title: 1772092289_H06


title: 1772092290_A06

status: Public on Dec 12 2017

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Processed data file: C1_expression_data.tab.gz

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e., Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: C1_expression_data.tab: Tab-delimited text file of total number of detected mRNA molecules from each gene in each cell.
Supplementary_files_format_and_content: datasetB_cellid_to_sampleid.txt: Tab-delimited text file shows the mapping from the sample IDs used in the referenced publication to the cell IDs in this dataset.

molecule: total RNA

organism: Mus musculus

source_name: dentate gyrus, CD-1, postnatal day 21

growth_protocol: Male and female wild type CD-1 mice (Charles River), as well as hGFAP-GFP reporter mice (Zhuo et al., Developmental Biology, 187(1), p36, 1997), between postnatal days 8 and 68 were used.

extract_protocol:
Mice were sacrificed by an overdose of Isoflurane or Ketamin/Xylazine, followed by perfusion through the left ventricle with artificial cerebrospinal fluid, equilibrated in 95%O2/5%CO2 on ice or 4°C. The dentate gyrus was then microdissected from 300 μ m vibratome brain sections. Single-cell suspensions were prepared using the Papain kit (Worthington) with 25-35min enzymatic digestion followed by manual trituration using a BSA-coated p1000 pipette or fire-polished Pasteur pipettes. For hGFAP-GFP mice, GFP-positive cells were sorted on a BD FACSAria II into oxygenated aCSF at 4°C. Cells were loaded at 500-800 cells/μ l at 4° on the C1 Fluidigm medium-sized chip.
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2x BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2x BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen QIAquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1x NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3' fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments, Ampure beads (Beckman Coulter) were used at 1.8x volume and eluted in 30 µL.

tag: strain/background

tag: genotype/variation

value: wild type

tag: hgfap-gfp mrna detected (0=no, 1=yes)

