title: sci3-me-614

description: sci-RNA-seq3 library


title: sci3-me-595

status: Public on Feb 20 2019

type: SRA

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq of co-assay was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
Genome_build: mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file
Supplementary_files_format_and_content: Cell annotation file: sample is cell id of each single cell with the reverse transcription and ligation barcode attached; tsne_1 and tsne_2 are cell coordinates after t-SNE dimension reduction.
Supplementary_files_format_and_content: Gene annotation file including gene id, gene type and gene short name.
Supplementary_files_format_and_content: A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryos

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer. The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%.
Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping.  The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi). Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer.    Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes).    After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including  4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.    After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen). 1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min.    For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter). In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate.    For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.

tag: developmental stage

tag: genetic background

value: B6 background


title: sci3-me-592

description: sci-RNA-seq3 library


title: sci3-me-593

description: sci-RNA-seq3 library


title: sci3-me-594

description: sci-RNA-seq3 library


title: sci3-me-587

description: sci-RNA-seq3 library


title: sci3-me-588

description: sci-RNA-seq3 library


title: sci3-me-586

description: sci-RNA-seq3 library


title: sci3-me-585

description: sci-RNA-seq3 library


title: sci3-me-584

description: sci-RNA-seq3 library


title: sci3-me-589

description: sci-RNA-seq3 library


title: sci3-me-591

description: sci-RNA-seq3 library


title: sci3-me-590

description: sci-RNA-seq3 library


title: sci3-me-583

description: sci-RNA-seq3 library


title: sci3-me-727

description: sci-RNA-seq3 library


title: sci3-me-728

description: sci-RNA-seq3 library


title: sci3-me-582

description: sci-RNA-seq3 library


title: sci3-me-581

description: sci-RNA-seq3 library


title: sci3-me-580

description: sci-RNA-seq3 library


title: sci3-me-579

description: sci-RNA-seq3 library


title: sci3-me-578

description: sci-RNA-seq3 library


title: sci3-me-577

description: sci-RNA-seq3 library


title: sci3-me-574

description: sci-RNA-seq3 library


title: sci3-me-571

description: sci-RNA-seq3 library


title: sci3-me-569

description: sci-RNA-seq3 library


title: sci3-me-575

description: sci-RNA-seq3 library


title: sci3-me-572

description: sci-RNA-seq3 library


title: sci3-me-576

description: sci-RNA-seq3 library


title: sci3-me-568

description: sci-RNA-seq3 library


title: sci3-me-567

description: sci-RNA-seq3 library


title: sci3-me-566

description: sci-RNA-seq3 library


title: sci3-me-562

description: sci-RNA-seq3 library


title: sci3-me-555

description: sci-RNA-seq3 library


title: sci3-me-561

description: sci-RNA-seq3 library


title: sci3-me-560

description: sci-RNA-seq3 library


title: sci3-me-556

description: sci-RNA-seq3 library


title: sci3-me-558

description: sci-RNA-seq3 library


title: sci3-me-563

description: sci-RNA-seq3 library


title: sci3-me-564

description: sci-RNA-seq3 library


title: sci3-me-554

description: sci-RNA-seq3 library


title: sci3-me-557

description: sci-RNA-seq3 library


title: sci3-me-553

description: sci-RNA-seq3 library


title: sci3-me-559

description: sci-RNA-seq3 library


title: sci3-me-551

description: sci-RNA-seq3 library


title: sci3-me-552

description: sci-RNA-seq3 library


title: sci3-me-550

description: sci-RNA-seq3 library


title: sci3-me-570

description: sci-RNA-seq3 library


title: sci3-me-573

description: sci-RNA-seq3 library


title: sci3-me-549

description: sci-RNA-seq3 library


title: sci3-me-548

description: sci-RNA-seq3 library


title: sci3-me-565

description: sci-RNA-seq3 library


title: sci3-me-547

description: sci-RNA-seq3 library


title: sci3-me-543

description: sci-RNA-seq3 library


title: sci3-me-544

description: sci-RNA-seq3 library


title: sci3-me-546

description: sci-RNA-seq3 library


title: sci3-me-542

description: sci-RNA-seq3 library


title: sci3-me-545

description: sci-RNA-seq3 library


title: sci3-me-539

description: sci-RNA-seq3 library


title: sci3-me-540

description: sci-RNA-seq3 library


title: sci3-me-541

description: sci-RNA-seq3 library


title: sci3-me-537

description: sci-RNA-seq3 library


title: sci3-me-538

description: sci-RNA-seq3 library


title: sci3-me-536

description: sci-RNA-seq3 library


title: sci3-me-535

description: sci-RNA-seq3 library


title: sci3-me-531

description: sci-RNA-seq3 library


title: sci3-me-534

description: sci-RNA-seq3 library


title: sci3-me-533

description: sci-RNA-seq3 library


title: sci3-me-532

description: sci-RNA-seq3 library


title: sci3-me-530

description: sci-RNA-seq3 library


title: sci3-me-529

description: sci-RNA-seq3 library


title: sci3-me-528

description: sci-RNA-seq3 library


title: sci3-me-527

description: sci-RNA-seq3 library


title: sci3-me-526

description: sci-RNA-seq3 library


title: sci3-me-524

description: sci-RNA-seq3 library


title: sci3-me-525

description: sci-RNA-seq3 library


title: sci3-me-520

description: sci-RNA-seq3 library


title: sci3-me-522

description: sci-RNA-seq3 library


title: sci3-me-523

description: sci-RNA-seq3 library


title: sci3-me-521

description: sci-RNA-seq3 library


title: sci3-me-518

description: sci-RNA-seq3 library


title: sci3-me-517

description: sci-RNA-seq3 library


title: sci3-me-516

description: sci-RNA-seq3 library


title: sci3-me-514

description: sci-RNA-seq3 library


title: sci3-me-510

description: sci-RNA-seq3 library


title: sci3-me-511

description: sci-RNA-seq3 library


title: sci3-me-509

description: sci-RNA-seq3 library


title: sci3-me-512

description: sci-RNA-seq3 library


title: sci3-me-513

description: sci-RNA-seq3 library


title: sci3-me-508

description: sci-RNA-seq3 library


title: sci3-me-504

description: sci-RNA-seq3 library


title: sci3-me-505

description: sci-RNA-seq3 library


title: sci3-me-507

description: sci-RNA-seq3 library


title: sci3-me-502

description: sci-RNA-seq3 library


title: sci3-me-500

description: sci-RNA-seq3 library


title: sci3-me-501

description: sci-RNA-seq3 library


title: sci3-me-519

description: sci-RNA-seq3 library


title: sci3-me-498

description: sci-RNA-seq3 library


title: sci3-me-496

description: sci-RNA-seq3 library


title: sci3-me-497

description: sci-RNA-seq3 library


title: sci3-me-494

description: sci-RNA-seq3 library


title: sci3-me-495

description: sci-RNA-seq3 library


title: sci3-me-493

description: sci-RNA-seq3 library


title: sci3-me-492

description: sci-RNA-seq3 library


title: sci3-me-515

description: sci-RNA-seq3 library


title: sci3-me-491

description: sci-RNA-seq3 library


title: sci3-me-490

description: sci-RNA-seq3 library


title: sci3-me-489

description: sci-RNA-seq3 library


title: sci3-me-487

description: sci-RNA-seq3 library


title: sci3-me-488

description: sci-RNA-seq3 library


title: sci3-me-506

description: sci-RNA-seq3 library


title: sci3-me-503

description: sci-RNA-seq3 library


title: sci3-me-486

description: sci-RNA-seq3 library


title: sci3-me-499

description: sci-RNA-seq3 library


title: sci3-me-485

description: sci-RNA-seq3 library


title: sci3-me-481

description: sci-RNA-seq3 library


title: sci3-me-483

description: sci-RNA-seq3 library


title: sci3-me-478

description: sci-RNA-seq3 library


title: sci3-me-480

description: sci-RNA-seq3 library


title: sci3-me-479

description: sci-RNA-seq3 library


title: sci3-me-476

description: sci-RNA-seq3 library


title: sci3-me-475

description: sci-RNA-seq3 library


title: sci3-me-477

description: sci-RNA-seq3 library


title: sci3-me-474

description: sci-RNA-seq3 library


title: sci3-me-472

description: sci-RNA-seq3 library


title: sci3-me-473

description: sci-RNA-seq3 library


title: sci3-me-471

description: sci-RNA-seq3 library


title: sci3-me-470

description: sci-RNA-seq3 library


title: sci3-me-468

description: sci-RNA-seq3 library


title: sci3-me-469

description: sci-RNA-seq3 library


title: sci3-me-467

description: sci-RNA-seq3 library


title: Smc1 ChIP-seq Smc1 RNAi replicate 2

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

library_source: genomic

data_processing:
Basecalling was performed by Torrent Suite version 5 software using default settings.
Aligmentment to the Drosophila release 5 genome sequence was performed using the TMAP map4 algorithm without soft clipping (-g 3 option)
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDTools genomecoveragebed (-d option)
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Dorsett and Misulovin. 2017. Methods Mol Biol 1515:125-139, DOI: 10.1007/978-1-4939-6545-8_8. Input sequence used for each sample is indicated above. Coverage in each window was normalized to total genome coverage prior to normalization to Input. For mapping early S phase DNA synthesis the sliding window was adjusted to 2,450 bp with 50 bp steps.
ChIP enrichment was averaged for all replicates to generate final processed data files
Genome_build: Drosophila melanogaster Release 5 (April 2006) with ChrU and Uextra removed
Supplementary_files_format_and_content: SGR

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cultured cells

growth_protocol: ML-DmBG3-c2 cells were cultured in Schneider's media with 10% fetal calf serum (FCS) and 10 micrograms per mL insulin at 25 degrees.

