title: L16373_M4-1m_07_C11

description: single cell


title: L16369_M4-1m_07_G10

status: Public on Sep 10 2019

type: SRA

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

description: single cell

library_source: transcriptomic

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: alignment of single-end data against mm10 with gsnap version 2017-03-17; splice sites were supported by using Ensembl version 87 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-87.ss.mm10.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.5.2 (-a EnsemblGene-87.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 87 gtf file
quality filtering: qc was done with the scater package and cells removed based on various quality metrics (ERCC content, chrM, total Features, total Counts and cell cycle)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e87.tsv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the sequenced single cell libraries
Supplementary_files_format_and_content: tab delimited file (scater.cpmlog10_counts.tsv.gz) created with the scater package; columns are the remaining cells and rows are genes

molecule: total RNA

organism: Mus musculus

source_name: adult mouse pancreas

extract_protocol:
To isolate Aldh1b1 expressing cells and their progeny, 1 mg of corn oil dissolved tamoxifen (20 mg/ml; Sigma) was injected intraperitoneally in Aldh1b1CreERT2 / ROSA26 LSLtdTomato double heterozygous adult mice for 5 consecutive days. Aldh1b1 expressing cells and their early progeny were isolated one day later from pancreata dissociated into single cells by virtue of their tdTomato (PE-Texas Red channel) expression from the lineage tracing mouse pancreas by FACS.
Pancreata were dissociated into single cells and cells were FACsorted into a 96 well plate containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. Lysis, reverse transcription of the RNA and cDNA amplification was performed according to the smartseq-2 protocol 6 with few modifications as detailed below. After thawing the samples, 2 ul of a primer mix (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)) was added. After filling up to 10 ul with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II, RNA was denatured for 3 minutes at 72°C and reverse transcription was performed at 42°C for 90 min. The reverse transcriptase was then inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 uM UP primer* under the following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and the DNA was eluted in 12 ul nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium). For library preparation 700 pg cDNA in 2 ul was mixed with 0.5 ul tagment DNA enzyme and 2.5 ul tagment DNA buffer (Nextera, Illumina) and tagmented at 55°C for 5 min. Subsequently, Illumina indices were added during PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.7 uM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina sequencing on a Nextseq500 aiming at an average sequencing depth of 0.5 mio reads per cell. Primers were as follows: dT primer: Aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACT(30)VN; Template Switch Oligo (TSO) primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG; Universal Part (UP) primer: AAGCAGTGGTATCAACGCAGAGT.

