title: H8_69: Carotid artery_16

description: H8_69: H8_69: Carotid artery_16

source_name: Atherosclerotic carotid artery

value: Atherosclerotic carotid artery


title: H93_96: Carotid artery_48

status: Public on Mar 07 2018

type: RNA

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

description: H93_96: H93_96: Carotid artery_48

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression microarrays (G4851B) 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). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, 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 (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to remove probes with low intensity values.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Macherey Nagel NucleoSpin columns. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2200 TapeStation system.

tag: tissue

tag: gender

value: female


title: GroupA_276 Fluoxetine exposed prelimbic cortex

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45oC.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: CEL files were preprocessed with RMA method provided by affy package, and called differentially expressed genes using limma package in R.

label: biotin

organism: Mus musculus

source_name: Prelimbic cortex isolated from prenatally Fluoxetine exposed male mice (postnatal day 90).

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT PLUS Reagent Kit User Manual, Affymetrix).

extract_protocol: Total RNA was extracted from punched samples of the mPFC using a RNeasy kit (Qiagen) followed by cDNA synthesis using a Quantitect Reverse Transcription kit (Qiagen).

value: Prelimbic cortex

tag: treatment

value: Fluoxetine exposed

value: male


title: GroupA_280 Fluoxetine exposed prelimbic cortex


title: H88_110: Femoral artery_43

description: H88_110: H88_110: Femoral artery_43

source_name: Atherosclerotic femoral artery

value: Atherosclerotic femoral artery


title: H90_62: Infra-popliteal artery_4

description: H90_62: H90_62: Infra-popliteal artery_4

source_name: Atherosclerotic infra-popliteal artery

value: Atherosclerotic infra-popliteal artery


title: 200 µM, experiment 2

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established neuroblastoma cell line after treatment with cobalt chloride

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on Human Exon 1.0ST Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using the RMA algorithm with Affymetrix Expression Console

source_name: SHSY5Y cells, 200µM CoCl2, exp2

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

growth_protocol: SHSY5Y cells were grown under standard conditions

extract_protocol: RNA was isolated using GeneMatrix Universal RNA Kit (roboklon, Berlin, Germany)

treatment_protocol: Cells were treated for 24 hrs with 0, 100, or 200 µM cobalt chloride

tag: cell type

value: neuroblastoma cell line

tag: cell line


title: 100 µM, experiment 1

source_name: SHSY5Y cells, 100µM CoCl2, exp1


title: H89_74: Femoral artery_29

description: H89_74: H89_74: Femoral artery_29


title: H87_171: Femoral artery_22

description: H87_171: H87_171: Femoral artery_22


title: H99_191: Infra-popliteal artery_8

description: H99_191: H99_191: Infra-popliteal artery_8


title: H74_65: Femoral artery_Control 17

description: H74_65: H74_65: Femoral artery_Control 17

source_name: Control femoral artery

value: Control femoral artery


title: H73_29: Infra-popliteal artery_11

description: H73_29: H73_29: Infra-popliteal artery_11


title: H66_91: Femoral artery_Control 06

description: H66_91: H66_91: Femoral artery_Control 06


title: H84_12: Femoral artery_14

description: H84_12: H84_12: Femoral artery_14


title: H72_198: Carotid artery_Control 22

description: H72_198: H72_198: Carotid artery_Control 22

source_name: Control carotid artery

value: Control carotid artery


title: H69_20: Carotid artery_37

description: H69_20: H69_20: Carotid artery_37


description: H65_94: H65_94: Infra-popliteal artery_Control 23

source_name: Control infra-popliteal artery

value: Control infra-popliteal artery


title: H60_186: Femoral artery_2

description: H60_186: H60_186: Femoral artery_2


title: H59_192: Infra-popliteal artery_5

description: H59_192: H59_192: Infra-popliteal artery_5


title: H53_52: Femoral artery_15

description: H53_52: H53_52: Femoral artery_15


title: H34_26b: Carotid artery_10

description: H34_26b: H34_26b: Carotid artery_10


title: H38_76: Infra-popliteal artery_9

description: H38_76: H38_76: Infra-popliteal artery_9


title: H40_24: Infra-popliteal artery_17

description: H40_24: H40_24: Infra-popliteal artery_17


title: H28_61: Femoral artery_17

description: H28_61: H28_61: Femoral artery_17


title: H51_151: Infra-popliteal artery_7

description: H51_151: H51_151: Infra-popliteal artery_7


title: H58_102: Carotid artery_21

description: H58_102: H58_102: Carotid artery_21


description: H61_155: H61_155: Infra-popliteal artery_Control 10


title: H35_97: Carotid artery_38

description: H35_97: H35_97: Carotid artery_38


title: H55_63: Carotid artery_Control 21

description: H55_63: H55_63: Carotid artery_Control 21


title: H184_196: Infra-popliteal artery_17

description: H184_196: H184_196: Infra-popliteal artery_17


title: H6_4: Femoral artery_Control 25

description: H6_4: H6_4: Femoral artery_Control 25


title: H52_141: Carotid artery_44

description: H52_141: H52_141: Carotid artery_44


title: H190_44: Femoral artery_Control 05

description: H190_44: H190_44: Femoral artery_Control 05


title: H185_163: Carotid artery_6

description: H185_163: H185_163: Carotid artery_6


title: H26_47: Carotid artery_26

description: H26_47: H26_47: Carotid artery_26


title: H191_82: Carotid artery_29

description: H191_82: H191_82: Carotid artery_29


title: H182_185: Femoral artery_27

description: H182_185: H182_185: Femoral artery_27


title: H21_53: Infra-popliteal artery_3

description: H21_53: H21_53: Infra-popliteal artery_3


title: H23_9: Carotid artery_5

description: H23_9: H23_9: Carotid artery_5


title: H27_183: Femoral artery_32

description: H27_183: H27_183: Femoral artery_32


description: H194_201: H194_201: Infra-popliteal artery_Control 11


title: H22_98: Carotid artery_92

description: H22_98: H22_98: Carotid artery_92


description: H36_173: H36_173: Infra-popliteal artery_Control 08


title: H29_33: Femoral artery_Control 11

description: H29_33: H29_33: Femoral artery_Control 11


title: H32_10: Carotid artery_81

description: H32_10: H32_10: Carotid artery_81


title: H177_153: Femoral artery_Control 22

description: H177_153: H177_153: Femoral artery_Control 22


title: H155_103: Carotid artery_33

description: H155_103: H155_103: Carotid artery_33


description: H154_194: H154_194: Infra-popliteal artery_Control 11


title: H162_59: Carotid artery_70

description: H162_59: H162_59: Carotid artery_70


description: H149_174: H149_174: Infra-popliteal artery_Control 18


title: H179_158: Carotid artery_22

description: H179_158: H179_158: Carotid artery_22


title: H18_75: Infra-popliteal artery_20

description: H18_75: H18_75: Infra-popliteal artery_20


title: H157_184: Femoral artery_40

description: H157_184: H157_184: Femoral artery_40


title: H168_182: Femoral artery_4

description: H168_182: H168_182: Femoral artery_4


title: H160_172: Femoral artery_41G

description: H160_172: H160_172: Femoral artery_41G


title: H17_200: Femoral artery_Control 25

description: H17_200: H17_200: Femoral artery_Control 25


title: H156_36: Carotid artery_12

description: H156_36: H156_36: Carotid artery_12


title: H159_140: Femoral artery_28

description: H159_140: H159_140: Femoral artery_28


title: H146_15: Carotid artery_Control 05

description: H146_15: H146_15: Carotid artery_Control 05


description: H147_112: H147_112: Infra-popliteal artery_Control 25


title: H188_149: Femoral artery_20

description: H188_149: H188_149: Femoral artery_20


title: H144_81: Carotid artery_44

description: H144_81: H144_81: Carotid artery_44


title: H173_170: Femoral artery_16

description: H173_170: H173_170: Femoral artery_16


title: MG-A-LL-2

city: Boston

first: David

middle: A.