extract_protocol:
Chromatin was prepared and ChIP-seq was conducted as described in Dorsett and Misulovin. 2017. Methods Mol Biol 1515:125-139, DOI: 10.1007/978-1-4939-6545-8_8.
For early S phase DNA synthesis, cells were removed from the plate after treatment by scraping, fixed with 1% formaldehyde in 20 mL volume per 100 million cells for 12 min at room temperature and fixation was stopped by adjusting to 0.25 M glycine. Cells were washed twice with phosphate buffered saline (PBS). Cells were permeablized in PBS containing 0.25% Triton X-100 (20 mL per 100 million cells) for 30 min at room termperature, and washed twice with PBS containing 0.5% bovine serum albumin. A click reaction (1 mL per 100 million cells) was conducted in PBS containing 100 micromolar Azide-PEG3-biotin conjugate, 10 mM sodium ascorbate and 2 mM copper sulftate for 60 min in the dark at room temperature. The cells were washed 3 times with PBS and chromatin was prepared as described for the ChIP-seq except the cells were suspended in 1 mL sonication buffer per 100 million cells, the sonication buffer contained 0.4% sodium dodecyl sulfate, and sonication was conducted for 5 cycles. The sonicated suspension was adjusted to 0.5% lauryl sarcosine and clarifed by centrifugation at 15 g for 10 min. Crosslinks were reversed by diluting 1 mL chromatin with 1 mL TE, adjusting to 800 micrograms per mL RNAse A, 500 micrograms per mL Proteinase K and 0.5% sodium dodecyl sulfate, and incubating at 65 degrees overnight. The solution was extracted with phenol:chloroform:isoamyl alcohol (25:24:1, pH 7.5) and the DNA purified using Qiagen QIAquick PCR purification columns, eluting twice with 55 microliters of provided elution buffer. EdU-containing DNA was isolated from the purified DNA using magnetic streptavidin beads (Dynabeads® M-280 Streptavidin, ThermoFisher). Twenty microliters of beads were washed twice before use with 1 mL of WB (5 mM Tris.HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.1% Tween 20). 100 microliters of DNA was diluted with 100 microliters of 2X WB and incubated with the streptavidin beads for 30 min at room temperature. Beads were collected with a magnet, and washed 3 times with 1 mL WB for 5 min. DNA was eluted from the beads by suspending in 400 microliters of 0.3X TE containing 1% SDS and 0.5 micrograms per mL Proteinase K and incubating at 65 degrees for 20 min. The bead suspension was extracted with 400 microliters of phenol:chloroform:isoamyl alcohol (25:24:1, pH 7.5) and DNA was purified from the supernatant using a column (Qiagen MinElute PCR Purification).
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Fragment Library Kit (ThermoFisher) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol:
For RNAi, media was replaced with 1 mL of Express Five SFM (Invitrogen) with 1% FCS and 10 micrograms per mL insulin for 3 hours. Depending on the target protein, from 10 to 40 microgram of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 mL and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters.Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.
For JQ1 treatment, JQ1 (stock 10 mM in DMSO) was added to the culture media at 10 micromolar final concentration for 8 hours.
For mapping early S phase DNA synthesis, culture media was adjusted to 1 mM hydroxyurea for 3 hours, and EdU thymidine analog (ThermoFisher) was then added at 10 micromolar final concentration overnight (~16 hours).

tag: antibody

value: Smc1, rabbit

tag: antibody source

value: Dale Dorsett

tag: normalization input


title: sci3-me-466

description: sci-RNA-seq3 library


title: sci3-me-484

description: sci-RNA-seq3 library


title: sci3-me-482

description: sci-RNA-seq3 library


title: Smc1 ChIP-seq mock treatment replicate 3


title: sci3-me-463

description: sci-RNA-seq3 library


title: sci3-me-465

description: sci-RNA-seq3 library


title: sci3-me-464

description: sci-RNA-seq3 library


title: sci3-me-462

description: sci-RNA-seq3 library


title: sci3-me-460

description: sci-RNA-seq3 library


title: Smc1 ChIP-seq mock treatment replicate 2


title: Smc1 ChIP-seq Smc1 RNAi replicate 1


title: Smc1 ChIP-seq JQ1 treatment replicate 2


title: Smc1 ChIP-seq JQ1 treatment replicate 1


title: Smc1 ChIP-seq mock treatment replicate 1


title: SA ChIP-seq Smc1 RNAi depletion replicate 1

value: SA, guinea pig


title: Smc1 ChIP-seq SA RNAi replicate 1


title: sci3-me-456

description: sci-RNA-seq3 library


title: SA ChIP-seq Rad21 RNAi depletion replicate 2


title: sci3-me-458

description: sci-RNA-seq3 library


title: sci3-me-461

description: sci-RNA-seq3 library


title: sci3-me-453

description: sci-RNA-seq3 library


title: sci3-me-455

description: sci-RNA-seq3 library


title: sci3-me-459

description: sci-RNA-seq3 library


title: sci3-me-452

description: sci-RNA-seq3 library


title: SA ChIP-seq MED30 RNAi depletion replicate 1


title: SA ChIP-seq MED30 RNAi depletion replicate 2


title: Smc1 ChIP-seq SA RNAi replicate 2


title: sci3-me-451

description: sci-RNA-seq3 library


title: SA ChIP-seq mock treatment replicate 4


title: sci3-me-457

description: sci-RNA-seq3 library


title: SA ChIP-seq mock treatment replicate 2


title: SA ChIP-seq mock treatment replicate 3


title: SA ChIP-seq JQ1 treatment replicate 2


title: SA ChIP-seq Rad21 RNAi depletion replicate 1


title: sci3-me-454

description: sci-RNA-seq3 library


title: SA ChIP-seq MED30 RNAi depletion replicate 3


title: SA ChIP-seq mock treatment replicate 1


title: SA ChIP-seq JQ1 treatment replicate 1


title: Rad21 ChIP-seq Smc1 RNAi depletion replicate 1

value: Rad21, rabbit


title: sci3-me-444

description: sci-RNA-seq3 library


title: sci3-me-449

description: sci-RNA-seq3 library


title: sci3-me-450

description: sci-RNA-seq3 library


title: sci3-me-447

description: sci-RNA-seq3 library


title: sci3-me-448

description: sci-RNA-seq3 library


title: sci3-me-445

description: sci-RNA-seq3 library


title: Rad21 ChIP-seq JQ1 treatment replicate 2


title: Rad21 ChIP-seq JQ1 treatment replicate 1


title: Rad21 ChIP-seq mock treatment replicate 1


title: sci3-me-440

description: sci-RNA-seq3 library


title: sci3-me-441

description: sci-RNA-seq3 library


title: sci3-me-439

description: sci-RNA-seq3 library


title: sci3-me-442

description: sci-RNA-seq3 library


title: sci3-me-443

description: sci-RNA-seq3 library


title: sci3-me-437

description: sci-RNA-seq3 library


title: sci3-me-438

description: sci-RNA-seq3 library


title: Preimmune serum ChIP-seq replicate 1

value: guinea pig preimmune serum


title: Rad21 ChIP-seq mock treatment replicate 2


title: sci3-me-446

description: sci-RNA-seq3 library


title: sci3-me-436

description: sci-RNA-seq3 library


title: sci3-me-435

description: sci-RNA-seq3 library


title: Rad21 ChIP-seq SA RNAi depletion replicate 2


title: Rad21 ChIP-seq SA RNAi depletion replicate 3


title: Nipped-B ChIP-seq SA RNAi depletion replicate 1

value: Nipped-B, rabbit


title: sci3-me-434

description: sci-RNA-seq3 library


title: sci3-me-433

description: sci-RNA-seq3 library


title: Nipped-B ChIP-seq SA RNAi depletion replicate 2


title: Rad21 ChIP-seq SA RNAi depletion replicate 1


title: Nipped-B ChIP-seq Rad21 RNAi depletion replicate 1


title: Nipped-B ChIP-seq Smc1 RNAi depletion replicate 1


title: Nipped-B ChIP-seq Rad21 RNAi depletion replicate 2


title: sci3-me-432

description: sci-RNA-seq3 library


title: Nipped-B ChIP-seq MED30 RNAi depletion replicate 2


title: sci3-me-430

description: sci-RNA-seq3 library


title: sci3-me-429

description: sci-RNA-seq3 library


title: Nipped-B ChIP-seq MED30 RNAi depletion replicate 3


title: Nipped-B ChIP-seq MED30 RNAi depletion replicate 1


title: sci3-me-428

description: sci-RNA-seq3 library


title: Nipped-B ChIP-seq mock treatment replicate 1


title: Nipped-B ChIP-seq mock treatment replicate 2


title: Nipped-B ChIP-seq JQ1 treatment replicate 2


title: Nipped-B ChIP-seq JQ1 treatment replicate 1


title: MED30 ChIP-seq Smc1 RNAi depletion replicate 1

value: MED30, guinea pig


title: sci3-me-422

description: sci-RNA-seq3 library


title: sci3-me-424

description: sci-RNA-seq3 library


title: sci3-me-423

description: sci-RNA-seq3 library


title: sci3-me-431

description: sci-RNA-seq3 library


title: sci3-me-427

description: sci-RNA-seq3 library


title: sci3-me-421

description: sci-RNA-seq3 library


title: MED30 ChIP-seq SA RNAi depletion replicate 2


title: MED30 ChIP-seq mock treatment replicate 1


title: MED30 ChIP-seq JQ1 treatment replicate 2


title: sci3-me-426

description: sci-RNA-seq3 library


title: sci3-me-417

description: sci-RNA-seq3 library


title: sci3-me-425

description: sci-RNA-seq3 library


title: sci3-me-419

description: sci-RNA-seq3 library


title: sci3-me-420

description: sci-RNA-seq3 library


title: MED30 ChIP-seq JQ1 treatment replicate 1


title: MED30 ChIP-seq SA RNAi depletion replicate 1


title: MED1 ChIP-seq mock treatment replicate 2

value: MED1, rabbit


title: sci3-me-418

description: sci-RNA-seq3 library


title: MED1 ChIP-seq mock treatment replicate 1


title: sci3-me-415

description: sci-RNA-seq3 library


title: sci3-me-414

description: sci-RNA-seq3 library


title: MED30 ChIP-seq Smc1 RNAi depletion replicate 2


title: Normalization input for early S phase DNA synthesis

description: Input.EdU.fastq.gz

value: normalization input


title: Fs(1)h ChIP-seq mock treatment replicate 2

value: Fs(1)hSL, rabbit

value: Igor Dawid


title: Fs(1)h ChIP-seq mock treatment replicate 1


title: MED30 ChIP-seq mock treatment replicate 2


title: sci3-me-412

description: sci-RNA-seq3 library


title: Fs(1)h ChIP-seq JQ1 treatment replicate 1


title: sci3-me-411

description: sci-RNA-seq3 library


title: Early S phase DNA synthesis (EdU) replicate 1


title: sci3-me-410

description: sci-RNA-seq3 library


title: sci3-me-416

description: sci-RNA-seq3 library


title: Early S phase DNA synthesis (EdU) replicate 2


title: PC9 NEO rep3

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

country: China

institute: The Affiliated Hospital of Southwest Medical University

data_processing:
Illumina bcl2fastq 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRch37.p13 whole genome using HISAT2 (version 2.1.0) with default parameters
Read counts are aggregated at the gene level using HTseq(version 0.9.1) and then identified DEGs using R package DESeq2
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each Sample

organism: Homo sapiens

extract_protocol:
Total RNA of stably infected cells was isolated with Trizol and the polyadenylated mRNAs were extracted using Dynabeads Oligo (dT) 25 beads
RNA libraries were constructed with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina ® (NEB, USA) with 3 independent replicates following the manufacturer’s instructions. One hundred and fifty bp paired-end sequencing was performing using Illumina HiSeq Xten.

