title: 5_Uninfected #5 Male

status: Public on Dec 21 2020

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

description:
sample name:
5

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”
The reads distribution across the genome was assessed using bamutils (from ngsutils)
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10
Quality control of sequencing and mapping results was summarized using MultiQC . Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept
The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow derived macrophages

growth_protocol: Mice we fed high fat diet for 4.5 weeks before 4.5 weeks (injection every other day) of either IL-4complex or PBS (For controls) injection and maintained on HFD throughout. Age matched mice on high fat diet were infected with S. mansoni concurrently.  At 4.5 weeks post injection or 10 weeks post infection, bone marrow was harvested and cultured in M-CSF for 6 days to generate macrophages.

extract_protocol:
cells were harvested, washed in 1X PBS and then RNA was harvested using Trizol reagent. RNA was DNase treated (NEB) and then cleaned with Qiagen MinElute Cleanup kit.
200 nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using KAPA mRNA Hyperprep Kit (Roche)

treatment_protocol: Cells are unstimulated Day 6 bone marrow derived macrophages

value: bone marrow derived macrophages

tag: Sex

value: male

tag: infection status

value: uninfected

value: PBS (control)


title: genomic DNA from eMRT case 20 [203952880054_R05C01]

status: Public on Dec 18 2020

type: genomic

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting.

data_processing:
Bioconductor (Version 3.10) package minifi (Version 1.32.0) using function 'preprocessNoob'
The Matrix_raw.txt.gz contains Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: primary eMRT sample (FFPE)

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA isolation from FFPE tissue, 10 x 10 µm sections were cut and DNA isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, either the HumanMethylation450 BeadChip array or the Infinium MethylationEPIC BeadChip Kit (both Illumina) were used to quantify the methylation status of 450,000 or 850,000 CpG sites, respectively, on an iScan device (Illumina).

tag: subject/case id

value: eMRT case 20

tag: subject status

value: extracranial malignant rhabdoid tumors (eMRTs)

value: female


title: genomic DNA from eMRT case 18 [203952880054_R02C01]

value: eMRT case 18


title: genomic DNA from eMRT case 19 [203952880054_R03C01]

value: eMRT case 19


title: Flu45

status: Public on Dec 15 2020

type: SRA

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

country: USA

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
Base Calling: Bcl2fastq, version 2.17.1.14. No mismatches allowed
Quality Filtering and Adapter Trimming: Bbduk tools (version 38.76)
Alignment: STAR version 2.7.0f to ENSEMBL GRCh38 human reference genome assembly release 33
Feature counting: featureCounts version 2.0.0
Genome_build: GRCh38, release 33
Supplementary_files_format_and_content: tab delimited text file; column 0 corresponds to gene ID, column 1 corresponds to gene counts

molecule: total RNA

source_name: Whole Blood

growth_protocol: Remnant clinical specimens

extract_protocol:
Direct-zol RNA Mini-Prep kit (Zymo Research)
SMART-Seq Stranded Kit (Takara Biosciences)
NP: MagBind viral DNA/RNA 96 kit (Omega Bio-tek) on the KingFisher Flex (Thermofisher), Whole blood: Directzol RNA mini prep kit (Zymo Research)
NP swabs: SMART-Seq Stranded Kit (Takara Biosciences), Whole blood: TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina)

treatment_protocol: DNase

tag: geographic location

tag: disease state

value: Bacterial sepsis

tag: pathogen

value: Escherichia coli, urine culture

tag: date collected

tag: disease severity

value: Hospitalized/ICU


title: Flu83_S110

value: Escherichia coli, blood culture


title: donor2_inlysate_vehicle

status: Public on Jan 22 2021

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

data_processing:
Total 36 fastq files for samples (single-end read) prepared with  Smart-3SEQ library were pre-processed by trimming the adapters, removing polyA tails and, extracting UMI sequence and G overhang as described in Foley et al., 2019. The fastq files were then aligned using HISAT2-2.1.0 (Kim De et al., 2019) and Homo sapiens GhCh38 NCBI Assembly (GCF_000001405.39,annotation-date 12/05/2019). Uniquely aligned reads  were counted using featureCounts from subread-1.6.4 package. 4  fastq files for each TruSeq sample (Paired read 1 and read 2 for same library across three lanes, total 72) were processed similarly to the Smart-3SEQ fastq files except for the pre-processing steps.
Differential gene expression was analyzed using DESeq2 1.26.0 using ~donor+treatment design.
genome build: GRCh38.p13NCBI assembly, accession :GCF_000001405.39, annotation-date 12/05/2019, annotation-source NCBI Homo sapiens Updated Annotation Release 109.20191205
processed data files format and content: merged tab delimited text file containing raw gene counts for each methods processed by featureCounts of subread package-1.6.4
processed data files format and content: gene length for all genes in raw gene counts

source_name: cultured human dermal fibroblast

growth_protocol: Human primary dermal fibroblasts were obtained using methods described in Vangipuram M etal,2013 . Cells were maintained in DMEM (Gibco, Dublin, Ireland, Item No. 11965-092) with 20% FBS (Gibco, Dublin, Ireland, Item No. 26140-079) and Pen/Strep 1:100 (Gibco, Dublin, Ireland, Item No. 15140-122)and gentamycin 25μg/mL (IBI Scientific, Dubuque, IA, Item No. IB02030), at 37℃ with 5% CO2 and were used at passage #4.

extract_protocol:
Total RNA was extracted and purified from cell cultures using RNeasy plus mini kit from QIAGEN (Hilden, Germany). For in-lysate RNA, cell cultures were washed with PBS, treated with a lysis buffer consisting of 0.1% (1mg/mL) BSA (New England Biolabs, Ipswich, MA, Item No. B9000S) / 0.3% Igepal CA 630 (Sigma-Aldrich, St. Louis, MO, Item No. I8896) for 5 minutes, and the supernatant was used for further library prep.
Extracted RNA and cell lysate were used for preparing sequencing libraries according to the Smart-3SEQ protocol (Foley et al., 2019). Illumina TruSeq libraries were prepared at the University of Iowa Genomics Facility using standard Illumina TruSeq stranded mRNA protocols. Concentration and fragment size of prepared library was measured using Qubit HS and bioanalyzer. Fragment size for Smart-3SEQ library was ~500bp which falls within the recommended 200-600bp

treatment_protocol: Samples were treated for 6 hours as indicated with DMSO,  10μM Calmidazolium chloride (Cayman Chemical Company, Ann Arbor, MI, Item No. 14442) or Fludrocortisone acetate (Sigma-Aldrich, St. Louis, MO, Item No. F6127).

tag: cell type

value: human dermal fibroblast

tag: donor

tag: treatment

value: DMSO

tag: library prep


title: FLU-27_S195

value: Group C Streptococcus, blood culture


title: FLU-22_S38


title: FLU-29_S179

value: Klebsiella pneumoniae, blood culture


title: WB41

value: Donor control

value: No pathogen

value: Asymptomatic


title: WB28


title: WB25

value: SARS-CoV-2, NP


title: WB26


title: WB23


title: WB19


title: WB32


title: WB34


title: WB48


title: WB15


title: WB35


title: genomic DNA from eMRT case 22 [204234160028_R03C01]

value: eMRT case 22

value: male


title: genomic DNA from eMRT case 23 [204234160028_R06C01]

value: eMRT case 23

value: extracranial malignant rhabdoid tumors (eMRTs)


title: WB44


title: WB47


title: WB46


title: WB14


title: WB55


title: WB43


title: WB13


title: FLU-30_S39

value: Klebsiella oxytoca, blood culture


title: WB52


title: WB12


title: WB27


title: WB36


title: WB53


title: WB50


title: WB51


title: WB31

value: Viral acute respiratory illness

value: Influenza


title: WB30


title: WB11


title: WB49


title: WB10


title: WB9


title: WB42


title: WB29


title: WB40


title: WB8


title: WB54


title: WB1


title: WB5


title: WB2


title: WB3


title: WB6


title: WB7


title: WB37


title: WB45


title: NPS-87

source_name: NP swab

extract_protocol:
Mag-Bind Viral DNA/RNA 96 kit (Omega Bio-Tek) on the KingFisher Flex (Thermofisher Scientific)
SMART-Seq Stranded Kit (Takara Biosciences)
NP: MagBind viral DNA/RNA 96 kit (Omega Bio-tek) on the KingFisher Flex (Thermofisher), Whole blood: Directzol RNA mini prep kit (Zymo Research)
NP swabs: SMART-Seq Stranded Kit (Takara Biosciences), Whole blood: TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina)

value: Human metapneumovirus


title: WB38


title: WB4


title: NPS-83

value: Rhinovirus


title: NPS-35

value: Non-viral acute respiratory illness


title: NPS-85


title: NPS-343


title: WB39


title: NPS-196

value: Coronavirus 229E


title: NPS-195

value: Coronavirus NL63


title: NPS-194

value: Coronavirus OC43


title: NPS-193

value: Coronavirus HKU1


title: NP79

extract_protocol:
easyMag (bioMérieux)
SMART-Seq Stranded Kit (Takara Biosciences)
NP: MagBind viral DNA/RNA 96 kit (Omega Bio-tek) on the KingFisher Flex (Thermofisher), Whole blood: Directzol RNA mini prep kit (Zymo Research)
NP swabs: SMART-Seq Stranded Kit (Takara Biosciences), Whole blood: TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina)