last: Sullivan

state: MA

address: 20 Staniford St.

country: USA

institute: Schepens Eye Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were were cubic spline normalized using Illumina Bead Studio software. After normalization the data were further processed by changing all negative values to zero and then adding 16 to each intensity.

label: Biotin

source_name: human meibomian gland  epithelial cell line, androgen, LPS and LBP treated

label_protocol: Biotinylated cRNA were prepared using a MessageAmp II-based protocol (Ambion Inc., Austin, TX) and one round of amplification.

growth_protocol: Cells were cultured in keratinocyte serum-free medium (KSFM) supplemented with bovine pituitary extract (BPE; 25 ug/mL HCEC and HCjE, 50 ug/mL HMGEC), 5 ng/mL epidermal growth factor (EGF), penicillin and streptomycin.

extract_protocol: Total RNA was extracted wth Rneasy Mini Kit(Qiagen) per manufacturer's recommendations. Quality control and quantification were performed with Agilent Bioanalyser. Quality and quantity were checked again before subjected to microarray by Asuragen.

treatment_protocol: After reaching confluence, cells were rinsed with PBS and cultured in medium containing DMEM/F12 with 10% FBS, 10 ng/ml EGF, penicillin and streptomycin and either dihydrotestosterone (DHT, 10 nM) or ethanol control for 2 days. After this time period, cells were incubated in serum-free DMEM/F12 and exposed to vehicle (1% bovine serum albumin [BSA]), or LPS (15 μg/ml) and LBP (150 ng/ml), for six hours.

value: HMGEC

tag: medium formulation

value: KSFM with bovine pituitary extract (BPE, 50 ug/mL), epidermal growth factor (EGF, 50 ng/ml), penicillin and streptomycin

tag: 2 day pre-treatment

value: DHT, 10 nM

tag: 6hr treatment

value: LPS, 15ug/mL; LBP, 150 ng/mL


title: H148_104: Carotid artery_95

description: H148_104: H148_104: Carotid artery_95


title: MG-A-LL-1


title: MG-A-LL-3


title: H142_189: Carotid artery_32

description: H142_189: H142_189: Carotid artery_32


title: H145_46: Carotid artery_40

description: H145_46: H145_46: Carotid artery_40


title: MG-LL-1

source_name: human meibomian gland  epithelial cell line, LPS and LBP treated

value: EtOH


title: MG-LL-2


title: H167_21: Carotid artery_42

description: H167_21: H167_21: Carotid artery_42


title: MG-LL-3


title: H143_39: Femoral artery_18

description: H143_39: H143_39: Femoral artery_18


title: H140_190: Femoral artery_23

description: H140_190: H140_190: Femoral artery_23


title: H135_17: Femoral artery_Control 01

description: H135_17: H135_17: Femoral artery_Control 01


title: MG-A-1

source_name: human meibomian gland  epithelial cell line, androgen treated

value: BSA


title: C-A-LL-3

source_name: human corneal epithelial cell line, androgen, LPS and LBP treated

value: HCEC

value: KSFM with bovine pituitary extract (BPE, 25 ug/mL), epidermal growth factor (EGF, 50 ng/ml), penicillin and streptomycin


title: MG-E-2

source_name: human meibomian gland  epithelial cell line, control


title: H139_13: Infra-popliteal artery_12

description: H139_13: H139_13: Infra-popliteal artery_12

value: female


title: MG-A-3


title: H14_23: Femoral artery_9

description: H14_23: H14_23: Femoral artery_9


title: H136_99: Carotid artery_55

description: H136_99: H136_99: Carotid artery_55

value: Atherosclerotic carotid artery


description: H141_93: H141_93: Infra-popliteal artery_Control 19

value: male


title: MG-A-2


title: H138_185b: Femoral artery_27

description: H138_185b: H138_185b: Femoral artery_27

value: Atherosclerotic femoral artery


title: H133_44b: Femoral artery_Control 05

description: H133_44b: H133_44b: Femoral artery_Control 05


title: MG-E-3


title: MG-E-1

source_name: human meibomian gland epithelial cell line, control


title: C-A-LL-2


title: C-LL-3

source_name: human corneal epithelial cell line, LPS and LBP treated


title: C-A-LL-1


title: C-LL-1


title: H132_88: Femoral artery_31

description: H132_88: H132_88: Femoral artery_31


title: C-LL-2


title: H129_168: Carotid artery_82

description: H129_168: H129_168: Carotid artery_82


title: H130_150: Infra-popliteal artery_19

description: H130_150: H130_150: Infra-popliteal artery_19

value: Atherosclerotic infra-popliteal artery


title: C-A-3

source_name: human corneal epithelial cell line, androgen treated


title: C-A-2


title: H128_73: Femoral artery_25

description: H128_73: H128_73: Femoral artery_25


title: H126_146: Carotid artery_27

description: H126_146: H126_146: Carotid artery_27

source_name: Atherosclerotic carotid artery


title: H131_28: Femoral artery_1

description: H131_28: H131_28: Femoral artery_1


title: H13_193: Infra-popliteal artery_10

description: H13_193: H13_193: Infra-popliteal artery_10


title: C-A-1


title: H122_169: Femoral artery_11

description: H122_169: H122_169: Femoral artery_11


title: H116_49: Carotid artery_2

description: H116_49: H116_49: Carotid artery_2


title: H113_77: Carotid artery_Control 27

description: H113_77: H113_77: Carotid artery_Control 27


title: C-E-3

source_name: human corneal epithelial cell line, control


title: HCjE-A-LL-2

source_name: human conjunctival epithelial cell line, androgen, LPS and LBP treated

value: HCjE


title: C-E-1


title: HCjE-A-LL-1


title: C-E-2


title: HCjE-LL-3

source_name: human conjunctival epithelial cell line, LPS and LBP treated


title: H121_92: Femoral artery_Control 21

description: H121_92: H121_92: Femoral artery_Control 21

value: Control femoral artery


title: HCjE-A-LL-3


title: H117_56: Femoral artery_Control 08

description: H117_56: H117_56: Femoral artery_Control 08


title: H112_26: Carotid artery_10

description: H112_26: H112_26: Carotid artery_10


title: HCjE-LL-2


title: H111_40: Infra-popliteal artery_1

description: H111_40: H111_40: Infra-popliteal artery_1

source_name: Atherosclerotic infra-popliteal artery


title: H114_84: Carotid artery_84

description: H114_84: H114_84: Carotid artery_84


title: HCjE-A-3

source_name: human conjunctival epithelial cell line, androgen treated


title: H109_78: Carotid artery_Control 19

description: H109_78: H109_78: Carotid artery_Control 19

value: Control carotid artery


title: H110_54: Carotid artery_Control 12

description: H110_54: H110_54: Carotid artery_Control 12


description: H108_34: H108_34: Infra-popliteal artery_Control 16

value: Control infra-popliteal artery


title: H105_25: Carotid artery_91

description: H105_25: H105_25: Carotid artery_91


title: H106_89b: Carotid artery_Control 10

description: H106_89b: H106_89b: Carotid artery_Control 10


title: HCjE-A-2


title: H103_90: Carotid artery_Control 14

description: H103_90: H103_90: Carotid artery_Control 14


title: HCjE-A-1


title: HCjE-E-1

source_name: human conjunctival epithelial cell line, control


title: H102_8: Femoral artery_Control 26

description: H102_8: H102_8: Femoral artery_Control 26

source_name: Control femoral artery


title: HCjE-E-2


title: HCjE-LL-1


title: HCjE-E-3


title: mac1 maize anthers, 0.5/0.6 mm, infected with MAC1 expressing U. maydis SG200, rep #4

