepared from the rRNA-depleted mRNA samples and constructed using the Ion Total-RNA Seq Kit v2 (Life Technologies).

treatment_protocol: High-fat diet (60%; HFD, D12492) and matching normal diet (ND, D12450J) pellets were purchased from Research Diets (New Brunswick, NJ, USA). The 30% sugar concentration in the sucrose solution was determined as described in a previous rodent study. Four groups: (i) WT administered ND + plain water; (ii) Tas1r3−/− administered ND + plain water; (iii) WT administered WD (HFD + 30% sugar solution); and (iv) Tas1r3−/− administered WD (HFD + 30% sugar solution). Foods and drinks were supplied ad libitum for 10 weeks; body weight and food and drink intake were monitored weekly.

value: Terminal ileum tissue

value: Western diet (WD)

value: Male


title: Tas1r3KO-WD_Female_rep1

value: Female


title: Tas1r3KO-WD_Female_rep2


title: MOLM13 500 nM VTP 1


title: 11A_M_1240


title: control 4H_S4

description: control


title: Tas1r3KO-WD_Male_rep1


title: IBC_4

value: Formalin-fixed paraffin embedded biopsy


title: CSC (Cancer stem cells) 3H_S3

description: CSC (Cancer stem cells)


title: 11A_M_124


title: NON-CSC 2H_S2

description: NON-CSC

value: tumor microenvironment (TME)-stimulation not CD44+/CD24low/-


title: WT-WD_Female_rep2

value: wild type


title: 11A_M_1239


title: WT-WD_Female_rep1


title: 11A_M_1238


title: Patient 17,Juxta-anastomotic AVF,Failed,T054

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
Female, age 80, non-Hispanic Black, diabetic (pre-access vein is sample GSM3369551 in GSE119296)
T054

data_processing:
Raw sequence data was processed by the on-instrument Real Time Analysis software (v.2.4.11) to basecall files.
Basecall files were converted to de-multiplexed FASTQ files with the Illumina supplied scripts in the BCL2FASTQ software (v2.17).
The quality of reads was determined with the FASTQC software to evaluate per base sequence quality, duplication rates, and overrepresented k-mers.
Illumina adapters were trimmed from the ends of the reads using the Trim Galore! Package.
Reads were aligned to the human reference genome (hg38) with the STAR aligner (v2.5.0a).
Gene count quantification was performed using the GeneCounts function within STAR against the GENCODE v38 human transcript .gtf file.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file of raw gene counts per sample

source_name: Juxta-anastomotic AVF

extract_protocol:
RNAlater-preserved samples were ground in liquid nitrogen and isolated with Trizol (Thermo Fisher Scientific) followed by column purification (EZNA Total RNA Kit I, Omega Bio-tek).
500 ng of total RNA was used as input for the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero to generate ribosomal RNA-depleted sequencing libraries. Each sample had a unique barcode to allow multiplexing, and was sequenced to >40 million raw reads in a single end 75 bp sequencing run on the Illumina NextSeq500.

value: Juxta-anastomotic AVF

tag: individual

value: Patient 17

tag: outcome

value: Failed

tag: gender

value: age 80

tag: ethnicity

value: non-Hispanic Black

tag: disease state


title: Patient 41,Juxta-anastomotic AVF,Failed,T483

description:
Female, age 46, non-Hispanic Black, non-diabetic
T483

value: Patient 41

value: age 46

value: non-diabetic


title: WT-WD_Male_rep2


title: Patient 39,Juxta-anastomotic AVF,Failed,T432

description:
Female, age 64, non-Hispanic Black, diabetic
T432

value: Patient 39

value: age 64

value: diabetic


title: Patient 40,Juxta-anastomotic AVF,Failed,T453B

description:
Female, age 47, Hispanic, non-diabetic
T453B

value: Patient 40

value: age 47

value: Hispanic


title: 11A_M_1237

value: male


title: 11A_M_1241


title: WT-WD_Male_rep1

value: Terminal ileum tissue

value: Western diet (WD)

value: Male


title: Patient 38,Juxta-anastomotic AVF,Failed,T414

description:
Female, age 74, White, diabetic
T414

value: Juxta-anastomotic AVF

value: Patient 38

value: Female

value: age 74

value: White


title: 11A_M_1236


title: Tas1r3KO-ND_Female_rep2

value: Normal diet (ND)


title: 11A_M_1235


title: Patient 34,Juxta-anastomotic AVF,Failed,T484

description:
Male, age 48, non-Hispanic Black, diabetic
T484

value: Patient 34

value: Failed

value: age 48

value: non-Hispanic Black


title: Patient 35,Juxta-anastomotic AVF,Failed,T452

description:
Male, age 68, non-Hispanic Black, non-diabetic
T452

value: Patient 35

value: age 68

value: non-diabetic


title: Patient 33,Juxta-anastomotic AVF,Failed,T472

description:
Male, age 67, Hispanic, diabetic
T472

value: Patient 33

value: age 67

value: Hispanic

value: diabetic


title: 11A_M_1233

value: male


title: control 1H_S1

description: control

tag: cell line

value: vehicles


title: Patient 32,Juxta-anastomotic AVF,Failed,T480

description:
Male, age 67, Hispanic, diabetic
T480

value: Juxta-anastomotic AVF

value: Patient 32

value: Male


title: Tas1r3KO-ND_Male_rep2

value: Terminal ileum tissue

tag: treatment

value: Normal diet (ND)