tag: cell type

value: non-small cell lung cancer cell line

tag: cell line

tag: genotype/variation

value: transfected with NEO


title: sci3-me-405

description: sci-RNA-seq3 library


title: sci3-me-404

description: sci-RNA-seq3 library


title: PC9 NEO rep2


title: PC9 HOXC6 rep2

value: transfected with HOXC6


title: PC9 HOXC6 rep3


title: sci3-me-408

description: sci-RNA-seq3 library


title: sci3-me-409

description: sci-RNA-seq3 library


title: PC9 NEO rep1


title: sci3-me-406

description: sci-RNA-seq3 library


title: A549 NEO rep3


title: sci3-me-402

description: sci-RNA-seq3 library


title: sci3-me-403

description: sci-RNA-seq3 library


title: sci3-me-407

description: sci-RNA-seq3 library


title: PC9 HOXC6 rep1


title: sci3-me-413

description: sci-RNA-seq3 library


title: sci3-me-400

description: sci-RNA-seq3 library


title: sci3-me-401

description: sci-RNA-seq3 library


title: A549 NEO rep1


title: A549 NEO rep2


title: sci3-me-399

description: sci-RNA-seq3 library


title: A549 HOXC6 rep3


title: A549 HOXC6 rep2


title: sci3-me-397

description: sci-RNA-seq3 library


title: sci3-me-396

description: sci-RNA-seq3 library


title: sci3-me-398

description: sci-RNA-seq3 library


title: A549 HOXC6 rep1


title: sci3-me-393

description: sci-RNA-seq3 library


title: sci3-me-392

description: sci-RNA-seq3 library


title: sci3-me-391

description: sci-RNA-seq3 library


title: sci3-me-394

description: sci-RNA-seq3 library


title: sci3-me-395

description: sci-RNA-seq3 library


title: W5 Replicate 3

city: Boston

first: Alejandro

last: Gutierrez

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
Alignments were performed with STAR aligner (version 2.3.1z4) against the hg19 w ERCC92 genome
Aligned files were processed to primary (raw) read counts using featureCounts, and primary read counts were normalized using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: [normalized counts.csv]  normalized mRNA reads for each individual sample and gene

molecule: total RNA

source_name: Jurkat cell line

growth_protocol: RPMI 10%FBS 1%PenStrep

extract_protocol:
RNA was extracted from BRCA2 wild-type or heterozygous mutant clones using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.  RNA samples were then treated with Ambion Turbo DNAse (Thermo Fisher Scientific, Waltham, MA), and DNA contamination was confirmed to be <10% for all samples.  RNA quantity was determined using the Qubit RNA Assay Kit (Thermo Fisher Scientific) and RNA quality was determined on an Agilent Bioanalyzer using the RNA Pico Kit (Agilent, Santa Clara, CA).
Using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA), 50-100 ng of total RNA was converted into a DNA library following the manufacturer’s protocol. Following library construction, DNA libraries were assessed for quality control.  Library quantity was determined using the Qubit High Sensitivity DNA Kit (Thermo Fisher Scientific) and library size was determined using the Bioanalyzer High Sensitivity Chip Kit (Agilent).

value: Jurkat cell line

tag: genotype

value: BRCA2 +/-


title: W5 Replicate 2


title: W5 Replicate 1


title: W4 Replicate 3


title: sci3-me-387

description: sci-RNA-seq3 library

value: B6 background


title: sci3-me-389

description: sci-RNA-seq3 library


title: sci3-me-388

description: sci-RNA-seq3 library


title: W4 Replicate 2


title: sci3-me-386

description: sci-RNA-seq3 library


title: sci3-me-385

description: sci-RNA-seq3 library


title: W4 Replicate 1


title: sci3-me-384

description: sci-RNA-seq3 library


title: Dox_shCTCF1_Rep3_RNA

type: RNA

city: Madison

first: Nathan

last: Damaschke

state: WI

address: 1111 Highland Ave Room 7048

department: Urology

institute: University of Wisconsin

description: Induced shRNA CTCF knockdonw rep 3

hyb_protocol: Samples were hybridized to the Human Transcriptome 2.0 Array (Affymetrix) and scanned at the University of Wisconsin-Madison Biotechnology Center.

scan_protocol: Gene chips were post processed on the AFX Fluidics 450 Station, and Chips were scanned on the GC3000 G7 Scanner (Serial #50208130)

data_processing: Raw data were processed with the Affymetrix Command Console version 4.0.0.1567G (Affymetrix) for background correction and normalization.  Data analysis were performed using the Transcriptome Analysis Console v3.0 (Affymetrix).  RMA expression value (Log2 transformed) derived from Expression Console Software

label: Biotin

source_name: Immortalized prostate epithelial cells

label_protocol: Single-stranded cDNA was generated from 15ug of total RNA with the Affymetrix WT Plus Expression kit and then fragmented and labeled with the Affymetrix WT Terminal Labiling Kit according to manufacturer's protocols.

growth_protocol: Cells were grown in Ham's F12 Medium supplemented with 1% fetal bovine serum, 100 U/ml penicillin/streptomycin, 2mM L-glutamine, 0.1mM non-essential amino acids, 2.7mg/ml dextrose, 5microgram/ml human transferrin, 1microgram/ml hydrocortisone, 0.25U/ml human insulin, 10ng/ml cholera toxin, and 0.25% bovine pituitary extract.  Cells were grown in 37C incubator at 5% CO2.  Cells were harvested following 5 days of treatment, and proceeded to RNA extraction

extract_protocol: RNA was extracted using the PerfectPure RNA Tissue Kit (5prime) according to manufacturer's instructions.  Quality assesment was conducted using an Agilent RNA Nanochip and by a Nanodrop spectrophotometer (Thermo).

treatment_protocol: Stable cell lines harboring doxycycline inducible shRNA targeting CTCF were maintained under selection with 1ug/ml puromycin on 10cm plates.  Doxycycline or vehicle only (DMSO) was added to media at 2ug/ml, media and doxycycline were refreshed every 48 hours until harvest.

tag: tissue

value: Immortalized prostate epithelial cells

tag: treatment

value: CTCF knockdown, doxycycline treated, 5 days


title: DMSO_shCTCF1_Rep2_RNA

description: Uninduced control rep 2

value: No knockdown control, vehicle treated, 5 days


title: Dox_shCTCF1_Rep1_RNA

description: Induced shRNA CTCF knockdonw rep 1


title: DMSO_shCTCF1_Rep1_RNA

description: Uninduced control rep 1


title: Dox_shCTCF1_Rep2_RNA

description: Induced shRNA CTCF knockdonw rep 2


title: DMSO_shCTCF1_Rep3_RNA

description: Uninduced control rep 3


title: Cas9 Replicate 3

value: BRCA2 WT


title: Normal_control_12

city: Guangzhou

first: Xinmei

last: Zhao

address: No 1838 Guangzhou North Avenue

institute: Nanfang Hospital, Southern Medical University

description: SAMPLE 60

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The  expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed before performing statistical analysis.

label: biotin

source_name: control

label_protocol: Total RNA was labled with the WG-DASL pre 1 MCS4 w/UDG Kit according to manufacturers suggested protocols.

extract_protocol: Standard Allprep RNA/DNA FFPE kit protocol

tag: disease state

value: Normal

tag: individual id

value: intestinal tissue


title: sci3-me-382

description: sci-RNA-seq3 library


title: sci3-me-390

description: sci-RNA-seq3 library


title: sci3-me-373

description: sci-RNA-seq3 library


title: Parental Replicate 2


title: Parental Replicate 3


title: sci3-me-379

description: sci-RNA-seq3 library


title: sci3-me-374

description: sci-RNA-seq3 library


title: sci3-me-378

description: sci-RNA-seq3 library


title: sci3-me-377

description: sci-RNA-seq3 library


title: Cas9 Replicate 1


title: sci3-me-380

description: sci-RNA-seq3 library


title: Cas9 Replicate 2


title: sci3-me-376

description: sci-RNA-seq3 library


title: sci3-me-383

description: sci-RNA-seq3 library


title: sci3-me-381

description: sci-RNA-seq3 library


title: sci3-me-372

description: sci-RNA-seq3 library


title: sci3-me-375

description: sci-RNA-seq3 library


title: sci3-me-371

description: sci-RNA-seq3 library


title: Parental Replicate 1


title: Normal_control_10

description: SAMPLE 58


title: sci3-me-369

description: sci-RNA-seq3 library


title: Normal_control_11

description: SAMPLE 59


title: Normal_control_7

description: SAMPLE 55


title: 40436_v13_mait

city: Silver Spring

first: Dohoon

last: Kim

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Henry M Jackson

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to hg38 whole genome using STAR v2.5.2b with parameters ;  BAM SortedByCoordinate --quantMode TranscriptomeSAM --outFileNamePrefix
The alignment data was normalized and analyzed using featureCount, RUVg, and edgeR
The alignment data was treated with RSEM and then used in GSEA(Gene Set Enrichment Analysis by Broad institute). The required .gct files were transfomed by Xcode.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample(featureCount) and gct files for GSEA

source_name: v13' is Visit 13th (13th visit)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen), and RNA-Seq cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) according to the manufacturer’s instructions.
Amplified material was purified using Agencourt AMPure XP beads (Beckman). cDNA quantity was assessed on a Qubit 3.0 (ThermoFisher) and fragment size was evaluated on a 2100 BioAnalyzer (Agilent). The PCR products were next indexed using the Nextera XT DNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Briefly, products were tagmented using the Amplicon tagment mix containing Tn5 transposase, and indexed using Nextera index 1 (i7) and index 2 (i5) primers. The libraries were again cleaned-up with Agencourt AMPure XP beads, quantified, pooled, and sequenced across 75 base pairs (bp) using a single-end strategy with a 75-cycle high output flow cell on a NextSeq 500 (Illumina).