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware and Donald Danforth Plant Science Center.
Genome_build: Maize AGP v4
Supplementary_files_format_and_content: tag count file

organism: Zea mays

source_name: Ustilago infected Maize anther

extract_protocol:
Total RNA for RNA-seq libraries was isolated using the PureLink Plant RNA Reagent (ThermoFisher) following the manufacturer’s instructions.
Total RNA quality and quantity were accessed by RNA 6000 Pico Kit (Agilent) and by the Qubit RNA BR Assay Kit (ThermoFisher), respectively. An aliquot of 500 ng of total RNA was treated with DNase I (New England BioLabs, Ipswich, MA) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research Corp., Irvine, CA). An aliquot containing 200 ng of treated RNA was used for library construction. The TruSeq Stranded Total RNA with RiboZero-Plant Kit (Illumina) was used for library construction following the manufacturer’s instructions. Libraries were sequenced in an Illumina HiSeq 2500 instrument with single-end mode with 101 bp reads. All of the sequencing runs were performed in the University of Delaware Sequencing and Genotyping Center in Newark, DE.

tag: male fertility

value: sterile

tag: pathogen

value: U. maydis SG200 carring ZmMAC1


title: mac1 maize anthers, 0.5/0.6 mm, infected with MAC1 expressing U. maydis SG200, rep #3


title: mac1 maize anthers, 0.5/0.6 mm, infected with MAC1 expressing U. maydis SG200, rep #2


title: mac1 maize anthers, 0.5/0.6 mm, infected with MAC1 expressing U. maydis SG200, rep #1


title: mac1 maize anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #2

value: U. maydis SG200


title: H1_87: Femoral artery_3

description: H1_87: H1_87: Femoral artery_3

source_name: Atherosclerotic femoral artery


title: H10_109: Femoral artery_7

description: H10_109: H10_109: Femoral artery_7


title: treated with active mixture for 24h_rep1

city: Pécs

first: Tamás

last: Czömpöly

address: Finn 1/1

department: Cancer research and drug development

country: Hungary

institute: Culevit Ltd.

description: 24h_replicate 1

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R.

source_name: Hela cell line_treated_24h

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

growth_protocol: Hela cells were cultered in MEM contaning 10% FBS. The cells were incubated in a humidified atmosphere of 5 % CO2, at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA concentration was measured using NanoDrop spectophotometer (Thermo scientific). The integrity of total RNA was confirmed with gel electrophoresis.

treatment_protocol: The cells were treated with a mixture of experimentally selected substances (amino acids and other small molecules), called active mixture for 3h, 6h and 24h. The active mixture was dissolved in MEM.

value: HeLa

value: treated with active mixture for 24h


title: mac1 maize anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #1


title: Control rep1

city: Flushing

first: Ye

last: Jin

state: NY

address: 6530 Kissena Blvd

department: Biology

institute: Queens College-CUNY

data_processing:
Genome for Xenopus laevis was downloaded from http://www.xenbase.org/other/static/ftpDatafiles.jsp. The version of the genome is X. laevis v7.1.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate < 0.05) at the end. After trimming, sequence reads shorter than 30 nucleotides were discarded.
Remaining sequence reads were aligned to the transcript sequences from X. laevis v7.1 genome with CLC Genomics Server program. Transcript hit counts were measured and Reads Per Kilobase of transcript per Million mapped reads (RPKM) values were calculated.
After quantile normalization and log2-transformation on RPKM values, unsupervised hierarchical clustering and Principal Component Analysis were performed. Transcript expression of samples 1 and 3 were compared with samples 2 and 4. Pair-wise Student t test was performed between the two groups. Fold-change of RPKMs, p values and False Discovery Rate (FDR) were calculated.
Genome_build: X. laevis v7.1
Supplementary_files_format_and_content: an excel file containing gene expression values, including gene hit counts, RPKM values, fold-change between groups and p values for transcript expression comparison

organism: Xenopus laevis

source_name: Animal cap explants

growth_protocol: Animal cap explants were isolated at late blastula stages, and cultured until mid-neurula stages.

extract_protocol:
Animal cap explants were isolated and cultured until mid-neurula stages. RNA was harvested using RNA-Bee reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols by Genewiz.

treatment_protocol: Synthetic RNA encoding pitx1 or water was injected into the animal pole of early cleavage stages embryos.

tag: genotype

value: wild type

tag: harvested stage

value: mid-neurula

tag: injected materials

value: nuclease-free water

value: animal cap explants


title: treated with active mixture for 24h_rep3

description: 24h_replicate 3


description: H104_154: H104_154: Infra-popliteal artery_Control 01

source_name: Control infra-popliteal artery


title: zeb1-tg-microglia-after mcao-rep2

city: Tianjin

first: Junwei

last: Hao

address: 154 Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

description:
Gene expression of zeb1-tg micorglia after tMCAO
MCAO-04

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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.

source_name: zeb1-tg-microglia-after mcao

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug 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 prepared using the Trizol reagent (Invitrogen) 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).

treatment_protocol: Microglia cells from the  brains of wild type mice, ZEB1-overexpression and ZEB1-knock down mice were isolated by MACS sorting using a mouse CX3CR1 cell enrichment kit before and after tMCAO.

value: microglia

tag: age

value: 8 weeks

value: tMCAO


title: Control rep2


title: treated with active mixture for 6h_rep2

description: 6h_replicate 2

source_name: Hela cell line_treated_6h

value: treated with active mixture for 6h


title: maize fertile anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #4

value: fertile


title: zeb1-tg-microglia-after mcao-rep1

description:
Gene expression of zeb1-tg micorglia after tMCAO
MCAO-03

value: male


title: treated with active mixture for 6h_rep3

description: 6h_replicate 3


title: wt-microglia-after mcao-rep2

description:
Gene expression of wt micorglia after tMCAO
MCAO-02

source_name: wt-microglia-after mcao


title: treated with active mixture for 3h_rep2

description: 3h_replicate 2

source_name: Hela cell line_treated_3h

value: treated with active mixture for 3h


title: treated with active mixture for 24h_rep2

description: 24h_replicate 2


title: wt-microglia-after mcao-rep1

description:
Gene expression of wt micorglia after tMCAO
MCAO-01


title: maize fertile anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #3


title: treated with active mixture for 3h_rep1

description: 3h_replicate 1


title: Pitx1 rep2

value: synthetic RNA encoding pitx1


title: maize fertile anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #2


title: treated with active mixture for 6h_rep1

description: 6h_replicate 1


title: treated with active mixture for 3h_rep3

description: 3h_replicate 3


title: maize fertile anthers, 0.5/0.6 mm, infected with U. maydis SG200, rep #1


title: Pitx1 rep1


title: untreated control_rep2

description: CTRL_replicate 2

source_name: Hela cell line_untreated

value: untreated


title: untreated control_rep3

description: CTRL_replicate 3


title: untreated control_rep1

description: CTRL_replicate 1


title: pMT vs. dGcn2 12hr rep3 (S110433)

city: CAMBRIDGE

first: Stefan

middle: J

last: Marciniak

state: Cambridgeshire

address: Cambridge Biomedical Campus, Hills Road

department: CIMR (Cambridge Institute for Medical Research )

country: United Kingdom

institute: University of Cambridge; School of Clinical Medicine

hyb_protocol: Add 140 µl of Ocimum hybridization buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridize for 16 hours at 51 °C. Perform post-hybridization washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing:
Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalized with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.
Spiked-in controls were removed before normalization with vsn

organism: Drosophila melanogaster

label_protocol: Mix together 50 µg total RNA, DEPC MilliQ water and spike mix to a total volume of 28 µl in an RNAse-free 1.5 ml tube. Add 1 µl of 500 ng/µl oligo (dT)23 anchored primer (Sigma). Incubate at 65 °C for 10 minutes in a hot-block to denature RNA tertiary structure, and then place on ice. Add µl of 5x first strand buffer (Invitrogen), 2 µl of low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl of 1 mM Cy3 or Cy5 dCTP (GE Healthcare), 2 µl of 0.1 M DTT (Invitrogen), 0.5 µl of RNAsin (Promega) and 2 µl of Superscript III reverse transcriptase (Invitrogen). Incubate at 42 °C for 1-2 hours. Hydrolyse the remaining RNA by mixing equal volumes of 0.5 M EDTA and 1 M NaOH. Then add 20 µl of this mix to the reaction and incubate at 65 °C for 15 minutes. Bring samples to room temperature and add 25 µl of 1 M Tris-HCl (pH 7.5) to neutralize. Reduce volume of probe to approximately 25 µl, by placing in a speed vac with medium heat. Then combine the Cy3- and Cy5-labelled probe (sample and control) into one 1.5 ml microfuge tube. Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: S2 cells were split into fresh Schneider medium (Sigma) plus 10% FBS (Sigma) + 100 U/ml Penicillin and 100 ug/ml Streptomycin the day before the experiment to a density of 1*10^6 cells/ml and grown at 25°C until harvest.

