title: G085_B09_232_ERJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ERJ, after resistance-type exercise training

value: vastus lateralis

value: ERJ


title: G085_B11_302_4057_PROM

status: Public on Jul 24 2018

type: RNA

city: Wageningen

first: Roland

last: Hangelbroek

address: Stippeneng 4

department: Division of Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of Affymetrix GeneChip Human Gene 1.1 ST arrays was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.

data_processing: Expression estimates were calculated applying the robust microarray analysis (RMA) algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4057, before or without resistance-type exercise training

label_protocol: One hundred nanogram of total RNA was labelled using Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow‐up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance‐type exercise training.

extract_protocol: Muscle samples were obtained with a 5 mm Bergstrom muscle biopsy needle from the Musculus vastus lateralis, after local anaesthesia of the skin and fascia. Samples were freed from any visible blood and non‐muscle tissue and immediately frozen in liquid nitrogen and then stored at −80°C. All samples were obtained in the morning, in an overnight fasted state, after at least 3 days of no heavy physical activity. Total RNA was isolated from the skeletal muscle tissue by using Trizol reagent (Invitrogen, Breda, Netherlands). Thereafter, RNA was purified using the Qiagen RNeasy Micro kit (Qiagen, Venlo, Netherlands), and RNA quality was checked using an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, Netherlands).

treatment_protocol: Training for both frail and healthy older subjects and consisted of progressive full‐body resistance‐type exercise training. However, the frail older group had training sessions twice per week, whereas the healthy older group trained three times per week. In addition, subjects took a protein or control drink for the duration of the study. The healthy older group received a 15 g portion of milk protein or control supplement at breakfast. The frail older group received a similar drink containing 15 g supplement drink (milk protein or control) at breakfast and lunch.

tag: tissue

tag: Sex

value: M

tag: subjectid

tag: age (yrs)

tag: height (m)

tag: weight (kg)

tag: bmi (kg/m2)

tag: supplement

value: placebo / no supplement

tag: received training

value: no

tag: group

value: Frail (baseline)


title: G085_B08_216_HUP_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HUP, after resistance-type exercise training

value: F

value: HUP

value: protein

value: yes

value: Healthy older (after training)


title: G085_B02_28_MZEPRE_SCRECOVERY_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject MZEpre, before or without resistance-type exercise training

value: MZEpre

value: Young (baseline)


title: G085_B04_138_8063_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8063, after resistance-type exercise training

value: Frail (after training)


title: G085_A12_333_BD34_CAS

source_name: Muscle biopsy from vastus lateralis, isolated from subject BD34, before or without resistance-type exercise training

value: Healthy older (baseline)


title: G085_C01_5_DSMT06

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 06, before or without resistance-type exercise training

value: DSMT 06


title: G085_B01_3_DSMT04

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 04, before or without resistance-type exercise training

value: DSMT 04


title: G085_A09_231_ERJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject ERJ, before or without resistance-type exercise training

value: vastus lateralis


title: G085_A07_207_HAP_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HAP, before or without resistance-type exercise training

value: HAP


title: G085_A06_153_8081_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8081, before or without resistance-type exercise training


title: G085_B06_154_8081_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8081, after resistance-type exercise training


title: G086_D04_69_4043_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4043, before or without resistance-type exercise training

value: M


title: G085_B03_71_4052_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4052, before or without resistance-type exercise training

value: placebo / no supplement


title: G085_A10_239_EVE_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject EVE, before or without resistance-type exercise training

value: EVE


title: G085_A11_301_4004_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4004, before or without resistance-type exercise training

value: no

value: Frail (baseline)


title: G085_B05_146_8075_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8075, after resistance-type exercise training

value: F


title: G085_A08_215_HUP_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HUP, before or without resistance-type exercise training

value: HUP

value: protein


title: G085_A04_137_8063_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8063, before or without resistance-type exercise training

value: yes


title: G085_A03_67_4034_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4034, before or without resistance-type exercise training


title: G084_H10_194_THH_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject THH, after resistance-type exercise training

value: THH

value: Healthy older (after training)


title: G085_A05_145_8075_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8075, before or without resistance-type exercise training


title: G085_A02_27_WLEPRE_SCRECOVERY

source_name: Muscle biopsy from vastus lateralis, isolated from subject WLEpre, before or without resistance-type exercise training

value: WLEpre

value: Young (baseline)


title: G084_H02_48_37IGS_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 37IGS, before or without resistance-type exercise training


title: G084_H08_162_8090_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8090, after resistance-type exercise training

value: Frail (after training)


title: G084_H07_136_8058_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8058, after resistance-type exercise training


title: G084_H04_108_8010_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8010, after resistance-type exercise training


title: G084_H01_32_NMIPRE_SCRECOVERY

source_name: Muscle biopsy from vastus lateralis, isolated from subject NMIpre, before or without resistance-type exercise training

value: NMIpre


title: G084_H09_176_COL_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject COL, after resistance-type exercise training

value: vastus lateralis

value: COL


title: G084_G04_107_8010_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8010, before or without resistance-type exercise training


title: G084_H03_90_THA_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject THA, before or without resistance-type exercise training

value: THA

value: Healthy older (baseline)


title: G084_H05_116_8026_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8026, after resistance-type exercise training

value: M


title: G084_G09_175_COL_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject COL, before or without resistance-type exercise training


title: G084_G08_161_8090_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8090, before or without resistance-type exercise training

value: placebo / no supplement


title: G084_G10_193_THH_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject THH, before or without resistance-type exercise training


title: G084_H06_128_8040_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8040, after resistance-type exercise training


title: HE8W-STR5

type: SRA

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell and these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: TPM(transcripts-per-million mapped reads) data was calculated as the total UMIs for a genes to be divided by the sum of UMIs from each cell and then multiply by 1,000,000

molecule: polyA RNA

source_name: Stromal cell of Week 8

extract_protocol: Chrion were scraped from human  placenta and the remaining villi were collected and minced into small pieces. The tissue were digested with an enzyme cocktail (0.125% trypsin 0.04% Dnase and 0.05% type Ⅳcollagenase) for 8 min twice at 37 ℃. Cell suspension were collected by filtering the ezyme mixture with 70 μm cell strainer and the enzyme reaction were stopped by addition of 5% DMEM. cells were centrifuged at 1200 g at 4 ℃ on a percoll gradient (7 layers: 10%, 20%, 30%, 40%, 50%, 60% and 70%) and cells from 30% - 50% percoll gradient were collected and washed with DMEM. EVT and CTB were sorted with MACS with PE-conjucted HLA-G and CDH1 antibody combined with anti-PE beads,STB were purified with mouth pipette based on their big size from the cell population and the remaning HLA-G and CDH1 double negative cells were stromal cells. For isolation of EVT from the basal plate of the 24 w placenta, basal plate were scaped from the placenta, minced and  digested with the method as described above,finally 24 w EVT were purified by MACs with HLA-G antibody.

treatment_protocol: human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h

tag: cell type

value: Stromal cell

tag: cell population

tag: Stage

value: Week 8


title: HE8W-STR7


title: HE8W-STR2


title: HE8W-STR6


title: HE8W-STR8


title: G084_G06_127_8040_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8040, before or without resistance-type exercise training

value: Frail (baseline)


title: HE8W-EVT9

source_name: Extravillous trophoblast of Week 8

value: Extravillous trophoblast

value: HLA-G+


title: G084_G02_47_32RUL_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 32RUL, before or without resistance-type exercise training

value: no


title: G084_G03_89_HEA_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject HEA, before or without resistance-type exercise training

value: F

value: HEA


title: G084_G07_135_8058_PRE_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8058, before or without resistance-type exercise training

value: yes


title: HE8W-STR4


title: HE8W-STR3


title: HE8W-EVT8


title: G084_F11_308_4081_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4081, before or without resistance-type exercise training


title: G084_G01_30_GTBPRE_IMMOB_3WKS

source_name: Muscle biopsy from vastus lateralis, isolated from subject GTBpre, before or without resistance-type exercise training

value: GTBpre

value: Young (baseline)


title: 8W_STR


title: HE8W-EVT7


title: G084_G05_115_8026_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8026, before or without resistance-type exercise training

value: vastus lateralis

value: protein


title: 8W_EVT


title: G084_F10_192_STE_POST_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject STE, after resistance-type exercise training

value: STE

value: Healthy older (after training)


title: G084_E02_45_02AET_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 02AET, before or without resistance-type exercise training

value: M


title: G084_F06_126_8035_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8035, after resistance-type exercise training

value: placebo / no supplement

value: Frail (after training)


title: G084_F04_106_8009_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8009, after resistance-type exercise training


title: G084_F08_160_8084_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8084, after resistance-type exercise training


title: G084_F07_134_8048_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8048, after resistance-type exercise training


title: G084_E10_191_STE_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject STE, before or without resistance-type exercise training

value: Healthy older (baseline)


title: G084_F01_26_NDOPRE_SCRECOVERY

source_name: Muscle biopsy from vastus lateralis, isolated from subject NDOpre, before or without resistance-type exercise training

value: NDOpre


title: G084_E03_85_BEC_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject BEC, before or without resistance-type exercise training

value: BEC


title: G084_D11_306_4074_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4074, before or without resistance-type exercise training

value: Frail (baseline)


title: G084_E04_105_8009_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8009, before or without resistance-type exercise training


title: G084_F09_174_AUH_POST_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject AUH, after resistance-type exercise training