title: NP78


title: NP77


title: NP76


title: NP80


title: NP74


title: NP75


title: NP73


title: NP68

value: Influenza A


title: NP72


title: NP71


title: NP70

value: Influenza B


title: NP32

extract_protocol:
EZ1 Advanced XL (Qiagen)
SMART-Seq Stranded Kit (Takara Biosciences)
NP: MagBind viral DNA/RNA 96 kit (Omega Bio-tek) on the KingFisher Flex (Thermofisher), Whole blood: Directzol RNA mini prep kit (Zymo Research)
NP swabs: SMART-Seq Stranded Kit (Takara Biosciences), Whole blood: TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina)

value: Donor control

value: No pathogen

value: Asymptomatic


title: NP33


title: NP31


title: NP66


title: NP30


title: NP27


title: NP28


title: NP25


title: NP24


title: NP21


title: NP20


title: NP198


title: NP199


title: NP22


title: NP197


title: NP17


title: NP14


title: NP15


title: Covid3


title: NP69


title: Covid1


title: NPS-694

value: ICU


title: NPS-187


title: NPS-334


title: NPS-336


title: NPS-333


title: NPS-339


title: NPS-319

value: Hospitalized, not ICU


title: NPS-341


title: NPS-294


title: NPS-337


title: NPS-338


title: NPS-335


title: NPS-332


title: NPS-330


title: NPS-329


title: NPS-331


title: NPS-328


title: Covid7


title: Covid5


title: NPS-326


title: NPS-327


title: NPS-325


title: NP26


title: NPS-324


title: NPS-323


title: NPS-322


title: NPS-321


title: NPS-290


title: NPS-186


title: NPS-218


title: NPS-289


title: NPS-292

value: Outpatient


title: NPS-293


title: NPS-177


title: NPS-299


title: NPS-173


title: NPS-306


title: NPS-172


title: NPS-98


title: NPS-314


title: NPS-96


title: NPS-95


title: NPS-92


title: NPS-99


title: NPS-311


title: NPS-310


title: NPS-291


title: NPS-307


title: NPS-296


title: NPS-308


title: NPS-183


title: NPS-176


title: NPS-170


title: NPS-142


title: NPS-182


title: NPS-139


title: NPS-141


title: NPS-165


title: NPS-138


title: NPS-135


title: NPS-133


title: NPS-132


title: NPS-129


title: NPS-131


title: NPS-309


title: NPS-126


title: NPS-125


title: NPS-130


title: NPS-124


title: NPS-123


title: NPS-127


title: NPS-120


title: NPS-111


title: NPS-122

value: Viral acute respiratory illness


title: NPS-112


title: NPS-116


title: NPS-113


title: NPS-117


title: NPS-109


title: NPS-106


title: NPS-108


title: NPS-105


title: NPS-118


title: NPS-104


title: NPS-102


title: NPS-107


title: NPS-103


title: NPS-101


title: NPS-100


title: NPS-128


title: NPS-315


title: NPS-110


title: NPS-302


title: NPS-115


title: NPS-181


title: NPS-169


title: NPS-167


title: NPS-166


title: NPS-168


title: NPS-160


title: NPS-164


title: NPS-153


title: NPS-155


title: NPS-156


title: NPS-158


title: NPS-163


title: NPS-148


title: NPS-157


title: NPS-146


title: NPS-147


title: NPS-140


title: NPS-145


title: NPS-137


title: NPS-134


title: NPS-90


title: NPS-91


title: NPS-316


title: NPS-171


title: NPS-318


title: NPS-178


title: NPS-180


title: NPS-317


title: NPS-184


title: NPS-151


title: NPS-152


title: NPS-149


title: NPS-150


title: NPS-175


title: NPS-136


title: NPS-288


title: NPS-305


title: NPS-262


title: NPS-154


title: NPS-260


title: NPS-287


title: NPS-271


title: NPS-270


title: NPS-252


title: NPS-259


title: NPS-250


title: NPS-275


title: NPS-234


title: NPS-242


title: NPS-243


title: NPS-254


title: NPS-249


title: NPS-231


title: NPS-226


title: NPS-278


title: NPS-267


title: NPS-285


title: NPS-233


title: NPS-282


title: NPS-245


title: NPS-247


title: NPS-235


title: NPS-286


title: NPS-236


title: NPS-237


title: NPS-265


title: NPS-255


title: NPS-272


title: NPS-224


title: NPS-240


title: NPS-210


title: NPS-207


title: NPS-211


title: NPS-256


title: NPS-273


title: NPS-223


title: NPS-208


title: NPS-274


title: NPS-209


title: NPS-244


title: NPS-202


title: NPS-205


title: NPS-284


title: NPS-200


title: NPS-201


title: NPS-206


title: NPS-266


title: NPS-276


title: NPS-269


title: NPS-253


title: NPS-246


title: NPS-238


title: NPS-214


title: NPS-263


title: NPS-228


title: NPS-239


title: NPS-203


title: NPS-222


title: NPS-283


title: NPS-279


title: NPS-280


title: NPS-212


title: NPS-241


title: NP65


title: NP42


title: NP41


title: NP43


title: NP59


title: NP64


title: NP51


title: NP52


title: NP56


title: NP63


title: NP57


title: NP53


title: NP62


title: NPS-213


title: NP61


title: NPS-215


title: NPS-220


title: NPS-216


title: NPS-451


title: NPS-532

value: Respiratory syncytial virus


title: NPS-453


title: NPS-230


title: NPS-268


title: NPS-526


title: NPS-313


title: NPS-221


title: NPS-531


title: NPS-528


title: NPS-527


title: NPS-452


title: NPS-416


title: NPS-398


title: NPS-404


title: NPS-421


title: NPS-481

value: Adenovirus


title: NPS-413


title: NPS-407


title: NPS-409


title: NPS-583

value: Human metapneumovirus


title: NPS-406


title: NPS-442


title: NPS-435


title: NPS-581


title: NPS-434


title: NPS-432


title: NPS-428


title: NPS-430


title: NPS-389


title: NPS-426


title: NPS-480


title: NPS-427


title: NPS-433


title: NPS-554

value: Parainfluenza


title: NPS-390


title: NPS-348


title: NPS-365


title: NPS-387


title: NPS-591


title: NPS-436


title: NPS-377


title: NPS-374


title: NPS-441


title: NPS-369


title: NPS-364


title: NPS-425


title: NPS-384


title: NPS-366


title: NPS-380


title: NPS-386


title: NPS-370


title: NPS-357


title: NPS-391


title: NPS-371


title: NPS-381


title: NPS-354


title: NPS-361


title: NPS-519


title: NPS-515


title: NPS-355


title: NPS-367


title: NPS-518


title: NPS-475

value: Rhinovirus


title: NPS-358


title: NPS-362


title: NPS-356


title: NPS-472


title: NPS-363


title: NPS-376


title: NPS-572


title: NPS-628


title: NPS-347


title: NPS-627


title: NPS-468


title: NPS-624


title: NPS-467


title: NPS-622


title: NPS-607


title: NPS-611


title: NPS-602


title: NPS-597


title: NPS-616


title: NPS-618


title: NPS-621


title: NPS-614


title: NPS-615


title: NPS-613


title: NPS-447


title: NPS-444


title: NPS-612


title: NPS-502


title: NPS-445


title: Patient#5_Pacli/Belinostat

status: Public on Dec 07 2020

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description: single cell RNA

data_processing:
We demultiplexed the reads from the FASTQ files using custom code.
Samples were aligned to GRCh38 using the STAR (020201) aligner using a GTF from GENCODE
We estimated the read counts using featurecounts (v1.5.2).
We checked data quality using CollectRnaSeqMetrics and CollectAlignmentSummaryMetrics from picard (1.129), as well as with custom code.
The pipelines were created and executed using BETSY.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each cell

source_name: AB-11A (97OVCZ)

growth_protocol: For single cell RNA sequencing, we thawed frozen viable breast cancer pleural effusions or ascites from patients and depleted dead cells with EasySepTM Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies) and CD45+ cells with EasySepTM Human CD45 Depletion Kit II (STEMCELL Technologies) according to manufacturer protocols. These purified cancer cells were then resuspended in Renaissance Essential Tumor Medium (RETM, Cellaria) containing 5% FBS, RETM supplement, antibiotic/antimycotic (anti-anti), and 20 ng/mL cholera toxin.