tag: donor

value: Primary human peripheral blood mononuclear cells (PBMC)

value: Mucosa-associated invariant T (MAIT) cells

tag: diagnosis

value: HIV+

tag: cell population

value: Va7.2+ CD161++ of CD3+ T cells


title: sci3-me-366

description: sci-RNA-seq3 library


title: 40436_v5_mait

source_name: v5' is Visit 5th (5th visit)


title: sci3-me-365

description: sci-RNA-seq3 library


title: 40363_v13_mait


title: sci3-me-368

description: sci-RNA-seq3 library


title: sci3-me-367

description: sci-RNA-seq3 library


title: 40436_va_mait

source_name: vA' is Visit 0th (First visit, control group)


title: Normal_control_8

description: SAMPLE 56


title: 40436_v11_mait

source_name: v11' is Visit 11th (11th visit)


title: sci3-me-364

description: sci-RNA-seq3 library


title: Normal_control_9

description: SAMPLE 57


title: Normal_control_5

description: SAMPLE 53


title: sci3-me-363

description: sci-RNA-seq3 library


title: sci3-me-362

description: sci-RNA-seq3 library


title: sci3-me-361

description: sci-RNA-seq3 library


title: 40363_v11_mait


title: Normal_control_6

description: SAMPLE 54


title: sci3-me-370

description: sci-RNA-seq3 library


title: Normal_control_4

description: SAMPLE 52


title: 40363_v5_mait


title: sci3-me-360

description: sci-RNA-seq3 library


title: sci3-me-359

description: sci-RNA-seq3 library


title: Normal_control_2

description: SAMPLE 50


title: Normal_control_1

description: SAMPLE 49


title: Normal_control_3

description: SAMPLE 51


title: sci3-me-358

description: sci-RNA-seq3 library


title: 40363_va_mait


title: sci3-me-356

description: sci-RNA-seq3 library


title: sci3-me-354

description: sci-RNA-seq3 library


title: sci3-me-355

description: sci-RNA-seq3 library


title: CD_uninvolved_23

description: SAMPLE 47

source_name: Crohn’s disease uninvolved

value: CD

tag: site

value: uninvolved


title: CD_uninvolved_24

description: SAMPLE 48


title: sci3-me-352

description: sci-RNA-seq3 library

tag: developmental stage


title: sci3-me-353

description: sci-RNA-seq3 library

tag: genetic background


title: sci3-me-351

description: sci-RNA-seq3 library


title: 40353_v11_mait


title: 40353_v5_mait


title: 40353_v13_mait


title: sci3-me-349

description: sci-RNA-seq3 library


title: sci3-me-350

description: sci-RNA-seq3 library


title: sci3-me-348

description: sci-RNA-seq3 library


title: CD_uninvolved_22

description: SAMPLE 46


title: CD_uninvolved_21

description: SAMPLE 45


title: sci3-me-347

description: sci-RNA-seq3 library


title: sci3-me-357

description: sci-RNA-seq3 library


title: sci3-me-346

description: sci-RNA-seq3 library


title: 10742_v13_mait


title: sci3-me-345

description: sci-RNA-seq3 library


title: sci3-me-344

description: sci-RNA-seq3 library


title: CD_uninvolved_20

description: SAMPLE 44


title: CD_uninvolved_19

description: SAMPLE 43


title: 10742_v11_mait


title: sci3-me-343

description: sci-RNA-seq3 library


title: 40353_va_mait


title: CD_uninvolved_18

description: SAMPLE 42


title: CD_uninvolved_16

description: SAMPLE 40


title: sci3-me-342

description: sci-RNA-seq3 library


title: sci3-me-341

description: sci-RNA-seq3 library


title: 10742_v5_mait


title: sci3-me-340

description: sci-RNA-seq3 library


title: 10723_v13_mait


title: CD_uninvolved_17

description: SAMPLE 41


title: 10742_va_mait


title: sci3-me-339

description: sci-RNA-seq3 library


title: sci3-me-337

description: sci-RNA-seq3 library


title: 10723_v11_mait


title: sci3-me-336

description: sci-RNA-seq3 library


title: CD_uninvolved_15

description: SAMPLE 39


title: sci3-me-333

description: sci-RNA-seq3 library


title: sci3-me-334

description: sci-RNA-seq3 library


title: sci3-me-335

description: sci-RNA-seq3 library


title: sci3-me-332

description: sci-RNA-seq3 library


title: CD_uninvolved_14

description: SAMPLE 38


title: CD_uninvolved_13

description: SAMPLE 37


title: 10723_va_mait


title: 10723_v5_mait


title: 10435_v13_mait


title: sci3-me-331

description: sci-RNA-seq3 library


title: CD_uninvolved_12

description: SAMPLE 36


title: CD_uninvolved_11

description: SAMPLE 35


title: sci3-me-338

description: sci-RNA-seq3 library


title: sci3-me-329

description: sci-RNA-seq3 library


title: sci3-me-330

description: sci-RNA-seq3 library


title: 10435_v11_mait


title: CD_uninvolved_10

description: SAMPLE 34


title: 10435_v5_mait


title: sci3-me-327

description: sci-RNA-seq3 library


title: sci3-me-326

description: sci-RNA-seq3 library


title: sci3-me-325

description: sci-RNA-seq3 library


title: 10435_va_mait


title: sci3-me-324

description: sci-RNA-seq3 library


title: sci3-me-323

description: sci-RNA-seq3 library


title: sci3-me-322

description: sci-RNA-seq3 library


title: CD_uninvolved_9

description: SAMPLE 33


title: sci3-me-320

description: sci-RNA-seq3 library


title: 10428_v13_mait


title: 10428_v5_mait


title: CD_uninvolved_8

description: SAMPLE 32


title: 10428_v11_mait


title: sci3-me-319

description: sci-RNA-seq3 library


title: sci3-me-318

description: sci-RNA-seq3 library


title: sci3-me-328

description: sci-RNA-seq3 library


title: sci3-me-317

description: sci-RNA-seq3 library


title: 10428_va_mait


title: sci3-me-316

description: sci-RNA-seq3 library


title: sci3-me-315

description: sci-RNA-seq3 library


title: 10220_v13_mait


title: sci3-me-321

description: sci-RNA-seq3 library


title: 10220_v11_mait


title: CD_uninvolved_5

description: SAMPLE 29


title: sci3-me-313

description: sci-RNA-seq3 library


title: sci3-me-314

description: sci-RNA-seq3 library


title: 10220_v5_mait


title: sci3-me-312

description: sci-RNA-seq3 library


title: CD_uninvolved_4

description: SAMPLE 28


title: sci3-me-311

description: sci-RNA-seq3 library


title: CD_uninvolved_7

description: SAMPLE 31


title: CD_uninvolved_2

description: SAMPLE 26


title: CD_uninvolved_6

description: SAMPLE 30


title: sci3-me-310

description: sci-RNA-seq3 library


title: 10220_va_mait


title: sci3-me-307

description: sci-RNA-seq3 library


title: sci3-me-306

description: sci-RNA-seq3 library


title: 10203_v13_mait


title: CD_uninvolved_3

description: SAMPLE 27


title: sci3-me-308

description: sci-RNA-seq3 library


title: 10203_v11_mait


title: sci3-me-304

description: sci-RNA-seq3 library


title: CD_involved_24

description: SAMPLE 24

source_name: Crohn’s disease involved

value: involved


title: CD_involved_23

description: SAMPLE 23


title: CD_uninvolved_1

description: SAMPLE 25


title: CD_involved_22

description: SAMPLE 22


title: CD_involved_21

description: SAMPLE 21


title: sci3-me-309

description: sci-RNA-seq3 library


title: 10203_v5_mait


title: sci3-me-302

description: sci-RNA-seq3 library


title: 10203_va_mait


title: sci3-me-301

description: sci-RNA-seq3 library


title: sci3-me-299

description: sci-RNA-seq3 library


title: CD_involved_20

description: SAMPLE 20


title: sci3-me-305

description: sci-RNA-seq3 library


title: sci3-me-300

description: sci-RNA-seq3 library


title: sci3-me-298

description: sci-RNA-seq3 library


title: sci3-me-297

description: sci-RNA-seq3 library


title: sci3-me-296

description: sci-RNA-seq3 library


title: sci3-me-295

description: sci-RNA-seq3 library


title: sci3-me-294

description: sci-RNA-seq3 library


title: sci3-me-303

description: sci-RNA-seq3 library


title: sci3-me-293

description: sci-RNA-seq3 library


title: CD_involved_19

description: SAMPLE 19


title: CD_involved_16

description: SAMPLE 16


title: sci3-me-291

description: sci-RNA-seq3 library


title: sci3-me-290

description: sci-RNA-seq3 library


title: sci3-me-289

description: sci-RNA-seq3 library


title: sci3-me-292

description: sci-RNA-seq3 library


title: CD_involved_17

description: SAMPLE 17


title: sci3-me-288

description: sci-RNA-seq3 library


title: sci3-me-286

description: sci-RNA-seq3 library


title: sci3-me-285

description: sci-RNA-seq3 library


title: CD_involved_18

description: SAMPLE 18


title: sci3-me-284

description: sci-RNA-seq3 library


title: CD_involved_15

description: SAMPLE 15


title: CD_involved_14

description: SAMPLE 14


title: sci3-me-283

description: sci-RNA-seq3 library


title: sci3-me-282

description: sci-RNA-seq3 library


title: SHR 215 male, 2 months of age, standart laboratory chow, left ventricle myocardium

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Left ventricle myocardium expression data obtained from SHR strain.

hyb_protocol: hybridization was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with PARTEK Genomics Suite 6.6 (Partek, Inc., Chesterfield, MO, USA) using GC-MRA as normalization method.

organism: Rattus norvegicus

label_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

growth_protocol: Both strains were bred in-house. Rats were kept under 12 hours light-dark cycle, fed standard laboratory chow and given access to water ad libitum. After 2 months rats were anesthetized and decapitated. Organs were snap frozen in liquid nitrogen, and left ventricular myocardium was used for RNA extraction and further analysis.

extract_protocol: Total heart RNA was isolated using TRIzol reagent (Invitrogen) and purification was performed using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. UV measurements at 280 and 260 nm and 2100 Bioanalyzer runs using the RNA-6000 Nano-LabChip (Agilent, Böblingen, Germany) were used to ensure the quality and quantity of the extracted RNA Only samples showing RNA integrity numbers (RIN) above 8 were used for furhter analysis.

tag: strain

value: SHR

tag: gender

value: male

tag: age

value: 2 months

value: left ventricular myocardium


title: SHR 218 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: CD_involved_13

description: SAMPLE 13


title: SHR 219 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: CD_involved_12

description: SAMPLE 12


title: SHR 213 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: PD5 210 male, 2 months of age, standart laboratory chow, left ventricle myocardium

description: Lef ventricle myocardium expression data obtained from PD5 strain.