value: AUH


title: G084_E07_133_8048_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8048, before or without resistance-type exercise training

value: F


title: G084_D10_180_GUJ_POST_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject GUJ, after resistance-type exercise training

value: GUJ


title: G084_F02_46_31CRR_PRO_CARB

source_name: Muscle biopsy from vastus lateralis, isolated from subject 31CRR, before or without resistance-type exercise training

value: no


title: G084_D09_170_8095_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8095, after resistance-type exercise training

value: yes


title: G084_F05_114_8013_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8013, after resistance-type exercise training


title: G084_E06_125_8035_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8035, before or without resistance-type exercise training


title: G084_E09_173_AUH_PRE_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject AUH, before or without resistance-type exercise training


title: G084_F03_86_WET_STOUD_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject WET, before or without resistance-type exercise training

value: WET


title: G084_E08_159_8084_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8084, before or without resistance-type exercise training

value: vastus lateralis


title: G084_D06_120_8028_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8028, after resistance-type exercise training

value: protein


title: G084_D03_84_8074_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8074, before or without resistance-type exercise training


title: G084_D05_112_8012_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8012, after resistance-type exercise training


title: G084_D04_104_8004_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8004, after resistance-type exercise training


title: G084_E01_20_DSMT28

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 28, before or without resistance-type exercise training

value: DSMT 28

value: Young (baseline)


title: G084_E05_113_8013_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8013, before or without resistance-type exercise training

value: M


title: G084_E11_307_4078_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4078, before or without resistance-type exercise training

value: placebo / no supplement


title: G084_D07_132_8046_POST_PROM_2

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8046, after resistance-type exercise training

value: Frail (after training)


title: G084_C07_131_8046_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8046, before or without resistance-type exercise training


title: G084_C09_169_8095_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8095, before or without resistance-type exercise training


title: G084_C10_179_GUJ_PRE_STOUD

source_name: Muscle biopsy from vastus lateralis, isolated from subject GUJ, before or without resistance-type exercise training

value: Healthy older (baseline)


title: G084_C06_119_8028_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8028, before or without resistance-type exercise training


title: G084_C03_70_4046_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4046, before or without resistance-type exercise training


title: G084_C01_17_DSMT24

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 24, before or without resistance-type exercise training

value: DSMT 24


title: G084_C02_40_08ACN_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 08ACN, before or without resistance-type exercise training


title: G084_B02_38_11ETK_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 11ETK, before or without resistance-type exercise training


title: G084_B09_166_8093_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8093, after resistance-type exercise training


title: G084_B05_110_8011_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8011, after resistance-type exercise training


title: G084_B08_156_8082_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8082, after resistance-type exercise training


title: G084_D01_18_DSMT25

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 25, before or without resistance-type exercise training

value: DSMT 25


title: G084_B06_118_8027_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8027, after resistance-type exercise training


title: G084_C11_305_4069_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4069, before or without resistance-type exercise training

value: Frail (baseline)


title: G084_B04_102_8003_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8003, after resistance-type exercise training


title: G084_B03_62_4010_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4010, before or without resistance-type exercise training


title: G084_B07_130_8044_POST_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8044, after resistance-type exercise training


title: G084_D02_42_12AEY_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 12AEY, before or without resistance-type exercise training


title: G084_C05_111_8012_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8012, before or without resistance-type exercise training


title: G084_A08_155_8082_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8082, before or without resistance-type exercise training


title: G084_B01_16_DSMT23

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT 23, before or without resistance-type exercise training

value: DSMT 23


title: G084_A11_303_4058_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4058, before or without resistance-type exercise training


title: G084_A09_165_8093_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8093, before or without resistance-type exercise training

value: F


title: G084_A04_101_8003_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8003, before or without resistance-type exercise training


title: G084_B11_304_4065_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4065, before or without resistance-type exercise training


title: G084_A05_109_8011_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8011, before or without resistance-type exercise training


title: G084_A06_117_8027_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8027, before or without resistance-type exercise training


title: G084_A03_61_4007_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 4007, before or without resistance-type exercise training


title: G084_A07_129_8044_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8044, before or without resistance-type exercise training


title: G084_A01_15_DSMT22

source_name: Muscle biopsy from vastus lateralis, isolated from subject DSMT22, before or without resistance-type exercise training


title: G084_A02_34_06OSN_MEAT_MILK

source_name: Muscle biopsy from vastus lateralis, isolated from subject 06OSN, before or without resistance-type exercise training


title: mfg1Δ/mfg1Δ vs WT  in hyphae condition 3h

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

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

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

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329. Expression array data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: WT under hyphal conditions (YPD 37°C)

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

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads). RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).

treatment_protocol: For ChIP-chip analysis, an overnight cultures in YPD were diluted to OD600nm =0.2 and grown to OD600nm=2 in 40 ml YPD at 30°C.  For gene expression profiling of yeast-form cells, saturated overnight cultures of all strains were diluted to a starting OD600 of 0.2 in 50 ml fresh YPD and grown at 30°C to an OD600of 0.8. Hyphae were induced by growing Candida cells in YPD to the mid-log phase, at which point  10% fetal bovine serum was added and cultures were incubated for 1 or 3h at 37°C . Cultures were harvested by centrifugation at 3,000 × g for 5 minutes, and the pellet rapidly frozen in liquid nitrogen.

tag: strain

tag: condition

value: hyphal condition

tag: time

tag: genotype

value: WT

source_name: mfg1Δ/mfg1Δ (YPD 3h-37°C)


title: flo8Δ/flo8Δ vs WT  in hyphae condition 1h

source_name: flo8Δ/flo8Δ (YPD 1h-37°C)


title: flo8Δ/flo8Δ vs WT  in hyphae condition 3h

source_name: flo8Δ/flo8Δ (YPD 3h-37°C)


title: mfg1Δ/mfg1Δ vs WT  in yeast condition

source_name: WT under yeast conditions (YPD 30°C)

value: yeast condition

source_name: mfg1Δ/mfg1Δ (YPD 30°C)


title: flo8Δ/flo8Δ vs WT  in yeast condition

description:
Arrays are organized in 48 sub-arrays containing 280 spots each.
3 replicates.

source_name: flo8Δ/flo8Δ (YPD 30°C)


title: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ vs WT  in hyphae condition 3h

source_name: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ (YPD 3h-37°C)


title: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ vs WT  in yeast condition

source_name: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ (YPD 30°C)


title: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ vs WT  in hyphae condition 1h

source_name: flo8Δ/ flo8Δ mfg1Δ/mfg1Δ (YPD 1h-37°C)


title: mfg1Δ/mfg1Δ vs WT  in hyphae condition 1h

source_name: mfg1Δ/mfg1Δ (YPD 1h-37°C)


title: Reconstituted BSA#1

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

country: Japan

institute: National Center for Global Health and Medicine

description: CD150+CD41-CD48-Flt3-CD34- LSK cells cultured for 7 days in the reconstituted BSA condition.

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used according to the manufacturer's instruction

scan_protocol: DNA Microarray Scanner (Agilent) was used according to the manufacturer's instruction

data_processing: The scaned images were analyzed with Feature Extraction Ver.9.5.3 (Agilent). Normalization method was 75 percentile shift for each sample.

organism: Mus musculus

source_name: HSC

label_protocol: Gene Expression Hybridization Kit (5188-5242 : Agilent) was used according to the manufacturer's instruction

growth_protocol: HSCs were cultured in SF-O3 medium containing 3ng/mL SCF + 0.1ng/mL TPO in the presence of 4% nBSA or 4% reconstituted BSA for 7 days.

extract_protocol: Fresh or cultured HSCs were sorted into SF-O3 medium and then centrifuged at 340 x g for 5 minutes at 4℃. Cell pellets were lysed in 75uL of RLT buffer plus 1% 2-ME, followed by RNA extraction using Qiagen RNeasy micro kit (74004 : Qiagen) according to the manufacturer's instruction.

treatment_protocol: CD150+CD41-CD48-CD34-Flt3-LSK cells of pooled bone marrow from 10 mice were sorted into SF-O3 medium and subjected to either lysis or 7-day culture.

value: Male

tag: age

value: 10 week old

tag: tissue

value: Bone marrow


title: Reconstituted BSA#2

tag: Sex


title: 16 hour 10% serum

description: CD150+CD41-CD48-Flt3-CD34- LSK cells cultured for 16 hours in the 10% serum condition.

growth_protocol: HSCs were cultured in SF-O3 medium containing 100ng/mL SCF + 100ng/mL TPO in the presence or absence of 10% serum at 37C for 16 hours.

treatment_protocol: CD150+CD41-CD48-CD34-Flt3-LSK cells of pooled bone marrow from 20 mice were sorted into SF-O3 medium and subjected to either lysis or 16-hour culture.


title: 16 hour serum-free

description: CD150+CD41-CD48-Flt3-CD34- LSK cells cultured for 16 hours in the serum-free condition.


title: Genome-wide occupancy of Mfg1p in hyphae condition 3h (R1)

type: genomic

description: Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

molecule: genomic DNA

source_name: WT under hyphal conditions (YPD 37°C)- Input sample

tag: chip antibody

source_name: Mfg1p-TAP under hyphal conditions (YPD 37°C)-ChIP sample

value: IgG Sepharose (GE Healthcare), Sigma catalog # GE17-0969-01


title: 0 hour Fresh

description: Freshly isolated CD150+CD41-CD48-Flt3-CD34- LSK cells.


title: nBSA

description: CD150+CD41-CD48-Flt3-CD34- LSK cells cultured for 7 days in the nBSA condition.