extract_protocol:
Cell organoids were collected by centrifugation at 300g for 5min, and dissociated with trypsin-EDTA for 5min at 37°C. Dead cells were depleted with EasySepTM Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899). Cells in suspension were stained with ReadyProbes Cell Viability Imaging Kit (Hoechst 33342 and Propidium Iodide, Thermo Fisher Scientific) by adding 80µL each dye at 500,000 cell/mL in basal DMEM medium and incubated for 20 minutes at 37°C + 5% CO2.  After incubation, cells were diluted with equal volume of 1X PBS (no Ca2+/Mg2+, pH 7.4, Thermo Fisher Scientific) then centrifuged for 5 minutes at 300 x g, 4°C.  Cells were resuspended to 5.0x105 to 2.0x106 cell/mL in 1X PBS and calculated concentrations on a hemocytometer using trypan blue then diluted to 50,000 cell/mL in 1x PBS + 0.2U/µL Superase· In RNase inhibitor (Thermo Fisher Scientific) + 1X Second Diluent (Takara Bio). Single-cell RNA-Sequencing (scRNA-Seq) was performed using the ICELL8® Single-Cell System (Takara Bio) using the SMARTer™ ICELL8 3’ DE Kit (Takara Bio).  Processing 8 samples at a time, 80µL of each 50,000 cell/mL cell sample, negative control, positive control (K-562 RNA), and fiducial reagent (dye control) were loaded into each well of a 384-well plate (A1 through D2) and dispensed 50nL per well into a 5,184 well SMARTer™ ICELL8® 3’ DE Chip (Takara Bio) using the ICELL8® Multisample NanoDispenser (MSND, Takara Bio).  After dispense, chip was sealed with imaging film, and centrifuged at 300 x g, 5 minutes, 4°C.  ICELL8® 3’ DE Chip was then imaged on an ICELL8® Imaging System (Takara Bio) featuring an Olympus BX43 upright florescent microscope equipped with an automated stage, camera, DAPI, and Texas Red filters and controlled by CellSelect® Software (Takara Bio) to visually identify and select wells containing one viable single-cell candidate per well (positive Hoechst 33342, negative Propidium Iodide) generating single-cell candidate list for each ICELL8® 3’ DE Chip.  After imaging, ICELL8® 3’ DE Chip were stored at -80°C overnight.  Each sample was ran twice on separate ICELL8® 3’ DE Chips in order to multiplex samples and minimize chip-to-chip variations.
The ICELL8® 3’ DE Chip is preprinted with a reverse transcription (RT) primer containing a unique molecular identifier (UMI), 11-base unique well barcode, and poly T sequence in each of the 5,184 wells. The ICELL8® 3’ DE Chip containing cells was thawed at room temperature for 10 minutes, then centrifuged for 3 minutes, 3,200 x g, 4°C and maintained on ice.  The ICELL8® 3’ DE Chip was placed on the ICELL8® MSND and loaded 50 µL of RT-PCR solution (Takara Bio; 56 µL 5M GC Melt, 24 µL 25mM dNTP Mix, 3µL 1M MgCl2, 9µL 100mM DTT, 62 µL 5X First-Strand Buffer, 33 µL 2X SeqAmp PCR Buffer, 16 µL 10% Triton X-100, 2 µL SMARTer ICELL8 3’ DE Oligo Mix, 29 µL 100U/µL SMARTScribe Reverse Transcriptase, 10µL SeqAMP DNA Polymerase) into four wells (A1 through A4) of a 384-well plate.  MSND then dispensed 50 nL to wells containing only live single-cell candidates according to the single-cell candidate file previously generated by the ICELL8® Imaging System.  The 3’ DE Chip containing single cell candidates with RT-PCR reagent sealed with PCR Sealing Film and centrifuged 3,200 x g, 3 min, 4°C and then placed in a BioRad T100 equipped with a ICELL8® Chip adapter to perform RT followed by 22 PCR cycles for cDNA amplification.  Amplified cDNA from the ICELL8® 3’ DE Chip individual cells was collected and pooled using the ICELL8® Collection Kit (Takara Bio) by centrifugation at 3,200 x g, 10 minutes, 4°C. The cDNA products were concentrated using cDNA Clean & Concentrator-5 Kit (Zymo Research) followed bead cleanup using 0.6X AMPure XP Beads (Beckman Coulter) and eluted in 12 µL DNase/RNase free water.  Libraries were prepared using 1ng of purified cDNA according to the ICELL8® 3’ DE instruction manual (Takara Bio) using the Nextera Primer P5 (ICELL8® 3’ DE Kit, Takara Bio), Nextera XT DNA Library Preparation Kit (Illumina) and i7 Index Primer (Nextera XT Index Kit, Illumina).  Unique i7 Indexes were used for each ICELL8® 3’ DE Chip.  Tagmented cDNA was amplified by PCR 12 cycles prior to dual-sided bead cleanup using AMPure XP beads, and eluted in 11µL DNase/RNase free water.  Library and cDNA quality and profile were confirmed prior to sequencing ran on an Agilent Bioanalyzer using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).  Prepared library was then sequenced using 150 paired-end cycles on a NovaSeq S4 flow cell (Illumina).
single-cell RNA-Seq

treatment_protocol: Patient cells were counted and plated at 10,000 per well in 100 µL RETM with 96-well spheroid plates with black walls (Corning 4520). After 18-24 hours, 100 µL culture medium with drug (2X dose) was added. After 72 hours, the medium was removed, and the organoids were washed with fresh medium once and replaced with 200 µL fresh medium containing CSL inhibitors.

value: breast cancer tumor cell

value: Paclitaxel (1µM)+Belinostat (1µM)

tag: patient


title: Patient#5_Pacli/DMSO

description: single cell RNA

value: Paclitaxel (1µM)+DMSO


title: Patient#5_Dox/Belinostat

description: single cell RNA

value: Doxorubicin (0.1µM)+Belinostat (1µM)


title: Patient#5_Carbo/Belinostat

description: single cell RNA

value: Carboplatin (0.1mM)+Belinostat (1µM)


title: Patient#5_Dox/DMSO

description: single cell RNA

value: Doxorubicin (0.1µM)+DMSO


title: Patient#5_Carbo/DMSO

description: single cell RNA

value: Carboplatin (0.1mM)+DMSO


title: Patient#6_Pacli/Belinostat

description: single cell RNA


title: Patient#5_DMSO/DMSO

description: single cell RNA

value: DMSO+DMSO


title: Patient#6_Carbo/Belinostat

description: single cell RNA


title: Patient#6_Pacli/DMSO

description: single cell RNA


title: NPS-619

value: Influenza B


title: Patient#6_Dox/DMSO

description: single cell RNA


title: Patient#6_Carbo/DMSO

description: single cell RNA


title: Patient#6_Dox/Belinostat

description: single cell RNA


title: ECT_E11.5_rep1

status: Public on Oct 05 2020

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
All scripts are available in https://github.com/lldelisle/scriptsForFernandezGuerreroEtAl2020
Adapters and bad-quality bases were removed with Cutadapt version 1.16 options -m 15 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 30.
Reads were further mapped using STAR version 2.6.0c with ENCODE parameters with the gtf file https://doi.org/10.5281/zenodo.3820859
FPKM values were computed with cufflinks version 2.2.1 omitting mitochondrial genes.
Strand  specific coverage  was  computed  with bedtools version 2.27.1 from uniquely-mapped  reads.
Mean between coverage normalized to million of uniquely mapped reads of both replicates was done.
Genome_build: mm10
Supplementary_files_format_and_content: AllCufflinks_Simplified.txt.gz: tabulation delimited table with FPKM values (lines with duplicated ensembl id were summed)
Supplementary_files_format_and_content: *_Uniq_fwd.bedGraph.gz: coverage of uniquely mapped reads not normalized of each sample on the positive strand
Supplementary_files_format_and_content: *_Uniq_rev.bedGraph.gz: coverage of uniquely mapped reads not normalized of each sample on the negative strand
Supplementary_files_format_and_content: normalized_*_neq2_Uniq_fwd.bw: mean coverage of uniquely mapped reads normalized to the million of uniquely mapped reads on the positive strand
Supplementary_files_format_and_content: normalized_*_neq2_Uniq_rev.bw: mean coverage of uniquely mapped reads normalized to the million of uniquely mapped reads on the negative strand

molecule: polyA RNA

organism: Mus musculus

source_name: Ectoderm of distal forelimb

extract_protocol:
The distal 150 microns of E9.5, E10.5, E11.5 and E12.5 forelimbs were dissected out in cold PBS and incubated in 0.25% trypsin (SV30037.01, GE Healthcare, Logan, Utah) on ice for 20 min. The distal limb stripes were then transferred to cold PBS where the ectoderm was separated from the mesoderm with fine forceps. Two biological replicates were collected for each stage and the same batch of embryos used for the ectoderm and mesoderm replicates. Total RNAs were purified using the RNeasy Plus Mini Kit (QIAGEN, 74134) for the first replicates and RNeasy Mini Kit (QIAGEN, 74104) for the second replicates.
RNA libraries were prepared using the Truseq® Stranded mRNA Library Prep Library Preparation kit (Illumina, 20020594)

tag: developmental stage

tag: strain

tag: tissue

value: Ectoderm of distal forelimb


title: ECT_E10.5_rep1


title: VC_UV Round 2

status: Public on Nov 17 2020

city: Saint Louis

first: Ryan

last: McCulla

state: Missouri

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

description:
Control - cells treated with 1% DMSO in VC and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
fpkm_genename-group 2.xls
fpkm_group-2.xls
fpkm_sample-group2.xls
readcount-group2.xls
readcount_genename-group2.xls
VC_UVvsVC_NoUV-2-DEG.xls
1-S_UVvsVC_UV_DEG.xls
Union for cluster-2.csv

data_processing:
QC and transcriptome data analysis :Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to reference genome :Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Quantification of gene expression level  :HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis :Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Adjusted P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Clustering  :To identify the correlation between difference, we clustered different samples using expression level FPKM to see the correlation using hierarchical clustering distance method with the function of pheatmap package in R
Genome_build: Homo_sapiens_hg19 (Sample 1,2,5,6 )  and Homo_sapiens_hg38 ( (Sample 3,4,7,8) :
Supplementary_files_format_and_content: xls files include FPKM count of each sample and DEG list for each comparison.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cell line was purchased from ATCC (Manassas,VA). The cells were incubated at 37°C in 95% relative humidity with 5% CO2. The cells were cultured in DMEM medium containing 10% FBS, and 1% L-glutamine. The cells were grown to 90% confluency and passaged by removing media, washing the cells with PBS buffer, and splitting the cells.