title: Tas1r3KO-ND_Female_rep1

value: Female


title: Patient 30,Juxta-anastomotic AVF,Matured,T474

description:
Female, age 75, Hispanic, diabetic
T474

value: Patient 30

value: Matured

value: age 75


title: 11A_M_1232


title: Patient 31,Juxta-anastomotic AVF,Failed,T462

description:
Male, age 38, Hispanic, non-diabetic
T462

value: Patient 31

value: Failed

value: age 38


title: 11A_M_1231


title: Patient 29,Juxta-anastomotic AVF,Matured,T433

description:
Female, age 64, White, diabetic
T433

value: Patient 29

value: age 64

value: White


title: Patient 28,Juxta-anastomotic AVF,Matured,T424

description:
Female, age 32, non-Hispanic Black, non-diabetic
T424

value: Patient 28

value: age 32

value: non-Hispanic Black

value: non-diabetic


title: 11A_M_125

value: male


title: WT-ND_Female_rep2

value: Terminal ileum tissue

value: wild type


title: Patient 26,Juxta-anastomotic AVF,Matured,T402

description:
Female, age 68, non-Hispanic Black, diabetic
T402

value: Juxta-anastomotic AVF

value: Patient 26

value: Female

value: age 68

value: diabetic


title: Patient 37,Juxta-anastomotic AVF,Failed,T455

description:
Male, age 60, non-Hispanic Black, diabetic
T455

value: Patient 37

value: Failed

value: Male

value: age 60


title: Patient 36,Juxta-anastomotic AVF,Failed,T453

description:
Male, age 40, non-Hispanic Black, non-diabetic
T453

value: Patient 36

value: age 40


title: 11A_M_123


title: Patient 27,Juxta-anastomotic AVF,Matured,T413

description:
Female, age 45, non-Hispanic Black, diabetic
T413

value: Patient 27

value: Matured

value: age 45


title: WT-ND_Female_rep1

value: Normal diet (ND)


title: Patient 25,Juxta-anastomotic AVF,Matured,T438

description:
Male, age 39, Hispanic, non-diabetic
T438

value: Patient 25

value: age 39

value: Hispanic

value: non-diabetic


title: 11A_M_1230

value: male


title: Patient 24,Juxta-anastomotic AVF,Matured,T436

description:
Male, age 48, non-Hispanic Black, diabetic
T436

value: Juxta-anastomotic AVF

value: Patient 24

value: age 48

value: non-Hispanic Black


title: Patient 22,Juxta-anastomotic AVF,Matured,T370

description:
Male, age 43, Hispanic, non-diabetic
T370

value: Patient 22

value: Male

value: age 43


title: 11A_M_1229


title: WT-ND_Male_rep1

value: Terminal ileum tissue

value: wild type


title: 11A_M_1228


title: Tas1r3KO-ND_Male_rep1


title: Patient 40,Basilic vein,Failed,V471

description:
Female, age 47, Hispanic, non-diabetic
V471

source_name: Basilic vein

value: Basilic vein

value: Patient 40

value: Failed

value: Female

value: age 47


title: 11A_M_1227


title: Patient 39,Basilic vein,Failed,V467

description:
Female, age 64, non-Hispanic Black, diabetic
V467

value: Patient 39

value: age 64

value: diabetic


title: 11A_M_1226

value: male


title: Patient 38,Basilic vein,Failed,V439

description:
Female, age 74, White, diabetic
V439

value: Patient 38

value: age 74

value: White


title: Ribo-ITP-K562-1cell-2

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description: RNA from Ribosome Protected Footprint

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA from the Ribo-ITP data using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”
After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy66 version 0.0.1
Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: Ribo-ITP

growth_protocol: Human K562 cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% Pen-Strep (Gibco) and incubated at 37 °C with 5% CO2 to a density of ~250,000 cells per mL. Cells were regularly tested for Mycoplasma contamination. The identity of the K562 cell line was authenticated using STR profiling from ATCC