tag: Sex

value: Male

tag: postnatal day

tag: tissue

value: dentate gyrus

tag: cell cluster

value: Granule-mature


title: 1772092290_A12


title: 1772092289_G11


title: 1772092289_H12


title: 1772092289_F12


title: 1772092289_F05


title: 1772092289_G09


title: 1772092290_B10

value: Astrocytes


title: 1772092289_G10


title: 1772092289_G04

value: VLMC


title: 1772092289_E09


title: 1772092289_F04


title: 1772092289_F03


title: 1772092289_E11


title: 1772092289_H09


title: 1772092289_D04


title: 1772092289_E04

value: OPC


title: 1772092289_D06


title: 1772092289_C10


title: 1772092289_E02


title: 1772092289_C07


title: 1772092289_B09


title: 1772092289_D01


title: 1772092289_C03


title: 1772092289_C11


title: 1772092289_A10


title: 1772092289_B05

value: PVM


title: 1772092289_A12


title: 1772092289_B08


title: 1772092289_B11


title: 1772092289_A09


title: 1772092289_C02


title: 1772092289_A01


title: 1772092284_H06

source_name: dentate gyrus, CD-1, postnatal day 25


title: 1772092284_H03


title: 1772092284_G07


title: 1772092284_H01


title: 1772092289_E01


title: 1772092289_C04


title: 1772092289_C05


title: 1772092289_C01


title: 1772092284_G04


title: 1772092289_A08


title: 1772092284_G03


title: 1772092284_E08


title: 1772092284_F08


title: 1772092289_A07


title: 1772092284_E01


title: 1772092284_D01


title: 1772092284_C11


title: 1772092284_E07


title: 1772092284_D03


title: 1772092284_E02


title: 1772092284_B04


title: 1772092284_A10


title: 1772092284_B02


title: 1772092284_C03


title: 1772092284_A05


title: 1772092284_D02


title: 1772092282_G06


title: 1772092282_G07


title: 1772092282_F12


title: 1772092282_E07


title: 1772092284_A01


title: 1772092282_F01


title: 1772092282_E01


title: 1772092282_D02


title: 1772092282_D04


title: 1772092282_D08


title: 1772092282_D01

value: Radial Glia-like


title: 1772092282_C12


title: 1772092282_D10


title: 1772092282_C11


title: 1772092284_A02


title: 1772092282_B05


title: 1772092282_C05

value: Endothelial


title: 1772092282_B09


title: 1772092282_B04


title: 1772092282_B06


title: 1772092282_C09


title: 1772092282_B03


title: 1772092282_G02


title: 1772092282_B02


title: 1772092284_D04


title: 1772092282_A10


title: 1772092282_A06


title: 1772092282_A05

value: Neuroblast


title: 1772092282_A11


title: 1772092270_H06

source_name: dentate gyrus, CD-1, postnatal day 23

value: Female


title: 1772092270_G12


title: 1772092270_H08


title: 1772092270_H11


title: 1772092282_B08


title: 1772092270_F05


title: 1772092270_G04


title: 1772092270_E06


title: 1772092270_E11


title: 1772092270_F11


title: 1772092270_F04


title: 1772092270_E03


title: 1772092270_F03


title: 1772092270_F09


title: 1772092270_E05


title: 1772092270_D10


title: 1772092270_D11


title: 1772092270_D04


title: 1772092270_D06


title: 1772092270_E01


title: 1772092282_B01


title: 1772092282_A01

value: OL


title: 1772092270_G06


title: 1772092270_C12


title: 1772092270_C02


title: 1772092270_C11


title: 1772092270_C06


title: 1772092270_D02


title: 1772092270_B09


title: 1772092270_A07


title: 1772092269_H11


title: 1772092270_A02


title: 1772092270_B03


title: 1772092269_H10


title: 1772092270_B07


title: 1772092270_A09


title: 1772092269_H01


title: 1772092269_H09


title: 1772092269_G10


title: 1772092269_G06


title: 1772092269_H02


title: 1772092269_F12


title: 1772092269_G01


title: 1772092269_F06


title: 1772092269_F08


title: 1772092270_C05


title: 1772092269_E06


title: 1772092269_F03


title: 1772092270_C03


title: 1772092269_E12


title: 1772092269_D11


title: 1772092269_D12


title: 1772092269_E04

value: Microglia


title: 1772092269_E05


title: 1772092269_D08


title: 1772092269_D06


title: 1772092269_D05


title: 1772092269_C07


title: 1772092269_C08


title: 1772092269_C05


title: 1772092269_C11


title: 1772092269_C04


title: 1772092269_B09


title: 1772092269_C03


title: 1772092269_B07


title: 1772092269_A12


title: 1772092269_B06


title: 1772092269_B04


title: 1772092269_B05


title: 1772092269_A09


title: 1772092269_A06


title: 1772092269_A04


title: 1772092269_A02


title: 1772092266_H10


title: 1772092266_H11

value: nIPC


title: 1772092266_H05


title: 1772092269_C12


title: 1772092282_G01


title: 1772092266_G09


title: 1772092266_G12


title: 1772092266_G04


title: 1772092266_F10


title: 1772092269_B02


title: 1772092266_F09


title: 1772092266_G01


title: 1772092266_F07


title: 1772092266_E12


title: 1772092266_E01


title: 1772092266_F05


title: 1772092266_D09


title: 1772092266_E04


title: 1772092266_C05


title: 1772092266_D02

value: Cajal-Retzius


title: 1772092266_B12


title: 1772092266_C02


title: 1772092266_B11


title: 1772092266_B08


title: 1772092266_A11


title: 1772092266_A09


title: 1772092266_A10


title: 1772092266_A07


title: 1772092266_A08


title: 1772092266_A02


title: 1772092261_H11


title: 1772092266_A01


title: 1772092261_H08


title: 1772092266_D10


title: 1772092261_H02


title: 1772092266_D05


title: 1772092261_H03


title: 1772092261_G05


title: 1772092261_F07


title: 1772092261_F06


title: 1772092266_F12


title: 1772092261_F03


title: 1772092261_G08


title: 1772092305_B04

value: Not determined


title: 1772092261_E10

value: wild type


title: 1772092261_E05

value: Male


title: 1772092261_D05

value: dentate gyrus


title: 1772092261_E01


title: 1772092261_D04

value: Granule-mature


title: 1772092261_H04


title: 1772092261_G10


title: 1772092261_B10


title: 1772092261_B06


title: 1772092261_A12


title: 1772092261_G06


title: 1772092261_D02


title: 1772092261_G07


title: 1772092261_A01


title: 1772092261_F12


title: 1772092261_C12


title: 1772092260_H09

value: Astrocytes


title: 1772092261_E12


title: 1772092261_A06


title: 1772092260_G12


title: 1772092260_H07


title: 1772092260_H12


title: 1772092261_A03


title: 1772092260_H02


title: 1772092261_E11


title: 1772092307_H10


title: 1772092260_G05


title: 1772092260_G09


title: 1772092260_H01


title: 1772092260_H04


title: 1772092260_F11


title: 1772092260_F06


title: 1772092260_E10


title: 1772092260_E11


title: 1772092260_F07


title: 1772092260_E06


title: 1772092260_E04


title: 1772092260_D09


title: 1772092260_D05


title: 1772092260_C11


title: 1772092260_A09


title: 1772092260_C10


title: 1772092260_B08

value: Granule-immature


title: 1772092260_E01


title: 1772092260_A05


title: 1772092260_A04


title: 1772092260_A06


title: 1772092260_A08


title: WT IFM 16h APF rep 1

status: Public on Dec 01 2017

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

country: USA

institute: University of Missouri Kansas City

description:
DESeq2_IFM_24hvs16h.xlsx
DESeq2_IFM_16hvs0h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf

data_processing:
basecalling and demultiplexing by the VBCF (Vienna, Austria) using Illumina software
quality assessment of the raw data using fastqc v.0.11.2
filtering and trimming of adapter residues and low quality reads with fthe FASTX toolkit v.0.0.14 and cutadapt v.1.4.1
Sequenced reads were mapped to the Ensembl BDGP6.80 whole genome using STAR v.2.4.2a
mapped reads were sorted and indexed using samtools v.1.2
bam files were converted into bigwig for visualisation on the UCSC server
Counting the mapped reads on the gene and exon level using featureCounts v.1.4.6
run the differentail expression analysis using the R package DESeq2 v.1.8.2
run the clustering using the R package Mfuzz v.2.28.0
Genome_build: BDGP6.80 from ENSEMBL

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol: flies were grown on standard cornmeal medium using a standard fly husbandry protocol

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP
RNA libraries were prepared for sequencing by the VBCF (Vienna, Austria) using standard Illumina protocols

treatment_protocol: dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction

value: indirect flight muscle

tag: developmental stage

value: 16h APF

tag: genotype

value: Mef2-Gal4, UAS-GMA-GFP

tag: growth protocol

value: grown at 27C, staged 0h white pre-pupae


title: WT wing disc hinge rep 1 (Myo1)

description:
DESeq2_IFM_16hvs0h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf

source_name: wing disc hinge region

value: wing disc hinge region

value: 3rd instar myoblast

tag: barcode

value: TGACCA


title: 1772092260_A02


title: salmIR IFM 72h APF rep1

description:
DESeq2_salm_72hvs30h.txt
DESeq2_salm_1dvs72h.txt
DESeq2_IFMvssalm_72h.txt
Mfuzz_salm_4TP_inputdata.xlsx

value: 72h APF

value: Mef2-Gal4, UAS-T3029 (salmIR)

value: ATCACG


title: WT IFM 48h APF rep 1

description:
DESeq2_IFM_72hvs48h.xlsx
DESeq2_IFM_48hvs30h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf

value: 48h APF


title: WT IFM 24h APF rep 1

description:
DESeq2_IFMvssalm_24h.txt
DESeq2_IFM_24hvs16h.xlsx
DESeq2_IFM_30hvs24h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf

value: 24h APF


title: salmIR IFM 30h APF rep2

description:
DESeq2_salm_72hvs30h.txt
DESeq2_salm_30hvs24h.txt
DESeq2_IFMvssalm_30h.txt
Mfuzz_salm_4TP_inputdata.xlsx

value: 30h APF

value: GTCCGC


title: salmIR IFM 24h APF rep2

description:
DESeq2_IFMvssalm_24h.txt
DESeq2_salm_30hvs24h.txt
Mfuzz_salm_4TP_inputdata.xlsx

value: ACTGAT


title: salmIR IFM 72h APF rep2

value: AGTCAA


title: 1772092260_D06

value: wild type

value: Male

value: dentate gyrus

value: Granule-mature


title: salmIR IFM 24h APF rep1

value: indirect flight muscle

value: grown at 27C, staged 0h white pre-pupae

value: GTTTCG


title: WT wing disc myoblast rep 3 (Myo3)

source_name: sorted wing disc myoblast

value: sorted wing disc myoblast

value: 3rd instar myoblast

value: Him-Gal4, UAS-BBM (RFP); salmEGFP

value: grown at 25C, collected crawling 3rd instar larvae

value: CAGATC


title: WT IFM 90h APF rep 2

description:
DESeq2_IFM_90hvs72h.xlsx
DESeq2_IFM_1dvs90h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf

value: 90h APF

value: Mef2-Gal4, UAS-GMA-GFP


title: WT IFM 48h APF rep 3

value: 48h APF

value: TGACCA


title: WT IFM 24h APF rep 3

value: 24h APF

value: CGATGT


title: 9970497062_R06C02

status: Public on Nov 23 2017

type: genomic

city: London

first: Matt

middle: J

last: Silver

address: Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

description:
replicate
genomic DNA from peripheral blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan with standard recommended Illumina scanner settings

data_processing: GenomeStudio and R/Bioconductor packages. The raw data are available on the series level in the file GSE_betas_raw.csv and includes unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood samples by desalting, proteinase K digestion, and ammonium acetate precipitation

value: blood

value: M

tag: season


title: WT IFM 16h APF rep 2

value: 16h APF

value: CTTGTA


title: WT IFM 48h APF rep 2

value: indirect flight muscle

value: grown at 27C, staged 0h white pre-pupae


title: 9970497062_R05C01

description:
sample
genomic DNA from peripheral blood

value: rainy


title: 9970497062_R05C02

value: F


title: 9970497062_R04C02

value: dry


title: 9970497062_R03C02


title: 9970497062_R06C01


title: 9970497062_R03C01


title: 9970497062_R04C01


title: salmIR IFM 30h APF rep1

value: 30h APF

value: Mef2-Gal4, UAS-T3029 (salmIR)