tag: strain

tag: tissue

value: pancreas

tag: genotype

tag: age

value: 8 weeks


title: L16372_M4-1m_07_B11

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title: L15255_M3_1d_04_C11

description: single cell


title: L15240_M3_1d_04_D09

description: single cell


title: L15237_M3_1d_04_A09

description: single cell


title: L15239_M3_1d_04_C09

description: single cell


title: L15238_M3_1d_04_B09

description: single cell


title: L15236_M3_1d_04_H08

description: single cell


title: L15235_M3_1d_04_G08

description: single cell


title: L15232_M3_1d_04_D08

description: single cell


title: L15230_M3_1d_04_B08

description: single cell


title: L15234_M3_1d_04_F08

description: single cell


title: L15233_M3_1d_04_E08

description: single cell


title: L15228_M3_1d_04_H07

description: single cell


title: L15227_M3_1d_04_G07

description: single cell


title: L15222_M3_1d_04_B07

description: single cell


title: L15226_M3_1d_04_F07

description: single cell


title: L15229_M3_1d_04_A08

description: single cell


title: L15218_M3_1d_04_F06

description: single cell


title: L15221_M3_1d_04_A07

description: single cell


title: L15220_M3_1d_04_H06

description: single cell


title: L15215_M3_1d_04_C06

description: single cell


title: L15212_M3_1d_04_H05

description: single cell


title: L15211_M3_1d_04_G05

description: single cell


title: L15209_M3_1d_04_E05

description: single cell


title: L15208_M3_1d_04_D05

description: single cell


title: L15210_M3_1d_04_F05

description: single cell


title: L15219_M3_1d_04_G06

description: single cell


title: L15206_M3_1d_04_B05

description: single cell


title: L15207_M3_1d_04_C05

description: single cell


title: L15205_M3_1d_04_A05

description: single cell


title: L15231_M3_1d_04_C08

description: single cell


title: L15203_M3_1d_04_G04

description: single cell


title: L15204_M3_1d_04_H04

description: single cell


title: L15202_M3_1d_04_F04

description: single cell


title: L15223_M3_1d_04_C07

description: single cell


title: L15201_M3_1d_04_E04

description: single cell


title: L15200_M3_1d_04_D04

description: single cell


title: L15213_M3_1d_04_A06

description: single cell


title: L15198_M3_1d_04_B04

description: single cell


title: L15214_M3_1d_04_B06

description: single cell


title: L15199_M3_1d_04_C04

description: single cell


title: L15193_M3_1d_04_E03

description: single cell


title: L15196_M3_1d_04_H03

description: single cell


title: L15197_M3_1d_04_A04

description: single cell


title: L15191_M3_1d_04_C03

description: single cell


title: L15190_M3_1d_04_B03

description: single cell


title: L15187_M3_1d_04_G02

description: single cell


title: L15185_M3_1d_04_E02

description: single cell


title: L15182_M3_1d_04_B02

description: single cell


title: L15188_M3_1d_04_H02

description: single cell


title: L15194_M3_1d_04_F03

description: single cell


title: L15195_M3_1d_04_G03

description: single cell


title: L15192_M3_1d_04_D03

description: single cell


title: L15183_M3_1d_04_C02

description: single cell


title: L15189_M3_1d_04_A03

description: single cell


title: L15186_M3_1d_04_F02

description: single cell


title: L15180_M3_1d_04_H01

description: single cell


title: L15184_M3_1d_04_D02

description: single cell


title: L15177_M3_1d_04_E01

description: single cell


title: L15179_M3_1d_04_G01

description: single cell


title: L15176_M3_1d_04_D01

description: single cell


title: L15178_M3_1d_04_F01

description: single cell


title: L15175_M3_1d_04_C01

description: single cell


title: L15174_M3_1d_04_B01

description: single cell


title: L14437_M2_1mth_03_H12

description: single cell


title: L15173_M3_1d_04_A01

description: single cell


title: L14436_M2_1mth_03_G12

description: single cell


title: L14435_M2_1mth_03_F12

description: single cell


title: L14434_M2_1mth_03_E12

description: single cell


title: L14433_M2_1mth_03_D12

description: single cell


title: L14432_M2_1mth_03_C12

description: single cell


title: L15181_M3_1d_04_A02

description: single cell


title: L14428_M2_1mth_03_G11

description: single cell


title: L14427_M2_1mth_03_F11

description: single cell


title: L14423_M2_1mth_03_B11

description: single cell


title: L14426_M2_1mth_03_E11

description: single cell


title: L14430_M2_1mth_03_A12

description: single cell


title: L14420_M2_1mth_03_G10

description: single cell


title: L14424_M2_1mth_03_C11

description: single cell


title: L14418_M2_1mth_03_E10

description: single cell


title: L14417_M2_1mth_03_D10

description: single cell


title: L14425_M2_1mth_03_D11

description: single cell


title: L14429_M2_1mth_03_H11

description: single cell


title: L14415_M2_1mth_03_B10

description: single cell


title: L14413_M2_1mth_03_H09

description: single cell


title: L14412_M2_1mth_03_G09

description: single cell


title: L14416_M2_1mth_03_C10

description: single cell


title: L14414_M2_1mth_03_A10

description: single cell


title: L14411_M2_1mth_03_F09

description: single cell


title: L14410_M2_1mth_03_E09

description: single cell


title: L14421_M2_1mth_03_H10

description: single cell


title: L14407_M2_1mth_03_B09

description: single cell


title: L14409_M2_1mth_03_D09

description: single cell


title: L14406_M2_1mth_03_A09

description: single cell


title: L14405_M2_1mth_03_H08

description: single cell


title: L14404_M2_1mth_03_G08

description: single cell


title: L14431_M2_1mth_03_B12

description: single cell


title: L14422_M2_1mth_03_A11

description: single cell


title: L14419_M2_1mth_03_F10

description: single cell


title: L14402_M2_1mth_03_E08

description: single cell


title: L14403_M2_1mth_03_F08

description: single cell


title: L14401_M2_1mth_03_D08

description: single cell


title: L14399_M2_1mth_03_B08

description: single cell


title: L14396_M2_1mth_03_G07

description: single cell


title: L14397_M2_1mth_03_H07

description: single cell


title: L14392_M2_1mth_03_C07

description: single cell


title: L14395_M2_1mth_03_F07

description: single cell


title: L14390_M2_1mth_03_A07

description: single cell


title: L14400_M2_1mth_03_C08

description: single cell


title: L14387_M2_1mth_03_F06

description: single cell


title: L14389_M2_1mth_03_H06

description: single cell


title: L14383_M2_1mth_03_B06

description: single cell


title: L14384_M2_1mth_03_C06

description: single cell


title: L14408_M2_1mth_03_C09

description: single cell


title: L14381_M2_1mth_03_H05

description: single cell


title: L14379_M2_1mth_03_F05

description: single cell


title: L14382_M2_1mth_03_A06

description: single cell


title: L14380_M2_1mth_03_G05

description: single cell


title: L14378_M2_1mth_03_E05

description: single cell


title: L14377_M2_1mth_03_D05

description: single cell


title: L14375_M2_1mth_03_B05

description: single cell


title: L14374_M2_1mth_03_A05

description: single cell


title: L14373_M2_1mth_03_H04

description: single cell


title: L14372_M2_1mth_03_G04

description: single cell


title: L14398_M2_1mth_03_A08

description: single cell


title: L14371_M2_1mth_03_F04

description: single cell


title: L14391_M2_1mth_03_B07

description: single cell


title: L14369_M2_1mth_03_D04

description: single cell


title: L14370_M2_1mth_03_E04

description: single cell


title: L14388_M2_1mth_03_G06

description: single cell


title: L14365_M2_1mth_03_H03

description: single cell


title: L14366_M2_1mth_03_A04

description: single cell


title: L14367_M2_1mth_03_B04

description: single cell


title: L14362_M2_1mth_03_E03

description: single cell


title: L14361_M2_1mth_03_D03

description: single cell


title: L14363_M2_1mth_03_F03

description: single cell


title: L14364_M2_1mth_03_G03

description: single cell


title: L14359_M2_1mth_03_B03

description: single cell


title: L14358_M2_1mth_03_A03

description: single cell


title: L14356_M2_1mth_03_G02

description: single cell


title: L14353_M2_1mth_03_D02

description: single cell


title: L14376_M2_1mth_03_C05

description: single cell


title: L14355_M2_1mth_03_F02

description: single cell


title: L14357_M2_1mth_03_H02

description: single cell


title: L14352_M2_1mth_03_C02

description: single cell


title: L14351_M2_1mth_03_B02

description: single cell


title: L14348_M2_1mth_03_G01

description: single cell


title: L14368_M2_1mth_03_C04

description: single cell


title: L14347_M2_1mth_03_F01

description: single cell


title: L14349_M2_1mth_03_H01

description: single cell


title: L14346_M2_1mth_03_E01

description: single cell


title: L14345_M2_1mth_03_D01

description: single cell


title: L14343_M2_1mth_03_B01

description: single cell


title: L14344_M2_1mth_03_C01

description: single cell


title: L14360_M2_1mth_03_C03

description: single cell


title: L14341_M2_1mth_02_H12

description: single cell


title: L14339_M2_1mth_02_F12

description: single cell


title: L14354_M2_1mth_03_E02

description: single cell


title: L14338_M2_1mth_02_E12

description: single cell


title: L14337_M2_1mth_02_D12

description: single cell


title: L14340_M2_1mth_02_G12

description: single cell


title: L14350_M2_1mth_03_A02

description: single cell


title: L14335_M2_1mth_02_B12

description: single cell


title: L14333_M2_1mth_02_H11

description: single cell


title: L14342_M2_1mth_03_A01

description: single cell


title: L14332_M2_1mth_02_G11

description: single cell


title: L14331_M2_1mth_02_F11

description: single cell


title: L14329_M2_1mth_02_D11

description: single cell


title: L14336_M2_1mth_02_C12

description: single cell


title: L14328_M2_1mth_02_C11

description: single cell


title: L14330_M2_1mth_02_E11

description: single cell


title: L14334_M2_1mth_02_A12

description: single cell


title: L14324_M2_1mth_02_G10

description: single cell


title: 3842 fruit, biological rep2

type: RNA

city: Rosario

first: Estela

middle: Marta

last: Valle

address: Ocampo y Esmeralda

country: Argentina

institute: IBR (CONICET-UNR)

description: fruit, biological rep2

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Tomato Genome Array. GeneChips were washed and stained according to Affymetrix procedures

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The data were analyzed using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Solanum lycopersicum

source_name: tomato ripe fruit

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Field crop trails were done at La Consulta Mendoza, Argentina (S 33° 43′ 59.16″, W 69° 7′ 4.44″; 1050 meters above sea level) during 2010 harvesting season. Seedlings were grown until four true leaves in 150-mL pots and transplanted spaced 30 cm in the row and a distance of 100 cm from row to row. A randomized parcel design with three replicates of six plants each was used, and a total of 18 plants per accession were grown. Fruit from all accessions were harvested at mature red stage and firmness in a sunny day between 10:00 am and 16:00 pm on March 9th and 10th 2010.

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

treatment_protocol: Pericarp tissue of the harvested fruits was obtained by removing the epicarp, locule tissues and seeds, and immediately frozen in liquid nitrogen and stored at –80 ºC until further analysis

value: fruit pericarp

tag: cultivar


title: 3815 fruit, biological rep1

description: fruit, biological rep1


title: 3815 fruit, biological rep2

description: fruit, biological rep2


title: 3836 fruit, biological rep2

description: fruit, biological rep2


title: 3806 fruit, biological rep3

description: fruit, biological rep3


title: 3836 fruit, biological rep3

description: fruit, biological rep3


title: 3836 fruit, biological rep1

description: fruit, biological rep1


title: 3842 fruit, biological rep1

description: fruit, biological rep1


title: LA1589 fruit, biological rep3

description: fruit, biological rep3

organism: Solanum pimpinellifolium


title: 3806 fruit, biological rep1

description: fruit, biological rep1


title: LA1589 fruit, biological rep2

description: fruit, biological rep2


title: 3842 fruit, biological rep3

description: fruit, biological rep3


title: 572 fruit, biological rep2

description: fruit, biological rep2


title: L14323_M2_1mth_02_F10

description: single cell


title: L14327_M2_1mth_02_B11

description: single cell


title: 572 fruit, biological rep3

description: fruit, biological rep3


title: L14322_M2_1mth_02_E10

description: single cell


title: L14326_M2_1mth_02_A11

description: single cell


title: 3806 fruit, biological rep2

description: fruit, biological rep2


title: L14321_M2_1mth_02_D10

description: single cell


title: L14320_M2_1mth_02_C10

description: single cell


title: L14325_M2_1mth_02_H10

description: single cell


title: LA1589 fruit, biological rep1

description: fruit, biological rep1


title: 572 fruit, biological rep1

description: fruit, biological rep1


title: L14318_M2_1mth_02_A10

description: single cell


title: L14317_M2_1mth_02_H09

description: single cell


title: 3815 fruit, biological rep3

description: fruit, biological rep3


title: L14319_M2_1mth_02_B10

description: single cell


title: L14316_M2_1mth_02_G09

description: single cell


title: 571 fruit, biological rep2

description: fruit, biological rep2


title: 571 fruit, biological rep1

description: fruit, biological rep1


title: 571 fruit, biological rep3

description: fruit, biological rep3


title: 560 fruit, biological rep3

description: fruit, biological rep3


title: L14314_M2_1mth_02_E09

description: single cell


title: L14313_M2_1mth_02_D09

description: single cell


title: L14315_M2_1mth_02_F09

description: single cell


title: L14311_M2_1mth_02_B09

description: single cell


title: L14312_M2_1mth_02_C09

description: single cell


title: L14310_M2_1mth_02_A09

description: single cell


title: L14309_M2_1mth_02_H08

description: single cell


title: 560 fruit, biological rep2

description: fruit, biological rep2


title: 560 fruit, biological rep1

description: fruit, biological rep1


title: 557 fruit, biological rep3

description: fruit, biological rep3


title: 557 fruit, biological rep1

description: fruit, biological rep1


title: 557 fruit, biological rep2

description: fruit, biological rep2


title: L14307_M2_1mth_02_F08

description: single cell


title: 549 fruit, biological rep2

description: fruit, biological rep2


title: 549 fruit, biological rep1

description: fruit, biological rep1


title: 549 fruit, biological rep3

description: fruit, biological rep3


title: L14306_M2_1mth_02_E08

description: single cell


title: L14303_M2_1mth_02_B08

description: single cell


title: L14308_M2_1mth_02_G08

description: single cell


title: L14304_M2_1mth_02_C08

description: single cell


title: L14302_M2_1mth_02_A08

description: single cell


title: L14301_M2_1mth_02_H07

description: single cell


title: L14300_M2_1mth_02_G07

description: single cell


title: L14305_M2_1mth_02_D08

description: single cell


title: L14296_M2_1mth_02_C07

description: single cell


title: L14294_M2_1mth_02_A07

description: single cell


title: L14293_M2_1mth_02_H06

description: single cell


title: pac3_highPi_III

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

description:
geneCounts_pac3_highPi.txt
DESeq_pac3_highPi_vs_mus52_highPi.csv

data_processing:
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the N. crassa genome using the Bowtie2 v2.3.4.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad NC12
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism: Neurospora crassa

source_name: Δpac-3 in high-Pi, replicate III

growth_protocol: All strains were maintained on solid Vogel’s Minimal (VM) medium supplemented with 2 % sucrose at 30 °C and pH 5.8. They were grown for 5 days (Δmus-52) or 10 days (Δpac-3), consisting of 3 days at 30 °C in the dark and 2 (Δmus-52) or 7 (Δpac-3) days at room temperature in ambient light.

extract_protocol:
The obtained mycelium was harvested, frozen in liquid nitrogen, and stored at - 80 °C until RNA isolation was performed. Total RNA was isolated using TRIzol™ Reagent (Invitrogen, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Conidia (approximately 10e7cells/mL−1) were germinated in an orbital shaker for 5 h at 30°C (200 rpm) in low- and high-Pi media (final concentrations, 10 μM or 10 mM Pi, respectively). Media was supplemented with 44 mM sucrose as the carbon source, and 50 mM of sodium citrate was used to adjust the pH to 5.4.

