title: LABD: 34245

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Labradoodle

value: whole blood


title: LABD: 34249

status: Public on Jul 17 2020

type: genomic

country: USA

molecule: genomic DNA

tag: tissue


title: CP73-6-Q20_9

type: SRA

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome build: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

molecule: total RNA

organism: Mus musculus

source_name: Striatum

extract_protocol:
TRAP: Striata or cortex were homogenized with a glass/Teflon power-driven Potter-Elvehjem homogenizer in an ice-cold lysis buffer (150 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5mM dithiothreitol, 100 μg/mL cycloheximide, 20 U/µL SUPERaseIn RNase Inhibitor, 40 U/µL RNasin Plus Rnase Inhibitor, and EDTA-free protease inhibitors).  Following homogenization, samples were centrifuged at 2,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  NP-40 (final concentration 1%) and 1,2-Diheptanoyl-sn-glycero-3-phosphocholine (DHPC, final concentration 15 mM) were subsequently added and samples were incubated on ice for 5 min.  Samples were centrifuged at 13,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  Streptavidin Dynabeads (ThermoFisher Scientific, Waltham MA) coated with biotin-linked mouse anti-GFP antibodies were then added to this supernatant and the samples were incubated overnight at 4°C with end-over-end rotation.  Beads were collected on a magnetic rack and washed three times with wash buffer (350 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/mL cycloheximide, 1% NP-40).  RNA was subsequently purified using the Absolutely RNA Isolation Nanoprep kit (Agilent Technologies, Santa Clara CA).
TRAP: Libraries were constructed using the Ovation RNA-Seq System v2 kit.

value: Striatum

tag: genotype

tag: tissue id


title: Acute - CTRL-2-INPUT

city: Melbourne

first: Anna

last: Trigos

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Cytosolic RNA
processed data file: Acute_input.txt

data_processing:
Sequencing reads were aligned with Tophat2 and reads counts were obtained with htseq (Anders et al., 2015) using the mouse genome (Ensembl release 78) as reference. We used our in-house bioinformatics pipeline, seqliner (http://bioinformatics.petermac.org/seqliner/).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Eμ-Myc B-lymphoma cells

growth_protocol: Eμ-Myc B-lymphoma cells (MSCV Gfp) were cultured in Anne Kelso DMEM, supplemented with 10% heat-inactivated (h.i.) fetal bovine serum (FBS), 100 μM L-asparagine (Merck), penicillin/streptomycin/glutamine (Thermo Fisher Scientific) and 0.5% beta-mercaptoethanol.

extract_protocol:
The cytoplasmic lysate was layered on top of a linear 10-40% sucrose gradient, ultracentrifuged (36,000 rpm, 2¼ hours, 4 °C) and fractionated using the Foxy Jr Fraction Collector with constant monitoring of absorbance at 260 nm by an ISCO UA-6 Absorbance Detector (Teledyne). Cytoplasmic (input) RNAs and polysomal RNAs from pooled fractions corresponding to four or more ribosomes were isolated using a TRIzol®- based method and purified using the Qiagen RNeasy® Minikit according to manufacturer’s instructions, and analysed by RNAseq.
cDNA libraries were generated using a ribodepletion method (TruSeq Ribo Profile Mammalian Kit, Illumina) from 1 µg of RNA sample. Fragment sizes were evaluated using the DNA 1000 kit and 2100 bioanalyzer (Agilent Technologies). Libraries were subjected to single-end sequencing (SE50bp) (Hiseq2500, Illumina) to generate ~30 million reads per sample using standard protocols.

treatment_protocol:
Acute study: Eµ-Myc B-cell lymphoma (MSCV Gfp; clone #4242) cells were transplanted into C57BL/6 mice as we performed previously (Bywater et al., 2012; Devlin et al., 2016). Lymphoma-bearing mice were treated on Day 10 post-transplant for 2 hours with CX-5461 (35 mg/kg), everolimus (EV; 5 mg/kg), or both (CX-5461+EV; 35 mg/kg CX-5461 and 5 mg/kg EV).
Resistance study: Early-passage Eμ-Myc B- lymphoma cells were isolated from the mice transplanted with Eµ-Myc B-cell lymphoma (MSCV Gfp; clone #107) cells who had succumbed to disease relapse following treatment with vehicles, everolimus, CX-5461 or CX-5461+EV at the end of a survival experiment in Figure 2B in Devlin et al. (Devlin et al., 2016). Specifically, lymph nodes isolated at endpoint of the in vivo experiment were manually disrupted by pressing with the plunger of a 3 ml syringe and the cell suspension was passed through 40 µm cell filters to obtain single cell suspensions. These cells were then cultured in Anne Kelso DMEM supplemented with 20% h.i. FBS (Gibco), 100 μM L-asparagine (Merck), penicillin/streptomycin/glutamine (Thermo Fisher Scientific) and 0.5% beta-mercaptoethanol until exponential growing phase was obtained (2-3 passages).

tag: cell type

value: MSCV Gfp; clone #4242

tag: treatment

value: Acute treatment to Vehicle/Vehicle


title: Acute - CTRL-1-INPUT


title: MN1+Smarca4_Input

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

library_source: genomic

data_processing:
BWA Alignment
MACS2 peak calling
samtools convert files
IGV 2.8.0
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: Transduced HSPC

growth_protocol: Cells were grown in IMDM medium supplemented with 15% heat inactivated FBS, 1% Penicillin/Streptomycin, 1% L-Glutamine, murine IL-3, murine IL-6 (10ng/mL), and murine SCF (20ng/mL).

extract_protocol:
HSPCs were isolated and transduced with the respective plasmid, then sorted. After 7-9 days in culture ChIP was performed. Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with the indicated antibody overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed at Genewiz, Illumina HiSeq, 2x150bp paired-end reads, multiplexed

value: Transduced HSPC

tag: chip antibody

value: none (input)


title: LABD: 34224


title: LABD: 34243


title: LABD: 34240


title: Histones_Input


title: CP73-6-Q20_8


title: LABD: 34229


title: Acute - CTRL-5-INPUT


title: CP73-6-Q20_7


title: LABD: 34215


title: LABD: 34208


title: CP73-6-Q20_6


title: CP73-6-Q20_5


title: noTD_H3K4me1

tag: transduced with


title: LAB: 33444

value: Labrador Retriever


title: LAB: 30656


title: LAB: 29561


title: MN1pQdel_H3K4me1


title: LAB: 29413


title: MN1_H3K4me1


title: CP73-6-Q20_4


title: LAB: 29399


title: LAB: 25261


title: CP73-6-Q20_3


title: LAB: 28481


title: MN1pQdel_H3K27ac


title: CP73-6-Q20_1


title: noTD_H3K27ac


title: CP73-6-Q20_2


title: LAB: 22113


title: CP73-6-Q20_10


title: MN1_H3K27ac


title: MCF7-Exosomes_(miRNA-4_0)

type: RNA

city: Beijing

first: Songjie

last: Shen

state: Beijing

address: No.1 Shuaifuyuan, Doncheng District

department: Department of Breast Surgery

country: China

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China

hyb_protocol: Hybridization was according to Biotin HSR RNA Labeling Kit

scan_protocol: Scanning was according to  Biotin HSR RNA Labeling Kit

data_processing: Affymetrix Expression Console™ Software

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the protocol of Affymetrix  Biotin HSR RNA Labeling Kit

growth_protocol: The MDA-MB-231 and MCF7 cells were cultured in DMEM Medium supplemented with 10% fetal bovine serum

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MCF7-Exosomes and MDA-MB-231-Exosomes isolation from cell culture supernatant

value: human breast adenocarcinoma cell line


title: noTD_Smarca4


title: LAB: 21325


title: MDA-MB-231-Cells_(miRNA-4_0).

value: Human breast cancer cell line


title: MCF7-Cells_(miRNA-4_0)


title: CP73-6-Q175_9


title: MDA-MB-231-Exosomes_(miRNA-4_0).


title: MN1pQdel_Smarca4


title: LAB: 12995


title: LAB: 12994


title: LAB: 13000


title: LAB: 7285


title: LAB: 2010


title: CP73-6-Q175_8


title: MN1_Smarca4


title: MN1leuk_H3K4me1

source_name: MN1-driven leukemia

value: AML


title: ALBD: Labradoodle7

value: Australian Labradoodle


title: CP73-6-Q175_7


title: CP73-6-Q175_6


title: LAB: 13001


title: LAB: 310


title: LAB: 12999


title: ALBD: Labradoodle16


title: MN1leuk_H3K27ac


title: CP73-6-Q175_5


title: ALBD: Labradoodle11


title: ALBD: Labradoodle20


title: CP73-6-Q175_4


title: CP73-6-Q175_3


title: MN1leuk_MN1_rep2

value: anti-HA


title: ALBD: Labradoodle13


title: ALBD: Labradoodle5


title: MN1leuk_Smarca4


title: ALBD: Labradoodle3


title: MN1leuk_MN1_rep1


title: ALBD: Labradoodle1


title: ALBD: Labradoodle12


title: LAB: 311


title: CP73-6-Q175_2


title: CP73-6-Q175_1


title: ALBD: Labradoodle18


title: CP73-6-Q175_10


title: ALBD: Labradoodle19


title: ALBD: Labradoodle22


title: ALBD: Labradoodle21


title: ALBD: Labradoodle14


title: CP73-6-Q170_9


title: DesminWTmouse3

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
adapter trimming using cutadapt v2.5
alignment to GRCm38 genome using STAR v2.5.4a
determination of raw counts using subread (v1.6.1) featureCounts
differential expression analysis using DESeq2
Genome_build: GRCm38.93
Supplementary_files_format_and_content: tab-separated text containing rlog-normalized count data

source_name: gastrocnemius muscle

growth_protocol: Mice were housed in cages that were maintained in a room with temperature 22 ± 1°C and relative humidity 50–60% on a 12h light/dark cycle. Water and food were provided ad libitum.

extract_protocol:
RNA was extracted using Trizol and Ambion Pure Link RNA Mini Kit according to the manufacturer's instructions.
Profiling of whole-genome transcriptomic patterns was performed with 1000ng high quality total RNA per sample. Libraries of the samples were generated using the Illumina stranded mRNA library kit according to the manufacturer's instructions.

tag: strain

value: Des wt/wt

value: striated muscle


title: ALBD: Labradoodle9


title: DesminWTmouse5


title: DesminWTmouse4


title: ALBD: Labradoodle4


title: DesminWTmouse2


title: ALBD: Labradoodle17


title: ALBD: Labradoodle6


title: CP73-6-Q170_7


title: CP73-6-Q170_6


title: ALBD: Labradoodle8


title: ALBD: Labradoodle15


title: 190913_R62_snRNA-H2

data_processing:
Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome build: GRCm38/mm10
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.