value: TAGCTT


title: 9970497054_R05C02


title: WT wing disc myoblast rep 2 (Myo2)

value: sorted wing disc myoblast

value: 3rd instar myoblast

value: Him-Gal4, UAS-BBM (RFP); salmEGFP

value: grown at 25C, collected crawling 3rd instar larvae

value: CAGATC


title: 9970497062_R02C02

value: blood


title: 9970497062_R01C02

value: M


title: WT IFM 24h APF rep 2

value: 24h APF

value: Mef2-Gal4, UAS-GMA-GFP

value: GAGTGG


title: 9970497062_R02C01


title: WT IFM 16h APF rep 3

value: indirect flight muscle

value: 16h APF

value: grown at 27C, staged 0h white pre-pupae


title: 9970497054_R05C01

value: F

value: rainy


title: 9970497054_R04C02

value: dry


title: 9970497054_R06C01


title: 9970497054_R06C02


title: 9970497054_R04C01


title: WT IFM 90h APF rep 1

value: 90h APF


title: 9970497054_R02C02


title: 9970497054_R03C01


title: 9970497054_R03C02


title: 9970497054_R02C01


title: 9970497054_R01C01


title: 9970497049_R06C02


title: 9970497054_R01C02


title: 9970497049_R06C01


title: 9970497049_R05C02


title: 9970497049_R04C01


title: 9970497062_R01C01


title: 9970497049_R03C02


title: 9970497049_R05C01


title: 9970497049_R04C02


title: 9970497049_R02C02


title: 9970497043_R04C02


title: 9970497049_R01C01


title: 9970497043_R05C02


title: 9970497049_R02C01


title: 9970497043_R02C02


title: 9970497043_R04C01


title: 9970497043_R03C02


title: 9970497043_R03C01


title: 9970497043_R02C01


title: 9970497043_R06C02


title: 9970497043_R05C01


title: 9970497043_R01C02


title: 9970497043_R06C01


title: 9970497018_R06C01


title: 9970497018_R06C02


title: 9970497043_R01C01


title: 9970497018_R05C01


title: 9970497018_R05C02


title: 9970497018_R04C01


title: 9970497018_R04C02


title: 9970497018_R01C02


title: 9970497018_R01C01


title: 9970497018_R02C01


title: 9970497018_R03C02


title: 9970497018_R03C01


title: 9970497049_R03C01


title: 9970497049_R01C02


title: 9970497018_R02C02


title: 9970497017_R06C02


title: 9970497017_R05C02


title: 9970497017_R02C02


title: 9970497017_R01C01


title: 9970497017_R03C01


title: 9970497013_R06C02


title: 9970497017_R05C01


title: 9970497017_R02C01


title: 9970497013_R06C01


title: 9970497017_R04C01


title: 9970497013_R05C02


title: 9970497017_R01C02


title: 9970497017_R03C02


title: 9970497013_R03C01


title: 9970497013_R04C01


title: 9970497013_R04C02


title: 9970497013_R02C02


title: 9970497013_R02C01


title: 9970497013_R03C02


title: 9970497017_R06C01


title: 9969489075_R05C02


title: 9970497013_R01C02


title: 9969489075_R06C02


title: 9969489075_R06C01


title: 9969489075_R05C01


title: 9969489075_R04C02


title: 9970497017_R04C02


title: 9969489075_R04C01


title: 9969489075_R03C02


title: 9969489075_R03C01


title: 9970497013_R05C01


title: 9969489075_R02C02


title: 9969489059_R04C01


title: 9969489059_R01C01


title: 9969489075_R01C01


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title: 200251580131_R02C02


title: 200251580131_R01C02


title: 200251580130_R05C02


title: 200251580130_R06C01


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title: TBI Chronic 3

status: Public on Oct 03 2017

city: La Jolla

first: Roeben

last: Munji

state: California

address: 9500 Gilman Dr.

department: Pharmacology

institute: University of California San Diego

data_processing:
Alignment: Aligned to mouse genome build "mm9" using the program Tophat 2.0.13. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search  --mate-inner-dist=150 --no-discordant --no-mixed
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: Raw per-gene count data table in plain text format, suitable for loading in Excel

source_name: Brain Endothelial cells

growth_protocol: FACS purification of endothelial cells

extract_protocol:
FACS purification of endothelial cells into Trizol. Phenol chloroform extraction was used to isolate RNA
Prepared at the Gladstone Genomics core: NuGEN Ovation RNA-seq V2 kit and NuGEN Ovation Ultralow kit wereused

tag: disease model

value: TBI

tag: timepoint

value: Chronic


title: TBI Chronic 1


title: TBI Subacute Control 2

value: TBI (control)

value: Control (subacute)


title: TBI acute 1

value: Acute


title: TBI Subacute Control 1


title: TBI subacute 1

value: Subacute


title: TBI acute Control 3

value: Control (acute)


title: TBI acute Control 1


title: TBI subacute 2


title: Stroke Chronic 2

value: MCAO stroke


title: TBI chronic control 2

value: Control (chronic)


title: 200251580130_R05C01

value: blood

value: M


title: 200251580130_R04C02


title: TBI acute 2


title: TBI acute 3


title: Stroke Chronic 3


title: 200251580130_R03C01


title: TBI acute Control 2


title: 200251580130_R03C02


title: Stroke Chronic 1


title: Stroke Subacute 3


title: Stroke Subacute 2


title: Stroke Subacute 1


title: 200251580130_R02C01


title: TBI chronic control 1


title: Stroke Acute 3


title: TBI subacute 3


title: TBI Chronic 2


title: Stroke Control 3

value: MCAO stroke (control)

value: Control


title: Stroke Acute 2


title: Stroke Control 1


title: EAE Subacute 3

source_name: Spinal Cord Endothelial cells

value: EAE


title: EAE Chronic 2


title: EAE Chronic 1


title: Stroke Control 2


title: EAE Acute 1


title: EAE Acute 2


title: EAE Chronic 3


title: EAE Subacute 2


title: EAE Subacute 1


title: EAE Acute 3


title: Stroke Acute 1


title: EAE Control 2

value: EAE (Control)


title: Epilepsy Chronic 3

value: Epilepsy


title: EAE Control 3


title: Epilepsy Chronic 1


title: Epilepsy Chronic 2


title: Epilepsy Acute 3


title: Epilepsy Subacute 1


title: Epilepsy Subacute 2


title: Epilepsy Subacute 3


title: Epilepsy Acute 1


title: Whole Brain 4

source_name: Whole Brain

value: Healthy


title: Epilepsy Control 2

value: Epilepsy (Control)