extract_protocol: Homogenize cell pellet in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle and add up to 700 µl of TRIzol. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes at 4 °C to pellet debris. Transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds and incubate at room temperature for 2-3 minutes. Centrifuge at 13,000 rpm for 15 minutes at 4 °C. Transfer upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.7 volumes of isopropanol to precipitate the RNA. Incubate at room temperature for 5 minutes or 1 hour at -20 °C and then centrifuge at 13,000 rpm for 15 minutes at 4 °C. Discard the supernatant and wash the RNA pellet with 1 ml 70% ethanol/DEPC MilliQ water. Centrifuge at 13,000 rpm for 10 minute at 4 °C. Air-dry the pellet briefly (~ 5 minutes). Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 20 to 50 µl. The RNA will dissolve more readily if the DEPC MilliQ water is preheated to 55 °C. Verify quality of RNA on a 1 % agarose gel and quantify with a Nanodrop.

treatment_protocol: Transgene expression was induced by adding directly into the media the appropriate volume of a sterile-filtered 50 mM copper sulphate to obtain final a 0.7 mM concentration

tag: expression

value: ctrl


title: H123_1: Carotid artery_Control 22

description: H123_1: H123_1: Carotid artery_Control 22

source_name: Control carotid artery

value: Control carotid artery


title: memory B cell BCR/CD40 rep1

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description:
replicate 1
SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol. 750ng of amplified cRNA per sample was hybridized a microarray chip.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with GeneSpring GX (Agilent Technologies).

source_name: B cell

label_protocol: We prepared amplified, biotinylated cRNA samples from extracted RNA with MessageAmp II aRNA Kit (Life Technologies) and Illumina TotalPrep RNA Amplification Kit (Illumina).

growth_protocol: Mononuclear cells were isolated from peripheral blood of healthy donor using density centrifugation with LSM (MP Biomedicals, LLC, Santa Ana, USA). We isolated B cells by positive selection with Dynabeads M450 CD19 and DETACHa-BEAD CD19 (Invitrogen, Carlsbad, CA, USA), whose viability and purity were greater than 99.5 % and 95 %, respectively (confirmed by flow cytometry). After staining B cells with mouse monoclonal antibody (mAb) against human CD19, CD27, IgD (all from BioLegend, San Diego, CA,  USA), we further purified switched-memory (IgD– CD27+) B cell by using BD FACS Aria III. One hundred thousand of FACS-sorted memory B cells were then cultured at 37˚C in a 5% CO2 humidified atmosphere for 24 hours.

extract_protocol: Total mRNA from cultured switched memory B cells was isolated with Isogen II reagent (Nippon Gene, Tokyo, Japan) following manufacturer's instruction.

treatment_protocol: 1. NS: No stimulation  2. BCR/CD40: An affiniPure F (ab’) Fragment Goat Anti-Human IgA/ IgG/IgM (H + L) (BCR, 10 μg/ml) was purchased from Jackson ImmunoResearch (West Grove, PA, USA). Anti- human CD40 monoclonal antibody (CD40, 2 μg/ml)  3. BCR/CD40/IFNg: BCR/CD40 + IFN-γ 20ng/ml (R&D Systems)  4. BCR/CD40/IL21: BCR/CD40 + IL21 20ng/ml (R&D Systems)

tag: b cell subset

value: memory B cell

tag: stimulation

value: Peripheral Blood


title: pMT vs. dGcn2 6hr rep1 (S110413)

extract_protocol: Homogenize tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle and add up to 700 µl of TRIzol. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes at 4 °C to pellet debris. Transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds and incubate at room temperature for 2-3 minutes. Centrifuge at 13,000 rpm for 15 minutes at 4 °C. Transfer upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.7 volumes of isopropanol to precipitate the RNA. Incubate at room temperature for 5 minutes or 1 hour at -20 °C and then centrifuge at 13,000 rpm for 15 minutes at 4 °C. Discard the supernatant and wash the RNA pellet with 1 ml 70% ethanol/DEPC MilliQ water. Centrifuge at 13,000 rpm for 10 minute at 4 °C. Air-dry the pellet briefly (~ 5 minutes). Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 20 to 50 µl. The RNA will dissolve more readily if the DEPC MilliQ water is preheated to 55 °C. Verify quality of RNA on a 1 % agarose gel and quantify with a Nanodrop.


title: memory B cell BCR/CD40/IFN-γ rep3

description:
replicate 3
SAMPLE 10

tag: tissue


title: pMT vs. dGcn2 6hr rep2 (S110415)


title: memory B cell no stimulation control rep1

description:
replicate 1
SAMPLE 4

value: NS


title: memory B cell no stimulation control rep3

description:
replicate 3
SAMPLE 12


title: memory B cell no stimulation control rep2

description:
replicate 2
SAMPLE 8


title: memory B cell BCR/CD40/IL21 rep1

description:
replicate 1
SAMPLE 1


title: memory B cell BCR/CD40/IFN-γ rep2

description:
replicate 2
SAMPLE 6


title: pMT vs. dGcn2 6hr rep3 (S110414)


title: memory B cell BCR/CD40/IL21 rep2

description:
replicate 2
SAMPLE 5


title: memory B cell BCR/CD40/IFN-γ rep1

description:
replicate 1
SAMPLE 2


title: pMT vs. dGcn2 6hr rep4 (S110429)


title: pMT vs. dGcn2 12hr rep2 (S110432)


title: memory B cell BCR/CD40 rep3

description:
replicate 3
SAMPLE 11


title: HA vs. HA-crc 6hr rep2 (S110178)

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalized with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

value: HA control

value: HAcrc


title: hNESC_MUT_COR_3

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description:
human iPSC derived
P4

hyb_protocol: Labeled, fragmented cDNA was hybridized to Human Gene 2.0 arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalogue number 900720). Arrays were washed and stained using the Affymetrix Fluidics Station 450

scan_protocol: Scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data was processed using R/bioconductor and GC-RMA with default parameters.

source_name: hNESC maintenance 6d

label_protocol: Human RNA samples (Xng) were processed and labeled for array hybridization using the Ambion WT Expression kit (Life Technologies, catalogue number 4411974, then Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, catalogue number 901524)

growth_protocol: 6 day maintenance N2B27 (Reinhardt et al., 2011)

extract_protocol: Quiagen miRNeasy Kit (quiazol interphase disolution) after metabolite extraction

treatment_protocol: No treatment performed

tag: mutation

value: patient


title: HA vs. HA-crc 6hr rep1 (S110123)


title: hNESC_MUT_BILL_3

description:
human iPSC derived
H3G2019S

value: inserted G2019S


title: memory B cell BCR/CD40/IL21 rep3

description:
replicate 3
SAMPLE 9


title: pMT vs. dGcn2 12hr rep1 (S110430)


title: HA vs. HA-crc 6hr rep3 (S110180)


title: HA vs. HA-crc 3hr rep3 (S110025)

growth_protocol: S2 cells were split into fresh Schneider medium (Sigma) plus 10% FBS (Sigma) + 100U/ml Pen and 100 ug/ml Streptomycin the day before the experiment to a density of and grown at 25°C until harvest.