title: 190913_R62_snRNA-H4


title: DesminKOmouse4

value: Des -/-


title: CP73-6-Q170_5


title: 190913_R62_snRNA-H1


title: 190913_R62_snRNA-H3


title: DesminWTmouse1


title: 190913_R62_snRNA-G12

value: CBAxC57 WT


title: DesminKOmouse2


title: 190913_R62_snRNA-G11


title: CP73-6-Q170_3


title: CP73-6-Q170_4


title: CP73-6-Q170_8


title: DesminKOmouse3


title: DesminKOmouse1


title: CP73-6-Q170_1


title: CP73-6-Q170_2


title: 190913_R62_snRNA-G9


title: 190913_R62_snRNA-G10


title: 190912_R62_snRNA-G8


title: 190912_R62_snRNA-G7


title: DesminKOmouse5


title: 190912_R62_snRNA-G5


title: CP73-6-Q170_10


title: 190912_R62_snRNA-G6


title: 190912_R62_snRNA-G3


title: 190912_R62_snRNA-G4


title: CP73-6-Q111_9


title: 190912_R62_snRNA-G2


title: CP73-6-Q111_8


title: Depleted_3 [T3_S3]

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10
Supplementary_files_format_and_content: Count table (csv); Normalised counts from DESEq2 (csv)

source_name: Rag KO_DSS_colon

extract_protocol:
Colons were extracted into RNA later and stored at -80 until processing. RNA was extracted with RNEasy plus micro kit (Qiagen)
Libraries were produced with TruSeq stranded total RNA library prep kit (Illumina)

treatment_protocol: Mice recived 2%DSS for the first 5 days in drinking water after which it was replaced with normal water. The mice were culled after 6 days.

tag: genotype/variation

value: Rag KO

value: DSS

value: Colon


title: Depleted_5 [T5_S5]


title: Depleted_2 [T2_S2]


title: CP73-6-Q111_7

value: Striatum


title: CP73-6-Q111_6


title: WT_Tn_15

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: Naïve CD4+ T cells

data_processing:
The raw reads were mapped onto the mouse genome build GRCm38 using STAR (version2.5.3) (Dobin et al.2013). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample

growth_protocol: All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.

extract_protocol:
PMA/Ionomycin stimulated for 4hr/37C prior to sort
Qiagen MiRNEasy micro kit

treatment_protocol: Naïve sorted cells cultured for 6 days with irradiated APCs and 2.5 ng/ml TGFb and 20ng/ml IL-6 or 63ng/ml HDS (hyper IL-6)

value: CD4+ T-cell

value: IL-17F/Thy1.1 Hz


title: Control_5 [C5_S10]

source_name: Rag KO_Control_colon

value: Control


title: KO_Tn_16

description: Naïve CD4+ T cells

value: IL6Ra-/-. IL-17F/Thy1.1 Hz


title: Depleted_1 [T1_S1]


title: Control_4 [C4_S9]


title: KO_HDS63_12

description: CD4+ Thy1.1+ Th17p


title: KO_Tn_14

description: Naïve CD4+ T cells


title: WT_Tn_13

description: Naïve CD4+ T cells


title: CP73-6-Q111_3


title: CP73-6-Q111_4


title: CP73-6-Q111_5


title: WT_HDS63_11

description: CD4+ Thy1.1+ Th17p


title: Control_2 [C2_S7]


title: CP73-6-Q111_2


title: Control_3 [C3_S8]


title: Depleted_4 [T4_S4]


title: WT_IL6_10

description: CD4+ Thy1.1+ Th17p


title: KO_HDS63_9

description: CD4+ Thy1.1+ Th17p


title: Control_1 [C1_S6]


title: CP73-6-Q111_10


title: WT_HDS63_8

description: CD4+ Thy1.1+ Th17p


title: RS_bisulfite-seq

city: Xi'an, Shaanxi

first: liu

middle: ying

last: dong

address: Shaanxi

department: College of Animal Science and Technology

institute: Northwest University of Agriculture and Forestry Science and Technology

description:
whole genome
ploidy: 1N

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “--s 16 -v 0.1 -n 1 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

source_name: testis

extract_protocol:
DNA is extracted through Wizard Genomic DNA Purification Kit（LOT 0000139127）.
The sequencing libraries were generated using the Pico Methyl-Seq Library Prep Kit  (D5456, Zymo Research) following the manufacturer's instructions.

value: testis

value: round spermatids

tag: development stage

value: 6-8 weeks


title: PS_bisulfite-seq

description:
whole genome
ploidy: 4N

value: pachytene spermatocytes


title: CP101_6_Q50_8


title: WT_IL6_7

description: CD4+ Thy1.1+ Th17p


title: CP101_6_Q50_7


title: Thy1_bisulfite-seq

description:
whole genome
marker: thy1
THY1-antibody  manufacturer : Biolegend   lot number:B284489

value: undifferentiated spermatogonia cells

value: 6-8 days post-natal


title: CP101_6_Q50_9


title: post_WT_2

description: WT Colonic Live CD4+TCRb+CD45.1+ cells

extract_protocol:
Cells were sorted into RPMI + 10% serum, then centrifuged and resuspended in Qiazol and stored at -80C overnight. RNA was extracted the following day using Qiagen miRNeasy kit.
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: 2 x 10^5 each of WT (CD45.1) and Il6ra-/- (CD45.2) Thy1.1+ Th17 precursors were transferred into Rag1-/- recipients


title: Kit_bisulfite-seq

description:
whole genome
marker: kit
KIT-antibody   manufacturer : Biolegend    lot number:B255217

value: differentiated spermatogonia cells


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 6

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: Leukemic Pax5+/- (CF)_W634

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in SPF (specific pathogen free facility) or in CF (conventional facility).

value: Total Bone Marrow CF


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 5

source_name: Leukemic Pax5+/- (CF)_W362


title: Leukemic IL6+/-; Pax5+/- mouse housed in CF, biological replicate 1

source_name: Leukemic IL6+/-; Pax5+/- (CF)_U971


title: CP101_6_Q50_6


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 3

source_name: Leukemic Pax5+/- (CF)_O338


title: Leukemic IL6+/-; Pax5+/- mouse housed in CF, biological replicate 3

source_name: Leukemic IL6+/-; Pax5+/- (CF)_L370


title: Leukemic IL6+/-; Pax5+/- mouse housed in CF, biological replicate 2

source_name: Leukemic IL6+/-; Pax5+/- (CF)_U572


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 4

source_name: Leukemic Pax5+/- (CF)_5748


title: RS Input

description: ploidy: 1N

data_processing:
Sequenced reads were trimmed for adaptor sequence, low quality. The processed reads were then aligned to the mouse genome (mm9) with bowtie2 (version 2.2.9) with default settings.
Peaks were called using macs14(v1.4.2) with the parameters "macs14 -g mm --nomodel --nolambda --shiftsize=73" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 callpeak function and normlized to one million eads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

extract_protocol:
All sorted cells and H3K9me3 antibody incubated by magnetic beads were immunoprecipitated and DNA was finally isolated. The amount of DNA used for the ChIP: 6pg.
The sequence libraries were generated using the KAPA Hyper Prep Kit for the  Illumina platform (kk8504), following the manufacturer's instructions. Paired-end  150-bp sequencing was performed on Illumina HiSeq X10.

value: H3K9me3 (Active Motif, 39161)


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 1

source_name: Leukemic Pax5+/- (CF)_5556


title: CP73-6-Q111_1


title: Leukemic Pax5+/- mouse housed in CF, biological replicate 2

source_name: Leukemic Pax5+/- (CF)_O361


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in SPF, biological replicate 3

source_name: Healthy Pax5+/- (SPF)_R468

value: Bone marrow:proB and preB SPF


title: CP101_6_Q50_5

source_name: Striatum


title: pre_WT_1

description: WT CD4+ Thy1.1+ Th17 precursors D6


title: ALBD: Labradoodle2

source_name: whole blood

value: Australian Labradoodle

value: whole blood


title: post_KO_2

description: IL-6Ra KO Colonic Live CD4+TCRb+CD45.2+ cells

value: Il6ra-/- Il17f/Thy1.1


title: CP101_6_Q50_4

value: Striatum


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in SPF, biological replicate 2

source_name: Healthy Pax5+/- (SPF)_R466


title: RS H3K9me3 rep2

description: ploidy: 1N


title: RS H3K9me3 rep3

description: ploidy: 1N


title: post_KO_1

value: CD4+ T-cell


title: CP101_6_Q50_3


title: pre_KO_1

description: IL-6Ra KO CD4+ Thy1.1+ Th17 precursors D6


title: post_WT_1

description: WT Colonic Live CD4+TCRb+CD45.1+ cells


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in SPF, biological replicate 1

source_name: Healthy Pax5+/- (SPF)_R465


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in CF, biological replicate 3

source_name: Healthy Pax5+/- (CF)_U425

value: Bone marrow:proB and preB CF


title: PS H3K9me3 rep3

description: ploidy: 4N


title: post_KO_0


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in CF, biological replicate 2

source_name: Healthy Pax5+/- (CF)_U424


title: PS H3K9me3 rep2

description: ploidy: 4N

source_name: testis


title: CP101_6_Q20_8


title: CP101_6_Q50_10


title: CP101_6_Q20_7


title: pre_WT_0

description: WT CD4+ Thy1.1+ Th17 precursors D6


title: Bone Marrow proB and preB cells of healthy Pax5+/- mouse housed in CF, biological replicate 1

source_name: Healthy Pax5+/- (CF)_Y564


title: PS H3K9me3 rep1

description: ploidy: 4N


title: pre_KO_0


title: PS Input

description: ploidy: 4N


title: Bone Marrow proB and preB cells of WT mouse housed in SPF, biological replicate 2

source_name: WT 2-SPF

value: WT


title: CP101_6_Q20_6


title: post_WT_0

description: WT Colonic Live CD4+TCRb+CD45.1+ cells


title: ATAC-seq_MPP6

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - Location AMC

data_processing:
First, NextSeq adapter sequences were trimmed from the FASTQ files with NGmerge 0.1 (Gaspar, 2018). Reads were mapped to the mouse genome mm10 with bowtie2 2.2.8 (Langmead and Salzberg, 2012) using the -X 2000 setting. BAM files were subsequently filtered for MAPQ > 30 with SAMTools 1.9 (Li et al., 2009) and duplicate reads were removed with picard 2.2.4. Reads mapping to the mitochondrial genome were removed from downstream analyses. BigWig files were generated using the bamCoverage function from DeepTools 3.3.1 (Ramírez et al., 2016) using the following settings: --outFileFormat=bigwig --binSize=10 --skipNonCoveredRegions --numberOfProcessors=12 --normalizeUsing RPKM.
Genome build: mm10

source_name: MPP

extract_protocol:
Omni-ATAC was performed as previously described (Corces et al., 2017) with optimization suited for both MPP cells (50,000 per sample) and HSCs (10,000 per sample). Cell pellets were resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and allowed to lyse for 3 minutes on ice. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were centrifuged for 10 minutes at 500 rcf at 4 °C. Nuclei were resuspended in 50 μl of transposition mix [25 μl 2× TD buffer, transposase (1.75 uL for MPP – 1 uL for HSC), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and water (5.75 uL for MPP – 6.5 uL for HSC)] by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 minutes in a thermomixer with shaking at 1,000 rpm. Reactions were cleaned with a Qiagen MinElute Reaction Cleanup kit.
The ATAC-seq library preparation was performed as previously described  (Buenrostro et al., 2015).