title: Sample_20375_SUBAR

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC

data_processing: From the CEL files, data was generated by correction and normalization parameters using frozen RMA (fRMA). Technical batches were then adjusted using ComBat using the surrogate variable analysis (SVA) package

source_name: Human Peripheral Blood

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

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

tag: phenotype

value: subclinical Acute Rejection


title: Fresh


title: Genome-wide occupancy of Flo8p in hyphae condition 1h (R2)

source_name: Flo8p-TAP under hyphal conditions (YPD 37°C)-ChIP sample


title: Genome-wide occupancy of Mfg1p in hyphae condition 1h (R2)


title: Genome-wide occupancy of Flo8p in hyphae condition 1h (R1)


title: Sample_20240_SUBAR


title: Sample_20300_SUBAR


title: Genome-wide occupancy of Mfg1p in hyphae condition 1h (R1)


title: Genome-wide occupancy of Flo8p in yeast condition (R1)

source_name: WT under yeast conditions (YPD 30°C)- Input sample

source_name: Flo8p-TAP under yeast conditions (YPD 30°C)-ChIP sample


title: Sample_20170_SUBAR


title: Sample_20108_SUBAR


title: Genome-wide occupancy of Flo8p in hyphae condition 3h (R1)


title: Genome-wide occupancy of Mfg1p in hyphae condition 3h (R2)


title: Genome-wide occupancy of Flo8p in yeast condition (R2)


title: Genome-wide occupancy of Mfg1p in yeast condition (R2)

source_name: Mfg1p-TAP under yeast conditions (YPD 30°C)-ChIP sample


title: Sample_20123_SUBAR


title: Genome-wide occupancy of Mfg1p in yeast condition (R1)


title: Sample_20063_SUBAR


title: Sample_20070_SUBAR


title: Sample_20055_SUBAR


title: Sample_20048_SUBAR


title: Genome-wide occupancy of Flo8p in hyphae condition 3h (R2)


title: Sample_20103_SUBAR


title: Sample_20017_SUBAR


title: Sample_20071_SUBAR


title: Sample_20005_SUBAR


title: Sample_20118_SUBAR


title: Sample_20069_SUBAR


title: Sample_20253_SUBAR


title: Sample_20325_TX

value: Transplant eXcellence


title: G084_C04_103_8004_PRE_PROM

source_name: Muscle biopsy from vastus lateralis, isolated from subject 8004, before or without resistance-type exercise training

value: vastus lateralis

value: M

tag: subjectid

tag: age (yrs)

tag: height (m)

tag: weight (kg)