tag: treatment

value: high-Pi

value: mycelium


title: L14292_M2_1mth_02_G06

description: single cell


title: pac3_highPi_II

source_name: Δpac-3 in high-Pi, replicate II


title: pac3_lowPi_III

description:
geneCounts_pac3_lowPi.txt
DESeq_pac3_lowPi_vs_mus52_lowPi.csv

source_name: Δpac-3 in low-Pi, replicate III

value: low-Pi


title: pac3_highPi_I

source_name: Δpac-3 in high-Pi, replicate I


title: L14288_M2_1mth_02_C06

description: single cell


title: L14291_M2_1mth_02_F06

description: single cell


title: whole blood rituximab treated baseline sample16 responder

city: Amsterdam

first: Saskia

last: Vosslamber

address: de Boelelaan 1118

country: Netherlands

institute: VU University medical center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina Scan protocol

data_processing: Data were normalized using quantile normalization

label: biotin

organism: Homo sapiens

source_name: whole blood

label_protocol: biotine labeled cRNA using the Illumina TotalPrep RNA amplification kit

extract_protocol: Total RNA was isolated using Bio robot MDX (Qiagen, Benelux b.v., Venlo, The Netherlands) according to the manufacturer’s instructions (PAXgene Blood RNA Mdx kit). Samples were cleaned from salts that may be present using Qiagen RNA MinElute procedure according to manufactures procedure (Qiagen, Venlo, The Netherlands).

value: baseline

tag: response

value: rituximab responder

value: blood

tag: disease state

value: rheumatoid arthritis

tag: gender

value: female


title: whole blood rituximab treated baseline sample33 responder


title: L14287_M2_1mth_02_B06

description: single cell


title: whole blood rituximab treated baseline sample40 responder


title: whole blood rituximab treated baseline sample24 non-responder

value: rituximab non-responder


title: pac3_lowPi_I

source_name: Δpac-3 in low-Pi, replicate I


title: whole blood rituximab treated baseline sample10 non-responder


title: whole blood rituximab treated baseline sample30 responder


title: whole blood rituximab treated baseline sample22 non-responder


title: L14299_M2_1mth_02_F07

description: single cell


title: whole blood rituximab treated baseline sample4 non-responder


title: whole blood rituximab treated baseline sample19 non-responder


title: whole blood rituximab treated baseline sample38 responder


title: mus52_highPi_III

description:
geneCounts_mus52_highPi.txt
DESeq_pac3_highPi_vs_mus52_highPi.csv

source_name: Δmus-52 in high-Pi, replicate III


title: whole blood rituximab treated baseline sample13 non-responder


title: L14295_M2_1mth_02_B07

description: single cell


title: whole blood rituximab treated baseline sample27 responder

value: male


title: L14286_M2_1mth_02_A06

description: single cell


title: L14285_M2_1mth_02_H05

description: single cell


title: mus52_lowPi_III

description:
geneCounts_mus52_lowPi.txt
DESeq_pac3_lowPi_vs_mus52_lowPi.csv

source_name: Δmus-52 in low-Pi, replicate III


title: whole blood rituximab treated baseline sample7 responder


title: L14284_M2_1mth_02_G05

description: single cell


title: whole blood rituximab treated baseline sample36 responder


title: pac3_lowPi_II

source_name: Δpac-3 in low-Pi, replicate II


title: mus52_lowPi_II

source_name: Δmus-52 in low-Pi, replicate II


title: L14282_M2_1mth_02_E05

description: single cell


title: mus52_highPi_II

source_name: Δmus-52 in high-Pi, replicate II


title: L14280_M2_1mth_02_C05

description: single cell


title: L14281_M2_1mth_02_D05

description: single cell


title: mus52_highPi_I

source_name: Δmus-52 in high-Pi, replicate I


title: L14279_M2_1mth_02_B05

description: single cell


title: mus52_lowPi_I

source_name: Δmus-52 in low-Pi, replicate I


title: L14277_M2_1mth_02_H04

description: single cell


title: L14278_M2_1mth_02_A05

description: single cell


title: L14283_M2_1mth_02_F05

description: single cell


title: L14276_M2_1mth_02_G04

description: single cell


title: L14274_M2_1mth_02_E04

description: single cell


title: L14273_M2_1mth_02_D04

description: single cell


title: L14272_M2_1mth_02_C04

description: single cell


title: L14275_M2_1mth_02_F04

description: single cell


title: L14269_M2_1mth_02_H03

description: single cell


title: L14270_M2_1mth_02_A04

description: single cell


title: L14268_M2_1mth_02_G03

description: single cell


title: L14266_M2_1mth_02_E03

description: single cell


title: L14267_M2_1mth_02_F03

description: single cell


title: L14271_M2_1mth_02_B04

description: single cell


title: L14265_M2_1mth_02_D03

description: single cell


title: L14262_M2_1mth_02_A03

description: single cell


title: L14264_M2_1mth_02_C03

description: single cell


title: L14263_M2_1mth_02_B03

description: single cell


title: L14261_M2_1mth_02_H02

description: single cell


title: L14259_M2_1mth_02_F02

description: single cell


title: L14260_M2_1mth_02_G02

description: single cell


title: L14258_M2_1mth_02_E02

description: single cell


title: L14256_M2_1mth_02_C02

description: single cell


title: ref1 vs. fcp1-trunc-1:666-tag-flag+cdk8-del-1-a

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: Full_protocols.txt

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction: Features were extracted using Imagene software from Biodiscovery.

data_processing: genes, no bg corr, dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0: see Full_protocols.txt

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: refpool

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: ref1 vs. fcp1-trunc-1:666-tag-flag-1-a


title: ref1 vs. fcp1-trunc-1:609-tag-flag-1-a


title: ref1 vs. fcp1-trunc-1:594-tag-flag-1-a


title: fcp1-trunc-1:666-tag-flag+cdk8-del-1-b vs. ref1


title: ref1 vs. fcp1-mut-tag-flag-1-a


title: L14254_M2_1mth_02_A02

description: single cell


title: ref1 vs. fcp1-trunc-1:713-tag-flag-1-a


title: fcp1-trunc-1:713-tag-flag-1-b vs. ref1


title: L14253_M2_1mth_02_H01

description: single cell


title: ref1 vs. fcp1-trunc-1:609-tag-flag+cdk8-del-1-a


title: L14252_M2_1mth_02_G01

description: single cell


title: ref1 vs. fcp1-trunc-1:594-tag-flag+cdk8-del-1-a


title: fcp1-trunc-1:666-tag-flag-1-b vs. ref1


title: fcp1-trunc-1:609-tag-flag-1-b vs. ref1


title: fcp1-trunc-1:594-tag-flag-1-b vs. ref1


title: fcp1-trunc-1:594-tag-flag+cdk8-del-1-b vs. ref1


title: fcp1-trunc-1:609-tag-flag+cdk8-del-1-b vs. ref1


title: fcp1-mut-tag-flag-1-b vs. ref1


title: L14249_M2_1mth_02_D01

description: single cell


title: L14250_M2_1mth_02_E01

description: single cell


title: L14248_M2_1mth_02_C01

description: single cell


title: L14255_M2_1mth_02_B02

description: single cell


title: L14247_M2_1mth_02_B01

description: single cell


title: L14246_M2_1mth_02_A01

description: single cell


title: L14245_M2_1mth_01_H12

description: single cell


title: L14244_M2_1mth_01_G12

description: single cell


title: L14242_M2_1mth_01_E12

description: single cell


title: L14240_M2_1mth_01_C12

description: single cell


title: L14241_M2_1mth_01_D12

description: single cell


title: L14238_M2_1mth_01_A12

description: single cell


title: L14257_M2_1mth_02_D02

description: single cell


title: L14233_M2_1mth_01_D11

description: single cell


title: L14235_M2_1mth_01_F11

description: single cell


title: L14251_M2_1mth_02_F01

description: single cell


title: L14234_M2_1mth_01_E11

description: single cell


title: L14231_M2_1mth_01_B11

description: single cell


title: L14236_M2_1mth_01_G11

description: single cell


title: L14229_M2_1mth_01_H10

description: single cell


title: L14230_M2_1mth_01_A11

description: single cell


title: L14232_M2_1mth_01_C11

description: single cell


title: L14237_M2_1mth_01_H11

description: single cell


title: L14239_M2_1mth_01_B12

description: single cell


title: L14223_M2_1mth_01_B10

description: single cell


title: L14227_M2_1mth_01_F10

description: single cell


title: L14226_M2_1mth_01_E10

description: single cell


title: L14224_M2_1mth_01_C10

description: single cell


title: L14225_M2_1mth_01_D10

description: single cell


title: L14228_M2_1mth_01_G10

description: single cell


title: L14221_M2_1mth_01_H09

description: single cell


title: L14220_M2_1mth_01_G09

description: single cell


title: L14243_M2_1mth_01_F12

description: single cell


title: L14218_M2_1mth_01_E09

description: single cell


title: L14222_M2_1mth_01_A10

description: single cell


title: L14217_M2_1mth_01_D09

description: single cell


title: L14215_M2_1mth_01_B09

description: single cell


title: L14211_M2_1mth_01_F08

description: single cell


title: L14212_M2_1mth_01_G08

description: single cell


title: L14208_M2_1mth_01_C08

description: single cell


title: L14214_M2_1mth_01_A09

description: single cell


title: L14216_M2_1mth_01_C09

description: single cell


title: L14209_M2_1mth_01_D08

description: single cell


title: L14213_M2_1mth_01_H08

description: single cell


title: L14206_M2_1mth_01_A08

description: single cell


title: L14204_M2_1mth_01_G07

description: single cell


title: L14199_M2_1mth_01_B07

description: single cell


title: L14203_M2_1mth_01_F07

description: single cell


title: L14207_M2_1mth_01_B08

description: single cell


title: L14195_M2_1mth_01_F06

description: single cell


title: L14196_M2_1mth_01_G06

description: single cell


title: L14197_M2_1mth_01_H06

description: single cell


title: IMR90_EMPTY_GM_input

city: Cambridge

first: Alessandra

last: Dall'Agnese

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

description:
input chromatin
processed data files:
H3K27Ac-EGM-17_S5_L005_R1_001_sorted_rmdup.pileup.bw
EGM_K3K27Ac_Macs14_p1e9_peaks.bed