treatment_protocol: Mice received 3 injections of MTP-HDL in 5 days, and were sacrificed the day after the last injection. Femurs and tibias were removed and bone marrow was extracted. After lineage depletion with magenetic bead sorting, cells were stained and MPPs and HSCs were sorted using a flowcytometric sorter.

tag: agent

value: Bone Marrow

value: MPP


title: kit Input

description:
marker: kit
KIT-antibody   manufacturer : Biolegend    lot number:B255217

value: testis


title: kit H3K9me3 rep3


title: CP101_6_Q20_5


title: Bone Marrow proB and preB cells of WT mouse housed in SPF, biological replicate 3

source_name: WT 3-SPF


title: Bone Marrow proB and preB cells of WT mouse housed in SPF, biological replicate 1

source_name: WT 1-SPF


title: CP101_6_Q20_9


title: CP101_6_Q20_4


title: Bone Marrow proB and preB cells of WT mouse housed in CF, biological replicate 4

source_name: WT 4-CF


title: RS H3K9me3 rep1

description: ploidy: 1N

value: round spermatids

value: 6-8 weeks


title: Bone Marrow proB and preB cells of WT mouse housed in CF, biological replicate 3

source_name: WT 3-CF


title: Bone Marrow proB and preB cells of WT mouse housed in CF, biological replicate 2

source_name: WT 2-CF


title: kit H3K9me3 rep2

value: 6-8 days post-natal


title: kit H3K9me3 rep1

value: differentiated spermatogonia cells


title: CP101_6_Q20_3


title: ATAC-seq_MPP3

value: PBS


title: thy1 Input

description:
marker: thy1
THY1-antibody  manufacturer : Biolegend   lot number:B284489

value: undifferentiated spermatogonia cells

value: H3K9me3 (Active Motif, 39161)


title: CP101_6_Q20_2


title: ATAC-seq_MPP4


title: fClipseq_1st_MTA1

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Library strategy: fCLIP-Seq
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the FTO peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include MTA1 binding peaks for each sample

source_name: colon

growth_protocol: HCT116 were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (HyClone) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate). Then, add 1% (vol/vol) 40U/ul Recombinant RNase Inhibitor（Takara,2313A） and 2% (vol/vol) 10mg/ml PMSF to the cell lysate, mix and rotate the mixture end over end at 4 °C for 30 min. Add 10 X RQ I buffer and DNase I(Promega,M610A). Incubate the tubes at 37 °C for 3 min,shaking at 1,000rpm. Immediately afterward a Stop solution was added to the lysates to quench DNase. Then, centrifuge 10,000 rpm for 10 min at 4 °C. Carefully collect the supernatant. Prepare a 1/50000 dilution of MNase(Thermo,EN0181).
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China) and Illumina GAIIx (Illumina, San Diego, CA, USA) 150 nt paird-end sequencing .

tag: cell line

value: colon

tag: morphology

value: epithelial

tag: disease

value: colorectal carcinoma


title: CP101_6_Q20_1

value: Striatum


title: ATAC-seq_MPP2


title: fClipseq_1st_IgG


title: thy1 H3K9me3 rep2


title: ATAC-seq_MPP5


title: CP101_6_Q175_9


title: thy1 H3K9me3 rep1


title: CP101_6_Q175_8


title: ATAC-seq_HSC5

source_name: HSC

value: Hematopoietic stem cells


title: ATAC-seq_HSC4


title: thy1 H3K9me3 rep3


title: Y1Y2_21_44H

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

description: RNASEQ

data_processing:
Sequencing libraries were constructed using the TruSeq RNA Sample preparation protocol (Illumina). RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to the following genomes: PlasmoDB-31_Pchabaudichabaudi from www.PlasmoDB.org and M14 GENCODE version of mouse genome from www.gencodegenes.org. An average of 57% of the uniquely mapped reads mapped to the parasite genome. Raw reads were quantified using featureCounts tool from Rsubread package followed by RPKM calculation using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment. Multidimensional scaling analysis was performed by plotMDS from limma package (50). Hierarchical clustering and heatmaps were obtain for each dataset by reordering of the timepoints according to gene expression using function heatmap.2 from the gplots package. Both hierarchical clustering analysis and heatmaps of Spearman correlations were performed on centered log2-transformed RPKM values. Plots were generated with ggplot2 package.
Genome_build: M14 From GENCODE; Plasmodium chabaudi chabaudi release 31 from plasmodb.org

molecule: polyA RNA

organism:
Plasmodium chabaudi
Mus musculus

source_name: P chabaudi infected blood

extract_protocol:
Blood was collected by cardiac puncture into 1.5mL of PBS, spin at 3,000 rpm for 2 min, added TRIzol LS and snap frozen
RNA was extracted using Trizol LS reagent according to manufactor's instructions.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Mice were infected with 10^6 Plasmodium chabaudi AS parasites

tag: mouse strain

tag: malaria strain

value: P. chabaudi AS

value: blood

tag: knockout

value: Arrhymithmic mutant (Cry1Cry2 KO)

tag: light condition

value: darkness

tag: feeding

value: ad libitum

tag: 1 mouse or pool of 3 mice

value: 1 mouse


title: CP101_6_Q175_7

source_name: Striatum

tag: tissue

tag: genotype

tag: tissue id


title: Y1Y2_20_28H

description: RNASEQ


title: ATAC-seq_HSC3

value: Bone Marrow

tag: cell type


title: CP101_6_Q20_10


title: CP101_6_Q175_6


title: Y1Y2_19_24H

description: RNASEQ


title: Y1Y2_18_20H

description: RNASEQ


title: ATAC-seq_MPP1

tag: strain

value: MPP


title: CP101_6_Q175_4


title: ATAC-seq_HSC6


title: MPP_PBS3

description: processed data file: GSE126793_MPP-counts.txt

data_processing:
Reads were aligned to the mouse genome mm10 by STAR 2.7.2a with default settings (Dobin et al., 2013). Differential expression between PBS and MTP10-HDL-treated samples was assessed using the DESeq2 1.24 bioconductor package in an R 3.6.1 environment.
Genome build: mm10

extract_protocol:
Total RNA was isolated using a Direct-zol RNA Kit (Zymo Research) with DNase treatment.
RNA with RIN greater than 7 underwent polyA selection. Insect carrier RNA Was added to allow low-input RNA library prep. Furthermore, samples were reverse transcribed to cDNA. cDNA libraries were prepared using 50-100ng of total RNA using the Nextflex Rapid Direction RNA-Seq kit (Perkin-Elmer).


title: CP101_6_Q175_5


title: ATAC-seq_HSC2


title: Y1Y2_17_16H

description: RNASEQ


title: CP101_6_Q175_3


title: Bone Marrow proB and preB cells of WT mouse housed in CF, biological replicate 1

source_name: WT 1-CF

value: Bone marrow:proB and preB CF

tag: genotype/variation

value: WT


title: Y1Y2_16_12H

description: RNASEQ


title: SAMPLE 8: miR-140-3p.1_b

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

description: replicate 2

hyb_protocol: Performed by service provider

scan_protocol: Performed by service provider

data_processing: global Lowess regression algorithm. Expression analysis was performed in R/bioconductor using the limma package

source_name: Human primary knee chondrocytes

label_protocol: Performed by service provider

growth_protocol: Human Primary chondrocytes cultured in DMEM with 10% Fetal calf serum and antibiotics

extract_protocol: Qiagen miRNeasy kit

treatment_protocol: Cells were transfected with the labelled small RNAs (100 nM) using DharmaFECT 1 transfection reagent. 48 hrs post-transfection RNA was isolated using a Qiagen miRNeasy kit

value: Human primary knee chondrocytes

tag: transfected


title: SAMPLE 6: miR-140-3p.2_c

description: replicate 3


title: SAMPLE 7: miR-140-3p.1_a

description: replicate 1


title: SAMPLE 9: miR-140-3p.1_c

description: replicate 3


title: SAMPLE 4: miR-140-3p.2_a

description: replicate 1


title: SAMPLE 3: mic_c

description: replicate 3

value: miControl


title: CP101_6_Q175_2


title: ATAC-seq_HSC1

tag: agent

value: PBS


title: Y1Y2_15_08H

description: RNASEQ


title: CP101_6_Q175_1


title: MPP_MTP2


title: Y1Y2_14_04H

description: RNASEQ


title: CP101_6_Q175_10


title: SAMPLE 1: mic_a

description: replicate 1


title: CP101_6_Q170_9


title: Y1Y2_13_00H

description: RNASEQ


title: Y1Y2_11_40H

description: RNASEQ


title: MPP_PBS2


title: Y1Y2_10_36H

description: RNASEQ


title: SAMPLE 5: miR-140-3p.2_b

description: replicate 2


title: Spinal motor neurons - WT rep1

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics. babraham.ac.uk/).
The raw trimmed reads were aligned to the mm9 mouse genome using the STAR aligner (github.com/alexdobin/STAR).
FPKM (fragments per kilobase of transcript per million reads) were generated with the edgeR package v.3.22.3.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Spinal motor neurons

extract_protocol:
RNA was extracted using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit (Cat# E7775L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for Illumina sequencing using NEBNext Library Prep Kit protocols

value: ES-derived spinal motor neurons

tag: mrna isolation

value: Oligo dT-based mRNA isolation


title: Spinal motor neurons - WT rep2


title: MPP_MTP3


title: CP101_6_Q170_7

data_processing:
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome build: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

extract_protocol:
TRAP: Striata or cortex were homogenized with a glass/Teflon power-driven Potter-Elvehjem homogenizer in an ice-cold lysis buffer (150 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5mM dithiothreitol, 100 μg/mL cycloheximide, 20 U/µL SUPERaseIn RNase Inhibitor, 40 U/µL RNasin Plus Rnase Inhibitor, and EDTA-free protease inhibitors).  Following homogenization, samples were centrifuged at 2,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  NP-40 (final concentration 1%) and 1,2-Diheptanoyl-sn-glycero-3-phosphocholine (DHPC, final concentration 15 mM) were subsequently added and samples were incubated on ice for 5 min.  Samples were centrifuged at 13,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  Streptavidin Dynabeads (ThermoFisher Scientific, Waltham MA) coated with biotin-linked mouse anti-GFP antibodies were then added to this supernatant and the samples were incubated overnight at 4°C with end-over-end rotation.  Beads were collected on a magnetic rack and washed three times with wash buffer (350 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/mL cycloheximide, 1% NP-40).  RNA was subsequently purified using the Absolutely RNA Isolation Nanoprep kit (Agilent Technologies, Santa Clara CA).
TRAP: Libraries were constructed using the Ovation RNA-Seq System v2 kit.