extract_protocol:
Cell processing: Cells were pelleted at 300 x g for 5 minutes. The cells were washed with 1x PBS and resuspended to achieve approximetly one million cells in 1 mL of PBS containing 0.1% BSA (Sigma) with 1 µg/ml of DAPI . The cells were passed through a strained cap to attain a single cell suspension and sorted with the Sony MA9000 Cell Sorter or BD FACSAria Fusion Flow Cytometer into Eppendorf LoBind 96-well plates containing 5 µL of cold lysis buffer with cycloheximide. Singlet cells were defined by gating on FSC-A/SSC-A, SSA-H/SSC-W, FSC-A/FSC-H, and FSC-A/Histogram. Live cells were selected using DAPI-negative gating. The plates were sealed and flash frozen in liquid nitrogen immediately after the sort was completed. The lysate was incubated at 37 °C with 1 µL of a 1:150 dilution of MNase stock (2,000 gel units/µL, NEB) for 30 minutes or 1 µL of a 1:300 dilution of RNase I (100 U/µL, Ambion) for 15 minutes. The MNase digestion was stopped by adding EGTA to a final concentration of 10 mM. SDS was added to a final concentration of 0.1% to samples digested with RNase I. The lysates were held on ice until processing through Ribo-ITP. Polydimethylsiloxane (PDMS) chip fabrication: Molds were 3D-printed by Proto Labs with WaterShed XC 11122 at high resolution (Fig. S1). Reusable molds were assembled by taping 3D-printed molds to glass slides (5” by 4”; Ted Pella). Sylgard 184 PDMS monomer and curing agent (Ellsworth Adhesives 4019862) were mixed at a 10:1 (w/w) ratio. The mixture was degassed using a desiccator connected to a vacuum pump, poured over the mold, and degassed again until there were no air bubbles. The mold was incubated for at least 16 h at 50°C. Individual PDMS chips were cut along the lines that form the outer rectangle on the design in Extended Data Fig. 1a. The 5 mm-diameter elution well, TE-, and LE-reservoirs were made with a biopsy punch (Extended Data Fig. 1b). Prior to the plasma treatment, glass slides (4’’ by 3’’; Ted Pella) and the feature-side of the PDMS slabs were thoroughly cleaned with tape to remove any dust particles. PDMS chips and glass slides were plasma cleaned with a 115V Expanded Plasma Cleaner (Harrick Plasma) connected to a Dry Scroll Pump (Agilent) for 2 minutes at high RF level. The plasma-treated surfaces of the glass and PDMS slabs were immediately brought together to form a covalent bond. Bonded chips were heated at 80°C on a heat block for at least two hours to enhance bonding. PDMS chip preparation for Ribo-ITP experiments: To ensure clean, RNAse-free chips, we pre-treated the channels and reservoirs of the Ribo-ITP chip by sequential treatment with the following solutions: RNaseZap (100% concentrate), nuclease-free water, 1 M NaOH, nuclease-free water, 1 M HCl, nuclease-free water, 10% (w/v) benzophenone in acetone (for 10 minutes, replenishing channels as needed to avoid bubble accumulation), methanol, and 0.1% Triton X-100. The channel was completely dried after final treatment by fully vacuuming out any remaining liquid in the channel. After securing the chips to a ProteinSimple 302/365nm UV Transilluminator with tape, we added 10% polyacrylamide (PA) prepolymer mix (Supplementary Table 6) to the size-selection channel through the elution well. Similarly, 5% PA prepolymer mix was loaded into the extraction channel through branch channel 2. To catalyze the polymerization of polyacrylamide on chip, we used a photoactivatable azo-initiator, 2,2'-Azobis[2-methyl-N-(2-hydroxyethyl)propionamide] (Wako Chemicals VA-086), at 0.5% final concentration in the prepolymer mixes. UV-driven polymerization (365 nm wavelength) was performed for one minute followed by a 30 second break. This on/off UV cycle was repeated two more times for a total UV exposure time of 3 minutes. UV intensity was measured as ~8.9 mW/cm2 using a G&R Labs Model 200 UV Light meter with a 365 nm probe. To avoid dehydration of the polyacrylamide gels after polymerization, we filled any open channels and reservoirs with storage buffer (Supplementary Table 6) until use. The chips were protected from light and used within six hours of preparation. Isotachophoresis setup: The prepared ITP chip was placed on a Dark Reader blue light transilluminator (Clare Chemical) and secured with tape. Storage buffer was removed from the channels and reservoirs using a vacuum. Leading electrolyte pluronic solution (LEp) and MOPS trailing electrolyte pluronic solution (TEp) (Supplementary Table 6) were kept on ice throughout the loading procedure. 200 µL pipet tips were kept at -20°C until the time of the experiment to facilitate manipulation of the pluronic-containing LEp and TEp solutions, which solidify within a minute above 4°C. 80 µL of LEp was loaded in LE reservoir 3, filling the reservoir to the top as well as the small section of the channel between the elution well and LE reservoir 3 (Extended Data Fig. 1b). LE reservoir 2 was filled with 30 µL LEp, ensuring contact with the polyacrylamide gel present in branch channel 2. The elution well was filled with 20 µL of RB. Fluorescent marker oligonucleotides containing a 5’ ATTO fluorophore and 3’ ddC blocking modification (Supplementary Table 7) were added to the sample followed by dilution with sample dilution buffer (SDB). The mixture was loaded into the lysate channel through LE reservoir 1. Finally, LE reservoir 1 was filled with 30 µL LEp and 70 µl TEp was added to the TE reservoir. The negative electrode was placed in the TE reservoir and the positive electrode in the LE reservoir. Positive and negative electrodes were placed in LE reservoir 3 and the TE reservoir, respectively. A constant current of 300 mA with a maximum voltage of 1.1 kV (Keithley 2410 Sourcemeter) was applied to the channel. Once the trailing end of the fluorescent markers entered the 5% PA gel, the branch channel electrode–with a lower current output due to a 510 kΩ (Xikon) resistor on a custom circuit board–was manually applied in LE reservoir 1 for ~10 seconds. When the leading edge of the shorter fluorescent marker reached the end of the size-selection channel, the current was suspended. The elution reservoir was thoroughly washed twice with 30 µL nuclease-free water and refilled with 10 µL dephosphorylation buffer (Supplementary Table 6). Current was applied again until the longer fluorescent marker began to enter the elution well. Finally, the purified sample with a 10 µL volume was collected from the elution well into a low-bind PCR tube and immediately stored at -80 °C.
D-Plex Small RNA-seq Kit (Diagenode C05030001) with minor modifications was used as detailed below. The dephosphorylation reaction was supplemented with 0.5 µL T4 PNK (NEB) and the reaction was incubated for 25 minutes. For reverse transcription, the template switching oligo (TSO) was diluted 1:2 in nuclease-free water. Samples were processed using the unique dual index (UDI) module. Half of the cDNA was amplified for 17 PCR cycles and a 1:4 dilution of the resulting library was assessed by Agilent Bioanalyzer High Sensitivity DNA kit. The concentrations of the target peaks were used to pool samples with approximately equimolar representation. AMPure XP bead cleanup (1.8x) was performed followed by size-selection using 3% agarose, dye-free gel cassettes with internal standards (Sage Science BDQ3010) on the BluePippin platform. Tight parameter settings of 173-207 bp range were used for samples prepared with the SDI module. Tight parameter settings of 183-217 bp range were used for MNase digested libraries. For the RNase I digested single cell libraries final size selection was performed by PAGE purification of 200 bp products.