library_source: genomic

data_processing:
ChIP-Seq - Read quality was determined using FASTQC. Reads were mapped using bowtie2-2.0.5/bowtie2 to the female Homo sapiens hg19 genomes with options: --very-sensitive-local. Peaks were called using macs1.4 with pvalue=1e-9
Genome_build: female Homo sapiens hg19 genome
Supplementary_files_format_and_content: [H3K27Ac-EGM-17_S5_L005_R1_001_sorted_rmdup.pileup.bw]  bigwig after duplicate removal and fragment size adjustment EMPTY GM H3K27Ac ChIPSeq
Supplementary_files_format_and_content: [EGM_K3K27Ac_Macs14_p1e9_peaks.bed]  EMPTY GM H3K27ac ChIP-seq peaks in BED format

molecule: genomic DNA

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% FBS

extract_protocol:
For ChIPSeq lysates were clarified from sonicated crosslinked nuclei and H3K27ac-DNA complexes were isolated with antibody.
ChIPSeq libraries were prepared as in http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf.

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and for 3days in EMEM 2% HS 1%ITS collected for DM time point.

tag: cell type

value: Lung fibroblast

tag: ectopic gene expression

value: EMPTY VECTOR

tag: passage from isolation

value: passage 21-28

tag: chip antibody


title: H3K27ac_IMR90_EMPTY_GM

description:
ChIP experiment for H3K27ac
processed data files:
H3K27Ac-EGM-17_S5_L005_R1_001_sorted_rmdup.pileup.bw
EGM_K3K27Ac_Macs14_p1e9_peaks.bed

value: H3K27ac (Active Motif, catalog# 39134)


title: L14191_M2_1mth_01_B06

description: single cell

value: pancreas

value: 8 weeks


title: NHDF_ChIP-seq

city: Shenzhen

first: Baohua

last: Liu

address: No.1066 Xueyuan Av. Nanshan District

country: China

institute: Shenzhen University

data_processing:
Illumina Casava (1.8) software used for basecalling.
Data were aligned to the hg38 human genome assembly using Bowtie (v2.2.5) with the settings ‘--very-sensitive’.
Low quality mapped reads were removed using SAMtools (v1.3.1) with the settings ‘-q 30’.
Peaks were called using MACS2 (v2.1.0) with the settings ‘--keep-dup 1 -q 0.05’, and further annotated by HOMER (v4.10)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deepTools (v 3.3.0)

source_name: NHDF

growth_protocol: Human fibroblasts were maintained in DMEM with 15% FBS, supplemented with NEAA, GlutaMax, and penicillin/streptomycin. Cells were cultured at  37 ℃ in a humidified incubator with 5% CO2.

extract_protocol:
Cells were scraped off in PBS containing 0.5% BSA and collected into a 50-mL Eppendorf tube. Pellet cells at 2,000 rpm for 8 min, and transfer cells into 1.5 mL tubes. Cells were lysed in sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF, cocktail) and sonicated using Bioruptor (Diagenode). The supernatant of Lysate was diluted at 1:10 using RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-doxycholate, cocktail), and incubated with Dynabeads M-280 streptavidin (11206D, Thermo Fisher Scientific) for affinity purification. The beads were washed once with low salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), once with high salt buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), once with LiCl buffer (250 mM LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were collected into new EP tubes with TE buffer and incubated on a Mixing Block at 65 ℃ overnight at 1,000 rpm to reverse the formaldehyde cross-links. The supernatant was incubated with 200 ng/μL of RNase A at 37 ℃ for 1 h and then 200 ng/μL of proteinase K at 55 ℃ for 2 h. DNA was extracted with phenol and precipitated with ethanol using 30 μg glycogen (10901393001, Roche) as the carrier. DNA pellet was dissolved in TE buffer
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Ultra™ DNA Library Prep Kit.
Libraries were sequenced on an Illumina HiSeq™ 2500 platform with 6G base PE150 reads.

treatment_protocol: 1×107 cells cultured in several 10 cm dishes were fixed with 2% PFA in PBS for 10 min at room temperature (RT) and then quenched with 0.1 M glycine in PBS for 10 min. After permeabilization with 0.5% Triton X-100 in PBS, endogenous peroxidase activity was quenched by 0.5% H2O2 in PBS for 10 min at RT. 3% BSA prepared in TST buffer (TS buffer, 100 mM Tris-HCl pH 7.5, 150 mM NaCl, with 0.05% Tween-20) were used to block cells for 1 h at RT, and then PML antibody conjugated with horse-radish peroxidase (PG-M3, sc-966 HRP, Santa Cruz) was diluted at 1:300 in pre-cold 3% BSA in TST and incubated at 4 ℃ overnight. Cells were rinsed with borate buffer solution (BBS, 100 mM boric acid, 25 mM sodium tetraborate, 75 mM NaCl, pH 8.5) and incubated with freshly prepared reaction buffer (3.3 μg/mL of biotinylated tyramide and 0.003% of H2O2 in BBS) for 3 min at 26 ℃. Stop the enzymatic reaction by incubating with 0.5% H2O2 in PBS at RT for 10 min.

value: Normal Human Dermal Fibroblasts (NHDF)


title: L14192_M2_1mth_01_C06

description: single cell

source_name: adult mouse pancreas


title: L14198_M2_1mth_01_A07

description: single cell


title: L14188_M2_1mth_01_G05

description: single cell


title: L14187_M2_1mth_01_F05

description: single cell


title: L14219_M2_1mth_01_F09

description: single cell


title: L14205_M2_1mth_01_H07

description: single cell


title: L14189_M2_1mth_01_H05

description: single cell


title: L14200_M2_1mth_01_C07

description: single cell


title: KO_1_IPN

city: New York

first: Zichen

last: Wang

state: NY

address: 1468 Madison Ave

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
135_7
featureCounts_matrix.csv

data_processing:
The paired-end sequencing reads were aligned to the rat genome, using the Spliced Transcripts Alignment to a Reference (STAR).
featureCount was employed to assign aligned reads to genes.
Genome_build: rn6
Supplementary_files_format_and_content: comma-delimited text files include read count values for each sample

organism: Rattus norvegicus

extract_protocol:
For RNA extraction and analysis, habenula tissues were homogenized in 500 µl TRIzol Reagent (ThermoFisher Scientific, Carlsbad, CA, USA) according to the manufacturer’s instructions. Samples were sonicated to complete homogenization. 100 µl of chloroform was added and samples were vigorously vortexed for 15 sec. After a 3 min incubation at room temperature, the samples were centrifuged at 12,000 x g at 4°C for 15 min. The aqueous phase of the sample was removed by angling the tube at 45° and pipetting the solution to a fresh tube. 250 µl of 100% isopropanol was added to the aqueous phase and incubated for 10 min at room temperature. Samples were then centrifuged at 12,000 x g for 10 min at 4°C. Supernatant was removed and discarded, leaving behind the RNA pellet. The pellet was washed with 500 μl 75% ethanol twice. The tube was allowed to dry for 5 min at room temperature. The pellet was resuspended in 20 µl nuclease-free water. Residual genomic DNA was removed using the DNA-free Kit (ThermoFisher Scientific, Carlsbad, CA, USA) per the manufacturer’s instructions. The concentration was measured using a NanoDrop machine (ThermoFisher Scientific, Carlsbad, CA, USA). Samples were stored at -80 °C until processing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: IPN