value: Striatum


title: E14_bulk_24hrs_endoderm_WT_rep2

city: Nijmegen

first: Chet

middle: H

last: Loh

address: Geert Grooteplein Zuid 28

institute: RIMLS

description:
Bulk-library
E14-APS-24h-rep2-6-17036

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads from this study and from Perino et al, Nat. Gen (2018) were trimmed to 42bp with fastx_trimmer (version 0.0.13.2), and in case of paired-end sequencing only read_1 was used for analysis
Raw reads were mapped and aligned to the mouse genome GRCm38/mm10 database using the Bowtie2 alignment tool.
Aligned reads were indexed and the final count table was derived using Htseq
R package ‘Scater’ was used for sample filtering and quality check, to remove dropouts (cells with < 5 reads) and cells with too few recovered genes (<500).
Bulk-RNA sequencing reads were quantified using Salmon and the count tables were analysed using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: Count tables in txt format

source_name: mouse embryonic stem cells

growth_protocol: mESC were grown in serum+LIF medium as described in Marks, H. et al. (doi:10.1016/j.cell.2012.03.026)

extract_protocol:
Standard RNA isolation protocol
Single-cell libraries were prepared according to the sort-seq/celseq2 method Hashimony et al.(https://doi.org/10.1186/s13059-016-0938-8). Bulk-RNA libraries were prepared according to the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using Kapa Pure Beads and sequenced on an Illumina NextSeq machine to obtain 75bp reads

treatment_protocol: Where indicated cells were treated to directed differentiation protocol towards either mesoderm or endoderm lineage

value: monolayer - endoderm

tag: timepoint

value: wild type


title: CP101_6_Q170_6


title: E14_bulk_5hrs_endoderm_WT_rep2

description:
Bulk-library
E14-APS-5h-rep2-4-17034


title: MPP_MTP1


title: Y1Y2_09_32H

description: RNASEQ

value: P. chabaudi AS

value: blood


title: E14_bulk_48hrs_endoderm_WT_rep2

description:
Bulk-library
E14-DE-48h-rep2-8-17038


title: E14_bulk_UD_endoderm_WT_rep2

description:
Bulk-library
E14-UD-rep2-2-17032

value: Undifferentiated


title: Y1Y2_08_28H

description: RNASEQ

value: Arrhymithmic mutant (Cry1Cry2 KO)

value: darkness

value: ad libitum


title: Y1Y2_07_24H

description: RNASEQ

value: 1 mouse


title: CP101_6_Q170_8


title: E14_bulk_UD_endoderm_MTF2null_rep2

description:
Bulk-library
MTF2-UD-rep2-10-17040

value: Mtf2 null


title: CP101_6_Q170_5


title: Y1Y2_06_20H

description: RNASEQ


title: E14_bulk_5hrs_endoderm_MTF2null_rep2

description:
Bulk-library
MTF2-APS1-5h-rep2-12-17042


title: CP101_6_Q170_4


title: CP101_6_Q170_3


title: Y1Y2_05_16H

description: RNASEQ


title: CP101_6_Q170_2


title: Y1Y2_04_12H

description: RNASEQ


title: E14_bulk_24hrs_endoderm_MTF2null_rep2

description:
Bulk-library
MTF2-APS1-24h-rep2-14-17044


title: E14_bulk_48hrs_endoderm_MTF2null_rep2

description:
Bulk-library
MTF2-DE-48h-rep2-16-17046


title: CP101_6_Q170_1


title: Y1Y2_03_08H

description: RNASEQ


title: E14_bulk_UD_endoderm_JARID2null_rep2

description:
Bulk-library
E4-UD-rep2-18-17048

value: Jarid2 null


title: Y1Y2_02_04H

description: RNASEQ


title: E14_bulk_5hrs_endoderm_JARID2null_rep2

description:
Bulk-library
E4-APS-5h-rep2-20-17050


title: CP101_6_Q170_10


title: CP101_6_Q111_9


title: E14_bulk_24hrs_endoderm_JARID2null_rep2

description:
Bulk-library
E4-APS-24h-rep2-22-17052


title: Y1Y2_01_00H

description: RNASEQ


title: CP101_6_Q111_8


title: WT21_44H

description: RNASEQ

value: WT mouse


title: E14_bulk_48hrs_endoderm_JARID2null_rep2

description:
Bulk-library
E4-DE-48h-rep2-24-17054


title: CP101_6_Q111_7


title: WT20_28H

description: RNASEQ


title: CP101_6_Q111_6


title: WT19_24H

description: RNASEQ


title: SAMPLE 2: mic_b

description: replicate 2

value: Human primary knee chondrocytes

value: miControl


title: E14_bulk_UD_endoderm_WT_rep1

description:
Bulk-library
E14-UD-rep1-1-17031


title: WT18_20H

description: RNASEQ


title: CP101_6_Q111_5


title: E14_bulk_5hrs_endoderm_WT_rep1

description:
Bulk-library
E14-APS-5h-rep1-3-17033


title: E14_bulk_24hrs_endoderm_WT_rep1

description:
Bulk-library
E14-APS-24h-rep1-5-17035


title: CP101_6_Q111_4


title: CP101_6_Q111_3


title: E14_bulk_48hrs_endoderm_WT_rep1

description:
Bulk-library
E14-DE-48h-rep1-7-17037


title: WT16_12H

description: RNASEQ


title: E14_bulk_UD_endoderm_MTF2null_rep1

description:
Bulk-library
MTF2-UD-rep1-9-17039


title: WT17_16H

description: RNASEQ


title: CP101_6_Q111_2


title: WT15_08H

description: RNASEQ


title: CP101_6_Q111_1


title: WT14_04H

description: RNASEQ


title: E14_bulk_24hrs_endoderm_MTF2null_rep1

description:
Bulk-library
MTF2-APS1-24h-rep1-13-17043


title: WT13_00H

description: RNASEQ


title: CP101_6_Q111_10


title: CP101_3_Q50_9


title: CP101_3_Q50_8


title: E14_bulk_48hrs_endoderm_MTF2null_rep1

description:
Bulk-library
MTF2-DE-48h-rep1-15-17045


title: E14_bulk_5hrs_endoderm_JARID2null_rep1

description:
Bulk-library
E4-APS-5h-rep1-19-17049


title: WT11_40H

description: RNASEQ


title: WT12_44H

description: RNASEQ


title: CP101_3_Q50_7


title: E14_bulk_24hrs_endoderm_JARID2null_rep1

description:
Bulk-library
E4-APS-24h-rep1-21-17051


title: WT10_36H

description: RNASEQ


title: E14_bulk_5hrs_endoderm_MTF2null_rep1

description:
Bulk-library
MTF2-APS1-5h-rep1-11-17041


title: CP101_3_Q50_6


title: E14_bulk_UD_endoderm_JARID2null_rep1

description:
Bulk-library
E4-UD-rep1-17-17047


title: WT09_32H

description: RNASEQ


title: E14_bulk_48hrs_endoderm_JARID2null_rep1

description:
Bulk-library
E4-DE-48h-rep1-23-17053


title: CP101_3_Q50_5


title: T47D_LTED_5month_biolrep2-techrep2

first: Perry

middle: D

last: Moerland

department: Epidemiology and Data Science

institute: Amsterdam UMC

description:
Infinium MethylationEpic
LTED_5m_2_2
201533480059_R04C01

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Pre-processing was performed using the R/Bioconductor package minfi. Detection p-values were calculated for each methylation probe. Data were normalized using functional normalization using the function preprocessFunnorm in the minfi package.

source_name: T47D, LTED, 5 month

label_protocol: Standard Illumina labelling protocol

growth_protocol: Parental T47D breast cancer cells were obtained from ATCC (HTB-133). Cell lines were regularly sent for cell line authentication to Multiplexion GmbH and tested for mycoplasma contamination. The cell lines were cultured in the respective media (WT: DMEM + 10% FBS + 1% P/S + 10-8M 17-ß-estradiol (E2);TAMR: DMEM + 10% FBS + 1% P/S + 100nM TAM (TAM); LTED: DMEM - phenol red + 10% charcoal stripped FBS + 1% P/S + 1% Glutamine + 1% Sodium Pyruvate), and incubated at 37  degrees Celsius with 5% CO2 in a humidified atmosphere.

extract_protocol: Total DNA was isolated by standard procedures

treatment_protocol: Parental sensitive T47D cells were cultured for 7 months (biological replicate 1) and 5 months (biological replicate 2) in the presence of 100nM tamoxifen or in estrogen deprivation to obtain T47D-TAMR and T47D-LTED respectively. The cells were passaged when they reached 80% confluency or reseeded in a new dish if they were not reaching confluency for more than 4 weeks. In this case, the medium was changed every week to ensure availability of nutrient. Two independent resistance acquisitions were performed in parallel therefore generating two replicates of resistant cell lines.