value: placebo / no supplement

value: yes


title: Sample_20316_TX


title: Sample_20340_TX


title: Sample_20250_TX


title: Sample_20337_TX


title: Sample_130326D2PX_SUBAR


title: X170317_PAXGR_H11_150707L3PX


title: Sample_20393_TX


title: Sample_20257_TX


title: Sample_20078_TX


title: X170317_PAXGR_H10_150901L1PX


title: Sample_20249_TX


title: Sample_20308_TX


title: Sample_20387_TX


title: Sample_20186_TX


title: Sample_20255_TX


title: Sample_20350_TX


title: X170317_PAXGR_H12_150813L2PX


title: Sample_20191_TX


title: Sample_20261_TX


title: Sample_20049_TX


title: Sample_20162_TX


title: Sample_20059_TX


title: Sample_20102_TX


title: Sample_20388_TX


title: X170317_PAXGR_H09_150929L1PX


title: X170317_PAXGR_H08_140206D1PX


title: X170317_PAXGR_H06_140225L1PX


title: X170317_PAXGR_H05_160428L1PX


title: Sample_20265_TX


title: X170317_PAXGR_H07_160510L1PX


title: X170317_PAXGR_H04_150115L2PX


title: X170317_PAXGR_H01_140828L2PX


title: X170317_PAXGR_H02_141111L3PX


title: X170317_PAXGR_G12_150623L4PX


title: X170317_PAXGR_H03_140722L3PX


title: X170317_PAXGR_G08_140325L1PX


title: X170317_PAXGR_G06_140619L1PX


title: X170317_PAXGR_G05_160407L3PX


title: X170317_PAXGR_G09_160304L1PX


title: X170317_PAXGR_G01_140708L5PX


title: X170317_PAXGR_G02_141009L1PX


title: X170317_PAXGR_G04_141016L2PX


title: X170317_PAXGR_G07_131219L3PX


title: X170317_PAXGR_F12_150827L3PX


title: X170317_PAXGR_F10_150908L3PX


title: X170317_PAXGR_F07_131205L2PX


title: X170317_PAXGR_G10_150908L1PX


title: X170317_PAXGR_F05_140107B1PX


title: X170317_PAXGR_F04_140930L1PX


title: X170317_PAXGR_F01_150331L1PX


title: X170317_PAXGR_F11_151124L1PX


title: X170317_PAXGR_G11_151119L1PX


title: X170317_PAXGR_E12_151110L4PX


title: X170317_PAXGR_E07_140227L2PX


title: X170317_PAXGR_E09_160209L4PX


title: X170317_PAXGR_F02_140918L1PX


title: X170317_PAXGR_E10_160310L3PX


title: X170317_PAXGR_E04_150205L1PX


title: X170317_PAXGR_E03_141120L1PX


title: X170317_PAXGR_E05_131114B2PX


title: X170317_PAXGR_E01_150120L2PX


title: X170317_PAXGR_D09_151008L1PX


title: X170317_PAXGR_D12_151112L4PX


title: X170317_PAXGR_E11_160121L4PX


title: X170317_PAXGR_E02_140717L3PX


title: X170317_PAXGR_D08_140123D1PX


title: X170317_PAXGR_D11_151027L1PX


title: X170317_PAXGR_D02_150331L2PX


title: X170317_PAXGR_D06_140107D3PX


title: X170317_PAXGR_D03_141014L2PX


title: X170317_PAXGR_C10_160317L1PX


title: X170317_PAXGR_C11_150903L2PX


title: X170317_PAXGR_D07_140619L2PX


title: X170317_PAXGR_C12_151112L5PX


title: X170317_PAXGR_D05_140211L1PX


title: X170317_PAXGR_D01_141104L2PX


title: X170317_PAXGR_C09_160407L2PX


title: X170317_PAXGR_D04_150514L1PX


title: X170317_PAXGR_C04_150305L2PX


title: X170317_PAXGR_C06_131119L2PX


title: X170317_PAXGR_C07_160503L1PX


title: X170317_PAXGR_C08_131212L2PX


title: X170317_PAXGR_C01_141002L3PX


title: X170317_PAXGR_C03_140717L4PX


title: X170317_PAXGR_C05_140327L1PX


title: X170317_PAXGR_G03_150507B2PX


title: X170317_PAXGR_F03_150212B2PX


title: X170317_PAXGR_B10_160308L2PX


title: X170317_PAXGR_B09_140107D2PX


title: X170317_PAXGR_E08_131226L1PX


title: X170317_PAXGR_B07_131219L1PX


title: X170317_PAXGR_B12_151203L2PX


title: X170317_PAXGR_B08_140311L5PX


title: X170317_PAXGR_B05_150519L2PX


title: X170317_PAXGR_B11_151029L2PX


title: X170317_PAXGR_B06_140213L4PX


title: X170317_PAXGR_B04_141218L2PX


title: X170317_PAXGR_A10_151022L5PX


title: X170317_PAXGR_A08_140701L1PX


title: X170317_PAXGR_A07_131121L1PX


title: Sample_170105_PGR_B01_1133101_04

value: subclinical acute rejection

value: peripheral blood


title: X170317_PAXGR_A05_150305L8PX


title: X170317_PAXGR_A09_140130L2PX


title: Sample_170105_PGR_H12_1127724_04


title: Sample_170105_PGR_A07_1137868_04


title: Sample_170105_PGR_D07_1132692_01


title: X170317_PAXGR_A04_141014L3PX


title: X170317_PAXGR_B02_141106L4PX


title: X170317_PAXGR_A03_150212B1PX


title: Sample_161221_PGR_F08_1136188_04


title: Sample_161221_PGR_B09_1134574_04


title: X170317_PAXGR_A06_140410L1PX


title: X170317_PAXGR_A02_141007L2PX


title: X170317_PAXGR_B01_150209L2PX


title: Sample_161221_PGR_B12_1137859_04


title: Sample_170105_PGR_C07_1121127_04


title: X170317_PAXGR_A01_140701L4PX


title: Sample_161221_PGR_D02_1134816_04


title: Sample_161221_PGR_D10_1135228_04


title: Sample_161221_PGR_D12_1136504_04


title: Sample_161221_PGR_B08_1128456_04


title: Sample_161221_PGR_D07_1130906_04


title: X170317_PAXGR_A12_150702L4PX


title: X170317_PAXGR_F06_160428L2PX


title: Sample_161221_PGR_D04_1126941_04


title: Sample_161221_PGR_E03_1127876_04


title: Sample_161221_PGR_H02_1124760_04


title: Sample_161221_PGR_E06_110439_04


title: Sample_161221_PGR_G04_1122539_04


title: Sample_161213_PGR_F10_1142891_04


title: Sample_161213_PGR_E09_1139772_04


title: Sample_161213_PGR_E01_1139768_04


title: Sample_161213_PGR_C03_1128588_04


title: Sample_161213_PGR_F03_1137232_04


title: Sample_161213_PGR_G12_110473_04


title: Sample_161213_PGR_B06_1133106_04


title: Sample_161213_PGR_A04_1134411_04


title: Sample_161209_PGR_D04_1140213_04


title: Sample_161213_PGR_A07_1136192_04


title: Sample_161209_PGR_E09_1139277_04


title: Sample_161213_PGR_A08_1121114_04


title: Sample_161209_PGR_H04_1137227_04


title: Sample_161213_PGR_D01_1128584_04


title: Sample_161213_PGR_A11_1139770_04


title: Sample_161213_PGR_E03_1128586_04


title: Sample_161209_PGR_F03_1125900_04


title: Sample_161209_PGR_D09_1140515_04


title: Sample_161209_PGR_D10_1137960_04


title: Sample_161207_PGR_E04_1140513_04


title: Sample_161207_PGR_H11_1137854_04


title: Sample_161209_PGR_B08_110465_04


title: Sample_161213_PGR_E07_1120149_04


title: Sample_161209_PGR_G04_1136007_04


title: Sample_161207_PGR_D02_1139276_04


title: Sample_161209_PGR_F02_1137853_04


title: Sample_161209_PGR_E06_1126488_04


title: Sample_161209_PGR_F01_1134822_04


title: Sample_161207_PGR_D10_1124573_04


title: Sample_161209_PGR_A01_1121659_04


title: Sample_161209_PGR_C05_1133110_04


title: Sample_161209_PGR_A05_1118965_04


title: Sample_161207_PGR_B11_1128874_04


title: Sample_161130_PGR_D11_1122538_04


title: Sample_161201_PGR_C08_1137360_04


title: Sample_161130_PGR_E09_111714_04


title: Sample_161201_PGR_A10_1134820_04


title: Sample_161207_PGR_B09_1121529_04


title: Sample_161121_PGR_C02_1142200_04


title: Sample_161121_PGR_F07_1128582_04


title: Sample_161117_PGR_D12_1135562_04


title: Sample_161201_PGR_C10_1123025_04


title: Sample_161201_PGR_B10_1133644_04


title: Sample_161121_PGR_C12_1129887_04


title: Sample_161201_PGR_B12_1131003_04


title: Sample_161130_PGR_F07_1122535_04


title: Sample_161130_PGR_B02_1136187_04


title: Sample_161121_PGR_D10_1130245_04


title: Sample_161130_PGR_H05_1135560_04


title: Sample_161121_PGR_A03_1138284_04


title: Sample_161201_PGR_A12_1124087_04


title: Sample_161117_PGR_D08_1122533_04


title: Sample_161117_PGR_F01_1133103_04


title: Sample_161201_PGR_C06_1134415_04


title: Sample_161121_PGR_G12_1140211_04


title: Sample_1124884_04


title: Sample_1118095_01


title: Sample_161117_PGR_E01_1142204_04


title: Sample_161117_PGR_D06_1128141_04


title: Sample_1116363_06


title: Sample_161117_PGR_E06_110467_04


title: Sample_170105_PGR_D02_1135220_04


title: Sample_1116101_05


title: Sample_170105_PGR_D09_1124962_04


title: Sample_1114650_05


title: Sample_170105_PGR_F05_1121523_04


title: Sample_170105_PGR_F10_1118904_04


title: Sample_1105690_06


title: Sample_170105_PGR_E03_1128453_04


title: Sample_170105_PGR_B04_1128858_04


title: Sample_161221_PGR_C08_1138740_04


title: Sample_161221_PGR_C12_1135227_04


title: Sample_170105_PGR_E02_1119855_04


title: Sample_170105_PGR_E06_1136206_04


title: Sample_170105_PGR_C04_1112195_04


title: Sample_161221_PGR_F05_1134587_04


title: Sample_161221_PGR_H07_1137357_04


title: Sample_161221_PGR_H01_1130473_04


title: Sample_161221_PGR_A12_1127730_04


title: Sample_170105_PGR_B11_1123946_04


title: Sample_161221_PGR_C09_1133137_04


title: Sample_161221_PGR_B06_1128455_04


title: Sample_161221_PGR_A08_1138309_04


title: Sample_161221_PGR_D01_1118356_04


title: Sample_161221_PGR_A04_1129335_04


title: Sample_161221_PGR_B03_1125790_04


title: Sample_161213_PGR_F12_1136006_04


title: Sample_161213_PGR_C11_1129066_04


title: Sample_161213_PGR_H09_1125791_04


title: Sample_161221_PGR_F10_1106501_04


title: Sample_161213_PGR_C09_1125793_04


title: Sample_161213_PGR_A05_1124764_04


title: Sample_161221_PGR_G07_1124571_04


title: Sample_161221_PGR_F11_113913_04


title: Sample_161213_PGR_H06_1134419_04


title: Sample_161213_PGR_D05_1141475_04


title: Sample_161213_PGR_B10_1133647_04


title: Sample_161221_PGR_E09_1132826_04


title: Sample_161213_PGR_B11_1134928_04


title: Sample_161213_PGR_H01_1124247_04


title: Sample_161213_PGR_E10_110463_04


title: Sample_161209_PGR_B02_1140536_04


title: Sample_161209_PGR_B01_1139260_04


title: Sample_161209_PGR_E01_1136207_04


title: Sample_161209_PGR_A12_1134819_04


title: Sample_161213_PGR_F11_1120410_04


title: Sample_161209_PGR_B09_1142201_04


title: Sample_161213_PGR_C01_1127210_04


title: Sample_161213_PGR_D12_1124572_04


title: Sample_161213_PGR_G10_1124569_04


title: Sample_161209_PGR_H05_1130249_04


title: Sample_161213_PGR_E12_1120812_04


title: Sample_161209_PGR_A04_1134812_04


title: Sample_161209_PGR_H10_1128143_04


title: Sample_161209_PGR_G03_1116467_04


title: Sample_161209_PGR_H02_1139257_04


title: Sample_161209_PGR_E05_1127879_04


title: Sample_161207_PGR_D04_1139261_04


title: Sample_161207_PGR_A02_1137957_04


title: Sample_161207_PGR_F12_1140650_04


title: Sample_161209_PGR_B06_110464_04


title: Sample_161207_PGR_H06_1140214_04


title: Sample_161209_PGR_H12_1134927_04


title: Sample_161209_PGR_C04_1115284_04


title: Sample_161207_PGR_D12_1137849_04


title: Sample_161207_PGR_B02_1137089_04


title: Sample_161207_PGR_F03_1136160_04


title: Sample_161207_PGR_E02_1132672_04


title: Sample_161207_PGR_A07_1138288_04


title: Sample_161207_PGR_C03_1137234_04


title: Sample_161209_PGR_F08_111713_04


title: Sample_161207_PGR_D05_1127692_04


title: Sample_161207_PGR_E09_1132676_04


title: Sample_161207_PGR_D06_1132675_04


title: Sample_161207_PGR_A06_1137601_04


title: Sample_161207_PGR_G03_1134582_04


title: Sample_161207_PGR_F02_1137603_04


title: Sample_161207_PGR_C07_1134811_04


title: Sample_161207_PGR_B04_1131504_04


title: Sample_161207_PGR_G05_1120148_04


title: Sample_161207_PGR_H09_1124252_04


title: Sample_161207_PGR_F01_1119057_04


title: Sample_161207_PGR_B01_1119853_04