value: Mut


title: WT_6_IPN

description:
135_6
featureCounts_matrix.csv

value: WT


title: WT_4_IPN

description:
135_4
featureCounts_matrix.csv


title: WT_3_IPN

description:
135_3
featureCounts_matrix.csv


title: KO_3_IPN

description:
135_9
featureCounts_matrix.csv


title: L14183_M2_1mth_01_B05

description: single cell


title: KO_2_IPN

description:
135_8
featureCounts_matrix.csv


title: L14186_M2_1mth_01_E05

description: single cell


title: WT_5_IPN

description:
135_5
featureCounts_matrix.csv


title: WT_2_IPN

description:
135_2
featureCounts_matrix.csv


title: L14210_M2_1mth_01_E08

description: single cell


title: KO_5_DHIP

description:
135_23
featureCounts_matrix.csv

value: DHIP


title: KO_6_DHIP

description:
135_24
featureCounts_matrix.csv


title: KO_4_DHIP

description:
135_22
featureCounts_matrix.csv


title: L14190_M2_1mth_01_A06

description: single cell


title: KO_3_DHIP

description:
135_21
featureCounts_matrix.csv


title: L14181_M2_1mth_01_H04

description: single cell


title: KO_2_DHIP

description:
135_20
featureCounts_matrix.csv


title: WT_1_IPN

description:
135_1
featureCounts_matrix.csv


title: NHDF_Input


title: L14180_M2_1mth_01_G04

description: single cell


title: L14182_M2_1mth_01_A05

description: single cell


title: L14185_M2_1mth_01_D05

description: single cell


title: WT_6_DHIP

description:
135_18
featureCounts_matrix.csv


title: WT_5_DHIP

description:
135_17
featureCounts_matrix.csv


title: L14179_M2_1mth_01_F04

description: single cell


title: L14178_M2_1mth_01_E04

description: single cell


title: WT_4_DHIP

description:
135_16
featureCounts_matrix.csv


title: KO_1_DHIP

description:
135_19
featureCounts_matrix.csv


title: L14177_M2_1mth_01_D04

description: single cell


title: WT_2_DHIP

description:
135_14
featureCounts_matrix.csv


title: WT_1_DHIP

description:
135_13
featureCounts_matrix.csv


title: KO_6_IPN

description:
135_12
featureCounts_matrix.csv


title: KO_5_IPN

description:
135_11
featureCounts_matrix.csv


title: L14175_M2_1mth_01_B04

description: single cell


title: L14176_M2_1mth_01_C04

description: single cell


title: L14174_M2_1mth_01_A04

description: single cell


title: WT_3_DHIP

description:
135_15
featureCounts_matrix.csv


title: L14173_M2_1mth_01_H03

description: single cell


title: RAT_KO_6

description:
133_6
featureCounts_matrix.csv

value: mHb


title: KO_4_IPN

description:
135_10
featureCounts_matrix.csv


title: RAT_WT_2

description:
133_8
featureCounts_matrix.csv


title: RAT_KO_5

description:
133_5
featureCounts_matrix.csv


title: RAT_KO_4

description:
133_4
featureCounts_matrix.csv


title: RAT_WT_3

description:
133_9
featureCounts_matrix.csv


title: RAT_WT_4

description:
133_13
featureCounts_matrix.csv


title: RAT_KO_1

description:
133_1
featureCounts_matrix.csv


title: RAT_KO_3

description:
133_3
featureCounts_matrix.csv


title: L14171_M2_1mth_01_F03

description: single cell


title: L14170_M2_1mth_01_E03

description: single cell


title: RAT_WT_1

description:
133_12
featureCounts_matrix.csv


title: RAT_WT_6

description:
133_11
featureCounts_matrix.csv


title: RAT_WT_5

description:
133_10
featureCounts_matrix.csv


title: L14169_M2_1mth_01_D03

description: single cell


title: L14168_M2_1mth_01_C03

description: single cell


title: L14172_M2_1mth_01_G03

description: single cell


title: L14167_M2_1mth_01_B03

description: single cell


title: RAT_KO_2

description:
133_2
featureCounts_matrix.csv


title: L14165_M2_1mth_01_H02

description: single cell


title: L14163_M2_1mth_01_F02

description: single cell


title: L14162_M2_1mth_01_E02

description: single cell


title: L14161_M2_1mth_01_D02

description: single cell


title: 15_SD Day 10 (43)_(RaGene-2_0-st)

city: Jackson

first: Kenji

middle: John

last: Maeda

state: MS

address: 2500 North State Street

department: Pharmacology & Toxicology

description: SD Day 10 (43)

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat GeneChip 2.0ST Arrays. GeneChips were automatically washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G.

data_processing: Analysis of microarray data was performed using Bioconductor, Limma and R Packages.

source_name: Uterine Implantation Site Day 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat GeneChip 2.0ST Arrays.

growth_protocol: Adult female Dahl S rats were obtained from Dr. Michael Garrett at the University of Mississippi Medical Center and adult female Sprague Dawley rats were purchased from Harlan Laboratories. Animals were bred at 16 weeks old. Gestational day 1 was defined by presence of sperm from vaginal swab.

extract_protocol: RNA was isolated using TRIzol® and Invitrogen PureLink Kit (Life Technologies) and evaluated for quality and integrity (Bio-Rad Experion™ System).

value: Sprague Dawley

value: Female

value: Uterine Implantation Site

tag: time point

value: Day 10


title: Pool 8_SD Placenta (56)_(RaGene-2_0-st)

institute: University of Mississippi Medical Center

description: SD Placenta (56)

source_name: Pooled Placental Tissue Day 14

value: Pooled Placental Tissue

value: Day 14


title: L14184_M2_1mth_01_C05

description: single cell


title: 12_SD Day 10 (59)_(RaGene-2_0-st)

description: SD Day 10 (59)


title: Pool 9_SD Placenta (64)_(RaGene-2_0-st)

description: SD Placenta (64)


title: 12_SD Day 7 (62)_(RaGene-2_0-st)

description: SD Day 7 (62)

source_name: Uterine Implantation Site Day 7

value: Day 7


title: L14166_M2_1mth_01_A03

description: single cell


title: Pool 10_SD Placenta (46)_(RaGene-2_0-st)

description: SD Placenta (46)


title: 10_SD Day 10 (49)_(RaGene-2_0-st)

description: SD Day 10 (49)


title: Pool 6_SD Placenta (50)_(RaGene-2_0-st)

description: SD Placenta (50)


title: Pool 7_SD Placenta (53)_(RaGene-2_0-st)

description: SD Placenta (53)


title: 11_SD Day 10 (57)_(RaGene-2_0-st)

description: SD Day 10 (57)


title: L14164_M2_1mth_01_G02

description: single cell


title: 8_SD Virgin (67)_(RaGene-2_0-st)

description: SD Virgin (67)

source_name: Uterine Tissue Day 0

value: Uterine Tissue

value: Day 0


title: L14159_M2_1mth_01_B02

description: single cell

value: pancreas


title: 14_SD Day 7 (45)_(RaGene-2_0-st)

description: SD Day 7 (45)


title: 10_SD Day 7 (55)_(RaGene-2_0-st)

description: SD Day 7 (55)


title: 9_SD Virgin (68)_(RaGene-2_0-st)

description: SD Virgin (68)


title: L14160_M2_1mth_01_C02

description: single cell

value: 8 weeks


title: L14157_M2_1mth_01_H01

description: single cell


title: 13_SD Day 7 (63)_(RaGene-2_0-st)

description: SD Day 7 (63)


title: 9_SD Virgin (47)_(RaGene-2_0-st)

description: SD Virgin (47)


title: 11_SD Day 7 (60)_(RaGene-2_0-st)

description: SD Day 7 (60)


title: 8_SD Virgin (65)_(RaGene-2_0-st)

description: SD Virgin (65)


title: Pool 5_Dahl S Placenta (M2447)_(RaGene-2_0-st)

description: Dahl S Placenta (M2447)

value: Dahl S


title: L14155_M2_1mth_01_F01

description: single cell


title: L14154_M2_1mth_01_E01

description: single cell


title: 7_SD Virgin (66)_(RaGene-2_0-st)

description: SD Virgin (66)


title: Pool 2_Dahl S Placenta (M2437)_(RaGene-2_0-st)

description: Dahl S Placenta (M2437)


title: L14153_M2_1mth_01_D01

description: single cell


title: Pool 4_Dahl S Placenta (M2434)_(RaGene-2_0-st)

description: Dahl S Placenta (M2434)


title: Pool 3_Dahl S Placenta (M2445)_(RaGene-2_0-st)

description: Dahl S Placenta (M2445)


title: L14158_M2_1mth_01_A02

description: single cell


title: 7_Dahl S Day 10 (M2453)_(RaGene-2_0-st)

description: Dahl S Day 10 (M2453)


title: Pool 1_Dahl S Placenta (M2452)_(RaGene-2_0-st)

description: Dahl S Placenta (M2452)


title: 4_Dahl S Day 10 (M2444)_(RaGene-2_0-st)

description: Dahl S Day 10 (M2444)


title: L14156_M2_1mth_01_G01

description: single cell


title: 3_Dahl S Day 7 (M2429)_(RaGene-2_0-st)

description: Dahl S Day 7 (M2429)


title: L14152_M2_1mth_01_C01

description: single cell


title: 6_Dahl S Day 7 (M2446)_(RaGene-2_0-st)

description: Dahl S Day 7 (M2446)


title: L14150_M2_1mth_01_A01

description: single cell


title: L16527_NC-wERCC_09_D07

description: single cell


title: L16431_NC-wERCC_08_D07

description: single cell


title: L16335_NC-wERCC_07_D07

description: single cell


title: L16239_NC-wERCC_06_D07

description: single cell


title: L15320_NC-wERCC_05_D07

description: single cell


title: L14393_NC-wERCC_03_D07

description: single cell


title: L14151_M2_1mth_01_B01

description: single cell


title: 6_Dahl S Day 10 (M2439)_(RaGene-2_0-st)

description: Dahl S Day 10 (M2439)


title: 5_Dahl S Day 10 (M2436)_(RaGene-2_0-st)

description: Dahl S Day 10 (M2436)


title: L16535_M5_50-1m_09_E07

description: single cell


title: L16439_M5_50-1m_08_E07

description: single cell


title: L14201_NC-wERCC_01_D07

description: single cell


title: 2_Dahl S Virgin (M2438)_(RaGene-2_0-st)

description: Dahl S Virgin (M2438)


title: L16343_M4_50-1m_07_E07

description: single cell


title: L15225_M2-cells_04_E07

description: single cell


title: L15321_M2-cells_05_E07

description: single cell


title: 1_Dahl S Virgin (M2435)_(RaGene-2_0-st)

description: Dahl S Virgin (M2435)


title: 4_Dahl S Day 7 (M2455)_(RaGene-2_0-st)

description: Dahl S Day 7 (M2455)


title: L14394_M2-cells_03_E07

description: single cell


title: 2_Dahl S Virgin (M2456)_(RaGene-2_0-st)

description: Dahl S Virgin (M2456)


title: L14298_M2-cells_02_E07

description: single cell


title: L14202_M2-cells_01_E07

description: single cell


title: L15224_NC-wERCC_04_D07

description: single cell


title: L16438_RNA-20pg_08_E06

description: single cell


title: L14297_NC-wERCC_02_D07

description: single cell


title: L16246_RNA-20pg_06_E06

description: single cell


title: 1_Dahl S Virgin (M2418)_(RaGene-2_0-st)

description: Dahl S Virgin (M2418)


title: L16247_M4_50-1m_06_E07

description: single cell


title: L15313_RNA-20pg_05_E06

description: single cell


title: L15217_RNA-20pg_04_E06

description: single cell


title: L14386_RNA-50pg_03_E06

description: single cell


title: 3_Dahl S Virgin (M2443)_(RaGene-2_0-st)

description: Dahl S Virgin (M2443)


title: L16534_RNA-20pg_09_E06

description: single cell


title: 5_Dahl S Day 7 (M2417)_(RaGene-2_0-st)

description: Dahl S Day 7 (M2417)


title: L14290_RNA-50pg_02_E06

description: single cell


title: L14194_RNA-50pg_01_E06

description: single cell


title: S_3.19_BR2

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

data_processing:
Sequencing quality was assessed using FastQC, and Illumina adapter sequences and some low-quality base pairs were removed using cutadapt version 1.9 (Martin, 2011). Reads were further trimmed in 3’ using “sickle” program version 1.33 with option -x and default values for all other parameters (implying Phred quality cut-off of 20).
The cleaned reads were then mapped against the whole repertoire of allelic variants for the 2,867 CDSs annotated in EGDe (GenBank accession No. NC_003210, length 2,944,528 bp) found in the 33 genomes.
Identification of allelic variants used “tblastn” version 2.6.0+ with options ‘-task tblastn -evalue 1e-10 -seg no’ (Camacho et al., 2009) and cut-offs corresponding to 80% identity at the amino-acid sequence and minimum coverage of 80% of the query.
Mapping used "bowtie2" version 2.2.6 (Langmead and Salzberg, 2012) with options ‘-N 1 -L 16 -R 4’ and converted to bam format using “samtools” version 1.9 (Li et al., 2009).
Read counts on each allelic variants were obtained using “htseq-count” version 0.10.0 (Anders et al., 2015) with options ‘-s reverse --nonunique all -a 1’. Read counts associated with all allelic variants were summed up to obtain a single read count per gene per sample. Importantly, “bowtie2” as used here mapped each read on a single allelic variant ensuring that each read could not be counted more than once and “htseq-count” options allowed to retrieve the reads that mapped equally well on several sequences as expected given the redundancy of the repertoire of allelic variants.
Read counts were normalized with the function “estimateSizeFactors” provided in the R package “DESeq2” (Love et al., 2014) version 1.20.0 based on the behaviour of the 2,456 conserved single copy genes (option ‘controlGenes’).
Genome_build: GenBank accession No. NC_003210
Supplementary_files_format_and_content: The file counts_bohyung_virulence_20190314.csv contains normalized read counts for 2867 CDSs of GenBank accession No. NC_003210 in the 66 samples, plus a column indicating which CDSs belong to the set of 2,456 conserved single copy genes.
Supplementary_files_format_and_content: ASCII text, tabulated separated values

organism: Listeria monocytogenes

source_name: cells grown in BHI medium, late exponential phase

growth_protocol: Mother cultures were inoculated into fresh BHI broth and grown at 37°C for 5-6 h to reach exponential phase.

extract_protocol:
The mixtures were pelleted by centrifugation (5,000g, 10 min, room temperature) and pellets were suspended in 5M Guanidine thiocyanate (Roth) lysis buffer with 10 µl/ml 2-Mercaptoethanol (Sigma-Aldrich). To lyse cell walls, 0.5mm glass beads (Roth) were added and bacterial cells were homogenized using Tissulyser (Qiagen) at a frequency of 30-1 for 6 min. After centrifugation (16,000g, 30 s, room temperature) supernatants were collected and RNA was purified using column-based RNA Clean & Concentrator-5 kit (Zymo Research). Quality of extracted RNA was assessed using Labchip GX II bioanalyzer (Perkin Elmer). To remove DNA contamination, total RNA was incubated with Baseline-Zero DNase (Epicentre) in the presence of RiboLock RNase inhibitor (40U/µl) (Thermo Fisher Scientific) for 30 min at 37°C followed by purification using RNA Clean & Concentrator-5 kit. RNA concentration was measured using fluorescence-based Qubit™ RNA HS Assay (Thermo Fisher Scientific).
To enrich mRNA and remove ribosomal RNA (rRNA), total RNA was treated with Ribo-Zero rRNA removal kit (Illumina). Briefly, beads were washed twice and hybridized with probes at 68°C for 10 min. Five hundred ng of total RNA was added to the mixture and incubated at RT and 50°C for 5 min each. rRNA bound to the beads was separated from mRNA using a magnetic stand. Enriched mRNA was then purified with RNA Clean & Concentrator-5 kit and and rRNA depletion was confirmed on Labchip GX II bioanalyzer (Perkin Elmer). Preparation of cDNA fragment libraries was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Illumina) with slight modifications. Briefly, the enriched mRNA was fragmented for 15 min at 94°C and reverse transcribed to synthesize the first-strand cDNA followed by second strand cDNA synthesis. Double-stranded cDNA (ds cDNA) was purified using NucleoMag (Macherey nagel) SPRI selection. End repair was performed on the ds cDNA library followed by ligation of adapters. High fidelity PCR was performed using KAPA Hifi polymerase (Kapa Biosystems) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers) to selectively enrich library fragments. The PCR products were purified twice using NucleoMag SPRI beads and the quality of the final library was assessed on Labchip GX II bioanalyzer. Indexed and purified libraries were sequenced on Illumina NextSeq 500 platform (paired-end, 2 X 75 bp per read).

treatment_protocol: RNAprotect (Qiagen) was immediately added and cultures were vortexed followed by incubation at room temperature for 5 min.

tag: lineage

value: Lineage 2

tag: growth medium

value: BHI

tag: growth phase

value: exponential phase

tag: growth temperature

tag: biological replicate


title: MSC_Input

city: Rochester

first: Andre

middle: J

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Data were processed by using HOMER [http://biowhat.ucsd.edu/homer/] and MACS.
Genome_build: mm9
Supplementary_files_format_and_content: *.bedgraph files are for display in the UCSC genome browser

source_name: marrow derived MSC

growth_protocol: Marrow derived MSC (mdMSC) were obtained from Dr. Janet Rubin, cryopreserved and expanded no more than 10 passages.  The MSCs were cultured in minimum Eagle’s medium alpha (MEMα) modification supplemented with 10% fetal bovine serum from Hyclone (Logan, UT), and 1% penicillin-streptomycin from Invitrogen.  For differentiation, cells were grown to confluency and then transferred to either osteogenic differentiation media (10 mM β–glycerophosphate and 50 µg/mL ascorbic acid) or adipogenic differentiation media (5 µg/mL insulin, 50 µM indomethacin, 0.1 µM dexamethasone) for the indicated lengths, replenishing the media every 2-3 days until assay.

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, Mol Endo. 2012). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody (bCat mixture of 3 antibodies, or TCF4).  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological replicate in the same manner (minimum of 2 replicates). Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Where indicated, MSC cells were treated with 50mM LiCl for 3 hours prior to ChIP assay.

tag: tissue

value: marrow-derived mesenchymal stem cells (MSCs)

value: vehicle

tag: antibody


title: MSC_TCF4LiCl_rep2

value: LiCl

value: TCF4 (Santa Cruz, H-125, sc13027, lot C0707)


title: HGT_CURED_2

first: Frederic

last: Sorgeloos

address: Addenbrookes Hospital, Hills Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol to the HumanHT-12 v4 BeadChip array.

scan_protocol: Standard scanning protocol using the Bead Array Reader from Illumina.

data_processing: The data were normalised using quantile normalisation in R by the lumi package [1] and the limma package [2].

source_name: IFN-cured HGT-1 cells that were bearing a GI Human norovirus replicon

label_protocol: 200ng of Total RNA underwent linear amplification using the Illumina TotalPrep RNA Amplification Kit (Life Technologies, Paisley, UK).

growth_protocol: Cells were maintained in Dulbecco’s minimal essential medium supplemented with 10% fetal calf serum, 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1X non-essential amino acid and in the case of HGT-NV cells with 1 mg/ml G418.

extract_protocol: RNA was extracted with Trizol reagent, precipitated using isopropanol and reususpended in water. RNA integrity was assessed using a SpectroStar (BMG Labtech, Aylesbury, UK) and a Bioanalyser (Agilent Technologies, Cheadle, UK).

treatment_protocol: Non applicable.

value: human gastric tumour

tag: cell line

value: HGT-1 (RRID:CVCL_A609)

tag: cell line reference


title: L16342_RNA-20pg_07_E06

description: single cell

tag: strain

tag: genotype

tag: age


title: HGT_CURED_3

description: replicate 3


title: S_3.19_BR1


title: S_3.17_BR2


title: HGT_CURED_1

description: replicate 1


title: HGT_NV_4

description: replicate 4

source_name: HGT-1 cells bearing a GI Human norovirus replicon


title: HGT_CURED_4

description: replicate 4


title: HGT_NV_2

description: replicate 2


title: HGT_4

description: replicate 4

source_name: HGT-1 cells wild-type


title: MSC_TCF4Veh_rep1

tag: treatment


title: MSC_TCF4LiCl_rep1


title: MSC_TCF4Veh_rep2


title: MSC_bCATLiCl_rep2

value: bCat1 (Santa Cruz, C-18, sc1496, lot J2110), bCat2  (Santa Cruz, E-5, sc7963, lot H2510), bCat3 (Santa Cruz, H-102, sc7199, lot L2010)


title: HGT_NV_3

description: replicate 3


title: HGT_2

description: replicate 2


title: HGT_3

description: replicate 3


title: HGT_1

description: replicate 1


title: S_3.17_BR1


title: MSC_bCATVeh_rep1


title: PHF2 ChIP-seq

city: Barcelona

last: Martínez-Balbás

state: Barcelona

address: C/ Baldiri Reixac 15-21

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

data_processing:
Read quality check was performed using FASTQ
Reads were mapped to the Mus musculus genome mm10 with Bowtie2
Peak calling was performed using MACS, using an effective genome size of 1870000000.0 and a p-value of 1e-10 for PHF2 ChIP-seq and a p-value of 0.001 and a q-value of 0.05 for H3K9me2 ChIP-seq
Genome_build: mm10
Supplementary_files_format_and_content: Bed files contain genomic coordinates of called peaks. Wig and bigWig files contain the information for displaying graphs.

source_name: Neural stem cells (NSCs)

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and -mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively

extract_protocol:
For Chip-seq lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the NEBNext® Ultra DNA Library Prep for Illumina® kit (ref. E7370) according to the manufacturer's protocol.

tag: cell type

value: Neural stem cells (NSCs)

tag: developmental stage

value: PHF2 (Cell signaling D45A2)

value: WT


title: MSC_bCATVeh_rep2


title: S_2.19_BR2

value: Lineage 1


title: ChIP-seq H3K9me2

tag: chip antibody

value: H3K9me2 (Abcam ab1220)


title: S_3.11_BR1


title: 18M+Nic-3

city: chongqing

first: jie

last: yang

address: 1 Youyi Road

institute: Chongqing Medical University

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20.
The clean reads were then aligned to mouse genome (version: mmu10, GRCm38) using the Tophat  program.
Genome_build: GRCm38 (mmu10)
Supplementary_files_format_and_content: RPKM data

source_name: tissue (hippocampus)

growth_protocol: APPswe/PS1dE9 transgenic mice, which overexpress the Swedish mutation of amyloid precursor protein together with presenilin 1 deleted in exon 9 , were purchased from Jackson Laboratories (#004462). In these mice, amyloid plaques develop at 4 months of age, and  impaired visuospatial learning occur as early as 6 months . Mice were housed in the 12/12 h light/dark cycle and were given food and water ad libitum.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using TruseqTM Small RNA sample prep Kit (Illumina) according to the manufacturer’s instructions. 1μg small RNA was used to add 3’ adaptor and 5’ adaptor to small RNA and RT-PCR was applied to the small RNA with adaptor to achieve the 1st cDNA; Truseq (Illumina) primer was used for PCR enrichment and introducing index sequence. Size selection was applied to obtain the 145-160bp library sequence. TBS380(Picogreen) was introduced to quantify the library concentration. We applied the cluster formation on flow cell utilizing cBot and sequencing on Hiseq2000 Platform.

treatment_protocol: Male mice were implanted subcutaneously with an osmotic mini pump (model 2002; Alzet,Cupertino,CA) that delivered 48 mg/kg/h nicotine hydrogen tartrate (Sigma, St.Louis)or saline for 14 days.

value: hippocampus

tag: mouse model

value: APP/PS1 mouse model of Alzheimer's disease

tag: drug

value: nicotine

value: C57BL/6 background (N9B6)

value: 18 month


title: S_3.11_BR2

tag: lineage

value: Lineage 2

tag: growth medium

value: BHI

value: exponential phase


title: S_2.19_BR1

tag: growth phase

tag: growth temperature


title: MSC_bCATLiCl_rep1

tag: tissue

value: marrow-derived mesenchymal stem cells (MSCs)

value: LiCl


title: S_2.18_BR2

tag: biological replicate


title: 18M+Nic-2


title: 18M-3

value: saline


title: 18M-2


title: S_2.18_BR1


title: 18M-1


title: 7M-3

value: 7 month


title: S_2.15_BR2


title: Input PHF2

value: Neural stem cells (NSCs)


title: 7M-2


title: 18M+Nic-1


title: 7M+Nic-2


title: S_2.15_BR1


title: HGT_NV_1

description: replicate 1

value: human gastric tumour

tag: cell line

value: HGT-1 (RRID:CVCL_A609)


title: S_2.13_BR2

value: Lineage 1


title: 7M-1


title: Input H3K9me2

value: WT


title: S_2.13_BR1


title: S_2.11_BR2


title: S_2.11_BR1


title: S_2.9_BR2


title: HGFTI_rep3

data_processing:
Illumina Casava (1.8) software used for basecalling.
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. Paired-end reads were aligned to the human reference genome hg19 with HISAT2 (v2.1.0).
HTSeq (v0. 6.0) was used to count the reads numbers mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: “xls” files include count and RPKM values for each sample.

source_name: HGFTI

extract_protocol:
Samples were isolated using the TRIzol™ Reagent (ThermoFisher Scientific, 15596026).
Fragmented RNA were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA)
Libraries were sequenced on an Illumina HiSeq™ 3000 platform with 6G base PE150 reads.

treatment_protocol: siRNA was transfected with DharmaFECT (T-2001, Thermo Fisher Scientific) in opti-MEM medium and the mix was incubated with cells for 6 h. At 72 h after transfection, cells were harvested for RNA extraction.

tag: disease

value: Hutchinson-Gilford progeria syndrome (HGPS)

value: dermal fibroblasts

tag: mutation

value: LMNA Exon 11, heterozygous c.1824C>T (p.Gly608Gly)

value: 2 uM of farnesylation inhibitor lonafarnib combined with 1 uM of zoledronate (HGFTI) for 3 days


title: HGFTI_rep2


title: HGFTI_rep1


title: HGI2si_rep3

tag: transfection

value: PML2 siRNA (HGI2si)


title: HGI2si_rep2


title: S_2.7_BR2

tag: strain

value: Lineage 2


title: S_2.4_BR1

value: BHI


title: S_2.4_BR2

value: exponential phase


title: S_2.9_BR1


title: S_2.7_BR1


title: S_1.13_BR1


title: Human stim MAIT 3

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Genes that were differentially expressed (>2 fold, P<0.01, FDR<0.05) between conditions and their normalised expression values, were generated with EdgeR R package(Robinson et al., 2010), Partek® Flow®, an online analysis platform for Next Generation Sequencing data (http://www.partek.com/partek-flow/).
RNA-seq data (logCPM) and ImmGen microarray data were integrated using a common set of Entrez(Maglott et al., 2011) annotated genes; batch effect removal was performed using ComBat algorithm in sva(Leek et al., 2012) R package. Hierarchical clustering analysis of transcription profiles was conducted in R employing highly variable genes (IQR >0.75(Gentleman et al., 2004)) and Euclidian distance.

source_name: PBMC

extract_protocol:
Cells were lysed in Agilent lysis buffer (Agilent Ltd., UK) containing 100 mM beta-mercaptoethanol and passed through a QIAshredder device (Qiagen, Valencia, US), then RNA extracted using the Absolutely RNA Nanoprep Kit according to the manufacturer’s instructions, including using of DNase I.
RNA libraries were prepared at the Melbourne Translational Genomics Platform, Department of Pathology (The University of Melbourne). Briefly, RNA quality and quantity were assessed using the Bioanalyzer 2100 RNA pico kit (Agilent technologies). The input total RNA was normalized to 250 pg per sample and median RIN was 9.7 (range 5.7-10.0). RNA was reverse transcribed and cDNA amplified by in vitro transcription with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). First strand cDNA synthesis and tailing by reverse transcription was performed using Clontech’s proprietary SMART (Switching Mechanism at 5’ End of RNA Template) technology. Following first strand synthesis, cDNA was amplified 12 cycles by LD PCR using blocked PCR primers. Amplified cDNA was purified using AMPure XP prior to QC using the bioanalyser 2100 HS DNA kit (Agilent technologies).
Library preparation of purified amplified cDNA was performed using Nextera XT library preparation (Illumina, AUS). Following QC, 150 pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposons. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalization and pooling before loading onto the HiSeq 2500 (Illumina, AUS) for paired end sequencing.

treatment_protocol: Single-cell suspensionswere generated from murine lungs which were finely chopped with a scalpel blade and treated with 3 mg.ml-1 collagenase III , 5ug/ml DNAse, and 2% foetal calf serum in RPMI for 90 min at 37'C with gentle shaking, and, where relevant, brefeldin A. Lung cells were then filtered (70 um) and washed with PBS/2% foetal calf serum. Red blood cells were lysed with hypotonic buffer TAC (Tris-based amino chloride) for 5 min at 37'C. Approximately 1.5x106 cells were filtered (40 um) and used for flow cytometric analysis. To obtain sufficient cells for sorting naïve CD8+CD44-CD62L+ cells from infection-naïve mice lungs from 2-3 mice per sample were pooled and stained with 0.18 ul anti-CD8-PE, then magnetically enriched using anti-PE beads (Miltenyi) prior to sorting. Human PBMC: cells were stained with surface antibodies (CD3-PE-CF594, CD8-PerCPCy5.5, CD45RA-FITC, TCR Va7.2-APC and FCg block for 15 mins at RT, followed by staining with MR1-5-OP-RU tetramer-PE for 20 mins at RT. Tetramer positive cells were positively selected using anti-PE microbeads (10 ul per 10-7 cells). Cells were sorted immediately into ice cold PBS with 10% FCS using an FACSAria III cell sorter selecting live CD3+TCR-Va7.2+MR1-5OP-RU-tetramer+ MAIT cells from the positive fraction and live CD3+CD8+CD45RA+MR1-Tetramer- cells from the negative fraction. The following day the remaining cells were stimulated for 6 h with 10 nM 5-OP-RU then magnetically enriched using MR1-5-OP-RU-tetramer-PE and anti-PE microbeads, and live CD3+TCR-Va7.2+MR1-5-OP-RU-tetramer+ MAIT cells sorted in the same manner. Purity was checked and with an average of 98%. Immediately after sorting cells were centrifuged at 400 g for 5 mins then resuspended in 100 uL of RNA lysis buffer (Agilent Ltd, UK) with 0.7uL beta-mercaptoethanol and stored at -80'C.

value: PBMC

tag: donor

value: Healthy volunteer

tag: treatment

value: Stimulated 6 h with 10nM 5-OP-RU


title: HGI2si_rep1

tag: cell type


title: Human stim MAIT 2


title: S_1.13_BR2


title: S_1.9_BR1


title: HGsi_rep3

source_name: HGsi

value: pan-PML siRNA (HGsi)


title: S_1.9_BR2


title: Human stim MAIT 1


title: HGsi_rep2


title: S_1.6_BR2


title: S_1.6_BR1


title: Human unstim MAIT 2

value: Unstimulated


title: Human unstim MAIT 3


title: S_1.3_BR2


title: HGsi_rep1


title: 7M+Nic-3

value: hippocampus

value: APP/PS1 mouse model of Alzheimer's disease

value: nicotine

tag: genotype

value: C57BL/6 background (N9B6)

tag: age

value: 7 month


title: 7M+Nic-1

tag: mouse model

tag: drug


title: HGcon_rep3

source_name: HGcon

value: Hutchinson-Gilford progeria syndrome (HGPS)

value: dermal fibroblasts

value: siRNA control


title: HGcon_rep2

value: LMNA Exon 11, heterozygous c.1824C>T (p.Gly608Gly)


title: S_1.3_BR1

tag: lineage

value: Lineage 2

tag: growth medium


title: Human unstim MAIT 1


title: Case_51: Second squamous cell carcinoma of the lung 20

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

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

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.444 based on the statistical language R version 3.4.2.

label: Cy5 and Cy3

source_name: Resection

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

tag: gender

value: Female

tag: smoking status (pack years)

value: Never smoker

tag: hpv genotyping

tag: p16 immunohistochemistry

value: Negative

tag: dna input [ng]

tag: tumor cell content (%)

tag: hnsc site of origin

value: Not applicable


title: Human unstim CD8+45RA+ 3

tag: tissue

value: PBMC

value: Live CD3+CD8+45RA+

value: Healthy volunteer


title: S_EGD.e_BR2

tag: strain

value: EGD-e

value: BHI

tag: growth phase

value: exponential phase

tag: growth temperature

tag: biological replicate


title: Case_30: Pulmonary metastasis of head and neck squamous cell carcinoma 30

source_name: Biopsy

value: Male

tag: age

value: Active (100 py)

value: Oral cavity


title: Case_50: Second squamous cell carcinoma of the lung 19

value: Active (40 py)


title: Human unstim CD8+45RA+ 2

tag: cell type

tag: donor

tag: treatment

value: Unstimulated


title: NFsi_rep3

source_name: NFsi

tag: disease

value: Normal

value: Normal Human Dermal Fibroblasts (NHDF)

tag: mutation

tag: transfection

value: pan-PML siRNA (NFsi)


title: Reference_sample_6: Primary lung squamous cell carcinoma 01

source_name: Lung resection

tag: gender

tag: smoking status (pack years)

tag: hpv genotyping


title: Reference_sample_5: Primary head and neck squamous cell carcinoma 05

tag: p16 immunohistochemistry

tag: dna input [ng]

tag: tumor cell content (%)

value: Larynx


title: S_EGD.e_BR1

tag: strain

tag: lineage

value: Lineage 2

tag: growth medium


title: Reference_sample_7: Primary lung squamous cell carcinoma 02

value: Former smoker (30 py)

value: Negative

tag: hnsc site of origin

value: Not applicable


title: Human unstim CD8+45RA+ 1

tag: tissue

value: PBMC

value: Live CD3+CD8+45RA+

value: Healthy volunteer


title: Reference_sample_4: Primary head and neck squamous cell carcinoma 04

value: Female

tag: age


title: NFsi_rep2

tag: cell type


title: S_Scott_A_BR2

value: Scott A

value: Lineage 1

value: BHI

tag: growth phase

value: exponential phase

tag: growth temperature

tag: biological replicate


title: NFsi_rep1

tag: disease

tag: mutation

tag: transfection


title: HGcon_rep1

value: Hutchinson-Gilford progeria syndrome (HGPS)

value: dermal fibroblasts

value: LMNA Exon 11, heterozygous c.1824C>T (p.Gly608Gly)

value: siRNA control


title: HiC_IMR90_MYOD_DM_Rep2

description: processed data file: GSE98509_M_GMvsM_DM_differentials.txt

data_processing:
ChIP-Seq - Read quality was determined using FASTQC. Reads were mapped using bowtie2-2.0.5/bowtie2 to the female Homo sapiens hg19 genomes with options: --very-sensitive-local. Peaks were called using macs2 2.1.1.20160309 with qvalue=0.01, macs2 2.1.1.20160309 was also used for differential peak calling among samples.
RNA-Seq - Spike-in were added based on number of nuclei but were not used for the analysis. Read quality was determined using FASTQC. Reads were mapped using TopHat2.1.1 to the female Homo sapiens hg19 genomes with options: -p 8 -g 1 --segment-length 17 --library-type fr-firststrand. HTSeq-0.6.1p1173 with --stranded=reverse option was used to assigned mapped reads to Homo Sapiens GRCh37.75 genes. Differential expression analysis was performed using DESeq2.
Hi-C - Read quality was determined using FASTQC. HiCPro-v2.7.7 was used for read mapping, valid ligation product detection, quality control, and sparse chromosomal interaction maps. HiTC was used to transform sparse matrices to NbyN matrices. Differential interactions 4kb resolution were called by DiffHiC. Requirement for significant differential interaction: Log(Fold Change) lower than -2 or higher than 2, pvalue lower than 0.05. Boundaries were called following a previously described method (Crane et al., 2015)
Genome_build: hg19

extract_protocol:
For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction. For Hi-C, DNA crossliked, digested and ligated, ligation products were isolated with streptavidine beads, Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications
RNASeq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations. Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and for 3days in EMEM 2% HS 1%ITS collected for DM time point. Cells were then treated or not with hTNF for 1hr prior collection

value: Lung fibroblast-derived myotube

tag: ectopic gene expression

value: mouse MYOD overexpression

tag: passage from isolation

value: passage 21-28


title: Reference_sample_10: Primary lung squamous cell carcinoma 05

tag: gender

value: Male

tag: smoking status (pack years)

value: Former smoker (40 py)

tag: hpv genotyping

tag: p16 immunohistochemistry

value: Positive

tag: dna input [ng]


title: Reference_sample_8: Primary lung squamous cell carcinoma 03

value: Active (10 py)

value: Negative

tag: tumor cell content (%)

tag: hnsc site of origin

value: Not applicable


title: Case_29: Pulmonary metastasis of head and neck squamous cell carcinoma 29

value: Female

tag: age

value: Active (80 py)

value: Oral cavity


title: Case_31: Pulmonary metastasis of head and neck squamous cell carcinoma 31

value: Former smoker (30 py)

value: Oropharynx


title: NFcon_rep3

source_name: NFcon

value: Normal

tag: cell type

value: Normal Human Dermal Fibroblasts (NHDF)


title: Reference_sample_9: Primary lung squamous cell carcinoma 04

value: Active (NA)


title: HiC_IMR90_MYOD_DM_Rep1

value: Lung fibroblast-derived myotube


title: S_LO28_BR2

tag: strain

tag: lineage

value: Lineage 2

tag: growth medium

value: BHI

tag: growth phase

value: exponential phase


title: Reference_sample_3: Primary head and neck squamous cell carcinoma 03

value: Male


title: S_LO28_BR1

tag: growth temperature

tag: biological replicate


title: NFcon_rep2

tag: disease

tag: mutation

tag: transfection

value: siRNA control


title: Reference_sample_1: Primary head and neck squamous cell carcinoma 01

tag: gender

tag: smoking status (pack years)

value: Active (10 py)

value: Positive


title: HiC_IMR90_MYOD_GM_Rep1

description: processed data file: GSE98509_E_GMvsM_GM_differentials.txt

value: Lung fibroblast-derived myoblast

tag: ectopic gene expression

value: mouse MYOD overexpression

tag: passage from isolation

value: passage 21-28


title: NFcon_rep1


title: HiC_IMR90_MYOD_GM_Rep2


title: Case_27: Pulmonary metastasis of head and neck squamous cell carcinoma 27

value: Active (60 py)

tag: hpv genotyping

tag: p16 immunohistochemistry

value: Negative

tag: dna input [ng]

tag: tumor cell content (%)

value: Oral cavity


title: S_Scott_A_BR1

tag: strain

value: Scott A

value: Lineage 1