tag: cell line

tag: treatment

value: LTED

tag: time

value: 5 months

tag: gender

value: Female


title: WT08_28H

description: RNASEQ

tag: mouse strain

tag: malaria strain

tag: knockout

tag: light condition


title: E14_bulk_UD_Mesoderm_WT_rep2

description:
Bulk-library
WT-UD2-16513

tag: tissue

value: monolayer - mesoderm

tag: genotype


title: T47D_TAM_5month_biolrep2-techrep1

description:
Infinium MethylationEpic
TAM_5m_2_1
201533480059_R07C01

source_name: T47D, TAM, 5 month

value: TAM


title: T47D_LTED_1month_biolrep2-techrep1

description:
Infinium MethylationEpic
LTED_1m_2_1
201533480059_R01C01

source_name: T47D, LTED, 1 month

value: 1 months


title: WT07_24H

description: RNASEQ

value: P. chabaudi AS

value: blood

tag: feeding

tag: 1 mouse or pool of 3 mice


title: T47D_TAM_2month_biolrep2-techrep2

description:
Infinium MethylationEpic
TAM_2m_2_2
201533480059_R06C01

source_name: T47D, TAM, 2 month

value: 2 months


title: E14_bulk_5hrs_Mesoderm_WT_rep2

description:
Bulk-library
WT-MPS2-5h-16515

tag: strain

value: wild type


title: T47D_TAM_5month_biolrep2-techrep2

description:
Infinium MethylationEpic
TAM_5m_2_2
201533480052_R08C01


title: T47D_TAM_2month_biolrep2-techrep1

description:
Infinium MethylationEpic
TAM_2m_2_1
201533480055_R06C01


title: CP101_3_Q50_3

value: Striatum

tag: tissue id


title: T47D_LTED_7month_biolrep1-techrep2

description:
Infinium MethylationEpic
LTED_7m_1_2
201364900141_R05C01

source_name: T47D, LTED, 7 month

value: 7 months


title: WT06_20H

description: RNASEQ

value: darkness

value: ad libitum

value: 1 mouse


title: E14_bulk_24hrs_Mesoderm_WT_rep2

description:
Bulk-library
WT-MPS2-24h-16517


title: CP101_3_Q50_2


title: E14_bulk_48hrs_Mesoderm_WT_rep2

description:
Bulk-library
WT-LM2-48-16519


title: T47D_LTED_1month_biolrep2-techrep2

description:
Infinium MethylationEpic
LTED_1m_2_2
201533480052_R02C01


title: T47D_LTED_2month_biolrep2-techrep1

description:
Infinium MethylationEpic
LTED_2m_2_1
201533480052_R03C01

source_name: T47D, LTED, 2 month


title: WT05_16H

description: RNASEQ

value: WT mouse


title: T47D_TAM_1month_biolrep2-techrep1

description:
Infinium MethylationEpic
TAM_1m_2_1
201533480052_R05C01

source_name: T47D, TAM, 1 month


title: CP101_3_Q50_1


title: WT04_12H

description: RNASEQ


title: T47D_WT_7month_biolrep1-techrep2

description:
Infinium MethylationEpic
WT_7m_1_2
201364900141_R03C01

source_name: T47D, WT, 7 month

value: WT


title: T47D_LTED_5month_biolrep2-techrep1

description:
Infinium MethylationEpic
LTED_5m_2_1
201533480055_R04C01

value: LTED


title: WT03_08H

description: RNASEQ


title: T47D_LTED_5month_biolrep1-techrep2

description:
Infinium MethylationEpic
LTED_5m_1_2
201364900141_R02C01

value: 5 months


title: E14_bulk_24hrs_Mesoderm_MTF2null_rep2

description:
Bulk-library
MTF2-MPS2-24h-16525

value: Mtf2 null


title: T47D_LTED_2month_biolrep2-techrep2

description:
Infinium MethylationEpic
LTED_2m_2_2
201533480055_R03C01

value: Female


title: CP101_3_Q20_9


title: CP101_3_Q20_8


title: T47D_WT_5month_biolrep1-techrep2

description:
Infinium MethylationEpic
WT_5m_1_2
201364900140_R08C01

source_name: T47D, WT, 5 month


title: E14_bulk_5hrs_Mesoderm_MTF2null_rep2

description:
Bulk-library
MTF2-MPS2-5h-16523

value: monolayer - mesoderm


title: T47D_WT_0month_biolrep2-techrep1

description:
Infinium MethylationEpic
WT_0m_2_1
201533480052_R01C01

source_name: T47D, WT, 0 month

value: 0 months


title: WT01_00H

description: RNASEQ

value: P. chabaudi AS


title: E14_bulk_48hrs_Mesoderm_MTF2null_rep2

description:
Bulk-library
MTF2-LM2-48h-16527


title: T47D_TAM_2month_biolrep1-techrep2

description:
Infinium MethylationEpic
TAM_2m_1_2
201364900140_R06C01

value: TAM


title: T47D_TAM_7month_biolrep1-techrep2

description:
Infinium MethylationEpic
TAM_7m_1_2
201364900141_R04C01

source_name: T47D, TAM, 7 month


title: T47D_TAM_5month_biolrep1-techrep2

description:
Infinium MethylationEpic
TAM_5m_1_2
201364900141_R01C01


title: T47D_WT_2month_biolrep1-techrep2

description:
Infinium MethylationEpic
WT_2m_1_2
201364900140_R05C01

source_name: T47D, WT, 2 month

value: 2 months


title: CP101_3_Q50_10

source_name: Striatum


title: CP101_3_Q20_7


title: E14_bulk_UD_Mesoderm_JARID2null_rep2

description:
Bulk-library
JARID2-UD2-16529

value: Undifferentiated

value: Jarid2 null


title: T47D_TAM_1month_biolrep2-techrep2

description:
Infinium MethylationEpic
TAM_1m_2_2
201533480055_R05C01

value: 1 months


title: T47D_WT_0month_biolrep2-techrep2

description:
Infinium MethylationEpic
WT_0m_2_2
201533480055_R01C01


title: T47D_LTED_2month_biolrep1-techrep2

description:
Infinium MethylationEpic
LTED_2m_1_2
201364900140_R07C01


title: AF23_44H

description: RNASEQ

source_name: P chabaudi infected blood

value: blood

value: Light/dark

value: spread-out fed


title: AF24_44H

description: RNASEQ

value: WT mouse

value: 1 mouse


title: WT02_04H

description: RNASEQ

value: darkness

value: ad libitum


title: E14_bulk_5hrs_Mesoderm_JARID2null_rep2

description:
Bulk-library
JARID2-MPS2-5h-16531


title: CP101_3_Q50_4

value: Striatum


title: CP101_3_Q20_6


title: AF22_40H

description: RNASEQ


title: CP101_3_Q20_5


title: CP101_3_Q20_4


title: E14_bulk_UD_Mesoderm_MTF2null_rep2

description:
Bulk-library
MTF2-UD2-16521

value: Mtf2 null


title: AF21_40H

description: RNASEQ


title: E14_bulk_48hrs_Mesoderm_JARID2null_rep2

description:
Bulk-library
JARID2-LM2-48h-16535

value: monolayer - mesoderm


title: E14_bulk_24hrs_Mesoderm_JARID2null_rep2

description:
Bulk-library
JARID2-MPS2-24h-16533


title: CP101_3_Q20_3


title: AF20_36H

description: RNASEQ


title: E14_bulk_UD_Mesoderm_WT_rep1

description:
Bulk-library
WT-UD1-16512

value: wild type


title: CP101_3_Q20_2


title: AF19_36H

description: RNASEQ

value: P. chabaudi AS


title: T47D_LTED_1month_biolrep1-techrep2

description:
Infinium MethylationEpic
LTED_1m_1_2
201364900140_R04C01

value: LTED

value: Female


title: CP101_3_Q20_1


title: E14_bulk_24hrs_Mesoderm_WT_rep1

description:
Bulk-library
WT-MPS1-24h-16516


title: AF18_32H

description: RNASEQ


title: CP101_3_Q170_7


title: CP101_3_Q170_5


title: AF17_32H

description: RNASEQ


title: T47D_WT_1month_biolrep1-techrep2

description:
Infinium MethylationEpic
WT_1m_1_2
201364900140_R02C01

source_name: T47D, WT, 1 month

value: WT


title: AF16_28H

description: RNASEQ


title: E14_bulk_UD_Mesoderm_MTF2null_rep1

description:
Bulk-library
MTF2-UD1-16520

value: Undifferentiated


title: CP101_3_Q170_4


title: AF15_28H

description: RNASEQ


title: T47D_LTED_7month_biolrep1-techrep1

description:
Infinium MethylationEpic
LTED_7m_1_1
201364900128_R05C01

value: 7 months


title: E14_bulk_5hrs_Mesoderm_MTF2null_rep1

description:
Bulk-library
MTF2-MPS1-5h-16522


title: CP101_3_Q170_3


title: T47D_TAM_1month_biolrep1-techrep2

description:
Infinium MethylationEpic
TAM_1m_1_2
201364900140_R03C01

value: TAM

value: 1 months


title: AF14_24H

description: RNASEQ

value: blood

value: Light/dark

value: spread-out fed


title: E14_bulk_24hrs_Mesoderm_MTF2null_rep1

description:
Bulk-library
MTF2-MPS1-24h-16524


title: CP101_3_Q170_2


title: E14_bulk_48hrs_Mesoderm_MTF2null_rep1

description:
Bulk-library
MTF2-LM1-48h-16526


title: AF12_20H

description: RNASEQ

value: WT mouse

value: 1 mouse


title: E14_bulk_UD_Mesoderm_JARID2null_rep1

description:
Bulk-library
JARID2-UD1-16528

value: Jarid2 null


title: AF13_24H

description: RNASEQ


title: CP101_3_Q111_9

value: Striatum


title: AF11_20H

description: RNASEQ


title: T47D_TAM_7month_biolrep1-techrep1

description:
Infinium MethylationEpic
TAM_7m_1_1
201364900128_R04C01


title: CP101_3_Q170_1


title: E14_bulk_5hrs_Mesoderm_JARID2null_rep1

description:
Bulk-library
JARID2-MPS1-5h-16530

value: monolayer - mesoderm


title: AF10_16H

description: RNASEQ


title: E14_bulk_24hrs_Mesoderm_JARID2null_rep1

description:
Bulk-library
JARID2-MPS1-24h-16532


title: CP101_3_Q111_8


title: AA6241

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
Data were pre-processed by ChAS and processed/analysed as described in Lesluyes et al. 2019 (PMID: 31243333)
Matrices include logRs (weighted for CytoScanHD), smooth signals (2N-centred for CytoScanHD) and allelic differences for all samples

source_name: Human sarcoma

label_protocol: Affymetrix standard procedure

growth_protocol: None (primary tumours)

extract_protocol: Affymetrix standard procedure

tag: histological subtype

value: Leiomyosarcoma

tag: group

value: Radiation-induced


title: CP101_3_Q111_7

first: Myriam

last: Heiman

institute: Massachusetts Institute of Technology


title: AA6240

value: Angiosarcoma


title: E14_bulk_48hrs_Mesoderm_JARID2null_rep1

description:
Bulk-library
JARID2-LM1-48h-16534

source_name: mouse embryonic stem cells

tag: timepoint


title: AF09_16H

description: RNASEQ

value: P. chabaudi AS


title: T47D_TAM_5month_biolrep1-techrep1

description:
Infinium MethylationEpic
TAM_5m_1_1
201364900128_R01C01

tag: cell line

value: 5 months

value: Female


title: E14_bulk_5hrs_Mesoderm_WT_rep1

description:
Bulk-library
WT-MPS1-5h-16514

value: wild type


title: E14_bulk_48hrs_Mesoderm_WT_rep1

description:
Bulk-library
WT-LM1-48h-16518


title: AA6239

value: Pleomorphic rhabdomyosarcoma


title: E14_EB_D0_JARID2null

description: Single-cell library

source_name: mouse embyroid bodies

value: embryoid bodies

value: Day 0


title: E14_EB_D0_EEDnull

description: Single-cell library

value: Eed null


title: T47D_WT_0month_biolrep1-techrep2

description:
Infinium MethylationEpic
WT_0m_1_2
201364900140_R01C01

tag: treatment

value: WT

value: 0 months


title: AA6237


title: AF06_08H

description: RNASEQ

value: blood

value: WT mouse

value: Light/dark

value: spread-out fed

value: 1 mouse


title: CP101_3_Q111_6

value: Striatum


title: CP101_3_Q111_5


title: E14_EB_D0_MTF2null

description: Single-cell library

value: Mtf2 null


title: AA6238

value: Leiomyosarcoma

value: Radiation-induced


title: CP101_3_Q111_4


title: CP101_3_Q111_3


title: AF05_08H

description: RNASEQ

value: P. chabaudi AS


title: AA6236


title: AF08_12H

description: RNASEQ


title: CP101_3_Q111_2


title: E14_EB_D0_WT

description: Single-cell library

value: wild type


title: AF04_04H

description: RNASEQ


title: E14_EB_D4_EEDnull

description: Single-cell library

value: Day 4


title: CP101_3_Q111_1


title: AF03_04H

description: RNASEQ


title: E14_EB_D4_JARID2null

description: Single-cell library

value: embryoid bodies

value: Jarid2 null


title: E14_EB_D4_MTF2null

description: Single-cell library


title: AF02_00H

description: RNASEQ


title: AA6235

value: Undifferentiated spindle cell sarcoma


title: T47D_LTED_2month_biolrep1-techrep1

description:
Infinium MethylationEpic
LTED_2m_1_1
201364900121_R07C01

value: LTED

tag: time

value: 2 months

value: Female


title: AA6234


title: AA6233

value: Extraskeletal osteosarcoma


title: D2_R62_4


title: CP101_3_Q111_10


title: AF01_00H

description: RNASEQ

value: blood

value: WT mouse

value: Light/dark


title: E14_EB_D4_WT

description: Single-cell library


title: AA6232


title: D2_R62_3

value: Striatum


title: T47D_WT_5month_biolrep1-techrep1

description:
Infinium MethylationEpic
WT_5m_1_1
201364900121_R08C01

value: WT

value: 5 months

tag: gender


title: AF07_12H

description: RNASEQ

tag: mouse strain

value: spread-out fed

value: 1 mouse


title: E14_EB_D7_EEDnull

description: Single-cell library

value: Day 7

value: Eed null


title: T47D_WT_7month_biolrep1-techrep1

description:
Infinium MethylationEpic
WT_7m_1_1
201364900128_R03C01

value: 7 months


title: N25_48H

description: RNASEQ

tag: malaria strain

value: P. chabaudi AS

value: nighttime fed


title: D2_R62_2


title: AA6230

value: Intimal sarcoma

value: Radiation-induced


title: E14_EB_D7_JARID2null

description: Single-cell library

value: embryoid bodies

value: Jarid2 null


title: D2_R62_1


title: E14_EB_D7_MTF2null

description: Single-cell library

value: Mtf2 null


title: AA6229

value: Undifferentiated pleomorphic sarcoma


title: N26_48H

description: RNASEQ

value: blood

tag: knockout

value: WT mouse

value: Light/dark


title: N23_44H

description: RNASEQ

tag: light condition


title: AA6228

value: Malignant mesenchymoma


title: D2_CTRL_4

tag: tissue

value: Striatum

value: CBAxC57 WT


title: T47D_TAM_2month_biolrep1-techrep1

description:
Infinium MethylationEpic
TAM_2m_1_1
201364900121_R06C01

value: TAM

value: 2 months

value: Female


title: N22_40H

description: RNASEQ

value: P. chabaudi AS

value: 1 mouse


title: N24_44H

description: RNASEQ

value: nighttime fed


title: E14_EB_D7_WT

description: Single-cell library

value: Day 7

tag: genotype

value: wild type


title: E14_EB_D10_EEDnull

description: Single-cell library

value: embryoid bodies

value: Day 10

value: Eed null


title: D2_CTRL_3


title: AA6227

value: Angiosarcoma

value: Radiation-induced


title: D2_CTRL_2


title: T47D_WT_2month_biolrep1-techrep1

description:
Infinium MethylationEpic
WT_2m_1_1
201364900121_R05C01

value: WT


title: T47D_LTED_1month_biolrep1-techrep1

description:
Infinium MethylationEpic
LTED_1m_1_1
201364900121_R04C01

value: LTED

value: 1 months


title: N21_40H

description: RNASEQ

value: blood

value: WT mouse

value: Light/dark

tag: feeding


title: E14_EB_D10_JARID2null

description: Single-cell library

value: Jarid2 null


title: T47D_WT_1month_biolrep1-techrep1

description:
Infinium MethylationEpic
WT_1m_1_1
201364900121_R02C01

value: Female


title: N20_36H

description: RNASEQ

value: P. chabaudi AS

tag: 1 mouse or pool of 3 mice

value: 1 mouse


title: AA6226

value: Undifferentiated pleomorphic sarcoma


title: D2_CTRL_1

value: Striatum

value: CBAxC57 WT


title: T47D_LTED_5month_biolrep1-techrep1

description:
Infinium MethylationEpic
LTED_5m_1_1
201364900128_R02C01

source_name: T47D, LTED, 5 month

value: 5 months


title: AA6225

value: Malignant mesenchymoma


title: E14_EB_D10_MTF2null

description: Single-cell library

tag: strain

value: embryoid bodies

value: Day 10

value: Mtf2 null


title: T47D_TAM_1month_biolrep1-techrep1

description:
Infinium MethylationEpic
TAM_1m_1_1
201364900121_R03C01

value: TAM


title: D1_R62_7

tag: tissue id


title: AA6224

tag: histological subtype

value: Angiosarcoma

value: Radiation-induced


title: N19_32H

description: RNASEQ

value: blood

value: WT mouse

value: nighttime fed


title: D1_R62_6


title: E14_EB_D10_WT

description: Single-cell library

value: wild type


title: AA6223

tag: group


title: T47D_WT_0month_biolrep1-techrep1

description:
Infinium MethylationEpic
WT_0m_1_1
201364900121_R01C01

value: WT

value: 0 months

value: Female


title: N18_32H

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: 1 mouse


title: 190807_zQ175_snRNA-B11

value: Striatum


title: D1_R62_4


title: N16_28H

description: RNASEQ


title: AA6222

value: Myxofibrosarcoma


title: D1_R62_3


title: 190807_zQ175_snRNA-B10


title: N15_28H

description: RNASEQ


title: AA6219

value: Undifferentiated pleomorphic sarcoma


title: N14_24H

description: RNASEQ


title: D1_R62_2


title: AA6220


title: 190807_zQ175_snRNA-B9


title: D1_R62_1


title: AA6218

value: Leiomyosarcoma


title: 190807_zQ175_snRNA-B6


title: N12_20H

description: RNASEQ


title: N13_24H

description: RNASEQ


title: 190807_zQ175_snRNA-B7


title: D1_CTRL_7

value: CBAxC57 WT


title: AA6216


title: AA6217


title: N11_20H

description: RNASEQ


title: D1_CTRL_6


title: D1_CTRL_5


title: D1_R62_5


title: 190807_zQ175_snRNA-B4


title: N17_32H

description: RNASEQ


title: AA6221

value: Angiosarcoma


title: N10_16H

description: RNASEQ


title: AA6215

value: Radiation-induced


title: miR140_KO_Rep4

description: 7 day old rib chondrocyte RNA

data_processing:
Quality of raw sequencing reads was checked using FastQC (v0.11.7)
Sequenced reads were mapped to the mm10 transcriptome using Salmon
Abundance measurements in transcripts per million (TPM) were generated using Salmon
Batch effects were estimated using RUVseq
Batch effects were incorporated into the differential expression analysis performed using DESeq2
Genome_build: mm10

source_name: costal chondrocytes

extract_protocol:
Primary mouse costal chondrocytes were isolated from 7-day-old miR-140null (knockout) and WT mice using collagenase digestion.  Total RNA, including miRNA was isolated using the miRVana miRNA Isolation Kit (with phenol)( Fisher Scientific).
Sequencing libraries were prepared from 500 ng of purified total RNA using the Illumina TruSeq Stranded mRNA sample preparation kit according to the manufacturer’s protocol, and sequenced on Illumina NextSeq500. Each sample provided >12 million single-end 75-bp sequencing reads.

tag: strain background

value: rib chondrocytes


title: N09_16H

description: RNASEQ

value: blood

value: WT mouse


title: AA6213


title: D1_CTRL_4


title: AA6214

value: Dedifferentiated liposarcoma


title: N08_12H

description: RNASEQ

value: nighttime fed


title: miR140_KO_Rep3

description: 7 day old rib chondrocyte RNA


title: miR140_KO_Rep2

description: 7 day old rib chondrocyte RNA


title: D1_CTRL_3


title: AA6212


title: D1_CTRL_2


title: 190807_zQ175_snRNA-B5

data_processing:
Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome build: GRCm38/mm10
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.


title: AA6211


title: miR140_WT_Rep4

description: 7 day old rib chondrocyte RNA

value: wild-type control


title: WtHSVtrap5IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

source_name: Cortex

value: Cortex


title: AA6210


title: N05_08H

description: RNASEQ

value: P. chabaudi AS


title: N07_12H

description: RNASEQ

value: Light/dark


title: miR140_WT_Rep3

description: 7 day old rib chondrocyte RNA


title: WtHSVtrap5IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: N06_08H

description: RNASEQ

value: 1 mouse


title: miR140_WT_Rep2

description: 7 day old rib chondrocyte RNA


title: AA6209


title: N03_04H

description: RNASEQ


title: WtHSVtrap5IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: N04_04H

description: RNASEQ


title: 190807_zQ175_snRNA-B8

value: Striatum


title: miR140_WT_Rep1

description: 7 day old rib chondrocyte RNA


title: AA6208


title: AA6207


title: WtHSVtrap4IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: D1_CTRL_1


title: DEN HFD -WT non-tumour 4

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

description:
Time Point: 30 weeks after IP
N4

data_processing:
Reads are mapped using STAR 2.5.0  to the mouse GRCm38 genome
Gene-level counts where generated using featureCounts (Subread 1.6.2) with Ensembl Transcript GTF V74
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with counts

source_name: Whole Liver Tissue

extract_protocol:
Frozen tissue samples were lysed using Trizol (Sigma-Aldrich) and mRNA was extracted with the qiagen RBNA easy column. Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
Sequencing library were constructed using Illumina mRNA library prep kit

treatment_protocol: Liver tissues were snap-frozen and stored at -80*C until RNA extraction

value: liver non-tumor

value: Wild Type

tag: Sex

value: male

value: DEN IP day 15 + 30 week HFD + SW -WT


title: AA6206

value: Angiosarcoma


title: miR140_KO_Rep1

description: 7 day old rib chondrocyte RNA


title: WtHSVtrap4IP-3

address: 77 Massachusetts Ave., Bldg 46-4285

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: CBAxC57 WT


title: DEN HFD -WT tumour 4

description:
Time Point: 30 weeks after IP
T4

value: liver tumor

tag: treatment


title: N01_00H

description: RNASEQ

value: blood


title: N02_00H

description: RNASEQ

value: WT mouse


title: DEN HFD -WT non-tumour 3

description:
Time Point: 30 weeks after IP
N3


title: WtHSVtrap3IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6205

value: Radiation-induced


title: FBPC_72B

description: RNASEQ

value: Long Period mutant (FBXL3 KO)

value: darkness

value: ad libitum


title: WtHSVtrap4IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: Cortex


title: DEN HFD -WT tumour 3

description:
Time Point: 30 weeks after IP
T3


title: WtHSVtrap3IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: FBPC_72A

description: RNASEQ

value: P. chabaudi AS


title: FBPC_68B

description: RNASEQ

value: 1 mouse


title: AA6203


title: AA6204

value: Dedifferentiated liposarcoma


title: DEN HFD -WT non-tumour 2

description:
Time Point: 30 weeks after IP
N2

value: liver non-tumor


title: WtHSVtrap3IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: DEN HFD -WT tumour 2

description:
Time Point: 30 weeks after IP
T2

value: Wild Type


title: WtHSVtrap2IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: FBPC_64B

description: RNASEQ


title: AA6231


title: AA6202


title: FBPC_68A

description: RNASEQ


title: AA6201


title: FBPC_64A

description: RNASEQ


title: AA6200

value: Undifferentiated pleomorphic sarcoma


title: DEN HFD -WT tumour 1

description:
Time Point: 30 weeks after IP
T1

value: male

value: DEN IP day 15 + 30 week HFD + SW -WT


title: WtHSVtrap2IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: CBAxC57 WT


title: FBPC_60B

description: RNASEQ


title: AA6198

value: Angiosarcoma


title: ACE2-A549-Trifluoperazone-drugonly-3

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App on Basespace (Illumina, CA).
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: Read counts for each sample and corresponding gene

growth_protocol: Human adenocarcinomic alveolar basal epithelial (A549) cells (ATCC, CCL-185) were maintained at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Corning). Undifferentiated human pluripotent stem cells (hPSCs) were maintained in feeder-free conditions. Briefly, hPSCs were cultured on Matrigel-coated 6-well plates in commercial StemFlex™ Medium (ThermoFisher). The medium was changed every day, and cells were passaged every ∼4 days using ReLeSR™ (STEM Technologies). In all normal hPSC cultures, 5 μM Rho-associated protein kinase (ROCK) inhibitor Y-27632 was only added into the culture media when passaging or thawing hPSCs. For pancreatic endocrine organoid differentiation, we adapted previous published protocols (Yang et al., 2020).

extract_protocol:
Total RNA from infected and mock infected cells was extracted using TRIzol Reagent (Invitrogen) and Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions and treated with DNase I. RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA-seq libraries for total ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced using an Illumina NextSeq 500 platform.

treatment_protocol: Approximately 1 x 10e6 A549 cells were infected with SARS-CoV-2. Infections with IAV were performed at a multiplicity of infection of 5 for 9 h in DMEM supplemented with 0.3% BSA, 4.5 g/L D-glucose, 4 mM L-glutamine and 1 µg/ml TPCK-trypsin. Infections with SARS-CoV-2 were performed at an MOI of 0.2 for 24 h in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES.

tag: cell line

value: lung alveolar (A549) transduced with vector expressing human ACE2

tag: drug

value: Trifluoperazine

tag: sars-cov-2 infected

value: No


title: WtHSVtrap1IP-3

city: Cambridge

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: FBPC_60A

description: RNASEQ

tag: mouse strain

tag: malaria strain

value: blood

value: Long Period mutant (FBXL3 KO)


title: FBPC_56C

description: RNASEQ

tag: knockout

tag: light condition

value: darkness

value: ad libitum


title: AA6197

value: Radiation-induced


title: ACE2-A549-Trifluoperazone-drugonly-2


title: FBPC_56B

description: RNASEQ

value: P. chabaudi AS

tag: tissue

value: 1 mouse


title: AA6196


title: ACE2-A549-Trifluoperazine-COV2-3

value: Yes


title: DEN HFD -WT non-tumour 1

description:
Time Point: 30 weeks after IP
N1

value: liver non-tumor

tag: genotype

value: Wild Type


title: FBPC_52B

description: RNASEQ

tag: feeding

tag: 1 mouse or pool of 3 mice


title: WtHSVtrap2IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: Cortex

tag: tissue id


title: R62HSVtrap5IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6194

tag: histological subtype

value: Undifferentiated pleomorphic sarcoma


title: ACE2-A549-Trifluoperazine-COV2-1


title: R62HSVtrap5IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6199

value: Malignant peripheral nerve sheath tumour

tag: group


title: FBPC_48B

description: RNASEQ


title: AA6193


title: R62HSVtrap4IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6192

value: Myxofibrosarcoma


title: FBPC_48A

description: RNASEQ


title: FBPC_44B

description: RNASEQ


title: R62HSVtrap4IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: ACE2-A549-Terfenadine-drugonly-3

value: lung alveolar (A549) transduced with vector expressing human ACE2

value: Terfenadine


title: ACE2-A549-Trifluoperazone-drugonly-1

value: Trifluoperazine

value: No


title: ACE2-A549-Terfenadine-drugonly-2


title: AA6191

value: Leiomyosarcoma


title: ACE2-A549-Terfenadine-drugonly-1


title: R62HSVtrap4IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: FBPC_44A

description: RNASEQ

value: blood

value: Long Period mutant (FBXL3 KO)

value: darkness


title: AA6190

value: Radiation-induced


title: ACE2-A549-Trifluoperazine-COV2-2


title: WtHSVtrap1IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: CBAxC57 WT


title: FBPC_40B

description: RNASEQ

value: P. chabaudi AS

value: ad libitum

value: 1 mouse


title: AA6195


title: R62HSVtrap3IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: Cortex


title: AA6189


title: R62HSVtrap5IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: R62HSVtrap3IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: FBPC_52A

description: RNASEQ


title: FBPC_40A

description: RNASEQ


title: ACE2-A549-Terfenadine-COV2-1

value: Yes


title: AA6188


title: FBPC_36B

description: RNASEQ


title: R62HSVtrap3IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6187

value: Extraskeletal osteosarcoma


title: ACE2-A549-RS504393-drugonly-3


title: R62HSVtrap1IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: AA6186

value: Myxofibrosarcoma


title: ACE2-A549-RS504393-drugonly-2

value: lung alveolar (A549) transduced with vector expressing human ACE2


title: FBPC_32B

description: RNASEQ


title: ACE2-A549-Terfenadine-COV2-3

value: Terfenadine


title: R62HSVtrap1IP-2

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: ACE2-A549-RS504393-drugonly-1


title: FBPC_32A

description: RNASEQ


title: AA6184

value: Undifferentiated pleomorphic sarcoma


title: ACE2-A549-Terfenadine-COV2-2


title: ACE2-A549-RS504393-COV2-3


title: FBPC_28B

description: RNASEQ


title: ChIP_input_BMDM_KLA

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: CMM

institute: University of California, San Diego

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
ChIP peak files were generated by HOMER ‘findPeaks’ by providing the corresponding input with parameters -size 200.
Tag density files were generated by HOMER ‘annotatePeaks’ by providing HOMER tag directories of p65 and p50 ChIP-seq data
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated HOMER peak files/HOMER annotation files

source_name: BMDMs (bone marow-derived macrophages)

extract_protocol:
Bone marrow was isolated from C57BL/6J mice and differentiated for 7 days using media containing M-CSF to bone marrow-derived macrophages (BMDMs) as described previously (Link et al., 2018). BMDMs were then treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 hour.
ChIP-Seq sequencing libraries were prepared from recovered DNA by blunting, A-tailing, and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific) as previously described (Heinz et al., 2010; Gosselin et al., 2014). Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (225-400 bp) by gel extraction (10% TBE gels, Life Technologies EC62752BOX). Libraries were single-end sequenced for 51 cycles with an average sequence depth >20 million on an Illumina HiSeq 4000 platform (Illumina, San Diego, CA) according to manufacturer’s instructions.

tag: strain

tag: cell type

value: BMDMs (bone marow-derived macrophages)

tag: antibody

value: input

value: KLA 1 hour


title: AA6183

value: Osteosarcoma


title: ChIP_p50_BMDM_KLA

value: p50 (2 micrograms each of p50 specific antibodies, Abcam:ab32360)

tag: treatment


title: ACE2-A549-RS504393-COV2-2

tag: cell line

tag: drug


title: WtHSVtrap1IP-4

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv


title: ACE2-A549-RS504393-COV2-1

tag: sars-cov-2 infected


title: FBPC_28A

description: RNASEQ

tag: mouse strain

tag: malaria strain

value: blood

value: Long Period mutant (FBXL3 KO)

value: darkness


title: AA6182

value: Undifferentiated spindle cell sarcoma

value: Radiation-induced


title: FBPC_24B

description: RNASEQ

value: P. chabaudi AS

tag: knockout

tag: light condition

value: ad libitum

value: 1 mouse


title: ChIP_p65_BMDM_KLA

value: p65 (2 micrograms each of p65 specific antibodies, Santa Cruz:sc-372X)


title: ACE2-A549-Mock-3

value: lung alveolar (A549) transduced with vector expressing human ACE2

value: mock

value: No


title: AA6181

value: Undifferentiated pleomorphic sarcoma


title: FBPC_36A

description: RNASEQ

tag: tissue


title: AA6180

value: Leiomyosarcoma


title: FBPC_24A

description: RNASEQ

tag: feeding


title: AA6185

value: Angiosarcoma


title: ACE2-A549-Mock-2


title: FBPC_20B

description: RNASEQ

tag: 1 mouse or pool of 3 mice


title: Dep_5

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10
Supplementary_files_format_and_content: Count table (csv)
Supplementary_files_format_and_content: Normalised counts from DESEq2 (csv)

source_name: Colon

extract_protocol:
Cells were sorted based on Live CD11b+ CX3CR1+ MHC-II+ Ly6C lo into RLT+ buffer. RNA extracted with RNEasy plus micro kit (Qiagen)
Libraries were produced with SMARTer stranded total RNAseq kit pico kit (Takara) as per manufactuers instructions

treatment_protocol: Mice recived 2%DSS for 6 days in drinking water

tag: genotype/variation

value: RagKO

tag: disease

value: DSS

value: anti CD94


title: Dep_6

value: anti CD95


title: AA6179

tag: histological subtype

tag: group


title: R62HSVtrap1IP-3

description:
Retro-TRAP
RPKM_R62_TRAP_CStrPN.tsv

value: Cortex

tag: genotype

tag: tissue id


title: FBPC_20A

description: RNASEQ

value: blood

value: Long Period mutant (FBXL3 KO)

value: darkness


title: Dep_4

tag: treatment

value: anti CD93


title: ACE2-A549-Loperamide-drugonly-3

tag: cell line

value: Loperamide


title: AA6178

value: Radiation-induced


title: FBPC_16B

description: RNASEQ

value: P. chabaudi AS

value: ad libitum

value: 1 mouse


title: Dep_3

value: anti CD92


title: AA6177

value: Leiomyosarcoma


title: Dep_2

value: anti CD91


title: ACE2-A549-Loperamide-drugonly-2

value: lung alveolar (A549) transduced with vector expressing human ACE2

tag: drug

value: No


title: ACE2-A549-Loperamide-drugonly-1

tag: sars-cov-2 infected


title: FBPC_12B

description: RNASEQ

tag: mouse strain


title: FBPC_16A

description: RNASEQ

tag: malaria strain


title: Dep_1

value: RagKO

value: DSS

value: anti CD90


title: Iso_6

value: Isotype control


title: FBPC_12A

description: RNASEQ

value: blood

tag: knockout

value: Long Period mutant (FBXL3 KO)


title: AA6175

value: Angiosarcoma


title: ACE2-A549-Loperamide-COV2-2

value: Loperamide

value: Yes


title: AA6174

value: Undifferentiated pleomorphic sarcoma

value: Radiation-induced


title: ACE2-A549-Loperamide-COV2-3


title: ACE2-A549-Loperamide-COV2-1


title: AA6173


title: Iso_5


title: Iso_4


title: AA6172


title: FBPC_08A

description: RNASEQ

value: P. chabaudi AS

tag: light condition

value: darkness

value: ad libitum

value: 1 mouse


title: ACE2-A549-DMSO-COV2-3

value: lung alveolar (A549) transduced with vector expressing human ACE2

value: DMSO


title: ACE2-A549-Mock-1

value: mock

value: No


title: AA6171


title: ACE2-A549-DMSO-COV2-2


title: FBPC_04A

description: RNASEQ

tag: tissue


title: AA6170


title: Iso_2

value: RagKO

value: DSS


title: AA6176


title: FBPC_00B

description: RNASEQ

value: blood

tag: feeding


title: Iso_1

value: Isotype control


title: ACE2-A549-DMSO-COV2-1


title: ACE2-A549-Berbamine-drugonly-3

value: Berbamine


title: AA6168

value: Undifferentiated spindle cell sarcoma


title: WTPC_72A

description: RNASEQ

value: WT mouse

tag: 1 mouse or pool of 3 mice


title: AA6169

value: Angiosarcoma


title: Iso_3

tag: genotype/variation


title: FBPC_00A

description: RNASEQ

value: Long Period mutant (FBXL3 KO)


title: FBPC_08B

description: RNASEQ

value: P. chabaudi AS


title: ACE2-A549-Berbamine-drugonly-2


title: AA6167

value: Radiation-induced


title: AA6166


title: WTPC_68B

description: RNASEQ

value: darkness

value: ad libitum


title: ACE2-A549-Berbamine-drugonly-1

value: lung alveolar (A549) transduced with vector expressing human ACE2


title: AA6165


title: ACE2-A549-Berbamine-COV2-2

value: Yes


title: FBPC_04B

description: RNASEQ

value: 1 mouse


title: 191108_HD_8_snRNA-H1

source_name: Putamen

value: Putamen

value: Control


title: WTPC_64B

description: RNASEQ


title: Tumor T89

city: Minneapolis

first: Timothy

last: Starr

state: MN

address: 420 Delaware St SE

department: Department of Obstetrics

institute: University of Minnesota

data_processing:
Fastq files were analyzed  using CellRanger (v3.0.2) software which performs indexing, demultiplexing, and alignment to produce bam files and a matrix of RNA abundance (cells x genes) using the Unique Molecular Identifier (UMI) counts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix files of UMI gene counts for every gene and every cell

source_name: tumor specimen

growth_protocol: Tumor specimens  taken from the operating room were used for clinical diagnoses and excess tissue was released to the study.

extract_protocol:
Cells were lysed and RNA was extracted and converted to cDNA and tagged with barcodes following the 10x Genomics Single Cell 3’ Protocol utilizing the ChromiumTM Single Cell 3’ v2 Library & Gel Bead Kit and ChromiumTM Single Cell A  Chip Kit (10x Genomics, Pleasanton, CA).
Barcoded cDNA was sequenced using an Illumina HiSeq 2500 flow cell with Rapid chemistry and 100 bp paired end sequencing, producing an average of 235 million reads per patient sample with an average of 11,502 cells/sample and 23,000 reads/cell

treatment_protocol: Tumor pieces were digested at  37C and gentle shaking following the Miltenyi GentleMacs Dissociation system protocol (Miltenyibiotec,  San Diego CA). This protocol uses a proprietary mix of enzymes and specially designed centrifuge tubes  to generate a single cell suspension. Cells were filtered through a 70 micron filter, washed 2x in PBS and incubated with red blood cell lysis to remove red blood cells. Cell viability was determined based on trypan blue exclusion. Cells were transported to the University of Minnesota core sequencing facility for  processing within 3 hours after excision from the patient.

value: omentum

tag: diagnosis

value: high-grade serous ovarian carcinoma

tag: tumor stage

value: IV

tag: tumor grade

tag: chemotherapy response

value: sensitive


title: WTPC_64A

description: RNASEQ

value: blood


title: ACE2-A549-Amoldipine-drugonly-3

value: Amlodipine

value: No


title: Tumor T90

value: IVa


title: WTPC_60B

description: RNASEQ

value: P. chabaudi AS

value: WT mouse


title: Tumor T76

value: IVb

value: resistant


title: ACE2-A549-Amoldipine-drugonly-2

value: lung alveolar (A549) transduced with vector expressing human ACE2


title: 191108_HD_7_snRNA-G12

source_name: Caudate

value: Caudate

tag: genotype

tag: tissue id


title: WTPC_60A

description: RNASEQ

value: darkness

value: ad libitum

value: 1 mouse


title: ACE2-A549-Berbamine-COV2-3

tag: cell line

value: Berbamine

value: Yes


title: WTPC_68A

description: RNASEQ


title: KPC3-PPT_244k

city: München

first: Sebastian

last: Mueller

address: Ismaninger Strasse 22

department: Institut für Molekulare Onkologie und Funktionelle Genomik

institute: Klinikum rechts der Isar

description: KPC mouse

hyb_protocol: The labelled DNA was hybridised onto the array slides in a 24h incubation at 65°C according to the manufacturers (Agilent) protocol.

scan_protocol: The slides were washed and scanned and the data extracted as tab-delimited text files according to the manufacturers protocol.

data_processing: Agilent Genomic Workbench software v7.0.4.0 was used for aCGH data preprocessing. Legacy centralization option was used for re-centralization of raw log ratios to the most common ploidy state. ADM-2 algorithm was applied for aberration calling. Normalized and curated data was imported into R.

source_name: primary pancreatic cancer cell culture

label_protocol: 250ng of genomic DNA were fluorescence labelled (Cy3 sample and Cy5 reference) by random primed labelling using the Enzo Oligo Array CGH Labelling kit according to the manufacturers protocol. The labelling activity was determined using a NanoDrop spectrophotometer.

growth_protocol: For all primary culture experiments, culturing medium (DMEM supplemented with 10% FCS and 1x P/S) and cultures with less than 10 passages were used.

extract_protocol: gDNA from murine primary cell culture pellets was isolated using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: No treatmant was applied.

value: pancreas

source_name: corresponding tail

value: tail


title: ACE2-A549-Amoldipine-drugonly-1

tag: drug


title: KPC4-PPT_244k

description: KPC mouse


title: KPC2-PPT_244k

description: KPC mouse


title: KPC1-PPT_244k

description: KPC mouse


title: WTPC_56B

description: RNASEQ

value: blood


title: Tumor T61

value: omentum

value: high-grade serous ovarian carcinoma

value: IIIc

value: refractory


title: NCI-H660_RNA-Seq rep2

city: Seattle

first: John

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
UC Santa Cruz Toil RNA-seq Pipeline (4.0.3)
Genome_build: hg38
Supplementary_files_format_and_content: CSV file with log-transformed FPKM+1 RSEM output for each gene and sample

source_name: Prostate cancer

growth_protocol: 22Rv1 and LNCaP95 cell lines were grown in RPMI medium supplemented with 10% FBS, 2 mM GlutaMAX, and penicillin/streptomycin. NCI-H660 and MSKCC EF1 cell lines were grown in Advanced DMEM/F12 medium supplemented with B27, 2 mM Glutamax, 10 ng/ml recombinant hEGF, 10 ng/ml recombinant hFGFb, and penicillin/streptomycin.

extract_protocol:
RNA from cell lines was extracted using the Qiagen Rneasy Mini Kit
RNA libraries were prepared for sequencing using the Illumina TruSeq Total RNA workflow

treatment_protocol: Cell lines were not treated

value: MSKCC EF1

tag: subtype

value: Neuroendocrine prostate cancer