tag: cell type

value: Chronic myelogenous leukemia

value: 0.33 units RNaseI


title: Ribo-ITP-K562-1cell-1

description: RNA from Ribosome Protected Footprint


title: 11A_M_1225


title: Patient 37,Basilic vein,Failed,V497

description:
Male, age 60, non-Hispanic Black, diabetic
V497

value: Patient 37

value: Male

value: age 60

value: non-Hispanic Black


title: Patient 35,Basilic vein,Failed,V487

description:
Male, age 68, non-Hispanic Black, non-diabetic
V487

value: Basilic vein

value: Patient 35

value: age 68

value: non-diabetic


title: Ribo-ITP-K562-1cell-3

description: RNA from Ribosome Protected Footprint


title: Patient 34,Basilic vein,Failed,V532

description:
Male, age 48, non-Hispanic Black, diabetic
V532

value: Patient 34

value: Failed

value: age 48


title: Patient 32,Basilic vein,Failed,V519

description:
Male, age 67, Hispanic, diabetic
V519

value: Patient 32

value: age 67

value: Hispanic

value: diabetic


title: DF68555 500 nM VTP scATAC Seq

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, detection of accessible chromatin peaks were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Patient-derived xenograft AML cells

extract_protocol:
Frozen patient derived AML BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 2 minutes until partially thawed and immediately transferred to a 50 mL conical tube with 1ml of prewarmed media (RPMI1640 supplemented with 10% FBS) and centrifuged (300 g for 5 min). Cells were sequentially diluted 1:1 3 times with prewarmed RPMI containing 10% FBS. Cells were centrifuged at 300 x g for 5 minutes in a swinging bucket centrifuge. After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 1 mL of 2% FBS/PBS, centrifuged at 300 x g for 5 minutes and resuspended in 900 uL of 2% FBS/PBS. To removed dead cells and debris, cells were passed through a 40 micron Flow-mi strainer and the cell concentration was determined with a Countess counting device. Nuclei were isolated following the demonstrated protocol for Nuclei isolation for single cell ATAC from 10X Genomics. Briefly, cells were lysed in chilled lysis buffer for 3 minutes, washed 3 times in chilled nuclei Wash Buffer, centrifuged for 5 minutes to remove the wash buffer and resuspened in Diluted Nuclei buffer (10X Genomics). The desired number of targeted nuclei (5000-10,000) in diluted Nuclei buffer were separated on the 10X Chromium Controller.
Single cell ATAC-Seq libraries were generated following the manufacturer's protocol provided by 10X Genomics for sc-ATAC seq analysis.

value: Patient-derived xenograft AML cells

value: Bone marrow


title: DF68555 Control scATAC Seq

value: Control


title: WT-ND_Male_rep2

value: Terminal ileum tissue

tag: genotype

value: wild type

value: Normal diet (ND)

value: Male


title: 11A_M_1224

value: male


title: Patient 23,Juxta-anastomotic AVF,Matured,T420

description:
Male, age 33, non-Hispanic Black, non-diabetic
T420

tag: tissue

value: Juxta-anastomotic AVF

value: Patient 23

value: Matured

value: age 33

value: non-Hispanic Black


title: Patient 30,Basilic vein,Matured,V522

description:
Female, age 75, Hispanic, diabetic
V522

value: Basilic vein

value: Patient 30

value: Female

value: age 75


title: 11A_M_1223


title: Patient 33,Basilic vein,Failed,V523

description:
Male, age 67, Hispanic, diabetic
V523

value: Patient 33

value: Failed

value: age 67

value: Hispanic

value: diabetic


title: Patient 31,Basilic vein,Failed,V501

description:
Male, age 38, Hispanic, non-diabetic
V501

value: Patient 31

value: age 38

value: non-diabetic


title: Patient 29,Basilic vein,Matured,V469

description:
Female, age 64, White, diabetic
V469

value: Patient 29

value: age 64

value: White


title: Patient 41,Basilic vein,Failed,V530

description:
Female, age 46, non-Hispanic Black, non-diabetic
V530

value: Patient 41

value: age 46


title: 11A_M_1222

value: male


title: DF68555 500 nM VTP scRNA Seq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Frozen patient derived AML BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 2 minutes until partially thawed and immediately transferred to a 50 mL conical tube with 1ml of prewarmed media (RPMI1640 supplemented with 10% FBS) and centrifuged (300 g for 5 min). Cells were sequentially diluted 1:1 3 times with prewarmed RPMI containing 10% FBS. Cells were centrifuged at 300 x g for 5 minutes in a swinging bucket centrifuge. After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 1 mL of 2% FBS/PBS, centrifuged at 300 x g for 5 minutes and resuspended in 900 uL of 2% FBS/PBS. To removed dead cells and debris, cells were passed through a 40 micron Flow-mi strainer and the cell concentration of the concentrated cell stock was determined with a Countess counting device.  The desired number of targeted cells (5000-10,000) from the concentrated cell stock were separated on the 10X Chromium Controller.
scRNA Seq libraries were constructed following the 10X Genomics protocol for single cell RNA Seq analysis.