title: Sample_161201_PGR_A11_1142203_04


title: Sample_161207_PGR_G02_1117053_04


title: Sample_161201_PGR_F02_1140514_04


title: Sample_161201_PGR_A08_1139255_04


title: Sample_161207_PGR_A05_110444_04


title: Sample_161201_PGR_D04_1137955_04


title: Sample_161207_PGR_G06_1117177_04


title: Sample_161201_PGR_D03_1136159_04


title: Sample_161201_PGR_H11_1135558_04


title: Sample_161201_PGR_F11_1120639_04


title: Sample_161201_PGR_G05_1119061_04


title: Sample_161201_PGR_G02_1126926_04


title: Sample_161207_PGR_D01_110468_04


title: Sample_161201_PGR_C09_1136485_04


title: Sample_161201_PGR_F01_1124964_04


title: Sample_161201_PGR_F07_1134414_04


title: Sample_161201_PGR_A05_1134576_04


title: Sample_161201_PGR_B03_1127507_04


title: Sample_161201_PGR_B07_1140512_04


title: Sample_161201_PGR_H06_1124963_04


title: Sample_161201_PGR_D05_1137956_04


title: Sample_161201_PGR_H04_1126316_04


title: Sample_161201_PGR_D01_1137229_04


title: Sample_161201_PGR_G07_1126005_04


title: Sample_161201_PGR_C11_1132811_04


title: Sample_161201_PGR_F08_1116622_04


title: Sample_161201_PGR_A06_1125897_04_2


title: Sample_161201_PGR_D09_1128587_04


title: Sample_161130_PGR_F11_1141474_04


title: Sample_161130_PGR_G08_1140207_04


title: Sample_161130_PGR_C01_1139767_04


title: Sample_161130_PGR_A11_1139769_04


title: Sample_161130_PGR_C08_1142892_04


title: Sample_161130_PGR_D09_1134821_04


title: Sample_161130_PGR_B08_1137231_04


title: Sample_161130_PGR_B01_1141470_04


title: Sample_161201_PGR_A09_1121520_04


title: Sample_161130_PGR_E02_1137092_04


title: Sample_161130_PGR_G01_1131004_04


title: Sample_161130_PGR_H10_1135229_04


title: Sample_161130_PGR_F09_1136490_04


title: Sample_161130_PGR_F08_1131594_04


title: Sample_161130_PGR_E08_1131506_04


title: Sample_161130_PGR_E01_1127884_04


title: Sample_161130_PGR_H02_1126001_04


title: Sample_161130_PGR_B11_1119851_04


title: Sample_161130_PGR_C05_1126925_04


title: Sample_161130_PGR_H11_1138287_04


title: Sample_161130_PGR_E11_1127889_04


title: Sample_161130_PGR_D06_1128872_04


title: Sample_161130_PGR_B05_1131606_04


title: Sample_161130_PGR_C02_1127875_04


title: Sample_161130_PGR_D12_1137226_04


title: Sample_161130_PGR_G11_1127508_04


title: Sample_161130_PGR_G03_1122536_04


title: Sample_161130_PGR_F10_1131590_04


title: Sample_161130_PGR_A09_1126490_04


title: Sample_161130_PGR_F06_110441_04


title: Sample_161130_PGR_C03_1117044_04


title: Sample_161130_PGR_A06_110438_04


title: Sample_161130_PGR_F05_110443_04


title: Sample_161121_PGR_G02_1140511_04


title: Sample_161130_PGR_H01_1116090_04


title: Sample_161121_PGR_G06_1141472_04


title: Sample_161121_PGR_D05_1137858_04


title: Sample_161121_PGR_B08_1139254_04


title: Sample_161121_PGR_E07_1137356_04


title: Sample_161121_PGR_H08_1137362_04


title: Sample_161121_PGR_G11_1136010_04


title: Sample_161121_PGR_D08_1134412_04


title: Sample_161121_PGR_B11_1130348_04


title: Sample_161121_PGR_C10_1137090_04


title: Sample_161121_PGR_A11_1133105_04


title: Sample_161121_PGR_F09_1131610_04


title: Sample_161130_PGR_G06_1137091_04


title: Sample_161121_PGR_B12_1123265_04


title: Sample_161121_PGR_H02_1129682_04


title: Sample_161121_PGR_A06_1126937_04


title: Sample_161121_PGR_F04_1124946_04


title: Sample_161121_PGR_A05_1127880_04


title: Sample_161121_PGR_H05_1127882_04


title: Sample_161121_PGR_A04_1127881_04


title: Sample_161121_PGR_C11_1124961_04


title: Sample_161121_PGR_G09_110469_04


title: Sample_161117_PGR_H02_1142887_04


title: Sample_161117_PGR_H12_1139259_04


title: Sample_161121_PGR_A07_1120645_04


title: Sample_161121_PGR_F10_1119067_04


title: Sample_161121_PGR_C04_1119059_04


title: Sample_161121_PGR_D04_1130343_04


title: Sample_161117_PGR_E12_1142890_04


title: Sample_161121_PGR_E10_1128868_04


title: Sample_161117_PGR_E10_1139258_04


title: Sample_161121_PGR_B07_1118078_04


title: Sample_161121_PGR_E05_1119065_04


title: Sample_161121_PGR_B05_1118359_04


title: Sample_161117_PGR_A06_1137600_04


title: Sample_161117_PGR_F04_1134416_04


title: Sample_161117_PGR_B07_1136488_04


title: Sample_161117_PGR_E05_1134566_04


title: Sample_161117_PGR_G08_1137225_04


title: Sample_161117_PGR_G01_1132242_04


title: Sample_161117_PGR_D11_1133099_04


title: Sample_161117_PGR_H07_1139256_04


title: Sample_161117_PGR_F09_1134815_04


title: Sample_161117_PGR_D09_1131607_04


title: Sample_161117_PGR_B09_1133098_04


title: Sample_161117_PGR_B04_1131596_04


title: Sample_161117_PGR_C04_1128876_04


title: Sample_161117_PGR_D01_1128873_04


title: Sample_161117_PGR_H05_1117295_04


title: Sample_161117_PGR_C01_1128871_04


title: Sample_161117_PGR_C07_1119740_04


title: Sample_161117_PGR_D04_1119866_04


title: Sample_1134569_05


title: Sample_161117_PGR_A09_1126930_04


title: Sample_161117_PGR_G03_1117849_04


title: Sample_1124083_04


title: Sample_161117_PGR_A01_110472_04


title: Sample_161117_PGR_A02_110445_04


title: Sample_1124957_05


title: Sample_1124216_04


title: Sample_161117_PGR_F08_1119857_04


title: Sample_161117_PGR_H06_110471_04


title: Sample_1128864_04


title: Sample_161117_PGR_B03_110440_04


title: Sample_1123274_04


title: Sample_1129702_04


title: Sample_1121656_04


title: Sample_1117266_01


title: Sample_161121_PGR_E01_1136005_04


title: Sample_1112915_04


title: Sample_1116627_01


title: Sample_1110282_04


title: Sample_1113999_06


title: Sample_1113328_04


title: Sample_1112264_04


title: Sample_1106752_04


title: Sample_1108703_06


title: Sample_1110265_03


title: Sample_1107532_04


title: Sample_1105463_06


title: Sample_1104563_04


title: Sample_1103754_04


title: Sample_1103436_03


title: Sample_1103032_03


title: Sample_161117_PGR_F10_1131599_04


title: HepaRG_BeP-2uM_72hrs_replicate 1

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (G4858A-072363) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: HepaRG, BeP-2uM, 72hrs, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human liver HepaRG cell line was obtained from Biopredic International (Overland Park, Kansas), and the cells were maintained according to the manufacturer’s recommendations. Briefly, the cells were seeded at a density of 1.3 × 104 cells/cm2 and maintained in William’s E medium supplemented with growth additives for HepaRG cells (Biopredic International) for 14 days. The cells were then differentiated by adding a differentiation supplement (Biopredic International) for an additional 14 days. The medium was changed every other day.

extract_protocol: Total RNA was extracted from HepaRG cells using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Twenty-eight days after the initial seeding, the terminally differentiated HepaRG cells were treated with BaP and BeP at dose 2 µM for 72 hours. Following the treatment, the cells were harvested by mild trypsinization, washed in phosphate-buffered saline, and immediately frozen at −80°C for subsequent analyses.

value: Differentiated HepaRG cells

tag: agent

value: benzo[e]pyrene (B[e]P)

tag: gender

value: Female


title: 6 lncRNA+mRNA

first: Fan

middle: Li

last: juan

state: Beijing

address: 11th Xizhimen south street,Xicheng district

department: Reproductive medical Center

institute: Peking University Peoples' Hospital

description: LncRNA expression at WOI

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: RIF lncRNA+mRNA at WOI

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: patients

value: RIF (recurrent implantation failure)

value: Endometrium

tag: collect time

value: Window of implantation


title: 13 lncRNA+mRNA

description: LncRNA expression at WOI

source_name: Control lncRNA+mRNA at WOI

value: Control


title: 7 lncRNA+mRNA

description: LncRNA expression at WOI


title: 9 lncRNA+mRNA

description: LncRNA expression at WOI


title: 14 lncRNA+mRNA

description: LncRNA expression at WOI


title: HepaRG_BeP-2uM_72hrs_replicate 2

source_name: HepaRG, BeP-2uM, 72hrs, replicate 2

tag: cell type


title: Sample_1106742_04


title: 12 lncRNA+mRNA

description: LncRNA expression at WOI


title: Sample_1103265_04


title: 3 lncRNA+mRNA

description: LncRNA expression at WOI


title: 15 lncRNA+mRNA

description: LncRNA expression at WOI


title: HepaRG_BaP-2uM_72hrs_replicate 1

source_name: HepaRG, BaP-2uM, 72hrs, replicate 1

value: benzo[a]pyrene (B[a]P)


title: 11 lncRNA+mRNA

description: LncRNA expression at WOI


title: 5 lncRNA+mRNA

description: LncRNA expression at WOI


title: Sample_1106515_05


title: Sample_1003267_04


title: HepaRG_BaP-2uM_72hrs_replicate 3

source_name: HepaRG, BaP-2uM, 72hrs, replicate 3


title: HepaRG_BeP-2uM_72hrs_replicate 3

source_name: HepaRG, BeP-2uM, 72hrs, replicate 3


title: HepaRG_72hrs_control_replicate 3

source_name: HepaRG, 72hrs, control, replicate 3


title: 2 lncRNA+mRNA

description: LncRNA expression at WOI


title: 4 lncRNA+mRNA

description: LncRNA expression at WOI


title: MCAL3

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

data_processing:
Sequenced reads have been trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. the reads mapped to mm10 whole genome using tophat v2.1.1 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver, control

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Sequencing libraries were performed by MIT Genome Core using Illumina TruSeq RNA Sample Prep Kit with 1 ug of total RNA.

tag: strain

tag: treatment

value: control

value: Liver

value: 8 week old


title: MEAL3

source_name: Liver, experimental

value: male parent chronically exposed to alcohol


title: MEAL1


title: MCAL1


title: MCAL2


title: HepaRG_BaP-2uM_72hrs_replicate 2

source_name: HepaRG, BaP-2uM, 72hrs, replicate 2


title: UM_28d_30

city: Madison

first: Laura

last: Knoll

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: UW-Madison

data_processing:
Base calling using standard Illumina HiSeq2500 software
The sequenced reads were aligned to the murine genome (GRCm38; database v87; Ensembl), using the Spliced Alignment to a Reference (STAR; v2.5.2b) program. Alignment parameters for STAR were kept at default except for the following: 2 base pair maximum mismatch, 70 base pair minimum intron length, and a 500,000 base pair maximum intron length.
Relative gene expression levels were then estimated using the RNA-seq by Expectation-Maximization (RSEM v1.2.31) program.
Genome_build: GRCm38; database v87; Ensembl
Supplementary_files_format_and_content: File lists genes with respective transcript names giving their total counts along with normalized expression representaed as TPM and FPKM values.