extract_protocol:
Following treatment protocol, cell media was aspirated and each well was washed with PBS. 350 µL of lysis buffer (included in Gen Elute™ Total RNA Purification Kit) was added. Wells were coated in lysis buffer for 5 minutes and transfered to seperate microcetrifuge tubes. 200 µL absolute ethanol was added and tubes were vortexed for 10 seconds. Columns were assembled with elution tubes and the lysates were applied directly onto seperately assembled columns. Tubes were centrifuged at 3,500 g for 1 minute. If lysate hasn't passed through the column. Centrifuge an additional minute at 14,000 g. Flowthrough was discarded. 400 µL of wash solution A was applied to each column and centrifuged for 1 minute at 3,500 g (or increased to 14,000 g as necessary). Flowthrough was discarded and the column was washed twice more with a 2 minute centrifuge time for the last wash. The columns were placed into fresh elution tubes and 50 µL of elution solution was added to each. The columns were centrifuged at 200 g for 2 minutes, followed by 14,000 g for 1 minute. The elution procedure was repeated to maximize yield. Samples were stored at -80 C until shipping at -20 C.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented by addition of fragmentation buffer. NEB library and strand specific libraries were then chosen. (Novogene Corporation - protocol associated with NEB library and strand specific library) Libraries were constructed using standard Illumina protocol.

treatment_protocol: "Two six well plates were plated with MDA-MB-231 cells (600,000 cells/1.8mL/well). Both plates were incubated with compounds (1-SO and 1-S) at final 10μM concentration for 24 hours (VC – 1% DMSO). One plate was irradiated with UV-A light by placing it in a Luzchem photoreactor with 8 LZC-UVA bulbs (fwhm, 325-375 nm) and another plate was kept in the dark by wrapping it in aluminium foil. After UV-exposure, RNA was extracted from these samples using Gen Elute™ Total RNA Purification Kit (Sigma Aldrich, Catalog #RNB100) and the protocol associated with the product kit. The samples were then shipped to Novogene Corporation Inc on dry ice. RNA sequencing and associated bioinformatics analysis (differential gene expression analysis) were performed by Novogene Corporation.  Heatmaps were generated using pheatmap package installed in R." - Isor A. et al., 2020 in prep

tag: cell line

tag: passage

tag: agent

value: 1percent  DMSO in VC and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs


title: VC_No UV Round 2

description:
Control - cells treated with 1%DMSO in VC
fpkm_genename-group 2.xls
fpkm_group-2.xls
fpkm_sample-group2.xls
readcount-group2.xls
readcount_genename-group2.xls
VC_UVvsVC_NoUV-2-DEG.xls
1-S_UVvsVC_NoUV_DEG.xls
1-S_NoUVvsVC_NoUV-DEG.xls
Union for cluster-2.csv

value: 1percent DMSO in VC


title: MES_E11.5_rep1

source_name: Mesoderm of distal forelimb

value: Mesoderm of distal forelimb


title: ECT_E12.5_rep1


title: ECT_E9.5_rep1


title: MES_E9.5_rep1


title: VC_No UV Round 1

description:
Control - cells treated with 1%DMSO in VC
fpkm_genename-group1.xls
fpkm_group-1.xls
fpkm_sample-group1.xls
readcount-group1.xls
readcount_genename_group1.xls
VC_UVvsVC_No UV-1-DEG.xls
1-SO_UVvsVC_No UV-DEG.xls
Union for cluster-1.csv


title: ECT_E9.5_rep2


title: MES_E12.5_rep1


title: MES_E12.5_rep2


title: MES_E10.5_rep2


title: MES_E9.5_rep2


title: MES_E10.5_rep1


title: Patient#6_DMSO/DMSO

description: single cell RNA


title: ECT_E12.5_rep2


title: VC_UV Round 1

description:
Control - cells treated with 1% DMSO in VC and UV-A irradiated for 30 minutes in a photoreactor with 8 LZC-UVA bulbs
fpkm_genename-group1.xls
fpkm_group-1.xls
fpkm_sample-group1.xls
readcount-group1.xls
readcount_genename_group1.xls
VC_UVvsVC_No UV-1-DEG.xls
1-SO_UVvsVC_UV-DEG.xls
Union for cluster-1.csv


title: ECT_E11.5_rep2


title: ECT_E10.5_rep2


title: Time Point 28d Dose 18µg (Tube_TiO2_NP), Sample 34

status: Public on Sep 12 2020

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via single intratracheal instillation of 0 µg (control) 18 µg (low), 54 µg (medium dose), and 162 µg (high dose) of  Tube TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

tag: gender

value: female

value: TiO2 Tube

tag: dose

tag: time

value: lung

tag: sample id

source_name: Universal Mouse Reference RNA

tag: reference

value: 11 mouse cell lines


title: Time Point 1d Dose 18µg (Tube_TiO2_NP), Sample 21


title: Time Point 28d Dose 162µg (Tube_TiO2_NP), Sample 27


title: Time Point 28d Dose 18µg (Tube_TiO2_NP), Sample 25


title: Time Point 1d Dose 0µg (Tube_TiO2_NP), Sample 24

value: CNTR


title: Time Point 28d Dose 54µg (Tube_TiO2_NP), Sample 35


title: MES_E11.5_rep2


title: Time Point 28d Dose 0µg (Tube_TiO2_NP), Sample 19


title: Time Point 28d Dose 0µg (Tube_TiO2_NP), Sample 28


title: Time Point 1d Dose 54µg (Tube_TiO2_NP), Sample 31


title: Time Point 1d Dose 54µg (Tube_TiO2_NP), Sample 22


title: Time Point 28d Dose 54µg (Tube_TiO2_NP), Sample 26


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 36


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 23


title: Time Point 1d Dose 0µg (Tube_TiO2_NP), Sample 29


title: Time Point 1d Dose 18µg (Tube_TiO2_NP), Sample 16


title: Time Point 28d Dose 18µg (Tube_TiO2_NP), Sample 20


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 14


title: Time Point 28d Dose 0µg (Tube_TiO2_NP), Sample 33


title: Time Point 28d Dose 54µg (Tube_TiO2_NP), Sample 12


title: Time Point 1d Dose 0µg (Tube_TiO2_NP), Sample 15


title: Time Point 1d Dose 18µg (Tube_TiO2_NP), Sample 30


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 32


title: Time Point 1d Dose 0µg (Tube_TiO2_NP), Sample 9


title: Time Point 28d Dose 18µg (Tube_TiO2_NP), Sample 11


title: Time Point 28d Dose 54µg (Tube_TiO2_NP), Sample 17


title: Time Point 28d Dose 162µg (Tube_TiO2_NP), Sample 18


title: Time Point 28d Dose 162µg (Tube_TiO2_NP), Sample 10


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 8


title: Time Point 1d Dose 54µg (Tube_TiO2_NP), Sample 13


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 7


title: Time Point 28d Dose 0µg (Tube_TiO2_NP), Sample 5


title: Time Point 1d Dose 54µg (Tube_TiO2_NP), Sample 3


title: Time Point 1d Dose 162µg (Tube_TiO2_NP), Sample 4


title: Time Point 28d Dose 54µg (Tube_TiO2_NP), Sample 6


title: Time Point 1d Dose 18µg (Tube_TiO2_NP), Sample 2


title: Time Point 28d Dose 54µg (DQ_TiO2_NP), Sample 37

treatment_protocol: Mice were dosed via single intratracheal instillation of 0 µg (control) 18 µg (low), 54 µg (medium dose), and 162 µg (high dose) of  DQ TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

value: TiO2 DQ


title: Time Point 1d Dose 0µg (Tube_TiO2_NP), Sample 1


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 34


title: Time Point 28d Dose 0µg (DQ_TiO2_NP), Sample 35


title: Time Point 28d Dose 18µg (DQ_TiO2_NP), Sample 36


title: Time Point 1d Dose 0µg (DQ_TiO2_NP), Sample 31


title: Time Point 1d Dose 18µg (DQ_TiO2_NP), Sample 32


title: Time Point 1d Dose 54µg (DQ_TiO2_NP), Sample 33


title: Time Point 28d Dose 0µg (DQ_TiO2_NP), Sample 30


title: Time Point 1d Dose 0µg (DQ_TiO2_NP), Sample 28


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 27


title: Time Point 1d Dose 18µg (DQ_TiO2_NP), Sample 25


title: Time Point 28d Dose 0µg (DQ_TiO2_NP), Sample 23


title: Time Point 1d Dose 54µg (DQ_TiO2_NP), Sample 26


title: Time Point 28d Dose 162µg (DQ_TiO2_NP), Sample 22


title: Time Point 28d Dose 18µg (DQ_TiO2_NP), Sample 24


title: Time Point 1d Dose 0µg (DQ_TiO2_NP), Sample 19


title: Time Point 1d Dose 54µg (DQ_TiO2_NP), Sample 17


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 18


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 38


title: Time Point 28d Dose 18µg (DQ_TiO2_NP), Sample 29


title: Time Point 28d Dose 54µg (DQ_TiO2_NP), Sample 21


title: Time Point 1d Dose 18µg (DQ_TiO2_NP), Sample 20


title: Time Point 28d Dose 54µg (DQ_TiO2_NP), Sample 16


title: Time Point 28d Dose 54µg (DQ_TiO2_NP), Sample 7


title: Time Point 28d Dose 0µg (DQ_TiO2_NP), Sample 5


title: Time Point 28d Dose 18µg (DQ_TiO2_NP), Sample 6


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 4


title: Time Point 1d Dose 18µg (DQ_TiO2_NP), Sample 2


title: Time Point 1d Dose 54µg (DQ_TiO2_NP), Sample 12


title: Time Point 28d Dose 0µg (Cube_TiO2_NP), Sample 35

treatment_protocol: Mice were dosed via single intratracheal instillation of 0 µg (control) 18 µg (low), 54 µg (medium dose), and 162 µg (high dose) of  Cube TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