value: Patient-derived xenograft AML cells

value: Bone marrow


title: Patient 27,Basilic vein,Matured,V445

description:
Female, age 45, non-Hispanic Black, diabetic
V445

value: Basilic vein

value: Patient 27

value: Matured

value: Female

value: age 45

value: non-Hispanic Black


title: 11A_M_1221


title: Patient 36,Basilic vein,Failed,V496

description:
Male, age 40, non-Hispanic Black, non-diabetic
V496

value: Patient 36

value: Failed

value: Male

value: age 40


title: Patient 26,Basilic vein,Matured,V413

description:
Female, age 68, non-Hispanic Black, diabetic
V413

value: Patient 26

value: age 68

value: diabetic


title: Patient 25,Basilic vein,Matured,V475

description:
Male, age 39, Hispanic, non-diabetic
V475

value: Patient 25

value: age 39

value: Hispanic

value: non-diabetic


title: Patient 24,Basilic vein,Matured,V462

description:
Male, age 48, non-Hispanic Black, diabetic
V462

value: Basilic vein

value: Patient 24

value: age 48


title: 11A_M_1220

value: male


title: S12-WT CutTag H3K27ac

city: Guangzhou

first: yuyan

last: wang

address: Zhongshan 2nd Road, Yuexiu

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: CutTag

growth_protocol: Ca Ski was maintained in RPMI-1640 supplemented with 10% fetal bovine serum (Gibco, 10270-106) and 100 U/ml penicillin and streptomycin (Invitrogen, 15140163). SiHa, HeLa, HEK293T, and C-33 A were cultured in DMEM supplemented with 10% fetal bovine serum and 100 U/ml penicillin and streptomycin (Invitrogen, 15140163). S12 and HaCaT cells were cultured in a 1:3 mixture of DMEM and Ham F-12 supplemented with 5% FBS (Gibco, 10270-106), 5 ug/ml insulin (Sigma-Aldrich, I5500), 8.4 ng/ml cholera toxin (Sigma-Aldrich, C8052), 24.3 ug/ml adenine (Solarbio, A8330), 10 ng/ml recombinant human EGF (Solarbio, P0033), and 0.5 ug/ml hydrocortisone (Solarbio, G8450) (5). All cells were cultured in a humidified 37 ℃ incubator at 5% CO2 and passaged 2-3 times weekly as recommended by ATCC.

extract_protocol:
Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
For short reads sequencing, PE100 bp read length sequencing was performed on the BGISEQ-500 sequencer after size selection by gel electrophoresis and 10 to 12 cycles of PCR. For long reads sequencing, size-select long DNA fragments used the BluePippin system and then libraries were constructed and sequenced following Nanopore standard protocol.

value: H3K27ac antibody


title: 11A_M_122

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: S12-L2-hR2-1 CutTag H3K27ac


title: Patient 22,Basilic vein,Matured,V176

description:
Male, age 43, Hispanic, non-diabetic
V176

value: Patient 22

value: Matured

value: age 43


title: S12-L1-hR1-1 CutTag H3K27ac


title: Patient 23,Basilic vein,Matured,V431

description:
Male, age 33, non-Hispanic Black, non-diabetic
V431

value: Patient 23

value: Male

value: age 33

value: non-Hispanic Black


title: 11A_M_1219


title: ACZ4-HM_S12

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

data_processing:
Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Alignment (STAR 2.7.3a): Default settings from Partek Flow
Quantify to annotation model (Partek E/M): Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Exclude features where maximum ≤ 1. Processed data file included with filtered raw gene counts
Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
ANOVA for DEGs: Factors: crosslinking density high1 to low 4 + Donor(Random). Shrinkage of error term variance: Limma-trend.

source_name: human engineered nasal constructs

growth_protocol: Constructs were cultured for 6 weeks in a 21% oxygen tension with the supplement of TGF-β3.

extract_protocol:
RNA was first extracted using conventional Trizol method then purified using LunaNano PureSPIN columns with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability. These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

treatment_protocol: Nasal chondrocytes were mixed with biopolymer solution (thiolate hyaluronic acid and gelatin) and crosslinker solution (PEGDA) in a solid content ratio of 2:1, 4:1, 6:1, 8:1 to create tissue engineered constructs

tag: crosslink density


title: ACZ3-HM_S11


title: ACZ1-HM_S9


title: ACW4-HM_S20


title: 11A_M_1218


title: HeLa-SE4-h2-3 CutTag H3K27ac

source_name: HeLa

value: HeLa


title: 11A_M_1217


title: ACZ2-HM_S10


title: ACW3-HM_S19


title: ACW2-HM_S18


title: HeLa-SE3-h2-5 CutTag H3K27ac


title: Patient 28,Basilic vein,Matured,V460

description:
Female, age 32, non-Hispanic Black, non-diabetic
V460

value: Patient 28

value: Female

value: age 32


title: HeLa-SE4-h2-2 CutTag H3K27ac


title: ACW1-HM_S17


title: DF68555 Control scRNA Seq

value: Patient-derived xenograft AML cells

value: Bone marrow

value: Control


title: 11A_M_1216


title: 11A_M_1215


title: ACV4-HM_S16


title: ACV3-HM_S15


title: 11A_M_1213


title: ACV2-HM_S14


title: TT-seq_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2_Batch2

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University

description: treated with dTAG13 for 3 hours

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameters “-outFilterMultimapNmax 1 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.02 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Dobin et al., 2013).
SAMtools v1.9 (Li et al., 2009) was used to quality filter SAM files with “-q 7 -f 2” and duplicated reads were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The counts of spike-in mm10 reads were used to generate normalization factors for coverage profiles.
Rsubread R package v2.0.1 (Liao et al., 2019) was used to perform gene expression quantification and DESeq2 R package v1.26.0 (Love et al., 2014) was used to perform differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Library strategy: TT-seq

source_name: INTS8-dTAG_INTS8-N211del DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 3h.

value: INTS8-dTAG_INTS8-N211del DLD1

value: colorectal adenocarcinoma cell lines

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-N211del expression

value: treated with dTAG13

tag: time

value: 3 hours


title: TT-seq_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1_Batch2

description: treated with dTAG13 for 3 hours


title: ACV1-HM_S13


title: ADL5.4-T3_S36

data_processing:
Partek Flow: Trim bases: Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25).
Partek Flow: Alignment (STAR 2.7.3a): Default settings from Partek Flow.
Partek Flow: Quantify to annotation model (Partek E/M): Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01.
Partek Flow: Filter features: Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts.
Partek Flow: Normalize counts: Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis.
Partek Flow: ANOVA for DEGs: Experiment I: Factors: Oxygen + TGF-B3 + Donor(Random) + Oxygen*TGF-B3. Shrinkage of error term variance: Limma-trend. Experiment II: Factors: Loading + TGF-B3 + Donor(Random) + Loading*TGF-B3. Shrinkage of error term variance: Limma-trend.
Assembly: hg38
Supplementary files format and content: ADL_CHP_ProcessedData_NormalizedCount.txt: Tab-delimited text file includes normalized counts. Samples are in rows, and genes are in columns.