source_name: cerebral cortex

extract_protocol:
Brain tissue was homogenized in Trizol (Ambion) using a pellet pestle (Kontes), and total RNA extracted using phenol/chloroform separation and ethanol precipitation. Illumina TrueSeq RNA Library Prep Kit v2 was used to process mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: CBA/J

value: Uninfected

tag: days post-infection

value: Male


title: UF_90d_18


title: UM_28d_32


title: UM_28d_31


title: UF_90d_17


title: UM_182d_37


title: UM_182d_36


title: MEAL2

tag: tissue

tag: age


title: UF_28d_12

tag: Sex


title: UF_28d_10


title: UF_28d_11


title: UF_180d_23


title: UF_21d_5


title: UF_21d_4


title: UF_90d_16


title: HepaRG_72hrs_control_replicate 1

source_name: HepaRG, 72hrs, control, replicate 1


title: HepaRG_72hrs_control_replicate 2

source_name: HepaRG, 72hrs, control, replicate 2


title: UF_21d_6


title: Lymphocyte-104_Nutlin, replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: PHA-stimulated human T-lymphocytes treated with 10 uM Nutlin-3 for 24 hr

hyb_protocol: 10 μg of fragmented amplified biotin -aRNAs were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: PHA-stimulated human T-lymphocytes from healthy volunteer # 104

label_protocol: According to the manufacturer's protocol (Affymetrix GeneChip 3' IVT Express kit)

growth_protocol: Human lymphocytes were isolated with Histopaque-1077 (Sigma-Aldrich) from the blood of healthy volunteers per IRB#07-E-0023 protocol. T- lymphocytes were activated with 1.5% vol/vol phytohemoagglutinin-M (PHA, Invitrogen) and grown in RPMI supplemented with 10% FBS (Fetal Bovine Serum, Invitrogen, Carlsbad, CA) and maintained at 37°C with 5% CO2. for 48h prior to drug treatment.  Cells were harvested 72h post PHA stimulation and 24h post drug treatment.

extract_protocol: 3-4 million cells were used per each replicate sample.  RNA from PHA-stimulated human T-lymphocytes treated ex vivo with various treatments were extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.

treatment_protocol: for Doxorubicin: 0.3 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs. Doxorubicin was dissolved in water, while Nutlin was dissolved in DMSO.

tag: subject id

value: PHA-stimulated human T-lymphocytes


title: Lymphocyte-104_DXR, replicate 3

description: PHA-stimulated human T-lymphocytes treated with 0.3 ug/ml Doxorubicin for 24 hr


title: Lymphocyte-104_DXR, replicate 1


title: Lymphocyte-104_DMSO, replicate 1

description: PHA-stimulated human T-lymphocytes treated with 0.1% DMSO for 24 hr (control cells)


title: Lymphocyte-104_Nutlin, replicate 3


title: SKOV3_sh_ZNF498_rep3

city: Kyoto

first: Koji

last: Yamanoi

address: 54 Shogoin Kawahara, Sakyo

institute: Kyoto University Graduate School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Adapter and low-quality sequences were removed by cutadapt (v1.2.1). After quality control, poly-A/T sequences were also removed by PRINSEQ (v0.19.2)
The trimmed reads were aligned to the reference human genome (GRCh37/hg19) using TopHat (v2.0.13).
Mapped reads were assembled by Cufflinks (v2.2.1) , and the transcripts across all samples were merged by Cuffmerge. The “fragments per kilo base per million map reads” (FPKM) was calculated with Cuffquant.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit (Qiagen) according to manufacturer's instructions
TruSeq RNA Sample Prep Kit v2 (Illumina) was used for the construction of sequencing libraries.RNA libraries were prepared according to standard Illumina protocols.

tag: cell line

value: human ovarian cancer cell line

tag: genotype/variation


title: Lymphocyte-104_DXR, replicate 2


title: Lymphocyte-90_DXR, replicate 3

source_name: PHA-stimulated human T-lymphocytes from healthy volunteer # 90


title: IM_28d_29

value: T. gondii strain ME49


title: Lymphocyte-90_Nutlin, replicate 1


title: Lymphocyte-104_DMSO, replicate 3


title: SKOV3_sh_ZNF498_rep1


title: Lymphocyte-104_DMSO, replicate 2


title: Lymphocyte-104_Nutlin, replicate 1


title: SKOV3_sh_ZNF498_rep2


title: Lymphocyte-90_Nutlin, replicate 2


title: Lymphocyte-90_DXR, replicate 2


title: Lymphocyte-90_Nutlin, replicate 3


title: Lymphocyte-90_DXR, replicate 1


title: Lymphocyte-90_DMSO, replicate 1


title: IM_28d_27


title: SKOV3_sh_TLE2_rep2


title: Lymphocyte-90_DMSO, replicate 3


title: SKOV3_sh_TLE2_rep1


title: IM_182d_33


title: IM_182d_34


title: SKOV3_sh_ITGB3BP_rep2


title: IF_90d_14


title: IF_90d_13


title: SKOV3_sh_ITGB3BP_rep1


title: Lymphocyte-90_DMSO, replicate 2


title: IF_90d_15


title: SKOV3_sh_TLE2_rep3


title: IF_28d_9


title: SKOV3_sh_ITGB3BP_rep3


title: SKOV3_control_rep3

value: control-sh


title: SKOV3_control_rep1


title: SKOV3_control_rep2


title: Lymphocyte-116_Nutlin_input

library_source: genomic

data_processing:
Sequenced reads were filtered to retain only those with average base quality score >20.
Filtered reads were mapped against the hg19 reference genome (exlcuding haplotype chromosomes) by bowtie v0.12.8 with parameters "-m 1 -v 2".
Alignments were deduplicated with MarkDuplicates.jar from the Picard tools suite v1.86.
For visualization of read depth, each uniquely-mapped non-duplicate read was extended to a length of 200nt.  Depth tracks were subsequently generated via BEDTools genomeCoverageBed v2.17.0 then UCSC utility bedGraphToBigWig .
Peak-calling was performed by SISSRs v1.4 at default parameters.  Any SISSRs peaks smaller than 200nt were re-defined as 200mers centered on the called peak midpoint.
Genome_build: hg19
Supplementary_files_format_and_content: Coverage of mapped reads (extended to 200nt) in bigWig format.
Supplementary_files_format_and_content: Called peaks (extended to minimum size of 200nt) in BED format.

source_name: PHA-stimulated human T-lymphocytes from healthy volunteer # 116

growth_protocol: Human lymphocytes were isolated with Histopaque-1077 (Sigma-Aldrich) from the blood of four healthy volunteers per IRB#07-E-0023 protocol. T- lymphocytes were activated with 1.5% vol/vol phytohemoagglutinin-M (PHA, Invitrogen) and grown in RPMI supplemented with 10% FBS (Fetal Bovine Serum, Invitrogen, Carlsbad, CA) and maintained at 37°C with 5% CO2. for 48h prior to drug treatment.  Cells were harvested 72h post PHA stimulation and 24h post drug treatment.

extract_protocol:
17-30 million cells were used per each ChIP-seq experiment. Treated cells were crosslinked with 1% formaldehyde, then cells were lysed and nuclei were collected.  Chromatin was sheared and immunoprecipitated with p53 DO-1 Ab overnight. Input DNA and p53 ChIP-DNA were reverse crosslinked and purified.
Libraries were prepared the using the Illumina ChIP-seq DNA Sample Prep Kit as per manufacturer's instructions .

tag: chip ab


title: Lymphocyte-116_Nutlin_p53

description: PHA-stimulated human T-lymphocytes treated with 10 uM Nutlin-3 for 24 hr and ChIP with p53

value: p53 DO-1 (Santa Cruz, sc-126)


title: CH1_sh_VPS45_rep3


title: test1 YAP

city: shanghai

first: Jing

last: Wang

address: 639 Zhizaoju Road

department: Depart of Plastic & Reconstructive Surgery

institute: Shanghai 9th People's Hospital, School of Medicine, Shanghai JiaoTong University

description: Chip-chip with YAP in mechancial streched interfollicular epidermal stem cells.