title: Whole Brain 2


title: Epilepsy Control 3


title: Whole Brain 3


title: Epilepsy Control 1


title: Whole Brain 1


title: Liver Endo 2

source_name: Liver Endothelial cells


title: EAE Control 1


title: Liver Endo 1


title: Kidney Endo 2

source_name: Kidney Endothelial cells


title: Brain Vascular 1


title: Lung Endo 2

source_name: Lung Endothleial cells


title: Brain Vascular 2


title: Kidney Endo 1


title: Heart Endo 1

source_name: Heart Endothelial cells


title: Lung Endo 1


title: Epilepsy Acute 2


title: BRAF OIS 1 - Dam-LaminB1

status: Public on Aug 17 2017

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description: Sample name: 3211_8_166_L_ND_39_ATGCCT_L007_R1_001

library_source: genomic

data_processing:
Reads were demultiplexed using bcl2fastq 1.8.4 with 1 mismatch allowed
DamID adaptors were trimmed from reads with cutadapt
Sequencing reads were mapped against the human genome build hg19 using Bowtie2 with parameters --local --phred33
Reads were filtered for those that mapped with qval 15 and unique mapping
Reads which aligned to GATC fragments were summarised as counts
Then summarised into 50kb bins as observed reads over expected in each bin
Genome_build: hg19
Supplementary_files_format_and_content: The file readcounts.txt contains the absolute gene expressions values for each of the samples.
Supplementary_files_format_and_content: OIS_LAD_CdG_GenomeResearch_Annot.csv: Lmnb1-Dam and DamOnly reads were binned into 50k regions and then rations of reads calculated to determine Lamin Associated Domains. Scripts for this are found at https://github.com/cadegraaf/DamIdSeq

source_name: Tig3ET cell line (diploid embryonic lung fibroblasts expressing the ecotropic receptor to allow infection with ecotropic retroviruses and hTERT to prevent replicative senescence)

growth_protocol: Cells were propagated in DMEM (GIBCO) supplemented with 9% fetal bovine serum.

extract_protocol:
Genomic DNA was isolated using the using Gentra Puregene Cell Kit according to the manufacturer’s instructions.  0.5 mg of gDNA was subjected to digestion with DpnI restriction enzyme, followed by ligation to a double-stranded adaptor. The adaptor-ligated fragments were subsequently PCR-amplified using primers identical to the adaptor sequence and the 5’ TC nucleotides of the gDNA fragment. Then the methylPCR products were cleaned up using the QIAquick PCR product purification kit. Then DNA fragments were end-repaired using the END ITTM end repair kit (Epicentre) according to manufacturer’s instruction. The end-repaired DNA was A-tailed by incubating with 0.4 mM ATP in the presence of 25U of klenow fragment (NEB) at 37°C for 30 min, then, 75°C for 20 min.
DNA was subsequently purified using AMPureXP beads (Agencourt Biosciences) and ligated to the Illumina Y adaptor in a reaction containing 2.5 mM Illumina Y adaptor and 2.5 U of T4DNA ligase and incubated at 16°C for 16 hours, followed by inactivation at 65°C for 10 min. The adaptor ligated DNA was purified with AMPureXP beads. 100 ng of purified DNA was amplified by 12 cycles in a reaction containing Illumina constant primer and Illumina index primer at a final concentration of 2.5 mM, and 10 ml of 2x MyTaq mix in a final volume of 20 ml. Samples were then pooled, bead purified and size-selected.

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with  empty vector (cycling). The infected population was selected using puromycin 1μg/ml. Eight days after retroviral infection (a time point at which cells have entered senescence) or after serum starvation, cells were transduced with Dam-Lamin B1-encoding lentiviruses. Twenty fours hours after transduction, cells were refreshed with medium supplemented with 0.5 μM Sh. After 24 hour of induction cells were harvested and processed for DamID sequencing.
Cells were maintained for 9 days after the treatment specified in Treatment

tag: cell line

tag: day treament

tag: cell stage

value: oncogene induced senescence

tag: transducer

value: Dam-Lamin B1-encoding lentiviruses


title: BRAF OIS 1 - Dam Only

description: Sample name: 3211_7_166_D_1_20_39_CAGATC_L007_R1_001

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with  empty vector (cycling). The infected population was selected using puromycin 1μg/ml. Eight days after retroviral infection (a time point at which cells have entered senescence) or after serum starvation, cells were transduced with Dam lentiviruses. Twenty fours hours after transduction, cells were refreshed with medium supplemented with 0.5 μM Sh. After 24 hour of induction cells were harvested and processed for DamID sequencing.
Cells were maintained for 9 days after the treatment specified in Treatment

value: Dam lentiviruses


title: BRAF OIS 2 - Dam-LaminB1

description: Sample name: 3211_12_166_L_ND_40_AGTGGT_L007_R1_001


title: Cycling 1 - Dam-LaminB1

description: Sample name: 3211_6_167_L_1_2_39_CGCTGA_L007_R1_001

value: cycling


title: Quiescent Serum Starvation 2 - Dam Only

description: Sample name: 3211_4_0F_D_R2_ACCACT_L007_R1_001

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, 0% FBS DMEM medium. Eight days after serum starvation, cells were transduced with Dam lentiviruses. Twenty fours hours after transduction, cells were refreshed with medium supplemented with 0.5 μM Sh. After 24 hour of induction cells were harvested and processed for DamID sequencing.
Cells were maintained for 9 days after the treatment specified in Treatment

value: quiescent


title: BRAF OIS 2 - Dam Only

description: Sample name: 3211_11_166_D_1_10_40_CATCAA_L007_R1_001

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with  empty vector (cycling). The infected population was selected using puromycin 1μg/ml. Eight days after retroviral infection (a time point at which cells have entered senescence) or after serum starvation, cells were transduced with Dam encoding lentiviruses. Twenty fours hours after transduction, cells were refreshed with medium supplemented with 0.5 μM Sh. After 24 hour of induction cells were harvested and processed for DamID sequencing.
Cells were maintained for 9 days after the treatment specified in Treatment


title: Cycling 2 - Dam-LaminB1

description: Sample name: 3211_10_167_L_1_2_40_AGTACA_L007_R1_001


title: Quiescent Serum Starvation 1 - Dam Only

description: Sample name: 3211_2_0F_D_R1_AAACAT_L007_R1_001


title: Quiescent Serum Starvation 2 - Dam-LaminB1

description: Sample name: 3211_3_0F_L_R2_ACATTG_L007_R1_001

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, 0% FBS DMEM medium. Eight days after serum starvation, cells were transduced with Dam-Lamin B1-encoding lentiviruses. Twenty fours hours after transduction, cells were refreshed with medium supplemented with 0.5 μM Sh. After 24 hour of induction cells were harvested and processed for DamID sequencing.
Cells were maintained for 9 days after the treatment specified in Treatment


title: Quiescent Serum Starvation 1 - Dam-LaminB1

description: Sample name: 3211_1_0F_L_R1_ACAAGC_L007_R1_001


title: Heart Endo 2


title: Cycling 1 - Dam Only

description: Sample name: 3211_5_167_D_1_10_39_AACGTG_L007_R1_001


title: BRx-213-3--08-26-15

status: Public on Aug 25 2016

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had less than 105 reads were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: candidate CTC