title: CD_involved_10

description: SAMPLE 10


title: sci3-me-287

description: sci-RNA-seq3 library

value: B6 background


title: CD_involved_9

description: SAMPLE 9


title: sci3-me-280

description: sci-RNA-seq3 library


title: sci3-me-279

description: sci-RNA-seq3 library


title: PD5 212 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: PD5 209 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: PD5 207 male, 2 months of age, standart laboratory chow, left ventricle myocardium


title: sci3-me-277

description: sci-RNA-seq3 library


title: sci3-me-281

description: sci-RNA-seq3 library


title: VAM2 BSA 1

city: NEW YORK

first: Hernandez

last: Moura Silva

state: NY

address: 430 E 29th street. 4th floor, Lab 460A

department: Kimmel Center for Biology and Medicine at the Skirball Institute

institute: New York University Langone Medical Center

description: Samples was prepared in the same way as the FBS ones. The only difference is that instead of FBS it was used BSA FFA free in the digestion buffer and other solutions to obtain the Adipose tissue SVF.

data_processing:
Illumina sequencing adapters and reads with Phred quality scores lower than 20 were removed with Trimmomatic. Trimmed reads were mapped to the Mus musculus genome Ensembl annotation release 91 using STAR v2.5.3a with default settings. The number of reads uniquely mapping to each gene feature in the corresponding annotation file was determined using featureCounts. The resulting count tables were passed to R for further analyses.
Differential expression and gene ontology analyses. Consistency between replicates was checked using principal component analysis (PCA) and Euclidean distance-based hierarchical clustering on normalized counts. Weakly expressed genes, defined as having less than 2 Fragment Per Kilobase of transcript per Million mapped reads (FPKM) in at least one group of replicates were removed from differential expression analysis. Counts normalization were performed using the method of Trimmed Mean of M-values (TMM) from edgeR package. Differential expression analyses were performed using limma. Genes were considered significant when the observed log2 fold-change was greater than 1 and the adjusted P value was less than 0.05. The set of significant genes for each contrast of interest was passed to Goseq for functional gene categories enrichment analyses.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx; It contains all normalized read counts for each gene for each subpopulation replicate. The table contains gene accession #, entrezgene, gene symbol, chromossome, Biotype, strand,

source_name: epididymal white adipose tissue

extract_protocol:
To isolate leukocytes from adipose tissue mice were anesthetized with a mixture containing 12.5mg/ml ketamine, 2.5mg/ml xylazine, and 25 mg/ml acepromazine and intracardially perfused with PBS with 5 mM EDTA. After dissection, the fat tissue was minced and incubated for 35 min at 37oC under gentle agitation (150rpm) in cRPMI (10% FBS, 1mM of Sodium Pyruvate (Gibco, 11360-070), Glutamax 1x (Gibco, 35050-061), MEM non-essential amino acids (Gibco, 11140-050), Hepes (Gibco, 15630-080), Pen Strep (Gibco, 15140-122) and RPMI (Gibco, 21870-076) containing 1mg/ml of collagenase type VIII (Sigma-Aldrich, C2139) and 100ug/ml of DNase I (Sigma-Aldrich, 10104159001). After digestion, the suspension was washed with ice-cold cRPMI and spun down. The floating fat layer was removed and the leukocyte-enriched pellet was ressuspended in cRPMI and filtered through a 70μm cell strainer. Although all results shown in this manuscript were obtained following the above extraction method, we also carried out a comparative experiment in which we used 2% FFA-free BSA (Fisher BP9704100) in the digestion and staining buffers instead of FBS. RNAseq results between the two extraction methods were highly similar without displaying a single gene with significant adjusted p-value. (data not shown).
Total RNA from sorted target cell populations was isolated using TRIzol LS (Invitrogen; 10296010) followed by DNase I (Qiagen, 79254) treatment and cleanup with RNeasy Plus Micro kit (Qiagen, 74034). RNA quality was assessed using pico bioanalyser chips (Agilent, 5067-1513). Only RNAs displaying a RNA integrity number (RIN) of 9 or higher were used for downstream procedures. RNAseq libraries were prepared using the Nugen Ovation Trio low input RNA Library Systems V2 (Nugen; 0507-08) according to the manufacturer’s instructions by the NYU Genome Technology Center. Pooled libraries were sequenced as 50 nucleotide, paired-end reads on an Illumina HiSeq 2500 using v4 chemistry.

treatment_protocol: HFD animals were submitted to High Fat Diet providing 60% calories from fat (Research Diets, D12492i) for 20 weeks starting at 6 weeks olf age

tag: diet

value: Normal Chow

value: Wild Type

tag: animal age

value: 15 weeks old


title: VAM2 BSA 4


title: VAM2 BSA 3


title: CD_involved_8

description: SAMPLE 8


title: CD_involved_11

description: SAMPLE 11


title: sci3-me-278

description: sci-RNA-seq3 library


title: VAM2 FBS 4


title: VAM2 FBS 1


title: VAM2 FBS 3


title: sci3-me-272

description: sci-RNA-seq3 library


title: sci3-me-274

description: sci-RNA-seq3 library


title: sci3-me-275

description: sci-RNA-seq3 library


title: sci3-me-276

description: sci-RNA-seq3 library


title: CD_involved_6

description: SAMPLE 6


title: CD_involved_7

description: SAMPLE 7


title: sci3-me-271

description: sci-RNA-seq3 library


title: CD_involved_5

description: SAMPLE 5


title: sci3-me-269

description: sci-RNA-seq3 library


title: sci3-me-270

description: sci-RNA-seq3 library


title: sci3-me-268

description: sci-RNA-seq3 library


title: CD_involved_4

description: SAMPLE 4


title: sci3-me-267

description: sci-RNA-seq3 library


title: sci3-me-273

description: sci-RNA-seq3 library


title: CD_involved_3

description: SAMPLE 3


title: sci3-me-266

description: sci-RNA-seq3 library


title: sci3-me-265

description: sci-RNA-seq3 library


title: sci3-me-264

description: sci-RNA-seq3 library


title: MPP control replicate 4

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the human genome by Rsubread version 1.22.3.
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Bone marrow

extract_protocol:
RNA was isolated from sorted HSC, MPP and HPC-1 cells derived from crushed bone marrow from the femurs, tibias, hips, and spine using a mortar and pestle. Lineage marker positive cell depletion used biotinylated antibodies against CD3, B220, GR1, and TER119 (BD). Cells were washed and incubated with MACS anti-biotin-beads, then run through MACS LS columns using a magnetic rack. Cells were stained with the following antibodies: strepdavidin-A700 (WEHI), cKIT-APC (WEHI), SCA1-PE/Cy7 (BD, 561024), CD150-BV421 (Biolegend, 566298) and CD48-PE (eBioscience, 12-0481-81) . Fluro-Gold (Sigma) was used to exclude dead cells and samples were sorted on an ARIA cell sorter (BD). RNA was isolated using an RNeasy Micro Kit (Qiagen).
For HSC and MPP samples, the SMART-Seq v4 Ultra Low Input RNAKit for Sequencing (Clontech) was used for cDNA synthesis and amplification followed by the Nextera XT DNA library Preparation Kit (Illumina).
For the HPC-1 samples, libraries were prepared using the TruSeq Stranded RNA Library Prep Kit (Illumina).
Libraries were sequenced with the NextSeq 500 high output (v2) kit to generate 80 bp paired end reads for data analysis.

tag: phf6 status

value: intact

tag: litter

tag: mouse id

tag: cell type

value: MPP

tag: library protocol

value: SMART-seq


title: HPC-1 control replicate 4

value: TruSeq


title: HSC control replicate 4

value: HSC


title: HPC-1 Phf6 delected replicate 4

value: deleted


title: A375/211_b RNA-seq

city: St. Petersburg

first: Piyush

last: Joshi

state: FL

address: 600 5th St S

department: Oncolog/JHACH

institute: Johns Hopkins University

data_processing:
For RNA-seq, Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped using HISAT2 v2.1.0, with --rna-strand -R option. StringTIe was used to quantify obtained alignment that was converted into read counts.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited csv files include reads counts for each sample

source_name: A375/211 (MIR211 overexpressing)

growth_protocol: A375 (ATCC CRL-1619) and A375/211 (MIR211 overexpressing cells were grown in Complete Tu Medium containing a 4:1 mixture of MCDB-153 medium with 1.5 g/L sodium bicarbonate and Leibovitz's L-15 medium with two mM L-glutamine, 2% FBS, and 1.68 mM CaCl2 (42). The cells were grown in a humidified incubator at 37°C, 5% CO2.

extract_protocol: RNA-Seq libraries were prepared using Truseq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA) with 1 ug of total RNA.

tag: cell line

value: A375/211 melanoma cell line


title: MPP Phf6 deleted replicate 4


title: sci3-me-262

description: sci-RNA-seq3 library


title: sci3-me-263

description: sci-RNA-seq3 library


title: CD_involved_2

description: SAMPLE 2

tag: disease state

value: CD

tag: individual id

tag: tissue

value: intestinal tissue


title: CD_involved_1

description: SAMPLE 1

tag: site

value: involved


title: A375/211_a RNA-seq


title: HSC Phf6 deleted replicate 4


title: A375_b RNA-seq

value: A375 melanoma cell line


title: sci3-me-261

description: sci-RNA-seq3 library

tag: developmental stage


title: sci3-me-260

description: sci-RNA-seq3 library

tag: genetic background


title: HPC-1 control replicate 3

tag: strain


title: sci3-me-256

description: sci-RNA-seq3 library


title: sci3-me-257

description: sci-RNA-seq3 library


title: sci3-me-258

description: sci-RNA-seq3 library


title: sci3-me-259

description: sci-RNA-seq3 library


title: A375_a RNA-seq


title: MPP control replicate 3


title: A375/211 BRIC-seq 6h

data_processing:
Library strategy: BRIC-seq
For RNA-seq, Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped using HISAT2 v2.1.0, with --rna-strand -R option. StringTIe was used to quantify obtained alignment that was converted into read counts.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited csv files include reads counts for each sample

source_name: Bru-labelled A375/211 (MIR211 overexpressing)

growth_protocol: A375 (ATCC CRL-1619) and A375/211 (MIR211 overexpressing cells were grown in Complete Tu Medium containing a 4:1 mixture of MCDB-153 medium with 1.5 g/L sodium bicarbonate and Leibovitz's L-15 medium with two mM L-glutamine, 2% FBS, and 1.68 mM CaCl2 (42) supplemented with 150 4μM 5-bromouridine for 24 h. The cells were grown in a humidified incubator at 37°C, 5% CO2.

extract_protocol: RNA-Seq libraries for BRIC-seq were prepared using Truseq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA) with 1 ug of total BrU labelled RNA extracted as per the instruction from the BRIC Kit (RN1007/1008; MBL International, Woburn, MA).

tag: treatment

value: Bru-labelled

tag: time


title: A375/211 BRIC-seq 3h


title: sci3-me-254

description: sci-RNA-seq3 library


title: sci3-me-253

description: sci-RNA-seq3 library


title: sci3-me-252

description: sci-RNA-seq3 library


title: A375/211 BRIC-seq 0h


title: HPC-1 Phf6 delected replicate 3


title: A375/211 BRIC-seq 1h


title: MPP Phf6 deleted replicate 3


title: sci3-me-250

description: sci-RNA-seq3 library


title: sci3-me-249

description: sci-RNA-seq3 library


title: sci3-me-251

description: sci-RNA-seq3 library


title: sci3-me-248

description: sci-RNA-seq3 library


title: HSC Phf6 deleted replicate 3


title: HPC-1 control replicate 2


title: sci3-me-247

description: sci-RNA-seq3 library


title: A375 BRIC-seq 6h

source_name: Bru-labelled A375


title: sci3-me-246

description: sci-RNA-seq3 library


title: sci3-me-255

description: sci-RNA-seq3 library


title: sci3-me-244

description: sci-RNA-seq3 library


title: MPP control replicate 2


title: A375 BRIC-seq 1h


title: HSC control replicate 3


title: HSC control replicate 2


title: A375 BRIC-seq 0h


title: sci3-me-242

description: sci-RNA-seq3 library


title: sci3-me-241

description: sci-RNA-seq3 library


title: HPC-1 Phf6 delected replicate 2


title: sci3-me-245

description: sci-RNA-seq3 library


title: sci3-me-240

description: sci-RNA-seq3 library


title: A375 BRIC-seq 3h


title: sci3-me-239

description: sci-RNA-seq3 library


title: sci3-me-238

description: sci-RNA-seq3 library


title: MPP Phf6 deleted replicate 2


title: sci3-me-237

description: sci-RNA-seq3 library


title: sci3-me-236

description: sci-RNA-seq3 library


title: HSC Phf6 deleted replicate 2


title: HPC-1 control replicate 1


title: sci3-me-235

description: sci-RNA-seq3 library


title: sci3-me-234

description: sci-RNA-seq3 library


title: MPP control replicate 1


title: sci3-me-233

description: sci-RNA-seq3 library


title: HSC control replicate 1


title: sci3-me-243

description: sci-RNA-seq3 library


title: sci3-me-232

description: sci-RNA-seq3 library


title: sci3-me-231

description: sci-RNA-seq3 library


title: HPC-1 Phf6 delected replicate 1


title: sci3-me-230

description: sci-RNA-seq3 library


title: sci3-me-229

description: sci-RNA-seq3 library


title: HSC Phf6 deleted replicate 1


title: sci3-me-225

description: sci-RNA-seq3 library


title: sci3-me-224

description: sci-RNA-seq3 library


title: sci3-me-223

description: sci-RNA-seq3 library


title: sci3-me-226

description: sci-RNA-seq3 library


title: sci3-me-222

description: sci-RNA-seq3 library


title: sci3-me-228

description: sci-RNA-seq3 library


title: sci3-me-221

description: sci-RNA-seq3 library


title: Sample F6_6 HCA+1 Se

city: White Plains

first: Rajiv

middle: R

last: Ratan

state: New York

address: 785 Mamaroneck Ave

department: Research

institute: Burke Neurological Institute

data_processing:
Followed the Illumina Stranded TruSeq protocol to generate standard fragment sizes (100-300bp, mean 150bp).
Libraries were quantified with the Quant-iT PicoGreen assay (Life Technologies) and validated on an Agilent 2200 TapeStation system. Libraries were prepared at core facility at UCLA and sequenced on HiSeq 4000 platform.
100bp paired-end reads were mapped to mouse GRCm38 genome build using Gencode M10 (Ensembl v85) annotations using rna-STAR. We used bias-aware quantification of genes and transcripts using Salmon.
DGE expression analysis was performed with expression levels normalized for gene length, library size, and G+C content (referred to as ‘normalized FPKM’) using the CQN package in R. A linear model framework was used to assess differential expression in log2[normalized FPKM] values for each gene
The R package weighted gene co-expression network analysis (WGCNA) was used to construct co-expression networks using normalized data after adjustment to remove variability from technical covariates. We used the biweight midcorrelation to assess correlations between log2[adjusted FPKM] and parameters for network analysis
Genome_build: mouse GRCm38 genome build using Gencode M10
Supplementary_files_format_and_content: raw counts

source_name: in vitro cortical neurons_HCA + 1 se

growth_protocol: Primary cortical neurons from E15 pups were plated on poly-d-lysine coated plastic 6 well plates for 24 hours.

extract_protocol:
Approximately 50-100µg of RNA was isolated from each sample using the miRNeasy kit with no modifications (Qiagen). For each RNA sample, RNA quality was initially quantified using the RNA Integrity Number (RIN) on an Agilent Bioanalyzer (Agilent Genomics).
We used rRNA depletion with the RiboZero Gold kit (Illumina) to prepare the library. RNA was depleted from 500ng total RNA with the Ribo-Zero Gold kit (Epicentre).

treatment_protocol: Cells were treated as described in the title heading with 0-1mM sodium selenite (Se) and/or 5mM of homocysteic acid for 6 hours.

value: e15 pups

value: primary cortical neurons cultures

tag: culture batch

value: Culture batch 6

value: 5mM of homocysteic acid (Hca) + 1mM sodium selenite (Se) for 6hrs


title: Sample F5_6 HCA+0.1Se

source_name: in vitro cortical neurons_HCA + 0.1 se

tag: animal age

value: 5mM of homocysteic acid (Hca) + 0.1mM sodium selenite (Se) for 6hrs


title: Sample F4_6 Hca

source_name: in vitro cortical neurons_Hca

value: 5mM of homocysteic acid (Hca) for 6 hrs


title: sci3-me-218

description: sci-RNA-seq3 library

source_name: mouse embryos

value: B6 background


title: sci3-me-220

description: sci-RNA-seq3 library


title: sci3-me-217

description: sci-RNA-seq3 library


title: Sample F3_6 1 se

source_name: in vitro cortical neurons_1 se

value: 1mM sodium selenite (Se) for 6hrs


title: sci3-me-219

description: sci-RNA-seq3 library


title: DP HFD 1

tag: diet

value: High Fat diet for 20 weeks (60% calories from fat)

tag: genotype

value: Wild Type

value: 26 weeks old


title: Sample F2_6 0.1 se

source_name: in vitro cortical neurons_0.1 se

value: 0.1mM sodium selenite (Se) for 6hrs


title: DP HFD 2


title: sci3-me-227

description: sci-RNA-seq3 library


title: sci3-me-215

description: sci-RNA-seq3 library


title: sci3-me-214

description: sci-RNA-seq3 library


title: sci3-me-216

description: sci-RNA-seq3 library


title: MPP Phf6 deleted replicate 1

tag: phf6 status

value: deleted

tag: litter

tag: mouse id

value: MPP

value: SMART-seq


title: PreVAM HFD 3


title: PreVAM HFD 2


title: Sample F1_6 control

source_name: in vitro cortical neurons_control

tag: cell type

value: control


title: sci3-me-212

description: sci-RNA-seq3 library


title: sci3-me-211

description: sci-RNA-seq3 library


title: Sample E6_5 HCA+1 Se

value: culture batch 5


title: DP HFD 3


title: sci3-me-210

description: sci-RNA-seq3 library


title: Sample E5_5 HCA+0.1Se

value: e15 pups


title: VAM2 HFD 2


title: sci3-me-207

description: sci-RNA-seq3 library


title: sci3-me-208

description: sci-RNA-seq3 library


title: Sample E3_5 1 se

value: primary cortical neurons cultures


title: sci3-me-206

description: sci-RNA-seq3 library


title: sci3-me-213

description: sci-RNA-seq3 library


title: VAM1 HFD 3


title: Sample E4_5 Hca


title: sci3-me-204

description: sci-RNA-seq3 library


title: PreVAM HFD 1


title: Sample E2_5 0.1 se


title: Sample E1 _5 control


title: VAM2 HFD 1


title: sci3-me-203

description: sci-RNA-seq3 library


title: sci3-me-202

description: sci-RNA-seq3 library


title: Sample D6_4 HCA + 1 se

value: culture batch 4


title: sci3-me-200

description: sci-RNA-seq3 library


title: VAM1 HFD 1


title: VAM1 HFD 2


title: CD11B-DCs ND 5

value: Normal Chow

value: 20 weeks old


title: sci3-me-198

description: sci-RNA-seq3 library


title: sci3-me-199

description: sci-RNA-seq3 library


title: sci3-me-209

description: sci-RNA-seq3 library


title: VAM2 HFD 3


title: sci3-me-197

description: sci-RNA-seq3 library


title: Sample D5_4 hca + 0.1 se

source_name: in vitro cortical neurons_hca + 0.1 se

value: 5mM of homocysteic acid (Hca) + 0.1mM sodium selenite (Se) for 6hrs


title: CD11B-DCs ND 2

value: 16 weeks old


title: sci3-me-196

description: sci-RNA-seq3 library

value: B6 background


title: Sample D4_4 hca

source_name: in vitro cortical neurons_hca

value: 5mM of homocysteic acid (Hca) for 6 hrs


title: sci3-me-201

description: sci-RNA-seq3 library


title: sci3-me-195

description: sci-RNA-seq3 library


title: sci3-me-194

description: sci-RNA-seq3 library


title: Sample D3_4 1 se

value: 1mM sodium selenite (Se) for 6hrs


title: sci3-me-192

description: sci-RNA-seq3 library


title: sci3-me-193

description: sci-RNA-seq3 library


title: CD11B+DCs ND 5

value: Wild Type


title: CD11B-DCs ND 1


title: CD11B+DCs ND 4

value: 12 weeks old


title: sci3-me-191

description: sci-RNA-seq3 library


title: CD11B+DCs ND 1


title: sci3-me-189

description: sci-RNA-seq3 library


title: sci3-me-190

description: sci-RNA-seq3 library


title: Sample D1_4 control


title: Sample C6_3 HCA+1 Se

value: culture batch 3

value: 5mM of homocysteic acid (Hca) + 1mM sodium selenite (Se) for 6hrs


title: sci3-me-188

description: sci-RNA-seq3 library


title: Sample C5_3 HCA+0.1Se


title: sci3-me-187

description: sci-RNA-seq3 library


title: sci3-me-184

description: sci-RNA-seq3 library


title: sci3-me-186

description: sci-RNA-seq3 library


title: sci3-me-185

description: sci-RNA-seq3 library


title: Sample C4 _3 Hca


title: eMON ND 1


title: eMON ND 4


title: eMON ND 5


title: Sample C3_3 1 se


title: Sample D2_4 0.1 se

value: 0.1mM sodium selenite (Se) for 6hrs


title: sci3-me-182

description: sci-RNA-seq3 library


title: sci3-me-183

description: sci-RNA-seq3 library


title: DP ND 5


title: sci3-me-181

description: sci-RNA-seq3 library


title: DP ND 4


title: sci3-me-180

description: sci-RNA-seq3 library


title: sci3-me-179

description: sci-RNA-seq3 library


title: sci3-me-205

description: sci-RNA-seq3 library


title: Sample B6_2 HCA+1 Se

value: culture batch 2


title: Sample C2_3 0.1 se


title: sci3-me-176

description: sci-RNA-seq3 library


title: sci3-me-178

description: sci-RNA-seq3 library


title: sci3-me-177

description: sci-RNA-seq3 library


title: PreVAM ND 5


title: sci3-me-175

description: sci-RNA-seq3 library


title: sci3-me-173

description: sci-RNA-seq3 library


title: Sample B5_2 HCA+0.1Se


title: sci3-me-174

description: sci-RNA-seq3 library


title: PreVAM ND 4


title: sci3-me-172

description: sci-RNA-seq3 library


title: sci3-me-171

description: sci-RNA-seq3 library


title: VAM2 ND 7


title: PreVAM ND 2


title: sci3-me-170

description: sci-RNA-seq3 library


title: sci3-me-169

description: sci-RNA-seq3 library


title: Sample B3_2 1 se


title: sci3-me-168

description: sci-RNA-seq3 library


title: Sample C1_3 control

value: control


title: Sample B2_2 0.1 se

value: e15 pups


title: sci3-me-166

description: sci-RNA-seq3 library


title: VAM2 ND 6


title: sci3-me-167

description: sci-RNA-seq3 library


title: sci3-me-165

description: sci-RNA-seq3 library


title: Sample B1_2 control

value: primary cortical neurons cultures


title: Sample A6_1 HCA+1 Se

value: culture batch 1


title: sci3-me-164

description: sci-RNA-seq3 library


title: Sample A5_1 HCA+0.1Se


title: Sample B4_2 Hca


title: VAM1 ND 2

value: Normal Chow


title: VAM1 ND 1


title: Sample A4_1 Hca


title: Sample A3_1 1 se


title: sci3-me-160

description: sci-RNA-seq3 library


title: sci3-me-159

description: sci-RNA-seq3 library


title: sci3-me-158

description: sci-RNA-seq3 library


title: Adult Nanog-tg MEPs +dox (treated) rep2

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

data_processing:
Illumina RTA software v1.18.66.3.
Fastq files extracted with bcl2fastq2 Conversion Software
Reads were pre-processed with Cutadapt to remove Illumina adaptors.
Resulting reads were mapped and quantified on the mouse transcriptome (Ensembl gene-build NCBIM37 v67) using RSEM
Data were normalized using TMM method from limma Bioconductor package
Genome_build: NCBIM37 v67 (mm9)
Supplementary_files_format_and_content: tab-delimited text files include normalized RSEM expected counts values for each sample

extract_protocol:
RNA was isolated following standard procedures
RNAseq libraries were constructed using the Illumina NEBNext Ultra™ RNA Library Prep Kit and established protocols.

treatment_protocol: Nanog expression induced by the administration of doxycycline for 5 days in the drinking water


title: sci3-me-161

description: sci-RNA-seq3 library


title: sci3-me-157

description: sci-RNA-seq3 library


title: Adult Nanog-tg MEPs +dox (treated) rep3


title: VAM2 ND 1


title: Sample A2_1 0.1 se


title: VAM1 ND 6


title: Adult Nanog-tg MEPs +dox (treated) rep1


title: Sample A1_1 control


title: sci3-me-156

description: sci-RNA-seq3 library


title: sci3-me-154

description: sci-RNA-seq3 library


title: sci3-me-162

description: sci-RNA-seq3 library


title: sci3-me-163

description: sci-RNA-seq3 library


title: sci3-me-153

description: sci-RNA-seq3 library


title: sci3-me-155

description: sci-RNA-seq3 library


title: sci3-me-152

description: sci-RNA-seq3 library


title: Adult Nanog-tg MEPs –dox (untreated) rep3


title: sci3-me-151

description: sci-RNA-seq3 library


title: PRO-Seq of infected 96 h flavopiridol-treated HFF (Towne BAC)

city: Iowa City

first: David

middle: H

last: Price

state: Iowa

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

description:
processed data file:
ROPE-Towne-BAC-FW.bb
ROPE-Towne-BAC-RV.bb

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to hg38 using bowtie 1.2 (retain unmapped reads).
Alignment of unmapped reads to Genbank FJ616285.1 using bowtie 1.2.
Generate bedgraphs using bedtools genomecov 2.26.
We have published the details on these tracks and their associated analyses in the manuscript, Parida, et al. 2019 (10.1128/mBio.02047-18).
Upload HCMV ROPE tracks to a custom track hub (https://github.com/P-TEFb/trackHub_HCMV)
Genome_build: hg38
Supplementary_files_format_and_content: bigbed files were generated from bed files using kentUtils bedToBigBed program

molecule: nuclear RNA

source_name: Primary human foreskin fibroblast (HFF)

growth_protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.

extract_protocol: All PRO-Seq and PRO-Cap protocols are detailed in the manuscript. Nuclei were rapidly isolated as described in Nilson, et al. 2017 (10.1093/nar/gkx724).  Please consult the manuscript, Nilson, et al. 2017 (10.1093/nar/gkx724), and Mahat, et al. 2016 (10.1038/nprot.2016.086).

treatment_protocol: HFF were kept at 100% confluence at least one week before infection.

tag: hcmv strain

value: Towne BAC

tag: infection duration

tag: method

value: PRO-Seq


title: Adult Nanog-tg MEPs –dox (untreated) rep1


title: sci3-me-149

description: sci-RNA-seq3 library


title: PRO-Seq of infected 96 h DMSO-treated HFF (Towne BAC)


title: sci3-me-147

description: sci-RNA-seq3 library


title: sci3-me-146

description: sci-RNA-seq3 library


title: sci3-me-143

description: sci-RNA-seq3 library


title: sci3-me-145

description: sci-RNA-seq3 library


title: sci3-me-141

description: sci-RNA-seq3 library


title: sci3-me-144

description: sci-RNA-seq3 library


title: sci3-me-150

description: sci-RNA-seq3 library


title: sci3-me-142

description: sci-RNA-seq3 library


title: hog1 vs WT - Replicate 1

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Microarray slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution. The scanning was performed using GenePix4000B scanner for the ChIP-chip slides.

data_processing: Data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: WT elutriated G1 cells  grown in YPD medium at 30°C for 10 min

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen). For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. Chromatin immunoprecipitation was performed by following the protocol available at http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html with the following exceptions: chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads). RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).

treatment_protocol: for both microarrays and Chip-chip experiments, overnight cultures of hog1 mutant and WT strains were diluted to an OD600 of 0.1 in 1 L fresh YPD-uridine medium, grown at 30°C to an OD600 of 0.8 and separated into size fractions by using the Beckman JE-5.0  elutriation system at 16°C. A total of 108 unbudded G1 phase cells were harvested, released into fresh YPD medium and grown for 10 min prior to harvesting by centrifugation and stored at -80°C.

tag: genotype/variation

value: WT

source_name: hog1 elutriated G1 cells  grown in YPD medium at 30°C for 10 min


title: hog1 vs WT - Replicate 2


title: sci3-me-139

description: sci-RNA-seq3 library

tag: developmental stage

value: B6 background


title: Adult Nanog-tg MEPs –dox (untreated) rep2


title: sci3-me-140

description: sci-RNA-seq3 library

tag: genetic background


title: sci3-me-137

description: sci-RNA-seq3 library


title: sci3-me-136

description: sci-RNA-seq3 library


title: Pat114N

city: Seoul

first: Jihae

last: Seo

address: 52 Ewhayeodae-gil, Seodaemun-Gu

department: Ewha Research Center for Systems BIology

country: South Korea

institute: Ewha Womans University

data_processing:
miRNA sequencing was performed on Illumina HiSeq 2000 platform using 1X50bp single-end runs.
For miRNA-Seq data, sequencing reads were mapped to the miRBase release 19 using Bowtie V.0.12.9 with the perfect match option after removing adapter sequences.
Genome_build: miRBase v19
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample

source_name: lung adenocarcinoma normal

extract_protocol:
cDNA size selection was carried out with the Sage Science’s Pippin prep electrophoresis platform. Sequencing of pooled libraries were performed on HiSeq 2000 sequencing system (Illumina) with the single end read of 50 bp length.
Small RNA sequencing libraries were prepared according to the manufacturer’s instructions using the Illumina Small RNA Prep kit.

tag: patient id

tag: disease

value: lung adenocarcinoma

tag: age

tag: gender

value: Female

value: smoker

tag: molecule subtype

value: microRNA

tag: tumor stage


title: Pat113N


title: Pat113T

source_name: lung adenocarcinoma tumor


title: sci3-me-138

description: sci-RNA-seq3 library

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq of co-assay was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
Genome_build: mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file
Supplementary_files_format_and_content: Cell annotation file: sample is cell id of each single cell with the reverse transcription and ligation barcode attached; tsne_1 and tsne_2 are cell coordinates after t-SNE dimension reduction.
Supplementary_files_format_and_content: Gene annotation file including gene id, gene type and gene short name.
Supplementary_files_format_and_content: A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer. The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%.
Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping.  The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi). Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer.    Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes).    After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including  4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.    After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen). 1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min.    For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter). In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate.    For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.


title: sci3-me-148

description: sci-RNA-seq3 library


title: sci3-me-135

description: sci-RNA-seq3 library


title: sci3-me-133

description: sci-RNA-seq3 library


title: sci3-me-132

description: sci-RNA-seq3 library


title: Pat112N


title: Pat111T


title: Pat114T


title: Pat112T


title: sci3-me-130

description: sci-RNA-seq3 library


title: sci3-me-129

description: sci-RNA-seq3 library


title: Pat111N


title: sci3-me-128

description: sci-RNA-seq3 library


title: Pat110T


title: sci3-me-131

description: sci-RNA-seq3 library


title: sci3-me-127

description: sci-RNA-seq3 library


title: sci3-me-125

description: sci-RNA-seq3 library


title: Pat109T


title: sci3-me-134

description: sci-RNA-seq3 library


title: PC3 -No Tx_CW036

city: New York

first: Wendy

last: Mao

department: Center for Translational Immunology

institute: Columbia University

data_processing:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: FPKM values in samplename_star_FPKM.txt,

source_name: PC3 -No Tx

growth_protocol: DU145 and PC3 cells were grown in cRPMI

extract_protocol:
Trizol extraction of RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either 0.1 uM JQ1, 1uM JQ1, 20 units/mL of hIFN-y, or combination thereof, overnight. Vehicle is DMSO.