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
scaled, log2 (ChIP/Input) ratio in gff files

source_name: YAP ChIP DNA from mechanical stretched cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: interfollicular epidermal stem cells were cultured on the collagen I coated silicon rubber membrane for 3 days to 50% confluency.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 0.5 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by twelve 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 30 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) over night at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 5 min at  4C; low-salt buffer (250 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: Cells were cultured on the flexceable silicon membrane and subjected to the mechanical stretched.Cyclic mechanical tension (CMT) at 0.5 Hz sinusoidal curve at 10% elongation was applied using an FX-5000T™ Flexercell® Tension Plus™ unit (Flexcell International Corporation).

value: interfollicular epidermal stem cells

tag: condition

value: mechanical stretched for 3 hours

source_name: Input DNA from mechanical stretched interfollicular epidermal stem cells .


title: IF_28d_7

tag: agent

value: Female


title: IF_28d_8


title: ctrl1 YAP

description: Chip-chip with YAP in mechancial unstreched interfollicular epidermal stem cells.

source_name: YAP ChIP DNA from mechanical unstretched cells

treatment_protocol: Cells were cultured on the same plates in the same incubator with the mechanical stretched groups but not subjected to stretch.

value: mechanical unstretched

source_name: Input DNA from interfollicular epidermal stem cells mechanical unstretched.


title: test2 YAP


title: Lymphocyte-116_DXR_p53

description: PHA-stimulated human T-lymphocytes treated with 0.3 ug/ml Doxorubicin for 24 hr and ChIP with p53


title: IF_21d_3


title: CH1_sh_VPS45_rep2


title: Lymphocyte-116_DMSO_p53

description: PHA-stimulated human T-lymphocytes treated with 0.1% DMSO for 24 hr and ChIP with p53 (control cells)


title: Lymphocyte-116_DXR_input


title: Lymphocyte-116_DMSO_input


title: ctrl2 YAP


title: CH1_sh_VPS45_rep1


title: CH1_sh_ZNF691_rep3


title: UF_180d_22


title: CH1_sh_ZNF691_rep2


title: Lymphocyte-104_DXR_p53


title: IF_21d_2


title: Lymphocyte-104_Nutlin_p53


title: Lymphocyte-104_Nutlin_input


title: Lymphocyte-104_DMSO_p53


title: IF_180d_21


title: IF_180d_20


title: Lymphocyte-104_DMSO_input


title: IF_180d_19


title: Lymphocyte-90_Nutlin_p53


title: Lymphocyte-90_Nutlin_input


title: Lymphocyte-90_DXR_input


title: CH1_sh_MSL3_rep2


title: Lymphocyte-90_DXR_p53


title: IF_21d_1


title: Lymphocyte-104_DXR_input


title: Lymphocyte-90_DMSO_p53


title: Lymphocyte-90_DMSO_input


title: CH1_sh_MSL3_rep1


title: Lymphocyte-45_Nutlin_p53

source_name: PHA-stimulated human T-lymphocytes from healthy volunteer # 45


title: Lymphocyte-45_DXR_p53


title: Lymphocyte-45_Nutlin_input


title: CH1_control_rep1


title: Lymphocyte-45_DMSO_input


title: CH1_control_rep2


title: Lymphocyte-45_DMSO_p53


title: CH1_sh_ZNF691_rep1


title: CH1_sh_MSL3_rep3


title: S33

city: Leiden

first: Janine

last: Melsen

address: Albinusdreef 2

department: Pediatrics

institute: LUMC

description: normalizedCountsTab.tab

data_processing:
FastQ files for each sample were generated using CASAVA version 1.8.4 software (Illumina).
In order to detect and remove the sequencing adaptors in the FastQ files, FASTQC version 0.10.0 and the cutadapt tool (version 1.4.2) were used, respectively.
Base quality trimming was performed using the sickle tool (version 1.200).
RNA paired-end reads were aligned to the Homo Sapiens (Human) reference genome version hg19 (GSNAP version 2014-05-15; npaths=1, quit_if_excessive=TRUE and novel splicing has been set to True).
The samtools tool (version 0.1.19-44428cd) was applied to compress, index and name-sort the resulting alignment file.
The count table, summarizing the total uniquely aligned reads per gene per sample, was generated using htseq-count (HTSeq suite version 0.6.1p1).
NKG2A+ and NKG2A- fractions of blood CD56dim and bone marrow ltNK samples were proportionally pooled (dummy samples were generated). Dummy samples were made for pools of the following sample pairs: [S1,S2], [S4,S5], [S15,S16], [S18,S19], [S22,S23], [S25,S26], [S29,S30], [S32,S33].
The read counts were normalized for library size with the ‘voom’ function of the limma package. Genes with averaged normalized counts below 4 counts per million of uniquely mapped reads (CPM) were excluded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes log2 normalized CPM values for each sample (including dummy samples).

source_name: bone marrow

growth_protocol: With approval of the institutional review board (P08.001), residual paired bone marrow and blood samples from 4 healthy bone marrow donors were used for RNA sequencing after informed consent was provided.

extract_protocol:
The different NK cell populations were FACS-purified on an ARIAIII cell sorter (Becton Dickinson (BD), Franklin Lakes, NJ, US). The gating strategy is depicted in Fig. 1A. The NK cell populations were collected in NucleoSpin RA1 lysis buffer (Machery Nagel, Düren, DE) and stored at -80oC prior to analyses. The total numbers of cells analyzed for each purified NK cell population are provided in Table S4. Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey Nagel), according to the instructions of the manufacturer. RNA concentration was measured using the Qubit (Thermo Fisher Scientific, Waltham, MA, US), and RNA integrity was analyzed using RNA Pico chips on 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, US). The RNA was converted to cDNA and pre-amplified using the SMARTer Ultra Low RNA kit (Clontech Laboratories, Montain View, CA, US) using 0.5-2ng total RNA input.
A sequencing library was generated from 1ng (Qubit measured) amplified cDNA using the Illumina Nextera XT kit (Illumina, San Diego, CA, US).

treatment_protocol: Bone marrow aspirates and blood were collected in EDTA tubes. Mononuclear cells  were isolated by Ficoll-Isopaque (Leiden University Medical Center Pharmacy, Leiden, NL) density gradient centrifugation and NK cells were enriched using the MACS untouched NK cell isolation kit (Miltenyi Biotec, Bergisch Gladbach, DE) according to manufacturers’ instructions. Lymphocytes were stained for surface markers with the antibodies listed in Table S3.

value: bone marrow

tag: nk cell type

value: ltNK

tag: nkg2a status

value: min

tag: donor


title: S35

description: normalizedCountsTab.tab


title: S34

description: normalizedCountsTab.tab


title: S32

description: normalizedCountsTab.tab

value: plus


title: CH1_control_rep3

tag: cell type


title: Lymphocyte-45_DXR_input


title: S31

description: normalizedCountsTab.tab

source_name: blood

value: blood


title: S30

description: normalizedCountsTab.tab


title: S28

description: normalizedCountsTab.tab


title: S27

description: normalizedCountsTab.tab


title: Cervix HPV16 idat 5826629088 rep2

city: Cambridge

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with CLC Genomics Workbench v4.8

source_name: Human cervix

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: cervix

value: human cervical keratinicoytes

tag: infection


title: Cervix HPV16 idat 5826629088 rep1

description: replicate 1


title: Cervix HPV16 idat 5885320010 rep2

description: replicate 2


title: S26

description: normalizedCountsTab.tab


title: S25

description: normalizedCountsTab.tab


title: S24

description: normalizedCountsTab.tab


title: Cervix Primary idat 5885320008 rep2

description: replicate 2


title: Cervix HPV16 idat 5885320010 rep1

description: replicate 1


title: Cervix Primary idat 5826629064 rep2

description: replicate 2


title: Cervix HPV16 idat 5885320008 rep2

description: replicate 2


title: Cervix Primary idat 5885320008 rep1

description: replicate 1


title: Cervix Primary idat 5885320010 rep1

description: replicate 1


title: S23

description: normalizedCountsTab.tab


title: Cervix HPV16 idat 5885320008 rep1

description: replicate 1


title: S29

description: normalizedCountsTab.tab


title: S21

description: normalizedCountsTab.tab


title: S22

description: normalizedCountsTab.tab


title: S20

description: normalizedCountsTab.tab


title: S19

description: normalizedCountsTab.tab


title: IM_28d_28

value: CBA/J

value: Male


title: S18

description: normalizedCountsTab.tab


title: S17

description: normalizedCountsTab.tab


title: Cervix Primary idat 5885320010 rep2

description: replicate 2


title: Fibroblasts, 23 years old

city: Yokohama

first: Kazuyuki

last: Yo

state: Kanagawa

address: 560 Kashio-cho, Totsuka-ku

department: Skin Research Department

institute: POLA Chemical Industries, Inc.

description: Gene expression in fibroblasts taken from 23 years old donor's abdominal skin

hyb_protocol: According to manufature's protocol using Gene Expression Hybridization Kit

scan_protocol: According to manufature's protocol using DNA Microarray Scanner

data_processing: Agilent Feature Extraction Ver.9.5.3 was used for analyzing scanned images. The method of baseline to median of all sample was employed for for normalization using Agilent GeneSpringGX11.

source_name: Fibroblasts taken from 23 years old donor's abdominal skin

label_protocol: After quality check, 100 ng of each sample was amplified and transcribed into fluorescent cRNA using Low Input Quick Amp Labeling Kit (Agilent)

growth_protocol: Primary human dermal fibroblasts taken from young (23 years old) and aged (70 years old) donors' abdomen were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin at 37℃ with 5% CO2.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) following manufacture's protocol, then quantified using a NanoDrop-1000 spectrophotometer. RNA integrity was assessed by 2100 Bioanalyzer.

value: Primary human dermal fibroblasts

tag: gender

value: female


title: L_Group_1

city: Jinan

first: X.

last: Xu

state: Shandong

address: Wenhuaxi Road 107

department: Department of Otolaryngology

institute: Qilu hospital of Shandong university

description: miRNA profile in FFPE tissue from patient (#1) with hypopharyngeal carcinoma who still survived at the time of research

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA,Release 21.0(8*60K,Design ID:070156) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: FFPE tissue of hypopharyngeal carcinoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by RecoverAll Total Nucleic Acid Isolation Kit for FFPE (AM1975) following the manufacturer's instructions.