extract_protocol:
Single CTCs were isolated from fresh whole blood following leukocyte depletion using the microfluidic CTC-iChip as described in PMID 23552373. Single cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer, and flash frozen in liquid nitrogen.
Clontech SMARTer Ultra Low Input Kit for RNA v3 for cDNA synthesis and the Nextera XT kit for library construction

tag: donor

tag: ptprc

value: low

value: high

tag: er

value: negative

tag: pr


title: BRx-183-7--3-10-15


title: BRx-183_4_031015


title: Cycling 2 - Dam Only

description: Sample name: 3211_9_167_D_1_10_40_CTGTAG_L007_R1_001


title: BRx-183-3--3-10-15


title: BRx-245-2--09-04-15


title: BRx-213-2--08-26-15


title: BRx-183_6_031015


title: BRx-183_5_031015


title: BRx-180-1--06-12-15


title: BRx-172-3--07-07-15


title: BRx-183_2_031015


title: BRx-172-1--09-09-15


title: BRx-172-2--08-25-15


title: BRx-180-1--07-02-15


title: BRx-172-2--07-07-15


title: BRx-183_1_031015


title: BRx-172-1--08-25-15


title: BRx-172-1--08-18-15


title: BRx-172-1-08-04-15


title: LKB1-K78I, rep2

status: Public on Dec 31 2016

type: RNA

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

description:
LW9
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with LKB1 K78I mutant.

hyb_protocol: The labeled cRNAs were hybridized onto the Agilent-045997 Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Human lung carcinoma cell line A549 transduced with pBabe LKB1 kinase-dead K78I mutant

label_protocol: Sample labeling was performed based on the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (Mediatech, Manassa, VA) supplemented with 10% inactivated fetal bovine serum (Life Technologies, Carlsbad, CA) and 1% penicillin/streptomycin (Corning Cellgro, Manassa, VA). Cells were grown in a 5% CO2 cell culture incubator at 37 °C. For retroviral production, the retroviral pBabe-based construct (LKB1, kinase death mutant LKB1 K78I or empty vector) together with packing plasmid pMD.MLV and pseudotyped envelope pMD2-VSV-G were transfected to 293T cells using Effectene transfection reagent (QIAGEN, Germantown, MD). Retroviruses were collected at 48 hours and 72 hours post transfection and used to infect the A549 cells on two consecutive dates. Cells were collected for RNA and proteins at 96 hours post infection.

extract_protocol: RNA was extracted using TRIzol (Life Technologies, Carlsbad, CA) and RNeasy mini kit (Qiagen, Germantown, MD).

treatment_protocol: (A) Two groups: LKB1-null, LKB1-wt; (B) Three groups: Control (vector), LKB1 (wt), LKB1 kinase-death (K78I).

tag: cell type

value: lung carcinoma cell line transduced with pBabe LKB1 kinase-dead K78I mutant

tag: genotype/variation


title: sulf8_H4

status: Public on Nov 01 2016

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data sperm cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix Equus caballus Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and Affymetrix Expression Console 1.1

label: biotin

organism: Equus caballus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: warmblood stallions at breeding age

extract_protocol: Total RNA was isolated from 4 x 108 sperms/stallion using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: kept at insemination center; 4 ejaculates per stallion were sampled during the breeding season

tag: gender

value: male

tag: tissue

value: spermatozoa

value: spring

tag: fertility class


title: BRx-172-1--06-25-15


title: LKB1-wt, rep2

description:
LW10
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with LKB1 wt.

source_name: Human lung carcinoma cell line A549 transduced with pBabe LKB1 wildtype

value: lung carcinoma cell line transduced with pBabe LKB1 wildtype


title: Control, rep2

description:
LW8
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with pBabe vector control.

source_name: Human lung carcinoma cell line A549 transduced with pBabe vector control

value: lung carcinoma cell line transduced with pBabe vector control


title: BRx-172-1--02-01-15


title: LKB1-wt, rep1

description:
LW7
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with LKB1 wt.


title: BRx-172_2_111114


title: BRx-172-1--4-16-15


title: auhf_M1

description: Gene expression data sperm cells


title: aulf5_S

description: Gene expression data sperm cells

value: autumn


title: BRx-172-5--11-11-14


title: BRx-172-1--9-30


title: BRx-172_1_111114


title: Control, rep1

description:
LW5
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with pBabe vector control.


title: BRx-170-2


title: BRx-16-4--09-09-15


title: sulf_D1

description: Gene expression data sperm cells


title: BRx-170-1


title: BRx-172_1_120114


title: suhf4_H2

description: Gene expression data sperm cells


title: auhf2_I

description: Gene expression data sperm cells


title: LKB1-K78I, rep1

description:
LW6
LncRNA expression data from LKB1-null lung cancer A549 cells transduced with LKB1 K78I mutant.


title: LKB1-wt cell line H3123

description:
LW4
LncRNA expression data from LKB1-positive lung cancer H3123 cells.

source_name: Human lung carcinoma cell line H3123

value: lung carcinoma cell line


title: BRx-16-3--09-09-15


title: BRx-132-1--06-09-15


title: BRx-16_3_120314


title: BRx-16_2_120314


title: BRx-139-1


title: BRx-131-1--09-15-15


title: BRx-16_2_102214


title: BRx-16_1_120314


title: LKB1-null cell line H460

description:
LW2
LncRNA expression data from LKB1-null lung cancer H460 cells.

source_name: Human lung carcinoma cell line H460


title: LKB1-wt cell line H322

description:
LW3
LncRNA expression data from LKB1-positive lung cancer H322 cells.

source_name: Human lung carcinoma cell line H322


title: sulf7_H3

description: Gene expression data sperm cells


title: suhf3_H1

description: Gene expression data sperm cells


title: BRx-111-2--10-08-15


title: BRx-146-1--4-16-15


title: BRx-146-1--08-06-15


title: BRx-111-1--10-08-15


title: LKB1-null cell line A549

description:
LW1
LncRNA expression data from LKB1-null lung cancer A549 cells.

source_name: Human lung carcinoma cell line A549


title: BRx-136_1_123014


title: BRx-111-3--10-08-15


title: BRx-136_2_123014


title: BRx-16_1_102214


title: aulf6_D

description: Gene expression data sperm cells


title: BRx-129_2_111814


title: BRx-129-2--9-29


title: BRx-111-1--10-19-15


title: auhf1_MH1

description: Gene expression data sperm cells


title: BRx-82_5_030915

extract_protocol:
Single CTCs were isolated from fresh whole blood following leukocyte depletion using the microfluidic CTC-iChip as described in PMID 23552373. Single cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer, and flash frozen in liquid nitrogen.
We used the Clontech SMARTer Ultra Low Input Kit for RNA v3 for cDNA synthesis and the Nextera XT kit for library construction. We spiked in a 1:50,000 dilution of the ERCC RNA Spike-In Mix, which is mix 1, before preparation with the SMARTer kit.

value: positive


title: BRx-82-2--11-13-14


title: BRx-82_6_030915


title: BRx-82_7_030915


title: BRx-82-8--3-9-15


title: BRx-82_3_030915


title: BRx-82_1_030915


title: BRx-82-1--1-12-15


title: BRx-82_2_030915


title: BRx-82_1_012015


title: BRx-82-3--9-15


title: BRx-42_2_110314


title: BRx-42_1_110314


title: BRx-82-2--9-15


title: BRx-42-3--9-29


title: BRx-42-1--9-22


title: BRx-42-1--9-14


title: BRx-42-2--9-14


title: BRx-42-1--9-29


title: BRx-42-1--10-20


title: BRx-82-1--11-13-14


title: BRx-42-2--9-29


title: 24hr RNAseH S 9.6 DRIP Seq

status: Public on Aug 23 2016

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
DESeq_differential_calls.tsv
library strategy: DRIP-seq

data_processing:
Base calling CASAVA v1.8.2
Reads were aligned to genome with bowtie2 -p 10 --qc-filter --no-unal -q -x hg19
Reads aligned over restriction digest intervals with bedtools coverage
DESEq2 (R package) was used to call enriched intervals over input
DESeq2 (R package) was again used to call regions with differential enrichment
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files include raw read counts over the intervals. For DESeq_differential_calls.tsv the file also includes the output from DESEq runs. "T0_DRIP_over_Input", "T2_DRIP_over_Input" and "T24 DRIP over input" refer to the enrichemnt of the mock, 2 hour and 24 hour samples over input respectively. "T0_T24_DRIP", "T0_T2_DRIP" and "T2_T24_DRIP" refer to the DESeq enrichment of 24 hour samples over mock, 2 hour samples over mock, and 2 hour over 24 hour respectively.

growth_protocol: MCF7 cells obtained from ATCC were cultured in DMEM (GIBCO) supplemented with 10% FBS in 5% CO2 at 37 °C.  For estrogen stimulation, MCF7 cells were plated in DMEM with 10% FBS for at minimum of 16 hours before being washed 3 times in 1X PBS. Phenol-red free DMEM (GIBCO) with 10% charcoal-stripped FBS (Invitrogen) was then added for 48 hours prior to the addition of E2 dissolved in EtOH or the vehicle control (100% EtOH).

extract_protocol:
DRIP was performed as described in Ginno et al., 2012. Briefly, DNA was extracted carefully by phenol/chroloform extraction in phase lock tubes, precipitated with EtOH/sodium acetate, washed with 70% EtOH, and resuspended in TE. DNA was digested with a cocktail of restriction enzymes (Bsrg1, EcoR1, HindIII, SspI, XbaI) overnight at 37˚C. For RNase H-treated samples, 8 ug of DNA was treated with RNase H overnight at 37˚C. DNA was purified by standard methods described above. 4ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. Protein A/G sepharose beads were added for 2 hours. Bound beads were washed 3 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 min at 55˚C. DNA was purified as described.
DNA libraries were prepared from 3 pooled DRIPs by sample. Briefly, input and DRIP DNA was sonicated to approximately 300 – 700 bp on a Bioruptor (Diagenode). End repair (NEB E6050S), A-tailing (NEB M0212S), ligation of adapters (NEB M2200S; Affymetrix Prep2Seq Adapters 79800), and PCR amplification were performed by standard methods as described (Ginno et al., 2012). Ampure XP beads (Beckman Coulter, A63880) were used for size selection. Libraries were pooled and sequenced on an Illumina HiSeq machine with single-end 50 bp reads by Elim BioPharm (Hayward, CA).

value: MCF7 breast cancer cells

tag: drug treatment

value: 24 hour treatment with 100 nM estradiol

tag: exogenous treatment

value: RNAseH


title: 24hr S 9.6 DRIP Seq

description:
count_data.tsv, DESeq_differential_calls.tsv
library strategy: DRIP-seq


title: 2hr input S 9.6 DRIP Seq

value: 2 hour treatment with 100 nM estradiol


title: 2hr S 9.6 DRIP Seq


title: 24hr input S 9.6 DRIP Seq


title: Mock input S 9.6 DRIP Seq

value: 24 hour vehicle (ethanol) treatment


title: Mock RNaseH S 9.6 DRIP Seq

value: RNaseH


title: Mock S 9.6 DRIP Seq


title: MI_day -1_27C_sample 3

status: Public on Jun 08 2016

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

institute: University of New South Wales

description: processed data file: day-1_MI_RSEM_genes.counts.matrix

data_processing:
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity > 90%) were removed from the assembled transcriptomes using cd-hit-est
Genome_build: the assembeled transcriptome
Supplementary_files_format_and_content: tab-delimited text files include expression count matrices for each sample at each time point

molecule: polyA RNA

organism: Cladocopium sp. C1

source_name: MI_day -1_27C

growth_protocol: Symbiodinium populations were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). For temperature experiments, 5x10^7 cells (1.5x10^6 cells/ml) of each population were added to eight replicate culture flasks per population. Light was provided at an intensity of 30 µmol quanta m-2 s-1 with a 12 h light-dark cycle.

extract_protocol:
Precisely after six hours of light exposure, 2-4 x 10^6 cells per population were immediately snap frozen in liquid nitrogen within 10 s of removal from experimental incubators and stored at -80°C. Snap frozen cells were thawed at room temperature and pelleted at 4°C (3,000 x g, 5 min). Media was removed, and pellets were lysed in buffer RLT (RNeasy plant mini kit, Qiagen) containing β-mercaptoethanol by bead beating with 0.3 g of 710-1,180 µm acid-washed glass beads (Sigma) using a TissueLyser II (Qiagen) for 90 s at 30 Hz. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) with an added on-column DNase I treatment (Qiagen).
Total RNA (150-500 ng) of each sample was sent to the Australian Genome Research Facility for confirmation of high quality RNA on an Agilent 2100 bioanalyzer, polyA-purification, Illumina TruSeq stranded library preparation, and sequencing on an Illumina HiSeq2500 (single end 100 bp, ~107 reads per sample)

treatment_protocol: Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C for two weeks. Two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C.

tag: population

value: Magnetic Island (MI)

tag: population source

value: Magnetic Island, Great Barrier Reef

tag: thermal tolerance phenotype

value: tolerant

tag: sampling time point

value: day -1

tag: temperature treatment

tag: incubator

value: incubator 2

tag: sample type

value: cell culture

tag: medium

value: filtered sea water + IMK nutrient supplement

tag: coral host from which it was isolated

value: Acropora tenuis


title: BRx-82-2--9-29

tag: donor

tag: ptprc

value: low

tag: er

tag: pr

value: negative


title: BRx-82-1--9-29

value: high

value: positive


title: BRx-82-1--9-15


title: MI_day -1_27C_sample 2

value: incubator 1


title: MI_day -1_27C_sample 1


title: RRBS_88_Mouse_Spleen_F_20w_NORMAL

status: Public on May 03 2015

city: Jerusalem

first: Howard

last: Cedar

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

data_processing:
100 bp paired-end sequencing reads from RRBS were obtained using the Hiseq 2500.  Adapter trimming and quality filtering was performed with the trim_galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)23using default parameters for RRBS analysis.  BSMAP24 was used for read alignment (using genome builds mm9 and hg19) and extraction of single base-resolution methylation levels.  100 bp tiles and DMRs were calculated with the MethylKit package25 using a minimum coverage of 10 per tile, methylation difference of 25%, and q value <= 0.01.  In order to increase sensitivity, DMRs were further filtered for multiple alignments in the genome using blat26 and excluding tiles that were mapped more than once.  The statistical significance of the DMR set was calculated by repeating the above steps on random permutations of male and female samples.  For each permutation the number of DMRs was calculated and a p-value was obtained by measuring the quantile of the original DMRs.  For tissues with at least 8 samples (Liver and Muscle) we included the condition that the difference between the second highest and second lowest values will not exceed 30%.
Genome_build: mm9 for mouse samples; hg19 for human samples
Supplementary_files_format_and_content: 100bpTiles_RRBS_Mouse.txt.gz (contains 100bp tiles methylation data of all the RRBS Mouse samples); 400bpTiles_WG_Mouse.bed.gz (contains 400bp tiles methylation data of all the WGBS Mouse samples); gene_exp.diff.gz (contains the expression data as processed by Cuffdiff).