source_name: human engineered cartilage constructs

growth_protocol: Tissue-engineered constructs were made from frozen human BM-MSCs seeded on HyStem-C hydrogels. Constructs were precultured for three weeks in a 3% oxygen condition with the supplement of TGF-β3.

extract_protocol:
RNA was extracted using LunaNano PureSPIN columns with a DNase digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability. These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads.

treatment_protocol: After pre-culture, two separate experiments were conducted. In experiment I, constructs were cultured in 3% and 20% oxygen environment with/without the supplement with TGF-β3 for 3 weeks. In experiment II, constructs were cultured under dynamic compression or cyclic hydrostatic pressure with/without the supplement with TGF-β3 for 3 weeks.

value: engineered cartilage constructs

tag: oxygen tension

value: HYP

tag: mechanical condition

value: CHP

tag: tgf-beta3 supplement

value: No


title: TT-seq_dTAG-1h_INTS8-dTAG_INTS8-N211del_DLD1_rep1_Batch2

description: treated with dTAG13 for 1 hours

value: 1 hours


title: 11A_M_1211

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: age

tag: strain

value: male


title: ADL5.3+T3_S25

value: DC

value: Yes


title: ADL5.2-T3_S24

value: Static


title: TT-seq_dTAG-0h_INTS8-dTAG_INTS8-N211del_DLD1_rep2_Batch2

description: treated with dTAG13 for 0 hours

value: 0 hours


title: ADL5.2+T3_S23


title: 11A_M_1210

tag: Sex


title: TT-seq_dTAG-0h_INTS8-dTAG_INTS8-N211del_DLD1_rep1_Batch2

description: treated with dTAG13 for 0 hours


title: 11A_M_121


title: ADL4.4-T3_S16


title: ADL5.1+T3_S29

value: NRX


title: ADL5.1-T3_S30


title: 11A_M_1209


title: TT-seq_dTAG-3h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 3 hours

source_name: INTS11-dTAG DLD1

value: INTS11-dTAG DLD1

value: INTS11 knock-in of a dTAG tag


title: 11A_M_1208


title: ADL4.3-T3_S33


title: TT-seq_dTAG-1h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 1 hours

value: colorectal adenocarcinoma cell lines


title: ADL4.2+T3_S20


title: 11A_M_1207


title: ADL4.2-T3_S32


title: 11A_M_1212


title: TT-seq_dTAG-1h_INTS8-dTAG_INTS8-N211del_DLD1_rep2_Batch2

description: treated with dTAG13 for 1 hours

value: INTS8-dTAG_INTS8-N211del DLD1

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-N211del expression


title: ADL4.1+T3_S31


title: ADL4.1-T3_S15


title: ADL3.4+T3_S19


title: 11A_M_1206


title: ADL3.4-T3_S14


title: 11A_M_1205


title: TT-seq_dTAG-0h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 0 hours

value: treated with dTAG13


title: TT-seq_dTAG-0h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 0 hours


title: ADL3.3-T3_S28

value: engineered cartilage constructs


title: TT-seq_dTAG-3h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 3 hours

value: 3 hours


title: 11A_M_1204


title: ADL4.4+T3_S22

value: HYP

value: CHP


title: ADL3.2-T3_S27

value: No


title: ADL5.4+T3_S35


title: ADL3.3+T3_S18


title: 11A_M_1203

value: male


title: PRO_dTAG-3h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 3 hours

data_processing:
The paired-end PRO-seq reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and fastp v0.21.0 (Chen et al., 2018b), and ribosomal RNA reads were removed using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012).
Resulting reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with “--local --sensitive-local” (Langmead and Salzberg, 2012), and PCR duplicates were removed by umi_tools v1.0.1 (Smith et al., 2017).
Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016) with "--Offset 1" for single-base files and "--Offset None" for full-length files.
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: PRO-Seq

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.


title: ADL3.2+T3_S17


title: ADL5.3-T3_S34

value: DC


title: ADL3.1-T3_S26


title: 11A_M_1202


title: ADL4.3+T3_S21

value: Yes


title: PRO_dTAG-3h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 3 hours


title: TT-seq_dTAG-1h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 1 hours

value: 1 hours


title: ADL3.1+T3_S60

value: Static


title: PRO_dTAG-1h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 1 hours


title: 11A_M_1201


title: S2-VP10_xenograft_ROR1high_ATAC

city: Kumamoto city

first: Masaya

last: Yamazaki

address: 1-1-1, Honjyo, Chuo-ku

institute: Kumamoto university

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human genome (hg19) by Bowtie2 (version 2.3.4.1).
Duplicate reads were removed.
ATAC-seq data was converted to bigwig files by bamCoverage with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: BAM files and Bigwig files.

source_name: human pancreatic adenocarcinoma

extract_protocol: ATAC-sequencing was performed with modifications based on a previous report (Corces et al., 2017).

value: S2-VP10 (human pancreatic adenocarcinoma)

tag: model

value: xenograft


title: S2-VP10_xenograft_ROR1low_ATAC


title: PRO_dTAG-1h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 1 hours

value: INTS11-dTAG DLD1

value: INTS11 knock-in of a dTAG tag


title: 11A_M_1200


title: S2-VP10_ATAC

value: 2D culture cell


title: S2-VP10_xenograft_ROR1low_CUT&RUN_H3K27ac

data_processing:
Library strategy: CUT&RUN
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human genome (hg19) by Bowtie2 (version 2.3.4.1).
Duplicate reads were removed.
The number of unique reads was normalized to spike-in yeast DNA (sacCer3).
CUT&RUN data were converted to bigwig files by bamCoverage (in the deepTools package, version 3.5.1) with the following parameters: --scaleFactor <each sample> --binSize 10.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files.

source_name: Pancreatic adenocarcinoma

extract_protocol:
CUT&RUN was performed using the CUT&RUN Assay Kit (CST) with a modification of the manufacturer’s protocol.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs).

tag: cut&run antibody

value: anti-H3K27ac (CST, 8173)


title: 11A_M_12


title: S2-VP10_xenograft_ROR1high_CUT&RUN_H3K27ac


title: S2-VP10_xenograft_ROR1low_CUT&RUN_H3K4me1

value: anti-H3K4me1 (Abcam, ab8895)


title: 11A_M_120


title: S2-VP10_xenograft_ROR1high_CUT&RUN_H3K4me1


title: HCC, scRNAseq

city: Baltimore

first: Elana

middle: J

last: Fertig

state: MD

address: 550 N Broadway, Suite 1101

department: Oncology

institute: Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center

description: 10x Genomics

data_processing:
Cell Ranger
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HCC

extract_protocol:
Tumors were dissociated using collagenase and enriched for tumor infiltrating leukocytes (TILs) using Percoll centrifugation gradient.
10x Chromium Next GEM Single Cell 5' Reagents Kits v2 following manufacturer’s instructions.

value: HCC

value: liver

value: cabozantinib+nivolumab


title: PRO_dTAG-0h_INTS11-dTAG_DLD1_rep1_Batch2

description: treated with dTAG13 for 0 hours

value: colorectal adenocarcinoma cell lines

value: treated with dTAG13

value: 0 hours


title: 11A_M_1199

value: male


title: S2-VP10_CUT&RUN_H3K27ac

data_processing:
Library strategy: CUT&RUN
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human genome (hg19) by Bowtie2 (version 2.3.4.1).
Duplicate reads were removed.
The number of unique reads was normalized to spike-in yeast DNA (sacCer3).
CUT&RUN data were converted to bigwig files by bamCoverage (in the deepTools package, version 3.5.1) with the following parameters: --scaleFactor <each sample> --binSize 10.
Peak detection was performed using MACS2 59 (version 2.2.7.1) with default parameters.
The Overlapping peaks between H3K4me1 and H3K27ac were obtained using the bedtools intersect function (version 2.30.0).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files. BED files.


title: PDAC, Visium

description: 10x Genomics

data_processing:
Space Ranger
Assembly: hg38
Supplementary files format and content: Outputs for each samples are provided in tar.gz files.
Library strategy: spatial transcriptomics

source_name: PDAC

extract_protocol:
Samples HCC and PDAClymphnode were surgically resected and embedded in optimal cutting temperature (OCT) reagent at stored at -80C. Sample PanIN, was formalin-fixed and paraffin-embedded upon surigcal resection. A 5um section from each sample was placed onto Visium slides.
Manufacturer's instructions for Visium (10x Genomics) frozen (HCC and PDAClymphnode) or FFPE (PanIN).

value: PDAC

value: pancreas

value: GVAX


title: S2-VP10_CUT&RUN_H3K4me3

value: S2-VP10 (human pancreatic adenocarcinoma)

value: anti-H3K4me3 (Millipore, 07-473)


title: 11A_M_1198


title: S2-VP10_CUT&RUN_H3K4me1


title: S2-VP10_xenograft_ROR1high_CUT&RUN_IgG

value: xenograft

value: rabbit IgG (Biolegend, 910805)


title: PanIN, Visium

description: 10x Genomics

source_name: PanIN

value: PanIN

value: naïve


title: 11A_M_1197


title: HCC, Visium

description: 10x Genomics


title: S2-VP10_CUT&RUN_IgG

value: 2D culture cell


title: 11A_M_1196


title: 11A_M_1195


title: WT strain F infection, 8 h p.i., PAA, replicate 2 [RNA-Seq]

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description:
Total RNA prepared using Trizol
Wt_F_8_hpi_plus_8hPAA_2

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene read counts

growth_protocol: Human fetal foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected at 60-80% confluency 24h after the last split. T-HF cells were cultured in DMEM supplements with 10% FBS and P/S. Expression of HA-ICP22 and HA-ICP22 + V5-ICP27 was induced by adding 5 μg/ml doxycycline for 48h.

extract_protocol:
Total RNA was prepared using Trizol.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat
35bp paired-end, NextSeq 500 (Illumina)

treatment_protocol: HFFF cells were infected for 15 minutes with HSV-1 strain F or ICP22-null virus at an MOI of 10 followed by PBS wash and media replacement. 350 µg/ml PAA was added to indicated samples for 8 or 12 hours. 5 μg/mL DOX was added to indicated samples 48 hours prior to collecting RNA. 80 mM KCl (salt stress) was added to indicated samples for 2 hours prior to collecting RNA.

value: human fetal foreskin fibroblasts

tag: time post infection

value: 8 hpi

tag: agent

value: Herpes simplex virus 1, strain F

value: PAA (350 microg/ml)


title: S2-VP10_xenograft_ROR1low_CUT&RUN_IgG


title: TT-seq_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1_Batch1

description: treated with dTAG13 for 3 hours

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameters “-outFilterMultimapNmax 1 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.02 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Dobin et al., 2013).
SAMtools v1.9 (Li et al., 2009) was used to quality filter SAM files with “-q 7 -f 2” and duplicated reads were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The counts of spike-in mm10 reads were used to generate normalization factors for coverage profiles.
Rsubread R package v2.0.1 (Liao et al., 2019) was used to perform gene expression quantification and DESeq2 R package v1.26.0 (Love et al., 2014) was used to perform differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.
TT-seq

tag: cell line

value: INTS8-dTAG_INTS8-N211del DLD1

value: colorectal adenocarcinoma cell lines

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-N211del expression

tag: treatment

value: treated with dTAG13

value: 3 hours


title: WT strain F infection, 8 h p.i., PAA, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_8_hpi_plus_8hPAA_1