value: TiO2 cube


title: Time Point 1d Dose 54µg (Cube_TiO2_NP), Sample 33


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 34


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 26


title: Time Point 1d Dose 0µg (Cube_TiO2_NP), Sample 31


title: Time Point 28d Dose 162µg (Cube_TiO2_NP), Sample 29


title: Time Point 28d Dose 18µg (Cube_TiO2_NP), Sample 28


title: Time Point 28d Dose 0µg (Cube_TiO2_NP), Sample 30


title: Time Point 1d Dose 54µg (Cube_TiO2_NP), Sample 25


title: Time Point 1d Dose 18µg (Cube_TiO2_NP), Sample 32


title: Time Point 28d Dose 162µg (Cube_TiO2_NP), Sample 21


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 17


title: Time Point 1d Dose 0µg (Cube_TiO2_NP), Sample 18


title: Time Point 28d Dose 18µg (Cube_TiO2_NP), Sample 15


title: Time Point 28d Dose 18µg (DQ_TiO2_NP), Sample 15


title: Time Point 1d Dose 54µg (Cube_TiO2_NP), Sample 12


title: Time Point 1d Dose 0µg (Cube_TiO2_NP), Sample 10


title: Time Point 28d Dose 0µg (DQ_TiO2_NP), Sample 14


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 9


title: Time Point 28d Dose 162µg (Cube_TiO2_NP), Sample 8


title: Time Point 1d Dose 162µg (DQ_TiO2_NP), Sample 9


title: Time Point 1d Dose 18µg (DQ_TiO2_NP), Sample 11


title: Time Point 28d Dose 18µg (Cube_TiO2_NP), Sample 6


title: Time Point 28d Dose 54µg (Cube_TiO2_NP), Sample 7


title: Time Point 1d Dose 0µg (DQ_TiO2_NP), Sample 10


title: Time Point 28d Dose 162µg (DQ_TiO2_NP), Sample 13


title: Time Point 1d Dose 54µg (Cube_TiO2_NP), Sample 3


title: Time Point 28d Dose 162µg (DQ_TiO2_NP), Sample 8


title: Time Point 28d Dose 54µg (Cube_TiO2_NP), Sample 37


title: Time Point 1d Dose 0µg (DQ_TiO2_NP), Sample 1


title: Time Point 1d Dose 54µg (DQ_TiO2_NP), Sample 3


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 38


title: Time Point 1d Dose 0µg (Cube_TiO2_NP), Sample 1


title: Time Point 28d Dose 18µg (Cube_TiO2_NP), Sample 36


title: Time Point 28d Dose 54µg (100_nm_TiO2_NP), Sample 39

treatment_protocol: Mice were dosed via single intratracheal instillation of 0 µg (control) 18 µg (low), 54 µg (medium dose), and 162 µg (high dose) of  100 nm TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

value: 100nm TiO2


title: Time Point 28d Dose 0µg (100_nm_TiO2_NP), Sample 37


title: Time Point 1d Dose 54µg (100_nm_TiO2_NP), Sample 35


title: Time Point 28d Dose 18µg (100_nm_TiO2_NP), Sample 38


title: Time Point 1d Dose 0µg (100_nm_TiO2_NP), Sample 33


title: Time Point 1d Dose 0µg (Cube_TiO2_NP), Sample 27


title: Time Point 1d Dose 18µg (Cube_TiO2_NP), Sample 24


title: Time Point 28d Dose 162µg (100_nm_TiO2_NP), Sample 31


title: Time Point 1d Dose 18µg (100_nm_TiO2_NP), Sample 34


title: Time Point 28d Dose 0µg (100_nm_TiO2_NP), Sample 32


title: Time Point 28d Dose 18µg (100_nm_TiO2_NP), Sample 29


title: Time Point 28d Dose 54µg (Cube_TiO2_NP), Sample 20


title: Time Point 28d Dose 0µg (Cube_TiO2_NP), Sample 22


title: Time Point 28d Dose 18µg (Cube_TiO2_NP), Sample 23


title: Time Point 1d Dose 54µg (100_nm_TiO2_NP), Sample 26


title: Time Point 28d Dose 0µg (100_nm_TiO2_NP), Sample 23


title: Time Point 28d Dose 54µg (100_nm_TiO2_NP), Sample 22


title: Time Point 1d Dose 18µg (100_nm_TiO2_NP), Sample 25


title: Time Point 28d Dose 54µg (Cube_TiO2_NP), Sample 16


title: Time Point 1d Dose 18µg (Cube_TiO2_NP), Sample 19


title: Time Point 28d Dose 162µg (Cube_TiO2_NP), Sample 13


title: Time Point 1d Dose 18µg (Cube_TiO2_NP), Sample 11


title: Time Point 1d Dose 0µg (100_nm_TiO2_NP), Sample 28


title: Time Point 28d Dose 54µg (100_nm_TiO2_NP), Sample 16


title: Time Point 1d Dose 0µg (100_nm_TiO2_NP), Sample 19


title: Time Point 28d Dose 18µg (100_nm_TiO2_NP), Sample 15


title: Time Point 28d Dose 0µg (Cube_TiO2_NP), Sample 14


title: Time Point 28d Dose 18µg (100_nm_TiO2_NP), Sample 6


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 4


title: Time Point 28d Dose 0µg (Cube_TiO2_NP), Sample 5


title: Time Point 1d Dose 18µg (100_nm_TiO2_NP), Sample 2


title: Time Point 28d Dose 162µg (100_nm_TiO2_NP), Sample 13


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 40

treatment_protocol: Mice were dosed via single intratracheal instillation of 0 µg (control) 18 µg (low), 54 µg (medium dose), and 162 µg (high dose) of  15 nm TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

value: 15nm TiO2NPs


title: Time Point 28d Dose 0µg (100_nm_TiO2_NP), Sample 5


title: Time Point 28d Dose 18µg (15_nm_TiO2_NP), Sample 38


title: Time Point 28d Dose 54µg (15_nm_TiO2_NP), Sample 39


title: Time Point 1d Dose 0µg (100_nm_TiO2_NP), Sample 1


title: Time Point 1d Dose 54µg (100_nm_TiO2_NP), Sample 3


title: Time Point 28d Dose 0µg (15_nm_TiO2_NP), Sample 37


title: Time Point 1d Dose 162µg (Cube_TiO2_NP), Sample 4


title: Time Point 28d Dose 54µg (100_nm_TiO2_NP), Sample 30


title: Time Point 1d Dose 18µg (Cube_TiO2_NP), Sample 2


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 40


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 36


title: Time Point 1d Dose 54µg (15_nm_TiO2_NP), Sample 35


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 36


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 27


title: Time Point 28d Dose 18µg (100_nm_TiO2_NP), Sample 21


title: Time Point 28d Dose 162µg (100_nm_TiO2_NP), Sample 24


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 20


title: Time Point 1d Dose 18µg (15_nm_TiO2_NP), Sample 34


title: Time Point 1d Dose 0µg (15_nm_TiO2_NP), Sample 33


title: Time Point 1d Dose 18µg (100_nm_TiO2_NP), Sample 17


title: Time Point 28d Dose 0µg (15_nm_TiO2_NP), Sample 32


title: Time Point 1d Dose 18µg (100_nm_TiO2_NP), Sample 11


title: Time Point 1d Dose 0µg (100_nm_TiO2_NP), Sample 10


title: Time Point 28d Dose 54µg (100_nm_TiO2_NP), Sample 7


title: Time Point 28d Dose 162µg (100_nm_TiO2_NP), Sample 8


title: Time Point 1d Dose 54µg (100_nm_TiO2_NP), Sample 12


title: Time Point 28d Dose 0µg (100_nm_TiO2_NP), Sample 14


title: Time Point 28d Dose 162µg (15_nm_TiO2_NP), Sample 31


title: Time Point 1d Dose 162µg (100_nm_TiO2_NP), Sample 9


title: Time Point 28d Dose 18µg (15_nm_TiO2_NP), Sample 29


title: Time Point 1d Dose 54µg (100_nm_TiO2_NP), Sample 18


title: Time Point 1d Dose 0µg (15_nm_TiO2_NP), Sample 28


title: Time Point 28d Dose 54µg (15_nm_TiO2_NP), Sample 30


title: Time Point 1d Dose 54µg (15_nm_TiO2_NP), Sample 26


title: Time Point 28d Dose 18µg (15_nm_TiO2_NP), Sample 24


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 27


title: Time Point 28d Dose 0µg (15_nm_TiO2_NP), Sample 23


title: Time Point 1d Dose 18µg (15_nm_TiO2_NP), Sample 20


title: Time Point 28d Dose 54µg (15_nm_TiO2_NP), Sample 21


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 18


title: Time Point 28d Dose 162µg (15_nm_TiO2_NP), Sample 22


title: Time Point 1d Dose 0µg (15_nm_TiO2_NP), Sample 19


title: Time Point 1d Dose 54µg (15_nm_TiO2_NP), Sample 17


title: Time Point 1d Dose 18µg (15_nm_TiO2_NP), Sample 25


title: Time Point 1d Dose 0µg (15_nm_TiO2_NP), Sample 10


title: Time Point 28d Dose 162µg (15_nm_TiO2_NP), Sample 13


title: Time Point 28d Dose 18µg (15_nm_TiO2_NP), Sample 15


title: Time Point 1d Dose 54µg (15_nm_TiO2_NP), Sample 12


title: poolD-92_S284

status: Public on Sep 05 2020

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm18) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2). Cells with less than 100,000 reads and/or 1000 genes expressed, more than 20% mitochondrial reads, and less than an average expression level of 3.0 of about 80 housekeeping genes 61 were discarded. 469 cells passed these stringent quality criteria
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: potential Csf1r lineage endothelial cell (CLEC)

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2 μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000 g for 1 min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9 min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).

tag: facs gating

value: CD45- CD31+ GFPlow

value: lymph node


title: poolD-90_S282


title: poolD-94_S286


title: poolD-91_S283

source_name: Csf1r lineage endothelial cell (CLEC)

value: CD45- CD31+ GFP+

value: blood


title: poolD-93_S285


title: poolD-96_S288


title: poolD-95_S287


title: Time Point 1d Dose 18µg (15_nm_TiO2_NP), Sample 11


title: poolD-88_S280


title: poolD-87_S279


title: poolD-86_S278


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 9


title: Time Point 28d Dose 54µg (15_nm_TiO2_NP), Sample 16


title: Time Point 28d Dose 18µg (15_nm_TiO2_NP), Sample 6


title: Time Point 28d Dose 0µg (15_nm_TiO2_NP), Sample 14


title: poolD-85_S277


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 8


title: Time Point 1d Dose 162µg (15_nm_TiO2_NP), Sample 4


title: Time Point 1d Dose 0µg (15_nm_TiO2_NP), Sample 1


title: poolD-84_S276


title: Time Point 28d Dose 54µg (15_nm_TiO2_NP), Sample 7


title: Time Point 1d Dose 54µg (15_nm_TiO2_NP), Sample 3


title: Time Point 28d Dose 0µg (15_nm_TiO2_NP), Sample 5


title: poolD-89_S281


title: poolD-82_S274


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source_name: no cell

value: no cell


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source_name: endothelial cell

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title: Time Point 1d Dose 18µg (15_nm_TiO2_NP), Sample 2


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title: KM2-F7_S150


title: KM2-E9_S165


title: KM2-E8_S157


title: KM2-E10_S173


title: KM2-E11_S181


title: KM2-E12_S189


title: KM2-G9_S167


title: KM2-E7_S149


title: KM2-E6_S141


title: KM2-E5_S133


title: KM2-E3_S117


title: KM2-E2_S109


title: KM2-E1_S101


title: KM2-D10_S172


title: KM2-D11_S180


title: KM2-E4_S125


title: KM2-D7_S148


title: KM2-D8_S156


title: KM2-D6_S140


title: KM2-C12_S187


title: KM2-D1_S100


title: KM2-D4_S124


title: KM2-D5_S132


title: KM2-D3_S116


title: KM2-C9_S163


title: KM2-C8_S155


title: KM2-C10_S171


title: KM2-C4_S123


title: KM2-F3_S118


title: KM2-C6_S139


title: KM2-C11_S179


title: KM2-C7_S147


title: KM2-D9_S164


title: KM2-C3_S115


title: KM2-C5_S131


title: KM2-C2_S107


title: KM2-B11_S178


title: KM2-D12_S188


title: KM2-B10_S170


title: KM2-B9_S162


title: KM2-B8_S154


title: KM2-B7_S146


title: KM2-B6_S138


title: KM2-D2_S108


title: KM2-B5_S130


title: KM2-B3_S114


title: KM2-B1_S98


title: KM2-A12_S185


title: KM2-A9_S161


title: KM2-A11_S177


title: KM2-A8_S153


title: KM2-A6_S137


title: KM2-A2_S105


title: KM1-H12_S96

source_name: macrophage


title: KM2-A1_S97


title: KM2-C1_S99


title: KM2-A3_S113


title: KM1-H11_S88


title: KM2-B12_S186


title: KM1-H9_S72


title: KM2-B4_S122


title: KM1-H10_S80


title: KM2-A4_S121


title: KM2-A10_S169


title: KM2-A5_S129


title: KM1-H8_S64


title: KM1-H7_S56


title: KM2-B2_S106


title: KM1-H3_S24


title: KM1-H4_S32


title: KM1-H5_S40


title: KM1-G12_S95


title: KM2-A7_S145


title: KM1-G10_S79


title: KM1-G9_S71


title: KM1-G7_S55


title: KM1-G8_S63


title: KM1-G11_S87


title: KM1-H2_S16


title: KM1-G5_S39


title: KM1-G4_S31


title: KM1-G6_S47


title: KM1-G2_S15


title: KM1-F12_S94


title: KM1-G1_S7


title: KM1-F11_S86


title: KM1-F10_S78


title: KM1-F5_S38


title: KM1-F6_S46


title: KM1-F4_S30


title: KM1-F9_S70


title: KM1-F7_S54


title: KM1-H6_S48


title: KM1-F8_S62


title: KM1-F3_S22


title: KM1-H1_S8


title: KM1-F2_S14


title: KM1-E10_S77


title: KM1-G3_S23


title: KM1-E8_S61


title: KM1-E12_S93


title: KM1-E11_S85


title: KM1-E6_S45


title: KM1-E9_S69


title: KM1-E7_S53


title: KM1-E1_S5


title: KM1-E5_S37


title: KM1-E2_S13


title: KM1-D12_S92


title: KM1-D11_S84


title: KM1-D9_S68


title: KM1-D6_S44


title: KM1-D8_S60


title: KM1-D10_S76


title: KM1-D5_S36


title: KM1-D1_S4


title: KM1-D4_S28


title: KM1-C11_S83


title: KM1-C10_S75


title: KM1-D3_S20


title: KM1-C12_S91


title: KM1-C9_S67


title: KM1-E4_S29


title: KM1-E3_S21


title: KM1-D7_S52


title: KM1-F1_S6


title: KM1-D2_S12


title: KM1-C6_S43


title: KM1-C8_S59


title: KM1-C7_S51


title: KM1-C4_S27


title: KM1-C3_S19


title: KM1-C5_S35


title: KM1-C1_S3


title: KM1-C2_S11


title: KM1-B8_S58


title: KM1-B6_S42


title: KM1-B3_S18


title: KM1-B12_S90


title: KM1-B1_S2


title: KM1-B2_S10


title: KM1-A11_S81


title: KM1-B10_S74


title: KM1-B11_S82


title: KM1-A8_S57


title: KM1-A10_S73


title: KM1-A7_S49


title: KM1-B9_S66


title: KM1-A6_S41


title: KM1-B5_S34


title: KM1-A12_S89


title: KM1-A9_S65


title: KM1-A5_S33


title: KM1-A4_S25


title: KM1-A1_S1


title: KM1-B7_S50


title: KM1-A3_S17


title: poolD-74_S266

organism: blank sample


title: KM1-A2_S9


title: CAMA-1_riboR_ribo_rep3

status: Public on Jun 22 2020

data_processing:
We verified the quality of sequence reads using FastQC.
Adapters were trimmed using Trimmomatic v 0.38 using default parameters.
Samples were aligned to hg19 using the STAR (v2.6.0.a) aligner using a GTF from RefSeq.
Transcripts were quantified as transcripts per million (TPM) by RSEM (v1.3.1).
The pipelines were created and executed using BETSY.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: breast cancer cell line

growth_protocol: CAMA-1 cells were continuously treated with 1 uM ribociclib for 1 month followed by 250 nM for 4 months to develop resistance. Dose response experiments confirmed the ribociclib-resistant nature of treated cells. Parental, sensitive and adapted, resistant cells were independently plated at 500,000 cells/well in 6-well cell culture plates in triplicate.

extract_protocol:
RNA was isolated using the commercially available kit (RNEasy Plus Mini Kit, Qiagen, Cat. No.: 74136) following the manufacturer's instruction.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA library Prep Ribo-zero Gold following manufacturer’s protocol.
RNA-Seq, paired-end reads, stranded

treatment_protocol: 24 hours after plating ribociclib treatment of 1 uM (final concentration) or same volume of vehicle control (DMSO) were initiated. After 12 hours of treatment, cells were trypsinized, washed and pellets were stored in -80C until RNA isolation.

value: 1 uM ribociclib

tag: ribociclib sensitivity

value: resistant


title: poolD-73_S265


title: CAMA-1_riboR_ribo_rep2


title: CAMA-1_riboR_DMSO_rep2

value: DMSO


title: KM1-B4_S26


title: CAMA-1_riboR_DMSO_rep3


title: CAMA-1_riboR_DMSO_rep1


title: CAMA-1_ribo_rep3

value: sensitive


title: CAMA-1_DMSO_rep3


title: CAMA-1_DMSO_rep1


title: 15435X7

status: Public on Jun 09 2020

description:
15435X7_S15_L008
processed data file: 15424R.15435R.RawCounts.txt.gz

data_processing:
Fastq files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger version 2.2 using default parameters (mkfastq)
Count matrices were generated from fastq files using 10X Genomics Cellranger version 2.2 using default parameters (count)
Aggregated counts matrices were generated for each sequencing run using 10X Genomics Cellranger version 2.2 (aggr)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include aggregated counts from each sample.
Supplementary_files_format_and_content: cell_annotations.txt file contains cell-level annotations of the cells from this data set.

source_name: PBMC

extract_protocol:
PBMC samples were thawed at 37ᵒC and washed with PBS followed by 0.04% non-acetylated BSA in PBS.
Chromium Single Cell 3’ Library & Gel Bead Kit V2 protocol

tag: subject status

value: advanced gastrointestinal cancer patient

tag: patient id

tag: cancer type

value: Colon

tag: response

value: Responder

tag: cell type

value: PBMC single cell


title: CAMA-1_ribo_rep2

tag: treatment


title: 15435X6

description:
15435X6_S14_L007
processed data file: 15424R.15435R.RawCounts.txt.gz


title: CAMA-1_DMSO_rep2


title: 15435X4

description:
15435X4_S12_L006
processed data file: 15424R.15435R.RawCounts.txt.gz

value: Esophagus


title: CAMA-1_ribo_rep1


title: 15435X5

description:
15435X5_S13_L007
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15435X1

description:
15435X1_S9_L005
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15435X8

description:
15435X8_S16_L008
processed data file: 15424R.15435R.RawCounts.txt.gz

value: Pancreas


title: 15435X3

description:
15435X3_S11_L006
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15435X2

description:
15435X2_S10_L005
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15424X6

description:
15424X6_S6_L003
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15424X8

description:
15424X8_S8_L004
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15424X5

description:
15424X5_S5_L003
processed data file: 15424R.15435R.RawCounts.txt.gz


title: CAMA-1_riboR_ribo_rep1


title: 15424X3

description:
15424X3_S3_L002
processed data file: 15424R.15435R.RawCounts.txt.gz

value: Liver


title: 15424X1

description:
15424X1_S1_L001
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15424X4

description:
15424X4_S4_L002
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 15424X2

description:
15424X2_S2_L001
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 14546X12

description:
14546X12_S12_L006
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X8

description:
14546X8_S8_L004
processed data file: 14546.14554.14562.RawCounts.txt.gz

value: EOT


title: 14546X7

description:
14546X7_S7_L004
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X9

description:
14546X9_S10_L005
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 15424X7

description:
15424X7_S7_L004
processed data file: 15424R.15435R.RawCounts.txt.gz


title: 14546X10

description:
14546X10_S9_L005
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X6

description:
14546X6_S6_L003
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14562X6

description:
14562X6_S6_L003
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X4

description:
14546X4_S4_L002
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X2

description:
14546X2_S2_L001
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14562X3

description:
14562X3_S3_L002
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14562X5

description:
14562X5_S5_L003
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14562X4

description:
14562X4_S4_L002
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X11

description:
14554X11_S13_L007
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14562X2

description:
14562X2_S2_L001
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X3

description:
14546X3_S3_L002
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X10

description:
14554X10_S16_L008
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X1

description:
14546X1_S1_L001
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X9

description:
14554X9_S15_L008
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X8

description:
14554X8_S14_L007
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14546X11

description:
14546X11_S11_L006
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X5

description:
14554X5_S11_L006
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X3

description:
14554X3_S9_L005
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X2

description:
14554X2_S8_L004
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X1

description:
14554X1_S7_L004
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: 14554X4

description:
14554X4_S10_L005
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: Clp1 knockdown mTEChi

status: Public on May 05 2020

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

description: mTEChi of a lentigenic mouse with expression of the anti-Clp1 shRNAs and of the GFP reporter

data_processing:
Illumina NextSeq 500 sequencer
Single-end reads were trimmed to 50bp
Alignment to the mm9 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution.
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include count numbers also in distal 3'UTRs and Deseq-normalized read counts with foldchange

source_name: medullary thymic epithelial cells

extract_protocol:
Total RNA was extracted by Trizol
Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina) was used for sequencing

treatment_protocol: Clp1 KD (GFP+) and Ctr (GFP-) mTEChi were isolated using a BD FACS Aria III cell sorter, following the typical isolation procedure.

tag: tissue

value: thymus

tag: type

value: MHCII high medullary epithelial cells

tag: genotype

value: Clp1 knockdown / GFP Plus


title: 14546X5

description:
14546X5_S5_L003
processed data file: 14546.14554.14562.RawCounts.txt.gz


title: Ctr mTEChi

description: mTEChi of a lentigenic mouse with NO expression of the anti-Clp1 shRNAs and of the GFP reporter

value: Ctr / GFP Minus


title: Aire-transfected Ctr KD HEK293 exp2

description:
Second experiment
Aire_Plus_CLP1_sh3_with_Ctr_counts_w_distalUTR.csv
Aire_Plus_CLP1_sh3_with_Ctr_Deseq.csv

data_processing:
Illumina HiSeq2000 and NextSeq 500 sequencers
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Alignment to the hg19 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution
Genome_build: hg19
Supplementary_files_format_and_content: csv text files include either read counts for each sample or Deseq-normalized read counts and foldchange

source_name: HEK293 cells

extract_protocol:
Total RNA was extracted by Trizol
non-directionnal TruSeq V3 RNA Sample Prep Kit on PolyA+ mRNA

treatment_protocol: HEK293 cells were maintained in DMEM high glucose medium complemented with 10% FBS, L-glutamate, sodium pyruvate 1mM, non-essential amino acids and pen/strep antibiotics. HEK293 cells were transfected with the pCMV-Aire-Flag plasmid (or the control empty plasmid) using the TransIT-293 transfection reagent (Mirus) for 48 hours

value: embryonic kidney

tag: cell line

tag: aire expression

value: Aire + / Aire_Plus


title: CLP1 KD (CLP1 sh3) HEK293

data_processing:
Illumina HiSeq2000 sequencer
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Alignment to the hg19 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution
Genome_build: hg19
Supplementary_files_format_and_content: csv text files include either read counts for each sample or Deseq-normalized read counts and foldchange

treatment_protocol: HEK293 cells were maintained in DMEM high glucose medium complemented with 10% FBS, L-glutamate, sodium pyruvate 1mM, non-essential amino acids and pen/strep antibiotics. HEK293 cells were seeded at a density of 250,000 per well in 6-well plates. The next day, cells were supplemented with 8mg/ml polybrene and infected with 20 μL of shRNA-bearing lentiviruses. The day after, the medium was changed to a fresh one containing 2 μg/ml puromycin. Cells were maintained in selective medium during 6 days and harvested for RNA extraction using TRIzol HEK293 cells.

tag: genotype/variation

value: CLP1 KD (sh3)


title: 14562X1

description:
14562X1_S1_L001
processed data file: 14546.14554.14562.RawCounts.txt.gz

tag: time


title: Aire-transfected Ctr KD HEK293 exp1

description:
First experiment
Aire_Plus_CLP1_sh2_with_Ctr_counts_w_distalUTR.csv
Aire_Plus_CLP1_sh2_with_Ctr_Deseq.csv


title: Aire-transfected CLP1 KD-sh2 HEK293 exp1

value: Aire + / Aire_Plus / CLP1 KD


title: CLP1 KD (CLP1 sh2) HEK293

value: CLP1 KD (sh2)


title: Ctr-transfected HEK293

value: Aire - / Ctr


title: Aire-transfected CLP1 KD-sh3 HEK293 exp2

value: Aire + / Aire_Plus/ CLP1 KD


title: Aire-transfected HEK293


title: 14554X6

description:
14554X6_S12_L006
processed data file: 14546.14554.14562.RawCounts.txt.gz

value: advanced gastrointestinal cancer patient

value: Responder


title: Ctr KD (LacZ shRNA) HEK293

value: Ctr KD


title: HEK293_SUPT16H_shRNA3_KD

description: b: second serie

hyb_protocol: The labeled DNA was then hybridized to Human Gene ST1.0 microarrays (Affymetrix), washed, stained, and scanned.

scan_protocol: Standard Affymetrix protocol

data_processing: Raw probe-level data (.CEL files) were normalized by the robust multiarray average (RMA) algorithm and summarized using the R-package aroma.affymetrix (www.aroma-project.org/).

label: biotin

source_name: HEK293, shRNA lenti-infection, 6 days

label_protocol: Single-stranded DNA in the sense orientation was synthesized from total RNA with random priming using the GeneChip WT Amplification kit (Affymetrix). The DNA was subsequently purified, fragmented, and terminally labeled using the GeneChip WT Terminal Labeling kit (Affymetrix) incorporating biotinylated ribonucleotides into the DNA.

growth_protocol: HEK293 cells were maintained in complemented DMEM high glucose medium

extract_protocol: HEK293 cells were harvested for RNA extraction using TRIzol (ThermoFischer).

treatment_protocol: The specific knowckdown of HEK293 cells was performed by infection with lentivirus-expressing shRNAs. shRNAs were cloned into the lentivirus vector pLKO with an expression driven by the ubiquitously active U6 promoter, and were provided by the RNAi Consortium of the Broad Institute, as lentiviral particles at ~10^7 VP/mL. HEK293s were seeded at a density of 250,000 per well in 6-well plates, were supplemented with 8mg/ml polybrene and infected with 20 μL of shRNA-bearing lentiviruses. The day after, the medium was changed to a fresh one containing 2 μg/ml puromycin. Cells were maintained in selective medium during 6 days and harvested for RNA extraction.