source_name: Spleen

growth_protocol: C57/bl mice were sacrificed at different ages and their liver, spleen, cerebellum and muscle were isolated.  Mice were anesthetized and either sham operated or castrated by removal of the gonads at the age of 3 or 20 weeks.  Testosterone (5 mg/ml) or vehicle alone was dissolved and then injected into an osmotic pump (Alzet, Model 2004) which was incubated for 48 h in saline at 37°C and then implanted subcutaneously into castrated males or females.  For long-term testosterone administration, the pumps were replaced every 28 days.

extract_protocol:
DNA was isolated from snap-frozen mouse tissues or from frozen human samples (purchased from Cancer Center Tissue and Tumor Bank of UMass Medical School) and incubated in lysis buffer (25  mM Tris-HCl (pH  8), 2  mM EDTA, 0.2% SDS, 200  mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
RRBS libraries were prepared as described (Boyle, P. et al. 2012)

tag: tissue

value: Spleen

tag: strain

tag: gender

value: F

tag: age

tag: condition

value: NORMAL


title: RRBS_86_Mouse_Spleen_F_1w_NORMAL


title: RRBS_10_Mouse_Cerebellum_F_20w_NORMAL

source_name: Cerebellum

value: Cerebellum


title: RRBS_12_Mouse_Liver_F_1w_NORMAL

source_name: Liver

value: Liver


title: aretIR IFM 72hAPF rep2

status: Public on Dec 23 2014

description:
DESeq2_analysisResults_AretIR72h_WTIFM72h_allGenes.txt
DEXSeqResults_AretIR_72h_vs_IFMWT_72h.txt

data_processing:
basecalling and demultiplexing by IMP sequencing core facility (Vienna, Austria) using Illumina software
quality assessment of the raw data using fastqc v0.10.1
filtering and trimming of adapter residues and low quality reads with fthe FASTX toolkit v0.0.13.2 and cutadapt v1.5
Sequenced reads were mapped to the Ensembl BDGP5.25 whole genome using tophat v2.0.11 with parameters -g 1 -p 10
mapped reads were sorted and indexed using samtools v0.1.19
bam files were converted into bigwig for  visualisation on the UCSC server
Counting the mapped reads on the gene and exon level using featureCounts v1.4.2
run the differentail expression analysis using the R package DESeq2 v1.6.1
calculate the differential exon usage with the R package DEXSeq v1.12.1
Genome_build: BDGP5.25 from ENSEMBL
Supplementary_files_format_and_content: tab delimited text files including log2fold change values, pval and padj as calculated by DESeq2 or DEXSeq

source_name: indirect flight muscle

growth_protocol: flies were grown on standard medium using standard fly husbandry protocol

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols

tag: developmental stage

value: 72h APF

tag: muscle type

value: fibrillar

tag: genotype

value: Mef2-Gal4, UAS:GMA::GFP, UAS-T41568 (aretIR)

tag: growth protocol

value: grown at 27C, staged 0h white pre-pupae

tag: barcode

value: GGCTAC


title: aretIR IFM 72hAPF rep1

value: GCCAAT


title: aretIR IFM 30hAPF rep2

description:
DESeq2_analysisResults_AretIR30h_WTIFM30h_allGenes.txt
DEXSeqResults_AretIR_30h_vs_IFMWT_30h.txt

value: 30h APF

value: ACTTGA


title: aretIR IFM 30hAPF rep1

value: GATCAG


title: H3118 CREB knock-down, biological rep3

status: Public on Oct 30 2015

description: Gene expression data from fusion positive salivary gland tumor cells, CREB knock down

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized using MAS5 normalization approach with Affymetrix GCOS software.

source_name: human mucoepidermoid carcinoma cell line derived from parotid, CREB knock-down

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% inactivated fetal bovine serum at 37°C under 5% CO2.

extract_protocol: RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Rneasy Column with in column DNase digestion

treatment_protocol: Cells were infected on two consecutive dates with the viruses in fresh complete medium plus 8ug/ml Polybrene for 6 to 8 hours and replaced with fresh medium. Cells were harvested at 72 hours  after the 1st infection.

tag: cell line

value: fusion-positive H3118 MEC cells

tag: genotype/variataion

value: CREB knock-down


title: H3118 CREB control, biological rep3

description: Gene expression data from fusion positive salivary gland tumor cells, control

source_name: human mucoepidermoid carcinoma cell line derived from parotid, scramble shRNA control

value: scramble shRNA control


title: aretIR IFM 1d rep2

description:
DESeq2_analysisResults_AretIR0d_WTIFM0d_allGenes.txt
DEXSeqResults_AretIR_03d_vs_IFMWT_03d.txt

value: 1d adult

value: grown at 27C from cross until eclosion

value: TTAGGC


title: H3118 CREB control, biological rep2


title: FRTsalmFRT mut IFM 1d rep1

description:
DESeq2_analysisResults_WTIFM0d_salm_allGenes.txt
DESeq2_analysisResults_AretIR0d_salm_allGenes.txt
DEXSeqResults_salm_ko_vs_IFMWT_03d.txt
DEXSeqResults_AretIR_03d_vs_salm_ko.txt

value: tubular converted

value: UAS-Flp;mef2-Gal4,salm1/ FRT-salm-FRT

value: grown at 18C, shifted to 30C at crawling 3rd instar stage until eclosion


title: WT jump muscle 1d rep2

description:
DESeq2_analysisResults_WTIFM0d_jump0d_allGenes.txt
DEXSeqResults_IFMWT_03d_vs_jump_0d.txt

source_name: tergal depressor of the trochanter muscle

value: tubular

value: Mef2-Gal4, UAS:GMA::GFP


title: aretIR IFM 1d rep1

value: fibrillar

value: Mef2-Gal4, UAS:GMA::GFP, UAS-T41568 (aretIR)

value: TAGCTT


title: HSY CREB knock-down, biological rep2

description: Gene expression data from fusion negative salivary gland tumor cells, CREB knock down

source_name: human parotid adenocarcinoma cell line, CREB knock-down

value: fusion-negative HSY parotid adenocarcinoma cells


title: H3118 CREB control, biological rep1


title: WT leg 1d rep1

description:
DESeq2_analysisResults_WTIFM0d_leg0d_allGenes.txt
DEXSeqResults_IFMWT_03d_vs_leg_0d.txt

source_name: whole leg


title: HSY CREB knock-down, biological rep1


title: 46 dpi LCMV Arm, repl.2

status: Public on Jun 01 2015

city: Aurora

first: Jens

last: Eberlein

state: CO

address: 1775 Aurora Court

department: Anesthesiology

institute: University of Colorado Denver

hyb_protocol: standard Affymetrix procedures

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA.)

data_processing: Samples were evaluated for quality control parameters using Gene Chip Operating System from Affymetrix. CEL files were then imported into GeneSpring (Agilent Technologies) and processed using the RMA algorithm.

source_name: adoptively transferred P14 cells isolated from spleen 46 days after LCMV Arm infection.

label_protocol: Ovation Biotin RNA Amplification and Labeling System, NuGen

growth_protocol: Mice were housed at the University of Colorado vivarium on a standard laboratory chow diet

extract_protocol: DNA-digested total RNA was extracted from highly purified p14 TE and TM using a MinElute kit (Qiagen) and RNA integrity confirmed by PicoChip RNA technology (Agilent) according to the manufacturer’s instructions.

treatment_protocol: 5e4 P14 cells were adoptively transferred into congenic BL6/C57 mice and infected with LCMV Armstrong 24 hours later. P14 cells were isolated at the indicated timepoints after infection using FACS.

tag: cell type

value: P14 CD8+ T cells

tag: infection

value: acute lcmv infection

tag: source tissue

value: spleen

tag: time

value: 46 days after infection with LCMV Armstrong

tag: genetic background


title: HSY CREB control, biological rep1

description: Gene expression data from fusion negative salivary gland tumor cells, control

source_name: human parotid adenocarcinoma cell line, scramble shRNA control

value: scramble shRNA control


title: 8 dpi LCMV Arm, repl.2

source_name: adoptively transferred P14 cells isolated from spleen 8 days after LCMV Arm infection.

value: 8 days after infection with LCMV Armstrong


title: H3118 CREB knock-down, biological rep1

value: fusion-positive H3118 MEC cells

value: CREB knock-down


title: WT jump muscle 1d rep1

value: 1d adult

value: grown at 27C from cross until eclosion

value: ACTTGA


title: HSY CREB control, biological rep3


title: HSY CREB control, biological rep2


title: salmIR IFM 1d rep1

value: tubular converted

value: Mef2-Gal4, UAS-T3029 (salmIR)


title: 46 dpi LCMV Arm, repl.4


title: 8 dpi LCMV Arm, repl.3


title: 46 dpi LCMV Arm, repl.1


title: 46 dpi LCMV Arm, repl.3


title: 8 dpi LCMV Arm, repl.1


title: HSY CREB knock-down, biological rep3


title: WT leg 1d rep2

value: tubular

value: Mef2-Gal4, UAS:GMA::GFP

value: GCCAAT


title: WT IFM 30hAPF rep2

value: 30h APF

value: fibrillar

value: grown at 27C, staged 0h white pre-pupae

value: GGCTAC


title: WT IFM 72hAPF rep1

value: 72h APF

value: CGATGT


title: WT IFM 1d rep2

description:
DESeq2_analysisResults_AretIR0d_WTIFM0d_allGenes.txt
DESeq2_analysisResults_WTIFM0d_jump0d_allGenes.txt
DESeq2_analysisResults_WTIFM0d_leg0d_allGenes.txt
DESeq2_analysisResults_WTIFM0d_salm_allGenes.txt
DEXSeqResults_AretIR_03d_vs_IFMWT_03d.txt
DEXSeqResults_IFMWT_03d_vs_jump_0d.txt
DEXSeqResults_IFMWT_03d_vs_leg_0d.txt
DEXSeqResults_salm_ko_vs_IFMWT_03d.txt

value: TGACCA


title: WT IFM 30hAPF rep1

value: ATCACG


title: WT IFM 72hAPF rep2

value: TTAGGC


title: Patient#4_CL#3

status: Public on Jul 11 2014

description: circulating cluster of cells in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: CTCs

extract_protocol:
Blood specimens from 10 patients with metastatic breast cancer were subjected to microfluidic depletion of RBCs and CD45 and CD66b-positive WBCs, leaving single CTCs and small CTC-clusters in the final product (Ozkumur et al., 2013). Unfixed tumor cells were stained for cell surface expression of EpCAM, EGFR, HER2, MET, and the mesenchymal marker CDH11, all conjugated with an Alexa488 fluorophore, as well as stained with TexasRed-conjugated antibodies against CD45, CD14 and CD16 to identify contaminating leukocytes. Individual CTC-clusters (median of 3 cells per cluster) were isolated using a micromanipulator and compared with numerically matched pools of single CTCs from the same specimen, followed by next generation RNA sequencing (SOLiD 5500). Samples that showed high expression of contaminant leukocyte markers at the RNA level were excluded from the analysis.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.

tag: patient

tag: single cells or cluster

value: CL

tag: also known as


title: WT IFM 1d rep1

value: 1d adult

value: grown at 27C from cross until eclosion


title: Patient#4_CL#2


title: Patient#4_CL#1


title: Patient#8_SC#2

description: circulating single cells in lysis buffer

value: SC


title: Patient#8_SC#3


title: Patient#4_SC#1


title: Patient#7_SC#1


title: Patient#8_CL#1


title: Patient#9_SC#1


title: Patient#7_SC#2


title: Patient#5_SC#1


title: Patient#9_CL#1


title: Patient#2_CL#1


title: Patient#7_CL#1


title: Patient#8_SC#1


title: Patient#4_SC#2


title: E75-BDF1-BDF1-5

status: Public on Mar 28 2012

city: San Francisco

first: Michelle

middle: M

last: Chan

institute: UCSF

description: Msp1 digested bisulfite converted genomic DNA

data_processing:
E75-BDF1-BDF1-5.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

growth_protocol: Isolated embryos were cultured in C02 buffered KSOM medium supplemented with amino acids (Millipore) until isolation at a perscribed stage.  Oocytes and embryos were isolated from gonadotropin primed females and sperm collected from the cauda epidinymis of recently mated male mice

extract_protocol:
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries
Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

treatment_protocol: NoPB embryos were subjected to laser assisted polar body biopsy using an 8 mm piezo pipette in batches of 5 embryos in M2 medium microdrops (Millipore) under mineral oil and cultured to the described stage.  ICM was isolated using rabbit anti mouse serum (Sigma Aldrich) and Guinea pig complement serum to ablate the outer trophectoderm of E3.5 blastocysts.  E6.5 and E7.5 embryos were dissected from the implanted decidua in PBS.

tag: strain

value: BDF1 x X1 cross


title: Patient#1_CL#1


title: Patient#3_SC#1


title: E75-BDF1-BDF1-3

data_processing:
E75-BDF1-BDF1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: H3118 CREB knock-down, biological rep2

value: fusion-positive H3118 MEC cells

value: CREB knock-down


title: Patient#8_CL#2


title: E75-BDF1-BDF1-1

data_processing:
E75-BDF1-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: E75-BDF1-BDF1-4

data_processing:
E75-BDF1-BDF1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.