tag: cell line

value: Human Prostate Cell Line

tag: passage

tag: treatment

tag: replicates


title: PC3 -No Tx_CW030

tag: cell type


title: Pat108T


title: Pat109N


title: Pat108N


title: PC3 -0.1 uM JQ1 + IFN-y_CW029

source_name: PC3 -0.1 uM JQ1 + IFN-y

value: 0.1 uM JQ1 + IFN-y


title: sci3-me-116

city: Seattle

first: Junyue

last: Cao

institute: University of Washington

description: sci-RNA-seq3 library


title: sci3-me-121

description: sci-RNA-seq3 library


title: sci3-me-118

description: sci-RNA-seq3 library


title: sci3-me-119

description: sci-RNA-seq3 library


title: sci3-me-122

description: sci-RNA-seq3 library


title: sci3-me-123

description: sci-RNA-seq3 library


title: PC3 -0.1 uM JQ1 + IFN-y_CW035


title: sci3-me-120

description: sci-RNA-seq3 library


title: sci3-me-124

description: sci-RNA-seq3 library


title: sci3-me-115

description: sci-RNA-seq3 library


title: Pat102N

value: never smoker


title: sci3-me-112

description: sci-RNA-seq3 library


title: sci3-me-113

description: sci-RNA-seq3 library


title: Pat110N


title: sci3-me-110

description: sci-RNA-seq3 library


title: PC3 -No Tx_CW024


title: Pat99T


title: sci3-me-109

description: sci-RNA-seq3 library


title: sci3-me-117

description: sci-RNA-seq3 library


title: Pat99N


title: sci3-me-108

description: sci-RNA-seq3 library


title: PC3 -1 uM JQ1 + IFN-y_CW022

source_name: PC3 -1 uM JQ1 + IFN-y

value: 1 uM JQ1 + IFN-y


title: sci3-me-114

description: sci-RNA-seq3 library


title: Pat102T


title: sci3-me-107

description: sci-RNA-seq3 library


title: sci3-me-126

description: sci-RNA-seq3 library


title: sci3-me-106

description: sci-RNA-seq3 library


title: PC3 -0.1 uM JQ1 + IFN-y_CW023


title: sci3-me-104

description: sci-RNA-seq3 library


title: sci3-me-111

description: sci-RNA-seq3 library


title: Pat95T


title: PC3 -IFN-y_CW033

source_name: PC3 -IFN-y

value: IFN-y


title: sci3-me-105

description: sci-RNA-seq3 library


title: PC3 -1 uM JQ1 + IFN-y_CW034


title: Pat89T


title: sci3-me-102

description: sci-RNA-seq3 library


title: Pat95N


title: sci3-me-103

description: sci-RNA-seq3 library


title: PC3 -IFN-y_CW021


title: Pat89N


title: sci3-me-101

description: sci-RNA-seq3 library


title: Pat88T


title: sci3-me-100

description: sci-RNA-seq3 library


title: PC3 -0.1 uM JQ1_CW032

source_name: PC3 -0.1 uM JQ1

value: 0.1 uM JQ1


title: sci3-me-098

description: sci-RNA-seq3 library


title: PC3 -0.1 uM JQ1_CW026


title: sci3-me-097

description: sci-RNA-seq3 library


title: sci3-me-099

description: sci-RNA-seq3 library


title: Pat88N


title: sci3-me-095

description: sci-RNA-seq3 library


title: sci3-me-094

description: sci-RNA-seq3 library


title: PC3 -IFN-y_CW027


title: PC3 -0.1 uM JQ1_CW020


title: PC3 -1 uM JQ1 + IFN-y_CW028


title: Pat85T


title: sci3-me-096

description: sci-RNA-seq3 library


title: PC3 - DMSO_CW025

source_name: PC3 - DMSO

value: DMSO


title: sci3-me-093

description: sci-RNA-seq3 library

source_name: mouse embryos


title: PC3 - DMSO_CW031


title: sci3-me-089

description: sci-RNA-seq3 library


title: sci3-me-092

description: sci-RNA-seq3 library


title: sci3-me-091

description: sci-RNA-seq3 library


title: Pat85N


title: Pat78N


title: sci3-me-086

description: sci-RNA-seq3 library


title: sci3-me-087

description: sci-RNA-seq3 library


title: DU145 - No Tx_CW012

source_name: DU145 - No Tx


title: sci3-me-084

description: sci-RNA-seq3 library


title: Pat76N


title: sci3-me-083

description: sci-RNA-seq3 library


title: Pat78T


title: sci3-me-090

description: sci-RNA-seq3 library


title: DU145 - No Tx_CW018


title: DU145 - No Tx_CW006


title: PC3 - DMSO_CW019


title: sci3-me-088

description: sci-RNA-seq3 library


title: Pat76T


title: DU145 - 0.1 uM JQ1 + IFN-y_CW017

source_name: DU145 - 0.1 uM JQ1 + IFN-y


title: Pat75T


title: sci3-me-082

description: sci-RNA-seq3 library


title: sci3-me-085

description: sci-RNA-seq3 library


title: Pat75N


title: DU145 - 0.1 uM JQ1 + IFN-y_CW011


title: sci3-me-081

description: sci-RNA-seq3 library


title: sci3-me-080

description: sci-RNA-seq3 library


title: sci3-me-078

description: sci-RNA-seq3 library


title: DU145 - 0.1 uM JQ1 + IFN-y_CW005


title: sci3-me-077

description: sci-RNA-seq3 library


title: sci3-me-079

description: sci-RNA-seq3 library


title: Pat69T


title: sci3-me-076

description: sci-RNA-seq3 library


title: Pat69N


title: sci3-me-075

description: sci-RNA-seq3 library


title: DU145 - 1 uM JQ1 + IFN-y_CW016

source_name: DU145 - 1 uM JQ1 + IFN-y


title: Pat68N


title: Pat68T


title: sci3-me-074

description: sci-RNA-seq3 library


title: sci3-me-072

description: sci-RNA-seq3 library


title: sci3-me-073

description: sci-RNA-seq3 library


title: sci3-me-070

description: sci-RNA-seq3 library


title: sci3-me-069

description: sci-RNA-seq3 library


title: DU145 - 1 uM JQ1 + IFN-y_CW010


title: sci3-me-068

description: sci-RNA-seq3 library


title: Pat67T


title: DU145 - IFN-y_CW009

source_name: DU145 - IFN-y


title: DU145 - IFN-y_CW015


title: sci3-me-067

description: sci-RNA-seq3 library


title: Pat66T


title: sci3-me-071

description: sci-RNA-seq3 library


title: sci3-me-066

description: sci-RNA-seq3 library


title: sci3-me-064

description: sci-RNA-seq3 library


title: Pat65T


title: sci3-me-065

description: sci-RNA-seq3 library


title: DU145 - 0.1 uM JQ1_CW014


title: sci3-me-063

description: sci-RNA-seq3 library


title: DU145 - IFN-y_CW003


title: DU145 - 0.1 uM JQ1_CW008


title: sci3-me-062

description: sci-RNA-seq3 library


title: sci3-me-061

description: sci-RNA-seq3 library


title: Pat65N


title: sci3-me-060

description: sci-RNA-seq3 library


title: sci3-me-059

description: sci-RNA-seq3 library


title: DU145 - 0.1 uM JQ1_CW002


title: sci3-me-058

description: sci-RNA-seq3 library


title: DU145 - 1 uM JQ1 + IFN-y_CW004


title: Pat67N


title: Pat64T


title: DU145 - DMSO_CW013

source_name: DU145 - DMSO


title: Pat64N


title: Pat66N


title: sci3-me-057

description: sci-RNA-seq3 library


title: sci3-me-056

description: sci-RNA-seq3 library


title: DU145 - DMSO_CW007


title: DU145 - DMSO_CW001


title: sci3-me-053

description: sci-RNA-seq3 library


title: sci3-me-049

description: sci-RNA-seq3 library


title: Pat60T


title: sci3-me-054

description: sci-RNA-seq3 library


title: sci3-me-050

description: sci-RNA-seq3 library


title: Pat61N


title: Pat60N


title: WT_3

city: rochester

first: Zhenkun

last: Lou

state: mn

address: 200 1st street sw

institute: mayo clinic

data_processing:
Paired-end RNA-seq data was generated with the Illumina HiSeq 4000 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg38 genome using star aligner (version v2.3.0e).
Following read alignment, featureCounts (v1.4.4) was used to quantify the gene expression at the gene level based on GENCODE gene annotation model GRCh38.p10 release 27.
Genes with 1 count per million in at least 1 sample were considered expressed and selected for further analysis, otherwise discarded.
The gene level read counts data was normalized using the trimmed mean of M-values normalization (TMM) method to adjust for sequencing library size difference. The data were transformed to log2 scale.
Genome_build: hg38

source_name: U2OS cells

growth_protocol: U2OS cells  were cultured in DMEM supplemented with 10% FBS and kept in a humidified 37°C 5% CO2 5%O2 incubator..

extract_protocol:
The transfected U2OS cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2OS cells were transfected with wildtype H4 plasmids or K31R H4 mutant.

tag: cell origin

value: osteosarcoma cells

tag: cell stock information

value: Parental U2OS odered from ATCC

tag: genotype

value: wild type


title: WT_2


title: sci3-me-052

address: Foege Building S-210, 3720 15th Ave NE

description: sci-RNA-seq3 library


title: sci3-me-048

description: sci-RNA-seq3 library


title: sci3-me-047

description: sci-RNA-seq3 library


title: WT_1


title: Pat59T


title: sci3-me-044

description: sci-RNA-seq3 library


title: sci3-me-046

description: sci-RNA-seq3 library


title: Pat61T


title: K31R_3

value: K31R mutant


title: Pat59N


title: sci3-me-043

description: sci-RNA-seq3 library


title: sci3-me-045

description: sci-RNA-seq3 library


title: Pat58T


title: sci3-me-042

description: sci-RNA-seq3 library


title: K31R_1


title: sci3-me-041

description: sci-RNA-seq3 library


title: sci3-me-039

description: sci-RNA-seq3 library


title: sci3-me-051

description: sci-RNA-seq3 library


title: sci3-me-038

description: sci-RNA-seq3 library