treatment_protocol: Transgene expression was induced by adding directly into the media the appropriate volume of a sterile-filteres 50 mM copper sulphate to obtain final a 0.7 mM concentration


title: hNESC_MUT_33897_3

description:
human iPSC derived
P6


title: memory B cell BCR/CD40 rep2

description:
replicate 2
SAMPLE 7


title: whole_blood-LPS-Patient_P5

city: Tuebingen

first: Alexander

middle: NR

last: Weber

address: Auf der Morgenstelle 15

department: Department of Immunology

institute: University of Tuebingen

description:
LPS_P5
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).

hyb_protocol: Hybridization was carried out according to the Illumina HumanHT-12 v4.0 Expression BeadChip Kit.

scan_protocol: Arrays were scanned on an Illumina HiScan array scanner.

data_processing: Illumina idat-files were read in, background corrected, normalized and log2-transformed and further analyzed using the R package 'limma' version 3.30.8. On average, 41-52 % of probes were found to be expressed on each array, and removal of genes detected in <4 arrays and/or lacking gene symbol annotation left a bit more than 21.000 genes for further analysis.

source_name: whole blood

label_protocol: aRNA synthesis was conducted using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (epicentre).

extract_protocol: RNA was isolated with (QIAamp RNA Blood Mini Kit, Qiagen) and genomic DNA digested (Turbo DNA-free Kit, ThermoFisher). Total RNA and aRNA were quantified on a NanoDrop 8000 spectrometer (Peqlab) and quality controlled using the Nano 6000 Kit for Bioanalyzer (Agilent).

treatment_protocol: For whole blood assays 1 ml freshly drawn heparinized blood was aliquoted into 24 well plates and stimulated for 3 h. Subsequently erythrocyte lysis was performed and the remaining cells were frozen at -80 °C in RLT buffer (QIAamp RNA Blood Mini Kit, Qiagen).

tag: patient


title: whole_blood-Unstimulated-Patient_P5

description:
Unstimulated_P5
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_13567_3

description:
human iPSC derived
P5


title: hNESC_GC_IM5_3

description:
human iPSC derived
P1GC

value: gene corrected


title: whole_blood-Chitin-Patient_P5

description:
Chitin_P5
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_GC_IM5_1

description:
human iPSC derived
P1GC


title: whole_blood-PAM3-Patient_P5

description:
PAM3_P5
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-LPS-Patient_P4

description:
LPS_P4
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Chitin-Patient_P4

description:
Chitin_P4
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_BILL_1

description:
human iPSC derived
H3G2019S


title: whole_blood-PAM2-Patient_P5

description:
PAM2_P5
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_IM5_3

description:
human iPSC derived
P1


title: hNESC_MUT_K7_3

description:
human iPSC derived
H1G2019S


title: HA vs. HA-crc 3hr rep2 (S110086)


title: hNESC_GC_IM5_2

description:
human iPSC derived
P1GC


title: hNESC_WT_BILL_2

description:
human iPSC derived
H3

value: healthy


title: whole_blood-LPS-Patient_P3

description:
LPS_P3
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_WT_BILL_3

description:
human iPSC derived
H3


title: HA vs. HA-crc 3hr rep1 (S110193)


title: whole_blood-PAM2-Patient_P4

description:
PAM2_P4
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-PAM3-Patient_P4

description:
PAM3_P4
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_BILL_2

description:
human iPSC derived
H3G2019S


title: whole_blood-Unstimulated-Patient_P4

description:
Unstimulated_P4
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Unstimulated-Patient_P3

description:
Unstimulated_P3
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_K7_2

description:
human iPSC derived
H1G2019S


title: whole_blood-PAM3-Patient_P3

description:
PAM3_P3
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_33897_1

description:
human iPSC derived
P6


title: hNESC_WT_BILL_1

description:
human iPSC derived
H3


title: hNESC_MUT_33897_2

description:
human iPSC derived
P6


title: whole_blood-PAM3-Patient_P2

description:
PAM3_P2
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Chitin-Patient_P3

description:
Chitin_P3
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-PAM2-Patient_P3

description:
PAM2_P3
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Unstimulated-Patient_P2

description:
Unstimulated_P2
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_WT_JAVI_3

description:
human iPSC derived
H5


title: hNESC_WT_JAVI_2

description:
human iPSC derived
H5


title: hNESC_WT_JAVI_1

description:
human iPSC derived
H5


title: HumAb 7F11

type: protein

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

description: purified recombinant human monoclonal antibody

hyb_protocol: Peptide arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with mAb diluted 1:200 for anti-human IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), arrays were incubated with an AlexaFluor®647-labelled anti-human secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a Powerscanner (Tecan Trading AG, Switzerland) and the 16-bit images were generated with Powerscanner software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data was performed using in-house developed software and R scripts. For each sample, the mean fluorescence intensity (MFI) of 3 replicated spots was determined, after subtraction of the background value surrounding each spot.

molecule: protein

source_name: recombinant antibody

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, AlexaFluor®647-conjugated anti-Human IgG secondary antibody (Jackson Immunoresearch) (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: Optimized gene fragments corrisponding to VH and VL of desired human monoclonal antibodies were inserted in a expression vector containing a human Ig gene signal peptide sequence and human IgG1, IgK or IgL costant regions under the CMV promoter. Transient production of recombinant antibodies was performed in suspesion Expi293 (Thermo Fisher Scientific) according to manufactoring protocol. Recombinant antibodies were purified from supernatants with protein G beads according to manufacturer's (GE Healthcare) instructions.

tag: antigen

value: NadA

tag: antibody subclass

tag: cell line used to produce recombinant antibody

value: Expi 293


title: hNESC_MUT_13567_2

description:
human iPSC derived
P6


title: whole_blood-Chitin-Patient_P1

description:
Chitin_P1
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Unstimulated-Patient_P1

description:
Unstimulated_P1
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: HumAb 2C4

label: AlexaFluor®647-labelled anti-human secondary antibody


title: hNESC_WT_COR_2

description:
human iPSC derived
H4


title: hNESC_WT_COR_1

description:
human iPSC derived
H4


title: hNESC_WT_EPIT_3

description:
human iPSC derived
H6


title: HumAb 3H12


title: hNESC_WT_K7_3

description:
human iPSC derived
H1


title: whole_blood-PAM2-Patient_P1

description:
PAM2_P1
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_WT_EPIT_2

description:
human iPSC derived
H6


title: whole_blood-PAM3-Patient_P1

description:
PAM3_P1
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: whole_blood-Chitin-Patient_P2

description:
Chitin_P2
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: hNESC_MUT_COR_1

description:
human iPSC derived
P4


title: hNESC_WT_COR_3

description:
human iPSC derived
H4


title: hNESC_MUT_COR_2

description:
human iPSC derived
P4


title: HumAb 5D11


title: hNESC_MUT_13567_1

description:
human iPSC derived
P6


title: whole_blood-PAM2-Patient_P2

description:
PAM2_P2
Sample '200793290055_I_Grn.idat' is not present to avoid confusion. Reason: it's treatment conditions (5h) is uncomparable to all other samples (3h).


title: HumAb 3A6


title: HumAb 1A12


title: hNESC_MUT_K7_1

description:
human iPSC derived
H1G2019S


title: HumAb 1C6


title: HumAb 2A3


title: HumAb 12H11


title: hNESC_WT_T12_2

description:
human iPSC derived
H2


title: HumAb 11F7


title: HumAb 10D12


title: Fab-anti-NadA 1C6

description:
purified fragment antigen binding
expressed in E.coli

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with Fabs diluted 1:50 for anti-human IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), arrays were incubated with an AlexaFluor®647-labelled anti-human IgG, fab specific secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before, then rinsed in sterile water and dried.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data was performed using in-house developed software and R scripts. For each sample, the mean fluorescence intensity (MFI) of replicated spots was determined, after subtraction of the background value surrounding each spot.

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: H and L chain V region genes of single plasmablasts isolated from peripheral blood were amplified separately and then joined by overlap extension PCR. Products were cloned into pET22 as bicistronic expression cassettes encoding for Fab antibody fragments and sequenced. Fab clones encoded by unique germ line were expressed in Escherichia coli Rosetta2 (DE3) strain (Novagen) in Enpresso B medium (Biosilta), according to manufacturer’s instructions. Induction was carried out with 1mM IPTG for 24h at 25°C. Total cell lysis was performed in CelLytic Express (Sigma-Aldrich). Recombinant Fabs were purified by Ni2+-affinity chromatographychromatography (Ni-NTA agarose resin, Qiagen), buffer-exchanged to Tris-HCl 20mM, NaCl 300mM, sodium azide 0.05%, pH8 and stored at 4°C. Recombinant Fabs were quantified by Bradford protein assay (Sigma-Aldrich) and their purity was assessed by SDS-PAGE after coomassie staining in non-reducing conditions.

value: fab

tag: cells used to produce the antibody

value: expressed in E.coli


title: hNESC_WT_T12_3

description:
human iPSC derived
H2


title: hNESC_WT_EPIT_1

description:
human iPSC derived
H6


title: Fab-anti-NadA 11F7


title: Fab-anti-NadA 5D11


title: Fab-anti-NadA 3H12


title: Fab-anti-NadA 3A6


title: hNESC_MUT_IM2_3

description:
human iPSC derived
P1.1


title: hNESC_WT_T12_1

description:
human iPSC derived
H2


title: hNESC_MUT_IM2_2

description:
human iPSC derived
P1.1


title: hNESC_MUT_IM2_1

description:
human iPSC derived
P1.1


title: hNESC_GC_IM2_1

description:
human iPSC derived
P1.1GC


title: hNESC_WT_K7_2

description:
human iPSC derived
H1


title: Fab-anti-NadA 2A3


title: Fab-anti-NadA 1A7


title: hNESC_MUT_T4.6_1

description:
human iPSC derived
P2


title: hNESC_GC_IM2_3

description:
human iPSC derived
P1.1GC


title: hNESC_GC_IM2_2

description:
human iPSC derived
P1.1GC


title: Fab-anti-NadA 1A12


title: Fab-anti-NadA 2C4


title: hNESC_MUT_T4.6_3

description:
human iPSC derived
P2


title: Fab-anti-NadA 1F7


title: Fab-anti-NadA 2A6


title: Fab-anti-NadA 7F11


title: Fab-anti-NadA 4F12


title: Fab-anti-NadA 1A3


title: Fab-anti-NadA 1E5


title: hNESC_MUT_T4.6_2

description:
human iPSC derived
P2


title: Fab-anti-NadA 10D12


title: Fab-anti-NadA 6B8


title: Fab-anti-NHBA 2H1

value: NHBA


title: hNESC_GC_T4.6_3

description:
human iPSC derived
P2GC


title: Fab-anti-NHBA 10C3


title: Fab-anti-NHBA 12E1


title: Fab-anti-NHBA 3D8


title: Fab-anti-NadA 12H11


title: hNESC_GC_T4.6_1

description:
human iPSC derived
P2GC


title: Fab-anti-NHBA 5H2


title: hNESC_GC_T4.6_2

description:
human iPSC derived
P2GC


title: Fab-anti-NHBA 4D11


title: Fab-anti-NHBA 3A5


title: Fab-anti-fHbp 1A3

value: fHbp


title: Fab-anti-fHbp 2A1


title: Fab-anti-fHbp 1A12


title: hNESC_MUT_IM5_2

description:
human iPSC derived
P1


title: Fibroblasts_UVB irradiation_60mJ/cm2_rep1

city: Nanjing

first: Ni

state: Jiangsu

address: 300 Guangzhou Rd

department: Department of Dermatology

institute: The First Affiliated Hospital of Nanjing Medical University

description: Gene expression in UVB irradiatied human skin fibroblasts

hyb_protocol: miRNA complete Labeling and Hyb Kit (Agilent) and miRNA Spike In Kit (Agilent) were used in process of Hybridization following the manufacturer's instructions. For microarray wash, Triton X-102 was added to Gene Expression wash buffers and Gene Expression Wash Buffer was prewarmed. Copious amounts of Milli-Q water was run through and emptied out  the staining dish  for at least 5 times, then Milli-Q water was discarded for preparation of equipment. The microarray slides were washed with GE Wash Buffer.

scan_protocol: Slides were assembled into an slide holder and assembled slide holders were placed into scanner carousel. Slides were scanned on the Agilent  Microarray Scanner(Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (version10.7.1.1, Agilent Technologies). Genespring Software(version13.1, Agilent Technologies) was used for quantile nomalization and following data processing. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared and purified from 100ng of the diluted RNA using miRNA complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Primary human skin fibroblasts were obtained from healthy volunteers by means of a foreskin circumcision. Cells were routinely cultured at 37˚C in an atmosphere of 95% air and 5% CO2. DMEM medium with 10% fetal bovine serum, 100 units/mL penicillin and 100 mg/mL streptomycin was supplied to promote cell growth.

extract_protocol: Culture medium was transferred to a centrifuge tube and centrifuged at 100,000rpm for 2h. Total RNA was extracted using the mirVana RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's recommendations.

treatment_protocol: Human skin fibroblasts was irradiated, then cultured in culture medium with 10% fetal bovine serum. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: skin fibroblasts

tag: protocol

value: UVB irradiation, 60mJ/cm2

tag: gender

value: male


title: Fibroblasts_UVA irradiation_20J/cm2_rep1

description: Gene expression in UVA irradiatied human skin fibroblasts

value: UVA irradiation, 20J/cm2


title: hNESC_WT_K7_1

description:
human iPSC derived
H1


title: hNESC_MUT_IM5_1

description:
human iPSC derived
P1


title: young Control

city: NanJing

first: Musheng

last: Li

address: sipailou 2

institute: Southeast University

hyb_protocol: Hybirdization mixture were prepared as CaptitalBio manual, incubated 3 minute at 95 °C , then 2 minutes on ice. 45ul mixture were used and hybridized for about 16hr.

scan_protocol: The arrays were washed twice, 5 minutes each time,  then scaned by Agilent G2565CA.

data_processing: Data were extacted from images by Agilent Feature Extraction software. then processed by Agilent GeneSpring. Raw data are available in the file "matrix_raw.csv" and in the file "all_expression_signal.xlsx". The raw data, normalized data and probe annotation are available in the file "all_expression_signal.xlsx".

source_name: Healthy

label_protocol: cDNA products obtained by reverse transcrition was concentrated and mixed with Random Primer , then labled with Cy using  Klenow Fragment Enzyme,

extract_protocol: After extracting from tissues by Trizol (Invitrogen, Gaithersburg, MD, USA) ,  total RNA were purified by NucleoSpin® RNA clean-up (MACHEREY-NAGEL,Germany). integrity were tested by Agilent 2100. RNA R 10X treatment to remove linear RNA , then remained RNA were used to synthsis cDNA,

value: Peripheral blood

value: PBMC

tag: diagnosis

value: Healthy


title: Fibroblasts_non-irradiation_rep1

description: Gene expression in non-irradiatied human skin fibroblasts

source_name: skin fibroblasts,non-irradiation

value: non-irradiation


title: senior TB

source_name: Tuberculosis

value: Tuberculosis


title: Fab-anti-fHbp 4F7


title: Fab-anti-fHbp 7B10


title: Fab-anti-fHbp 3F10


title: young TB


title: Fab-anti-fHbp 2D2


title: zeb1-kd-microglia-before mcao-rep2

description:
Gene expression of zeb1-kd micorglia before tMCAO
NORMAL-06

source_name: zeb1-kd-microglia-before mcao

value: microglia

value: 8 weeks

tag: genotype

value: ZEB1-knock down

tag: treatment

value: control


title: Fab-anti-fHbp 2C1

value: fab


title: zeb1-tg-microglia-before mcao-rep1

description:
Gene expression of zeb1-tg micorglia before tMCAO
NORMAL-03

source_name: zeb1-tg-microglia-before mcao

tag: age


title: zeb1-kd-microglia-before mcao-rep1

description:
Gene expression of zeb1-kd micorglia before tMCAO
NORMAL-05


title: zeb1-tg-microglia-before mcao-rep2

description:
Gene expression of zeb1-tg micorglia before tMCAO
NORMAL-04


title: HumAb 1A12

extract_protocol: Optimized gene fragments corresponding to VH and VL of desired human monoclonal antibodies were inserted in a expression vector containing a human Ig gene signal peptide sequence and human IgG1, IgK or IgL costant regions under the CMV promoter. Transient production of recombinant antibodies was performed in suspension Expi293 (Thermo Fisher Scientific) according to manufactoring protocol. Recombinant antibodies were purified from supernatants with protein G beads according to manufacturer's (GE Healthcare) instructions.

value: Expi 293


title: senior Control


title: wt-microglia-before mcao-rep2

description:
Gene expression of wt micorglia before tMCAO
NORMAL-02

source_name: wt-microglia-before mcao

value: wild type


title: wt-microglia-before mcao-rep1

description:
Gene expression of wt micorglia before tMCAO
NORMAL-01


title: Fab-anti-fHbp 3H8

value: fHbp

value: expressed in E.coli


title: zeb1-kd-microglia-after mcao-rep2

description:
Gene expression of zeb1-kd micorglia after tMCAO
MCAO-06

source_name: zeb1-kd-microglia-after mcao

value: tMCAO


title: HumAb 2C1

description: purified recombinant human monoclonal antibody


title: HumAb 12E1

value: NHBA

tag: cell line used to produce antibody


title: HumAb 1G3


title: Fab-anti-fHbp 10G7


title: HumAb 10C3


title: Fab-anti-fHbp 1G3


title: PE-Term-CH, rep4 (methylation)

type: genomic

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

hyb_protocol: Illumina HumanMethylation450 BeadChip protocol

scan_protocol: Arrays were imaged using an Illumina HiScan on a two-colour channel

data_processing: Data was processed in R 3.1.3. Loading was performed with the ChAMP package, functional normalization with the minfi package, batch correction for slide and array position with the sva package (ComBat)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human placenta

extract_protocol: Genomic DNA was purified using the Wizard® Genomic DNA Purification Kit from Promega followed by bisulphite conversion using Zymo's EZ DNA Methylation Kit following manufacturers' protocols

value: PE

value: placenta

tag: maternal age

tag: bmi

tag: maternal ethnicity

value: East Indian

tag: maternal blood type

value: O

tag: nulliparous

value: No

tag: previous miscarriage

tag: previous hypertensive pregnancy

value: Yes

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

value: C-Section

tag: ga week

tag: ga day

value: F

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: HumAb 7B10

tag: antigen

tag: antibody subclass

tag: cell line used to produce recombinant antibody


title: PE-PreT-AGA, rep10 (methylation)

label_protocol: Illumina HumanMethylation450 BeadChip protocol

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: gender


title: HumAb 5H2

tag: antigen

tag: antibody subclass

tag: cell line used to produce antibody


title: HumAb 1A3

tag: cell line used to produce recombinant antibody


title: zeb1-kd-microglia-after mcao-rep1

description:
Gene expression of zeb1-kd micorglia after tMCAO
MCAO-05

tag: tissue

value: microglia

value: male

tag: age

value: 8 weeks

tag: genotype

value: ZEB1-knock down

tag: treatment


title: PE-Term-AGA, rep7 (methylation)

tag: diagnosis

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: nulliparous

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

value: Vaginal

tag: ga week

tag: ga day

value: M

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Fab-anti-fHbp 4A9

tag: antigen

value: fHbp

tag: antibody subclass

value: fab

tag: cells used to produce the antibody

value: expressed in E.coli


title: HumAb 4D11

value: NHBA

tag: cell line used to produce antibody

value: Expi 293


title: subject HD274 cytotoxic CD8 T cells

status: Public on Mar 06 2018

city: Gosselies

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Total RNA was amplified with the Illumina TotalPrep RNA Amplification Kit (Ambion) and hybridized with the HumanHT-12 v4 array, containing 47,323 probes for 44,053 annotated genes, according to the instructions of the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina)

scan_protocol: Chips were scanned with the HiScan Reader (Illumina).

data_processing: Raw data were quantile normalized using the normalization method from the lumi package (Du et al, Bioinformatics 2008). Control probes have been filtered out (replace by null). Log2-transformed data are provided.

source_name: cytotoxic CD8 T cells

label_protocol: standard Illumina protocol

growth_protocol: direct ex-vivo analysis

extract_protocol: Total RNA was extracted using the Qiagen AllPrep DNA/RNA micro or mini kit according to the manufacturer's instructions.Nucleic acid concentration and purity were assessed by spectrophotometry using a nanodrop instrument (Thermoscientific). Median (interquartile range) of A260/A280 ratios were 1.91 (1.73-2.11). RNA integrity number (RIN) was measured using the Eukaryote Total RNA Nano assay and a Bioanalyzer (Agilent). One sample out of 20 had a RIN below 7 and was excluded from the analyses.

treatment_protocol: Isolation of PBMC from fresh blood using Ficoll. Enrichement of target populations by negative selection using Miltenyi Automacs technology. FACS-staining and sorting by positive selection on a BD FACS Aria III sorter.

tag: subject id

tag: subject status

value: CMV-seropositive healthy adult

tag: age (yrs)

tag: gender

value: female

tag: tissue

value: peripheral blood

tag: cell type

value: blood lymphocytes

tag: sorted population

value: cytotoxic CD8 T cells


title: subject HD240 central memory Th1 cells

source_name: central memory Th1 cells

value: Female

value: central memory Th1 cells

tag: sorted population markers


title: subject HD189 central memory Th1 cells


title: subject HD274 central memory Th1 cells


title: subject HD189 cytotoxic CD8 T cells


title: subject HD240 cytotoxic CD4 T cells

source_name: cytotoxic CD4 T cells

value: cytotoxic CD4 T cells


title: subject HD274 cytotoxic CD4 T cells


title: subject HD194 naive CD8 T cells

source_name: naive CD8 T cells

value: male

value: naive CD8 T cells


title: subject HD361 central memory Th1 cells

value: Male


title: subject HD194 central memory Th1 cells


title: subject HD274 naive CD4 T cells

source_name: naive CD4 T cells

value: naive CD4 T cells


title: subject HD189 naive CD4 T cells


title: subject HD194 naive CD4 T cells


title: C1-195-C2

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

data_processing:
Illumina Casava software used for basecalling
FastQC used for reporting the fundamental quality parameters
To avoid adapter contamination and higher error rates in reads boundary, we trimmed 12 nucleotides in 5’-end and 13 nucleotides in 3’-end, leaving 75 nucleotide long reads for sequence alignment. We employed STAR (v2.4.0) to uniquely align the filtered reads to mouse reference genome (mm9) with default parameters.
We used RSEQTools and SAMtools to calculate gene expression. We used HTSeq (v0.6.1) to calculate gene read count values for each annotation entry.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each sample

source_name: Brain

extract_protocol:
Clontech Smart-seq v4
Illumina Nextera
Poly-A capture followed by full-length cDNA reverse transcription

tag: strain

value: dMGE

tag: age

value: Brain


title: C1-195-C3


title: C1-195-C1


title: subject HD240 cytotoxic CD8 T cells


title: subject HD361 cytotoxic CD4 T cells


title: subject HD361 naive CD8 T cells


title: subject HD361 cytotoxic CD8 T cells


title: subject HD240 naive CD4 T cells


title: subject HD189 naive CD8 T cells


title: subject HD189 cytotoxic CD4 T cells


title: subject HD194 cytotoxic CD4 T cells


title: C1-195-C12


title: C1-195-C11


title: subject HD274 naive CD8 T cells


title: subject HD361 naive CD4 T cells


title: C1-195-B8


title: C1-195-B9


title: C1-195-B7


title: C1-195-B6


title: PE-Term-SGA, rep3 (methylation)

tag: diagnosis

value: PE

value: placenta

tag: maternal age

tag: bmi

tag: maternal ethnicity

value: Other

tag: maternal blood type

value: A

tag: nulliparous

value: Yes

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

value: No

tag: iugr

tag: attempted vaginal delivery

tag: mod

value: C-Section

tag: ga week

tag: ga day

value: F

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter


title: C1-195-B5

tag: strain

tag: tissue

tag: age


title: Cont-preT-AGA, rep1 (methylation)

tag: diagnosis

value: non-PE

tag: maternal age

tag: bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

value: O

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: gender

tag: nicu transfer

tag: chorioamnionitis


title: C1-195-C10

tag: strain


title: C1-195-B4

tag: tissue


title: C1-195-B2

tag: age


title: C1-195-B11


title: C1-195-B3


title: C1-195-A6


title: C1-195-A3


title: C1-195-A1


title: C1-195-A11


title: C1-195-A12


title: C1-195-A10


title: C1-187-H5

value: CGE


title: C1-187-H8


title: C1-187-H6


title: C1-187-H2


title: C1-187-H3


title: C1-187-H11


title: C1-187-G9


title: C1-187-H12


title: subject HD240 naive CD8 T cells

tag: subject id

tag: subject status

value: CMV-seropositive healthy adult

tag: age (yrs)

value: female

value: peripheral blood

tag: cell type

value: blood lymphocytes

tag: sorted population

value: naive CD8 T cells


title: C1-187-G4

value: Brain


title: C1-187-G8


title: C1-187-H10


title: C1-187-G5


title: C1-187-G6


title: C1-195-B1

value: dMGE


title: C1-187-G3


title: C1-187-G2


title: C1-187-G1


title: C1-187-G12


title: C1-195-A4


title: C1-187-F9


title: C1-187-G10


title: C1-187-F8


title: C1-187-F7


title: C1-187-F6


title: C1-187-H4


title: C1-187-F5


title: C1-187-F1


title: C1-187-F4


title: C1-187-F11


title: C1-187-F10


title: C1-187-E9


title: C1-187-E5


title: C1-187-E8


title: C1-187-E6


title: C1-187-G11


title: C1-187-D8


title: C1-187-E4


title: C1-187-E3


title: C1-187-E11


title: C1-187-E2


title: C1-187-E12


title: C1-187-E1


title: C1-187-E10


title: C1-187-D7


title: C1-187-D6


title: C1-187-D5


title: C1-187-D2


title: C1-187-D1


title: C1-187-D3


title: C1-187-F12


title: C1-187-F2


title: C1-187-D12


title: C1-187-D11


title: C1-187-C9


title: C1-187-D10


title: C1-187-C7


title: C1-187-C8


title: C1-187-C6


title: C1-187-C4


title: C1-187-C5


title: C1-187-C3


title: C1-187-C2


title: C1-187-D4


title: C1-187-C11


title: C1-187-B8


title: C1-187-B7


title: C1-187-C10


title: C1-187-C12


title: C1-187-B1


title: C1-187-B4


title: C1-187-B6


title: C1-187-A9


title: C1-187-B5


title: C1-187-A8


title: C1-187-B11


title: C1-187-B2


title: C1-187-A6


title: C1-187-B12


title: C1-187-A7


title: C1-187-A3


title: C1-187-A2


title: C1-187-A1


title: C1-187-A11


title: C1-187-B9


title: C1-186-H8


title: C1-186-H7


title: C1-186-H5


title: C1-186-H3


title: C1-186-H12


title: C1-186-H9


title: C1-186-H1


title: C1-186-G5


title: C1-186-G8


title: C1-187-A10


title: C1-186-G7


title: C1-186-H4


title: C1-186-G2


title: C1-186-G1


title: C1-187-A5


title: C1-186-G3


title: C1-186-G12


title: C1-186-F5


title: C1-186-H2


title: C1-186-F8


title: C1-186-F7


title: C1-186-H10


title: C1-186-G9


title: C1-186-F6


title: C1-186-F4


title: C1-186-G10


title: C1-186-F3


title: C1-187-A12


title: C1-186-F2


title: C1-186-F1


title: C1-186-F12


title: C1-186-G6


title: C1-186-F11


title: C1-186-E4


title: C1-186-E9


title: C1-186-E5


title: C1-186-E2


title: C1-186-E6


title: C1-186-E3


title: C1-186-E1


title: C1-186-E11


title: C1-186-E12


title: C1-186-D7


title: C1-186-D8


title: C1-186-E10


title: C1-186-D3


title: C1-186-D6


title: C1-186-D5


title: C1-186-D1


title: C1-186-C9


title: C1-186-D11


title: C1-186-D10


title: C1-186-C8


title: C1-186-E8


title: C1-186-F10


title: C1-186-C3


title: C1-186-C4


title: C1-186-C2


title: C1-186-E7


title: C1-186-C7


title: C1-186-D2


title: C1-186-B8


title: C1-186-C10


title: C1-186-B7


title: C1-186-B9


title: C1-186-C1


title: C1-186-B5


title: C1-186-C12


title: C1-186-D12


title: C1-186-B4


title: C1-186-B1


title: C1-186-B12


title: C1-186-B10


title: C1-186-B11


title: C1-186-A9


title: C1-186-A7


title: C1-186-A8


title: C1-186-A5


title: C1-186-A1


title: C1-186-A3


title: C1-186-A12


title: C1-186-A10


title: C1-185-H9

value: vMGE


title: C1-186-A11


title: C1-186-C11


title: C1-186-B6


title: C1-186-B2


title: C1-185-H6


title: C1-185-H4


title: C1-185-H12


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title: Lgr5 positive  rep2

city: Philadelphia

first: Michal

last: Shoshkes-Carmel

state: PA

address: 3400 Civic Center Blvd, 12-161

department: Genetics

institute: University of Pennsylvania

description:
FGC0259_s_8
2_Female_GFP_Positive_ISC

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Excel format file of transcript raw or FPKM read counts of each sample

source_name: Lgr5 positive

extract_protocol:
Intestine mesenchyme was dissociated to single cells by 7mg/ml DispaseII/0.05% trypsin solution 15 minutes 37℃. Cells were sorted lysed and total RNA was isolated by column purification (Absolutely RNA Nanoprep kit; Agilent Technologies)
NEB Next RNA library prep kit (New England BioLabs, Inc)

tag: strain background

value: mixed

tag: genotype

value: Lr5-EGFP-IRES CreERT2

value: intestine mesenchyme


title: Differentiated epithelium rep1

description:
FGC0265_s_4_GATCAG
DC_mRNA

source_name: Differentiated epithelium

value: wild type


title: Differentiated epithelium rep2

description:
FGC0302_s_2_TTAGGC
dif-mRNA


title: Lgr5 positive  rep1

description:
FGC0244_s_6
1_Male_GFP_Positive_ISC


title: C1-190-2-G11


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