tag: kd gene


title: HEK293_PRKDC_shRNA3_KD

description: b: second serie

value: PRKDC


title: HEK293_CTR_rep_KD

description: b: second serie

value: lacZ


title: HEK293_SUPT16H_shRNA1_KD

description: b: second serie


title: mTEClo Exp2

data_processing:
Illumina HiSeq2000 sequencer
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Paired-end reads were concatenated and trimmed to 50bp. Single-end reads were 50bp length
Alignment to the mm9 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution. 3'UTRs of all genes in the ActinoD-treated mTEChi were not considered for read count
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include Deseq-normalized count numbers and read count numbers for ActinoD-treated mTEChi

extract_protocol:
Total RNA was extracted by Trizol
Non-directionnal TruSeq V3 RNA Sample Prep Kit on PolyA+ mRNA was used for WT and Aire-KO mTEChi, as well as for mTEChi used as the reference timepoint (ActinoD 0h), or for mTEChi and lo from the same mice. Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina) was used for ActinoD-treated mTEChi

treatment_protocol: MHC-II high or low mTECs were isolated from pooled thymic of B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure. ActinoD-treated mTEChi were treated with actinomycin D (1 μM) in MEM medium for 3, 6 and 12 hours

value: MHCII low medullary epithelial cells

value: WT


title: HEK293_PRKDC_shRNA1_KD

description: b: second serie


title: HEK293_PABPC1_shRNA2_KD

description: b: second serie


title: HEK293_SUPT16H_shRNA2_KD

description: b: second serie


title: HEK293_PARP1_shRNA1_KD

description: b: second serie


title: HEK293_PARP1_shRNA2_KD

description: b: second serie


title: HEK293_PABPC1_shRNA3_KD

description: b: second serie


title: HEK293_HNRNPL_shRNA1_KD

description: a: first serie

value: HNRNPL


title: HEK293_PABPC1_shRNA1_KD

description: b: second serie


title: HEK293_CTR_KD_bis

description: b: second serie


title: HEK293_DDX17_shRNA3_KD

description: a: first serie


title: HEK293_PARP1_shRNA3_KD

description: b: second serie


title: HEK293_HNRNPL_shRNA3_KD

description: a: first serie


title: mTEChi Exp2

value: thymus

value: MHCII high medullary epithelial cells


title: HEK293_CPSF6_shRNA_KD

description: a: first serie


title: HEK293_HNRNPL_shRNA2_KD

description: a: first serie


title: HEK293_DDX17_shRNA2_KD

description: a: first serie


title: HEK293_DDX5_shRNA2_KD

description: a: first serie


title: HEK293_CLP1_shRNA1_KD

description: a: first serie


title: HEK293_PRKDC_shRNA2_KD

description: b: second serie


title: HEK293_DDX17_shRNA1_KD

description: a: first serie


title: HEK293_CLP1_shRNA2_KD

description: a: first serie


title: HEK293_CLP1_shRNA3_KD

description: a: first serie


title: HEK293_DDX5_shRNA3_KD

description: a: first serie


title: HEK293_DDX5_shRNA1_KD

description: a: first serie


title: HEK293_CTR_KD

description: a: first serie


title: ActinomycinD-treated mTEChi 3h

description: ActinomycinD-treated for 3h

extract_protocol:
Total RNA was extracted by Trizol
NNon-directionnal TruSeq V3 RNA Sample Prep Kit on PolyA+ mRNA was used for WT and Aire-KO mTEChi, as well as for mTEChi used as the reference timepoint (ActinoD 0h), or for mTEChi and lo from the same mice. Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina) was used for ActinoD-treated mTEChi

value: ActinomycinD-treated for 3h


title: ActinomycinD-treated mTEChi 6h

description: ActinomycinD-treated for 6h

value: ActinomycinD-treated for 6h


title: ActinomycinD-treated mTEChi 1h30

description: ActinomycinD-treated for 1h30

value: ActinomycinD-treated for 1h30


title: Aire-KO mTEChi 2

value: Aire-/-


title: ActinomycinD-treated mTEChi 0h

description: ActinomycinD-treated for 0h (reference timepoint)


title: ActinomycinD-treated mTEChi 12h

description: ActinomycinD-treated for 12h

value: ActinomycinD-treated for 12h


title: Aire-KO mTEChi replicate

data_processing:
Illumina HiSeq2000 sequencer
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Paired-end reads were concatenated and trimmed to 50bp
Alignment to the mm9 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include count numbers for each sample

treatment_protocol: WT and Aire-KO MHC-II high mTECs were isolated from a pool of four B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure


title: Aire-KO mTEChi


title: mTEChi 2


title: ACP11-QD-D4

status: Public on Apr 07 2020

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

source_name: ACP11 QD D4

extract_protocol:
RNA was extracted per manufacturer's instructions (RNAeasy kit, Qiagen, Germantown, MD or ZR-Duet kit, Zymo Research, Irvine, CA).
Libraries were prepared with TruSeq Stranded total RNA Library Preparation Gold Kit (Illumina, San Diego, CA).

treatment_protocol: CD19+ PBMCs were purified by positive immunomagnetic selection (Miltenyi Biotec, Bergisch Gladbach, Germany).

tag: sample type

value: LN


title: mTEChi replicate


title: mTEChi


title: ACP11-QD-Pre

source_name: ACP11 QD Pre


title: PBMMC_2

status: Public on Jan 30 2020

city: Montreal

first: Guillaume

last: Bourque

state: QC

address: 740 Dr penfield

department: Human Genetics

institute: Mcgill university

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98  nt RNA sequence.
Reads were processed using 10x Genomics cellranger v2.1.0 on the ENSEMBL 84 gene annotation
Genome_build: ENSEMBL GRCh38.84
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: PBMMC

extract_protocol:
Mononuclear cells were isolated from bone marrow (BM) aspirates or peripheral blood cells at diagnosis and cryopreserved in FBS with 10% DMSO
10X Genomics Chromium single cell RNA 3’ v2

tag: disease state

value: Healthy pediatric control

value: Healthy pediatric bone marrow mononuclear cells


title: PRE-T_2

source_name: PRE-T

value: Childhood acute lymphoblastic leukemia

value: Pre-T acute lymphoblastic leukemia cells


title: PBMMC_1

description: pool of two libraries


title: PRE-T_1


title: HHD_1

source_name: HHD

value: Pre-B High hyper diploid [HHD] acute lymphoblastic leukemia cells


title: ETV6-RUNX1_3

value: Pre-B t(12;21) [ETV6-RUNX1] acute lymphoblastic leukemia cells


title: ETV6-RUNX1_1


title: ETV6-RUNX1_2


title: Zfc3h1_KO_3_ESC_D0_RNAseq

status: Public on Nov 12 2019

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
Quality control of RNAseq reads were done using FastQC v0.11.2 , reads were trimmed using Trimmomatic v0.32 with settings  “ILLUMINACLIP:<TrueSeq3_PE_2>:2:30:10 HEADCROP:12 LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25”
RNAseq reads were aligned to mm10 using HISAT v0.1.6.beta with --rna-strandness RF --minins 0 --maxins 1000  and a list of GENCODE M12 annotated splice sites was also provided.
Paired and uniquely mapped exonic reads for GENCODE M12 genes were counted using featureCounts from the R package Rsubread (1.32.1)
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

growth_protocol: ES cells were cultured on 0.2% gelatin coated plates in 2i/LIF containing medium.

extract_protocol:
Total RNA for RNAseq  was isolated using the RNeasy Mini Kit (Qiagen)
RNAseq libraries were prepared from 1 µg RNA using the TruSeq Stranded Total RNA library prep kit (Illumina) following rRNA depletion using Ribozero Gold (Illumina)

value: Embryonic stem cells


title: Klf3 KO BMDM 8h LPS 3

status: Public on Mar 24 2020

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

description: F09_KNI2057A22 KO3 LPS 8h

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Partek Genomics Suite software was used to analyse CEL files

source_name: Klf3 KO bone marrow-derived macrophages

label_protocol: not provided

growth_protocol: Animals were housed in a specific pathogen-free environment at a constant ambient temperature of 22°C on a 12 h light dark cycle, with ad libitum access to standard chow food and water. Femora and tibiae were collected and flushed using cold sterile PBS then seeded into tissue culture dishes in 80% DMEM-F12 (containing 10% FCS and 1% penn-strep-glut) and 20% L929 conditioned media (containing M-CSF growth factor). BMDMs were grown over 7-10 days before treatment, with L929 media topped up every 2-3 days.

extract_protocol: Cells were lysed and homogenised in TRI reagent, and RNA isolated using phenol/chloroform extraction. RNA was then purified using a Qiagen RNeasy Mini Kit and eluted in RNase-free water.

treatment_protocol: Media was removed, cells washed with PBS then replaced with regular DMEM-F12 (10% FCS 1% PSG). 0 h samples were harvested for RNA extraction, and 8 h samples were treated with 100 ng/mL lipopolysaccharide (LPS) or vehicle (PBS). After 8 h these samples were harvested for RNA extractions.

tag: strain

value: FVB/NJ

tag: Sex

value: male

value: bone marrow-derived macrophages

value: Klf3 KO


title: PBMMC_3


title: WT BMDM 8h LPS 3

description: F07_KNI2057A14 WT3 LPS 8h

source_name: WT bone marrow-derived macrophages

value: WT


title: WT BMDM 8h vehicle 3

description: D07_KNI2057A12 WT3 PBS 8h


title: WT BMDM 8h LPS 2

description: E09_KNI2057A21 WT2 LPS 8h


title: Klf3 KO BMDM 8h LPS 2

description: F05_KNI2057A6 KO2 LPS 8h


title: HHD_2


title: Klf3 KO BMDM 0h 3

description: B09_KNI2057A18 KO3 0h


title: Klf3 KO BMDM 8h LPS 1

description: E07_KNI2057A13 KO1 LPS 8h


title: WT BMDM 0h 3

description: B07_KNI2057A10 WT3 0h


title: Klf3 KO BMDM 8h vehicle 3

description: D09_KNI2057A20 KO3 PBS 8h


title: ETV6-RUNX1_4


title: WT BMDM 8h vehicle 1

description: C05_KNI2057A3 WT1 PBS 8h


title: Klf3 KO BMDM 8h vehicle 2

description: D05_KNI2057A4 KO2 PBS 8h


title: Klf3 KO BMDM 8h vehicle 1

description: C07_KNI2057A11 KO1 PBS 8h


title: Zfc3h1_KO_1_ESC_D0_RNAseq


title: WT_3_ESC_D0_RNAseq

value: Wildtype


title: WT BMDM 8h vehicle 2

description: C09_KNI2057A19 WT2 PBS 8h


title: WT BMDM 0h 1

description: A05_KNI2057A1 WT1 0h


title: Klf3 KO BMDM 0h 2

description: B05_KNI2057A2 KO2 0h


title: Klf3 KO BMDM 0h 1

description: A07_KNI2057A9 KO1 0h


title: WT BMDM 0h 2

description: A09_KNI2057A17 WT2 0h