tag: cell type


title: WT strain F infection, 8 h p.i. replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_8_hpi_1

value: no treatment


title: WT strain F infection, 12 h p.i., PAA,  replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_12_hpi_plus_12hPAA_2

value: 12 hpi


title: WT strain F infection, 12 h p.i., PAA,  replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_12_hpi_plus_12hPAA_1


title: WT strain F infection, 8 h p.i. replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_8hpi_2


title: 11A_M_1194

city: La Jolla

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute

value: male


title: PRO_dTAG-0h_INTS11-dTAG_DLD1_rep2_Batch2

description: treated with dTAG13 for 0 hours

value: INTS11-dTAG DLD1

tag: genotype

value: INTS11 knock-in of a dTAG tag

value: 0 hours


title: TT-seq_dTAG-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2_Batch1

description: treated with dTAG13 for 3 hours


title: WT strain F infection, 12 h p.i. replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_12_hpi_2


title: TT-seq_dTAG-3h_INTS8-dTAG_DLD1_rep2_Batch1

description: treated with dTAG13 for 3 hours

source_name: INTS8-dTAG DLD1

value: INTS8-dTAG DLD1

value: INTS8 knock-in of a dTAG tag


title: mock infection, 8h p.i., PAA, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_8_hpi_plus_8hPAA_2

value: human fetal foreskin fibroblasts

value: mock


title: TT-seq_dTAG-3h_INTS8-dTAG_DLD1_rep1_Batch1

description: treated with dTAG13 for 3 hours


title: 11A_M_1193


title: 11A_M_1192


title: TT-seq_dTAG-3h_INTS11-dTAG_DLD1_rep2_Batch1

description: treated with dTAG13 for 3 hours


title: 11A_M_1191


title: mock infection, 12h p.i., PAA, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_12h_plus_12hPAA_1


title: mock infection, 12h p.i., PAA, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_12_hpi_plus_12hPAA_2


title: mock infection, 12h p.i., replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_12h_1

source_name: mock infection, 12h p.i., replicate 1


title: mock infection, 8h p.i., replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_8_hpi_2

source_name: mock infection, 8h p.i., replicate 2


title: TT-seq_dTAG-3h_INTS11-dTAG_DLD1_rep1_Batch1

description: treated with dTAG13 for 3 hours


title: 11A_M_1190


title: TT-seq_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep2_Batch1

description: untreated

value: treated with DMSO


title: HA-ICP22 cells, salt stress, DOX, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_Salt_stress_plus_DOX_RNA_2

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: no infection

value: DOX (5 μg/mL) + KCl (80 mM)


title: mock infection, 12h p.i., replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Mock_12_hpi_2

source_name: mock infection, 12h p.i., replicate 2


title: HA-ICP22 cells, salt stress, DOX, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_Salt_stress_plus_DOX_RNA_1


title: WT strain F infection, 12 h p.i. replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Wt_F_12_hpi_1

value: Herpes simplex virus 1, strain F


title: HA-ICP22 cells, salt stress, no DOX, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_Salt_Stress_minus_DOX_RNA_2

value: KCl (80 mM)


title: TT-seq_DMSO-3h_INTS8-dTAG_INTS8-N211del_DLD1_rep1_Batch1

description: untreated

value: INTS8-dTAG_INTS8-N211del DLD1

value: colorectal adenocarcinoma cell lines

value: INTS8 knock-in of a dTAG tag, then ectopic INTS8-N211del expression

value: 3 hours


title: HA-ICP22+V5-ICP27 cells, DOX, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_plus_V5_ICP27_cells_plus_DOX_RNA_2

value: DOX (5 μg/mL)


title: HA-ICP22 cells, salt stress, no DOX, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_Salt_Stress_minus_DOX_RNA_1


title: 11A_M_119

value: male


title: HA-ICP22+V5-ICP27 cells, DOX, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_plus_V5_ICP27_cells_plus_DOX_RNA_1


title: TT-seq_DMSO-3h_INTS8-dTAG_DLD1_rep2_Batch1

description: untreated


title: TT-seq_DMSO-3h_INTS8-dTAG_DLD1_rep1_Batch1

description: untreated


title: ICP22-null infection, 12h p.i., PAA, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICPP22_12hpi_plus_12hPAA_1

value: 12 hpi

value: ICP22-null mutant of herpes simplex virus 1, strain F

value: PAA (350 microg/ml)


title: 11A_M_1186


title: ICP22-null infection, 8h p.i., PAA, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICP22_8hpi_plus_8hPAA_2

value: human fetal foreskin fibroblasts

value: 8 hpi


title: 11A_M_1188


title: ICP22-null infection, 8h p.i., PAA, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICPP22_8hpi_plus_8hPAA_1


title: HA-ICP22+V5-ICP27 cells, no DOX, replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_plus_V5_ICP27_cells_minus_DOX_RNA_1

value: no treatment


title: 11A_M_1187


title: TT-seq_DMSO-3h_INTS11-dTAG_DLD1_rep1_Batch1

description: untreated

value: INTS11-dTAG DLD1

value: INTS11 knock-in of a dTAG tag

value: treated with DMSO


title: ICP22-null infection, 8h p.i., replicate 1 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICP22_8hpi_1


title: TT-seq_DMSO-3h_INTS11-dTAG_DLD1_rep2_Batch1

description: untreated


title: 11A_M_1184


title: HA-ICP22+V5-ICP27 cells, no DOX, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
HA_ICP22_plus_V5_ICP27_cells_minus_DOX_RNA_2

value: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line

value: no infection


title: ICP22-null infection, 12h p.i., PAA, replicate 2 [RNA-Seq]

description:
Total RNA prepared using Trizol
Delta_ICP22_12hpi_plus_12hPAA_2