treatment_protocol: All patients underwent surgery and chemoradiotherapy,

value: hypopharyngeal carcinoma

tag: survival status

value: Survived

tag: survival time (month)


title: L_Group_3

description: miRNA profile in FFPE tissue from patient (#3) with hypopharyngeal carcinoma who still survived at the time of research

tag: tissue


title: S16

description: normalizedCountsTab.tab


title: L_Group_2

description: miRNA profile in FFPE tissue from patient (#2) with hypopharyngeal carcinoma who still survived at the time of research


title: S15

description: normalizedCountsTab.tab


title: CRS_6625

city: Baltimore

first: Hailun

address: 1550 Orleans Street

institute: Johns Hopkins University

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse lung tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

treatment_protocol: Add doxycycline in drinking water to induce KrasG12D and EMT genes expression

tag: strain

value: FVBN

tag: mutation


title: CRS_7499


title: CRS_6769


title: S7

description: normalizedCountsTab.tab


title: Cervix Primary idat 5826629064 rep1

description: replicate 1


title: Fibroblasts, 70 years old

description: Gene expression in fibroblasts taken from 70 years old donor's abdominal skin

source_name: Fibroblasts taken from 70 years old donor's abdominal skin

tag: age


title: CRT_2874


title: S5

description: normalizedCountsTab.tab


title: CRT_7824


title: L_Group_4

description: miRNA profile in FFPE tissue from patient (#4) with hypopharyngeal carcinoma who still survived at the time of research


title: D_Group_3

description: miRNA profile in FFPE tissue from patient (#3) with hypopharyngeal carcinoma who died at the time of research

value: Dead


title: 2_deletion

city: Nashville

first: Antonis

last: Rokas

address: VU Station B 35-1364

department: Biological Sciences

institute: Vanderbilt University

description:
ChIP DNA from wetA deletion spores used as the control for the second ChIP experiment
2_all_peaks.narrowPeak

data_processing:
Reads were trimmed using version 0.36 of Trimmomatic.
Version 0.7.15 of BWA-MEM was used to map reads to the A. nidulans (A4) genome.
SAM files were converted to the BAM format using version 1.3 of SAMtools.
BAM files were sorted and then reads with any of the following flags were removed: unmapped, secondary alignment, or supplementary mapped read.
Reads with a MAPQ score of 0 were also removed.
Duplicate reads were removed using the rmdup command in SAMtools, and samples were pooled using the merge command in SAMtools.
Extension sizes were calculated using SPP.
Version 2.1.1.20160309 of MACS2 with the settings –g 2.93e7 –s 101 --nomodel --extsize was used to call peaks.
Genome_build: FungiDB-32_AnidulansFGSCA4
Supplementary_files_format_and_content: Each processed data file is in narrowPeak format (http://www.genome.ucsc.edu/FAQ/FAQformat.html) and contains all peaks called by MACS2

organism: Aspergillus nidulans

source_name: 2-day-old spores

extract_protocol:
109 conidia were cross-linked with 1% formaldehyde, lysed and broken as described in Park and Yu, 2012. Cell lysates were sonicated to shear DNA to 300-500 bp in length and were immunoprecipitated with the rabbit anti-WetA polyclonal antibody.
Libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina, San Diego, CA), and sequenced on a HiSeq2500 with single reads of 101 bp.

tag: antibody

value: WetA polyclonal antibod


title: 2_WT

description:
ChIP DNA from wild type spores used as the experimental sample for the second ChIP experiment
2_all_peaks.narrowPeak


title: nidu_dwetA

data_processing:
genome build:  FungiDB-32_AnidulansFGSCA4
Mapping of the raw sequence reads to the genome was carried out with version 2.1.1 of Tophat2, and the default settings were used except that the max intron length was set to 4,000 bases (--max-intron-length 4000).
The alignment BAM files were compared against the gene annotation GFF file, and raw counts for the number of reads mapping to each gene were generated using version 0.6.1p1 of HTSeq-count.
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each gene in each sample

extract_protocol:
2-day-old conidia of WT and DwetA strains were harvested from solid minimal media
mRNA was extracted from total RNA using poly-A selection, followed by RNA fragmentation. The strand-specific library was constructed by first-strand cDNA synthesis using random primers, sample cleanup, and second-strand synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to the cDNA fragments followed by ligation of the adapters. The final cDNA library was achieved by further purification and enrichment with PCR

tag: genotype/variation

value: wetA deletion mutant


title: D_Group_5

description: miRNA profile in FFPE tissue from patient (#5) with hypopharyngeal carcinoma who died at the time of research


title: CRT_3178


title: nidu_WT

value: Wild Type


title: D_Group_1

description: miRNA profile in FFPE tissue from patient (#1) with hypopharyngeal carcinoma who died at the time of research


title: CR_2873


title: D_Group_2

description: miRNA profile in FFPE tissue from patient (#2) with hypopharyngeal carcinoma who died at the time of research


title: CR_6771


title: CR_2871


title: Patient 6

city: Chang Sha

first: Chen

last: Hequn

address: xiangya road

institute: Xiangya Hospital, Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

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 with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Normal renal papillary tissues

label_protocol: Sample labeling and array hybridization were performed according to 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). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: patients with renal tumor who underwent nephrectomy

tag: Sex

value: Female


title: S2

description: normalizedCountsTab.tab

value: min


title: S3

description: normalizedCountsTab.tab

value: blood


title: S6

description: normalizedCountsTab.tab

value: bone marrow


title: 1_input

description:
input DNA used as a control for the first ChIP experiment
1_all_peaks.narrowPeak

value: input


title: fumi_WT

data_processing:
genome build:  FungiDB-32_AfumigatusAf293
Mapping of the raw sequence reads to the genome was carried out with version 2.1.1 of Tophat2, and the default settings were used except that the max intron length was set to 4,000 bases (--max-intron-length 4000).
The alignment BAM files were compared against the gene annotation GFF file, and raw counts for the number of reads mapping to each gene were generated using version 0.6.1p1 of HTSeq-count.
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each gene in each sample

organism: Aspergillus fumigatus


title: Patient 4

source_name: Randall’s plaques tissues of CaOx renal stones patients

value: CaOx renal stones patients


title: S1

description: normalizedCountsTab.tab

value: plus


title: 1_ChIP

description:
ChIP DNA used as the experimental sample for the first ChIP experiment
1_all_peaks.narrowPeak


title: S4

description: normalizedCountsTab.tab

value: ltNK


title: fumi_dwetA


title: Patient 3

value: Male


title: Patient 2


title: Patient 5


title: AB4171

status: Public on Jul 23 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
POU2F3_WT_CD45+Il25r+_mouse36
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample. Meta data file associating each single cell with its amplification batch and index sorting readouts is available on the series record in the file "metadata.txt".

source_name: Thymus

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Thymus: Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

value: Thymus

tag: selection marker

tag: treatment

value: untreated

tag: mouse age

value: 4-6 weeks


title: AB4381

description:
Thymic_CD45+ Il25r+_mouse39
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4181

description:
POU2F3_KO_CD45+Il25r+_mouse37
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4383


title: AB4385

description:
Thymic_CD45+ Il25r+_mouse40
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4184

description:
POU2F3_KO_CD45+Il25r+_mouse38
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4389


title: AB4386


title: AB4387


title: AB4170

description:
POU2F3_WT_CD45+Il25r+_mouse35
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4388


title: Patient 1


title: AB4172


title: AB4183


title: AB4382


title: AB4384


title: AB4168

description:
POU2F3_WT_CD45+Il25r+_mouse34
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB4167


title: AB4182


title: AB3988

description:
Thymic_CD45+ Il25r+_mouse33
paired-end sequencing.  Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB3990


title: AB3987


title: AB4169


title: E15.5_Liver_Pdx1-Cre_1_02

city: Beijing

first: Cheng-ran

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description:
Sample 672
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz

data_processing:
Bulk-cell RNA-seq (Sample 001-016)
Sequencing reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat (v2.1.0) with parameter "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2".
Reads aligned to genes were counted by HTSeq (v 0.6.0) with parameters "-f bam -r pos -s reverse -a 30".
Reads of biological replicates were pooled.
Gene expression levels were quantified as reads per kilobase of longest transcript per million mapped reads (RPKM).
Single-cell RNA-seq (Sample 023-541, 568-586, 607-631, 671-674)
Sequencing reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat (v2.1.0) with parameter "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq".
Reads aligned to genes were counted by HTSeq (v 0.6.0) with parameters "-f bam -r pos -s no -a 30".
Gene expression levels were quantified as reads per kilobase of longest transcript per million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and RPKM values for each sample

source_name: Liver

extract_protocol:
Bulk-cell RNA-seq (Sample 001-016)
For E10.5, E14.5 and E17.5 dorsal and ventral pancreases, a total of 5-7 x 10e4 sorted cells were used to isolate total RNA using the Rneasy Micro Kit (Qiagen, 74004). Poly(A) RNA was further purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) according to the manufacturer's instructions.
Single-cell RNA-seq (Sample 023-541, 568-586, 607-631, 671-674)
Libraries were prepared according the Smart-seq2 method as previously reported (Picelli et al., 2014).
2 ng cDNA were subjected to prepare the libraries using the TruePrep DNA Library Prep Kit (TD502, Vazyme).

tag: embryonic day

tag: culture time

tag: sorting

value: Pdx1-Cre, ROSA26-tdTomato+


title: E15.5_Liver_Pdx1-Cre_1_04

description:
Sample 674
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E15.5_Liver_Pdx1-Cre_1_03

description:
Sample 673
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: AB3989


title: E15.5_Liver_Pdx1-Cre_1_01

description:
Sample 671
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz