title: Independent sample hyb 28

status: Public on Dec 31 2005

city: Singapore

first: Jianhua

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description:
wild-type S. pombe strain LJY1014 (h- leu1-32) at early-log growth phase in YES medium
Self-self hybridization of Independent sample of wild-type fission yeast cells at early-log growth phase
Cells were harvested from a series of independent cultures.  Total RNA was extracted using a hot-phenol protocol.  ~10 ? was annealed with oligo dT12-18, and reverse-transcribed into cDNA in presence of Cy3- or Cy5-coupled dUTP.  Free Cy3- or Cy5-coupled dUTP was removed with a Microcon-30 concentrator.  Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.
Keywords = Independent S. pombe wild-type cell sample

organism: Schizosaccharomyces pombe

source_name: Independent sample of early-log phase wild-type cells


title: Independent sample hyb 17

type: RNA

molecule: total RNA


title: Independent sample hyb 16


title: Independent sample hyb 24


title: Independent sample hyb 23


title: Independent sample hyb 27


title: Independent sample hyb 22


title: Independent sample hyb 20


title: Independent sample hyb 21


title: Independent sample hyb 25


title: Independent sample hyb 13


title: Independent sample hyb 10


title: Independent sample hyb 14


title: Independent sample hyb 19


title: Independent sample hyb 12


title: Independent sample hyb 18


title: Independent sample hyb 11


title: Independent sample hyb 26


title: Independent sample hyb 15


title: Independent sample hyb 9


title: Independent sample hyb 7


title: Independent sample hyb 8


title: Independent sample hyb 5


title: Independent sample hyb 3


title: Independent sample hyb 2


title: Low Glucose Transcriptome Profiling {rpt 2}

status: Public on Jan 01 2006

city: Detroit

first: Lalit

middle: P

last: Singh

state: MI

address: 4646 John R.

department: Internal Medicine/Nephrology & Physiology

country: USA

institute: Wayne State University School of Medicine

description:
Identification of genes regulated by low glucose, high glucose and glucosamine treatments
Keywords = hexosamine
Keywords = glucose
Keywords = mesangial
Keywords = diabetes
Keywords = diabetic glomerulopathy

organism: Mus musculus

source_name: Mesangial Cells


title: Independent sample hyb 6


title: Independent sample hyb 4


title: Glucosamine Transcriptome Profiling


title: Independent sample hyb 1


title: Lymph node 08

city: Mannheim

first: Alexei

last: Gratchev

department: Department of Dermatology

country: Germany

institute: Medical Centre Mannheim, University of Heidelberg

description: Lymph node sample 08

organism: Homo sapiens

source_name: Fresh tissue


title: Tonsil 09

description: Tonsil sample 09


title: Tonsil 04

description: Tonsil sample 04


title: Lymph node 09

description: Lymph node sample 09


title: Tonsil 03

description: Tonsil sample 03


title: Tonsil 08

description: Tonsil sample 08


title: NRH -arg4

city: Providence

first: Xianne

last: Leong

state: RI

department: Medical Oncology

institute: Rhode Island Hospital; Brown University

description:
Biosource strain/age/gender/disease state:
normal diploid hepatic epithelial cell line WB-F344 isolated from liver of an adult male Fischer-344 rat

Growth protocol:
Cells were routinely cultured in  modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS. Cells used in experiments were of low passage (<15)

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum without L-Arginine HCl  for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Keywords = arginine, hepatocyte, cancer, rat, amino acid, gene regulation, microarray

organism: Rattus norvegicus

source_name: WB normal rat hepatic cells cultured in arginine-deficient media for 18 hours


title: san/san no.1

city: Oxford

first: Teresa

last: Lambe

country: United Kingdom

institute: Oxford University

description: Male C57BL/6 mice were treated with ENU to generate single base substitutions,  the variant genome sequences were breed to homozygosity in inbreeding pedigrees, and screened for antinuclear autoantibodies (ANA). The sanroque pedigree contained multiple progeny with ANA of mixed homogeneous nuclear and cytoplasmic immunofluorescence pattern by 12 weeks of age, due to an autosomal recessive gene variant. Comparsion of the gene expression profile of CD4 cells from  sanroque to wildtype was performed.

source_name: CD4 cells from sanroque


title: Tonsil 07

description: Tonsil sample 07


title: Lymph node 04

description: Lymph node sample 04


title: Tonsil 10

description: Tonsil sample 10


title: Tonsil 06

description: Tonsil sample 06


title: Lymph node 10

description: Lymph node sample 10


title: Tonsil 01

description: Tonsil sample 01


title: 10Mm175.2

city: San Francisco

first: Michael

middle: E.

last: Salazar

state: CA

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: Total RNA from alveolar macrophages from wild type mice treated with doxycycline

source_name: Mac Ref


title: Lymph node 07

description: Lymph node sample 07


title: 10Mm174.2


title: Tonsil 05

description: Tonsil sample 05


title: 10Mm231.2

description: Total RNA from alveolar macrophages from integrin beta6 deficient mice reconstituted with TGF-b1 treated with doxycycline


title: Lymph node 06

description: Lymph node sample 06


title: Tonsil 02

description: Tonsil sample 02


title: 10Mm173.2

description: Total RNA from alveolar macrophages from integrin beta6 deficient mice treated with doxycycline


title: Lymph node 05

description: Lymph node sample 05


title: Lymph node 02

description: Lymph node sample 02

source_name: fresh tissue


title: Lymph node 01

description: Lymph node sample 01


title: san/san pt 2

source_name: CD4 cells from Sanroque


title: Lymph node 03

description: Lymph node sample 03


title: C3H/HeJBir-Il10tm1Cgn, sample 1

city: Hannover

first: Andre

last: Bleich

institute: Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School

description: Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is the first of two independent microarray experiments using mice of this strain.

source_name: Total colon, pooled sample


title: +/+ pt 1

source_name: CD4 cells from wildtype


title: C57BL/6J-Il10tm1Cgn, sample 1

description: Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is the first of two independent microarray analyses using this strain of mice.


title: 10Mm.179.1


title: 10Mm.232.1


title: C3H/HeJBir, sample-1

description: Equal amounts (7 micro-gram) of RNA were pooled from four animals. This is the first of two independent microarray experiments using mice of this strain.


title: 10Mm.178.1


title: C57BL/6J, sample 1


title: 10Mm.176.1


title: C3H/HeJBir, sample 2

description: Equal amounts (7 micro-gram) of RNA were pooled from four animals. This is an independent replicate of sample 1.


title: 10Mm.177.1


title: 10Mm.172.1


title: 10Mm.171.1


title: C57BL/6J-Il10tm1Cgn, sample 2

description: Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is an independent replicate of sample 1.


title: 10Mm.168.2


title: 10Mm.170.1


title: C57BL/6J, 4 week old, sample 2


title: 10Mm.180.2


title: +/+ no.2

description: Male C57BL/6 mice were treated with ENU to generate single base substitutions,  the variant genome sequences were breed to homozygosity in inbreeding pedigrees, and screened for antinuclear autoantibodies (ANA). The sanroque pedigree contained multiple progeny with ANA of mixed homogeneous nuclear and cytoplasmic immunofluorescence pattern by 12 weeks of age, due to an autosomal recessive gene variant. Comparsion of the gene expression profile of CD4 cells from  Sanroque to wild type was performed.

source_name: CD4 cells from wildtype mouse


title: C3H/HeJ male control

status: Public on Dec 29 2005

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

country: Canada

institute: McGill University

description:
RNA was extracted from lung tissue using a Trizol protocol.  The RNA of 3-5 mice was pooled and one RNA sample of the pool analysed.  Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.

Keywords = mouse, lung, bleomycin, strain differences

source_name: whole right lung


title: C3H/HeJ female 6 weeks, 125

source_name: whole right lung, 6 weeks after a bleomycin dose of 125mg/kg, given by osmotic minipump.


title: C57BL/6 female control


title: C3H/HeJ female 3 weeks, 125

source_name: whole right lung, 3 weeks after a bleomycin dose of 125mg/kg, given by osmotic minipump.


title: C57BL/6 female 3 weeks, 125


title: C3H/HeJ female control


title: C57BL/6 male control


title: C3H/HeJ male 3 weeks, 100

source_name: whole right lung, 3 weeks after a bleomycin dose of 100mg/kg, given by osmotic minipump.


title: C57BL/6 male 3w, 100


title: C3H/HeJ male 6 weeks, 100

source_name: whole right lung, 6 weeks after a bleomycin dose of 100mg/kg, given by osmotic minipump.


title: C57BL/6 female sick, 125

source_name: whole right lung, when moribund after a bleomycin dose of 125mg/kg, given by osmotic minipump.


title: A/J female 6w, 125


title: C57BL/6 male sick, 100

source_name: whole right lung, when moribund after a bleomycin dose of 100mg/kg, given by osmotic minipump.


title: C3H/HeJBir-Il10tm1Cgn, sample 2


title: 10Mm.169.1


title: A/J female 3w, 125


title: A/J male 3w, 100


title: A/J female 3w, 100


title: A/J male 6w, 100


title: A/J male control


title: A/J male 3w, 80

source_name: whole right lung, 3 weeks after a bleomycin dose of 80mg/kg, given by osmotic minipump.


title: Tumor 19A

status: Public on Dec 14 2005

city: Little Rock

first: Radhakrishnan

last: Nagarajan

state: AR

address: 4301 W Markham, Slot 781, Room: 3234

department: Department of Biostatistics

institute: University of Arkansas for Medical Sciences

description: Tumor

source_name: Neck


title: C57BL/6 female 6 weeks, 125


title: Tumor 18A

description: Tumor


title: Tumor 15A

description: Tumor


title: Tumor 17A

description: Tumor


title: Tumor 17B

description: Tumor Sample


title: A/J female control


title: Tumor 16A

description: Tumor


title: Tumor 18B

description: Tumor Sample


title: Tumor 13A

description: Tumor


title: Tumor 19B

description: Tumor Sample


title: Tumor 10A

description: Tumor


title: Tumor 12A

description: Tumor


title: Tumor 15B

description: Tumor Sample


title: Tumor 14A

description: Tumor


title: Tumor 13B

description: Tumor Sample


title: Tumor 14B

description: Tumor Sample


title: Tumor 16B

description: Tumor Sample


title: Tumor 11B

description: Tumor Sample


title: Ren-2 Control 2

status: Public on Dec 15 2005

city: Melbourne

first: Maria

last: Schache

country: Australia

institute: St Vincents Institute

description: Sprague Dawley compared to Ren-2 study

source_name: Ren-2 control kidney total RNA

source_name: Reference kidney total RNA


title: Sprague Dawley Diabetic 1

description: Sprague Dawley compared to Ren-2 study

source_name: Sprague Dawley diabetic kidney total RNA


title: Ren-2 Diabetic 1

description: Sprague Dawley compared to Ren-2 study

source_name: Ren-2 diabetic kidney total RNA


title: Tumor 12B

description: Tumor Sample


title: Sprague Dawley Diabetic 2

description: Sprague Dawley compared to Ren-2 study


title: Sprague Dawley Control 2

description: Sprague Dawley compared to Ren-2 study

source_name: Sprague Dawley control kidney total RNA


title: Tumor 9A

description: Tumor


title: Ren-2 Control 1

description: Sprague Dawley compared to Ren-2 study


title: Tumor 11A

description: Tumor


title: Tumor 9B

description: Tumor Sample


title: Sprague Dawley Control 1

description: Sprague Dawley compared to Ren-2 study


title: Tumor 10B

description: Tumor Sample


title: Ren-2 Diabetic 2

description: Sprague Dawley compared to Ren-2 study


title: Tumor 7B

description: Tumor Sample


title: Tumor 4A

description: Tumor


title: Tumor 8A

description: Tumor


title: Tumor 1A

description: Tumor


title: Tumor 2A

description: Tumor


title: Tumor 7A

description: Tumor


title: Tumor 6B

description: Tumor Sample


title: Tumor5B

description: Tumor Sample


title: Tumor 8B

description: Tumor Sample


title: Tumor 2B

description: Tumor Sample


title: Tumor 6A

description: Tumor


title: Tumor 1B

description: Tumor Sample


title: Tumor 3A

description: Tumor


title: Tumor 4B

description: Tumor Sample


title: Chemosensitive and chemoresistant ovarian cancers RNA profiling

status: Public on Dec 11 2005

city: BOSTON

first: Kuan-Chun

last: Huang

state: MA

address: 221 Longwood Ave. BLI-431

department: OB-GYN

institute: Brigham and Women's Hospital

description:
We analyzed the expression profiles between pooled RNAs prepared from 3 serous ovarian cancers that respond to the taxol-carboplatin treatment and 3 serous ovarian cancers that are resistant to taxol-carboplatin treatment.
Keywords = ovarian cancer
Keywords = chemoresistance

source_name: 3 chemotherapy sensitive ovarian cancers

source_name: 3 chemotherapy resistant ovarian cancers


title: Tumor 3B

description: Tumor Sample


title: 137a: Kidney-liver

status: Public on Dec 02 2005

city: Stillwater

first: Zhongming

last: Chen

state: OK

address: 264 McElroy Hall

department: Deptment of Physiological Sciences

institute: Oklahoma State University

description: Normal organ tissue cDNA hybridizations.

source_name: Kidney

source_name: Liver


title: 137b: Brain-spleen

source_name: Brain

source_name: Spleen


title: 136c: Kidney-heart

source_name: Heart


title: 136b: Brain-liver


title: 135b: Kidney-brain


title: 137c: Heart-lung

source_name: Lung


title: 134c: Spleen-kidney


title: 135a: Spleen-heart


title: 133b: Brain-heart


title: 135c: Liver-lung


title: 134a: Lung-brain


title: 136a: Spleen-lung


title: 133c: Liver-spleen


title: 134b: Heart-Liver


title: 131a: Liver-heart


title: 130c: Liver-kidney


title: 132b: Brain-kidney


title: 132a: Lung-liver


title: 130b: Lung-heart


title: 131c: Kidney-spleen


title: 132c: Heart-spleen


title: 130a: Spleen-brain


title: 129c:Spleen-liver


title: 133a: Lung-kidney


title: 129a: Kidney-lung


title: 129b: Heart-Brain


title: 128c:Liver-brain


title: 128b: Lung-spleen


title: 128a:Heart-kidney


title: 127c: Liver-Kidney


title: 127b:Heart-Spleen

source_name: spleen


title: 125b: Liver-heart


title: 123a: Lung-kidney


title: 127a: Brain-lung


title: 122c:Heart-liver


title: 124b:Heart-lung


title: E12 wt.2

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

institute: The Walter and Eliza Hall Institute

description:
total RNA from wild-type mouse embryo, stage E12
Keywords = RUNX1, AML1, transcription, knockout, network, mouse

source_name: E12 embryo proper


title: 123c: Spleen-liver


title: E12 ko.2

description:
total RNA from Runx1 knockout mouse embryo, stage E12
Keywords = RUNX1, AML1, transcription, knockout, network, mouse


title: 123b:Brain-heart


title: 125c:Kidney-Brain


title: E12 wt.1


title: 121c: Kidney-lung

description: Normal organ tissue hybridization: CHI=Cy3-cDNA, CH2=Alexa 647-cDNA


title: E12 ko.1


title: 125a: Spleen-lung


title: 124c: Liver-brain


title: E8.5 wt.2

description:
total RNA from wild-type mouse embryo, stage E8.5
Keywords = RUNX1, AML1, transcription, knockout, network, mouse

source_name: E8.5 embryo proper


title: E8.5 ko.2

description:
total RNA from Runx1 knockout mouse embryo, stage E8.5
Keywords = RUNX1, AML1, transcription, knockout, network, mouse


title: E8.5 wt.1


title: 121a: Heart-Brain


title: 122b:Lung-spleen


title: 122a: Brain-Kidney


title: E8.5 ko.1


title: 121b: Liver-Spleen


title: 124a: Spleen-kidney


title: 118c: Brain-liver

description:
Normal organ tissue samples. Cy3- Brain cDNA, Alexa 647-liver cDNA.
Keywords = Brain-liver


title: FPD.3

status: Public on Dec 01 2005

description:
RNA from EBV-transformed lymphoblasts derived from a FPD-AML patient is compared to RNA from EBV-transformed lymphoblasts derived from a related unaffected individual.
Keywords = RUNX1, AML1, transcription factor, network, overexpression, haploinsufficiency

source_name: Lymphoblasts from affected FPD-AML individual (V:1)

source_name: Lymphoblasts from unaffected individual (IV:1)


title: 119c: Liver-lung

description:
Normal organ tissue samples. Cy3- Liver cDNA, Alexa 647-lungcDNA.
Keywords = Liver-lung


title: 118a: Lung-heart

description:
Normal organ tissue samples. Cy3- Lung cDNA, Alexa 647-heart cDNA.
Keywords = Lung-heart


title: 118b: Kidney-spleen

description:
Normal organ tissue samples. Cy3- kidney cDNA, Alexa 647-spleen cDNA.
Keywords = Lung-heart


title: FPD.2

source_name: Lymphoblasts from affected FPD-AML individual (V:2)


title: FPD.1

source_name: Lymphoblasts from unaffected individual (V:3)


title: TELRUNX1.2

description:
"HeLa cells infected by adenovirus (serotype 5, MOI 100) expressing EGFP are compared to HeLa cells infected with adenovirus expressing the fusion protein TELRUNX1. The cells are incubated for 48h before extracting total RNA."
Keywords = RUNX1, AML1, transcription factor, network, overexpression, haploinsufficiency

source_name: "HeLa overexpressing EGFP, Cy3"

source_name: "HeLa overexpressing TELRUNX1, Cy5"


title: FPD.4


title: RUNX1/CBFb.6

description:
"HeLa cells infected by adenovirus (serotype 5, MOI 100) expressing EGFP are compared to HeLa cells infected with adenoviruses expressing RUNX1 and CBFb. The cells are incubated for 48h before extracting total RNA."
Keywords = RUNX1, AML1, transcription factor, network, overexpression, haploinsufficiency

source_name: "HeLa overexpressing RUNX1 and CBFb, Cy5"


title: RUNX1/CBFb.7

source_name: "HeLa overexpressing RUNX1 and CBFb, Cy3"

source_name: "HeLa overexpressing EGFP, Cy5"


title: RUNX1/CBFb.5


title: TELRUNX1.3

source_name: "HeLa overexpressing TELRUNX1, Cy3"


title: 119a: Heart-Kidney

description:
Normal organ tissue samples. Cy3- heart cDNA, Alexa 647-kidney cDNA.
Keywords = Heart-Kidney

source_name: Kidney


title: 119b: Spleen-Brain

description:
Normal organ tissue samples. Cy3- spleen cDNA, Alexa 647-brain cDNA.
Keywords = spleen-brain

source_name: Spleen

source_name: Brain


title: RUNX1/CBFb.4


title: TELRUNX1.1


title: LJMJDW17

city: Nashville

first: James

middle: Daryl

last: West

state: TN

address: 23rd Ave at Pierce

department: Biochemistry

institute: Vanderbilt University

description: MeOH control--6h--Replicate #3

source_name: RKO human colorectal carcinoma cells


title: RUNX1/CBFb.2


title: RUNX1/CBFb.3


title: 120c: Kidney-liver

description:
Normal organ tissue samples
Keywords = Lung
Keywords = heart
Lot batch = 10KE118c

source_name: Liver


title: RUNX1/CBFb.1


title: 120b: Spleen-heart

description:
Normal organ tissue samples
Keywords = Spleen-Heart

source_name: Heart


title: LJMJDW9

description: MeOH control--6 h--Replicate #2


title: LJMJDW1

description: MeOH Control--6h--Replicate #1


title: LJMJDW13

description: MeOH control--24h--Replicate #2


title: LJMJDW5

description: MeOH Control--24 h--Replicate #1


title: RIE vs RIE - TGF-beta x 1 hr; #4

city: Houston

first: Carl

last: Allen

state: TX

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

description:
RIE (rat intestinal epithelial) cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #4 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Lot batch = Experiment #4/4

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36418/suppl/GSM36418 - RIE vs RIETGFb #4.TIF.gz

source_name: RIE (rat intestinal epithelial) cells

source_name: RIE cells treated with TGF-beta x 1 hr


title: RIE vs RIE - TGF-beta x 1 hr; #3

description:
RIE (rat intestinal epithelial) cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #3 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Lot batch = Experiment #3/4

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36417/suppl/GSM36417 - RIE vs RIETGFb #3.TIF.gz

source_name: RIE (rat intestinal epithlial) cells


title: RIE-Ras vs RIE-Ras - TGF-beta x 1 hr; #1

description:
RIE-Ras cells were established by stable transfection of the parental cells with pSV2-H-Ras(12V) which contain human sequences encoding the constitutively active H-Ras(12V) protein. RIE-Ras cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #1 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Keywords = Ras

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36419/suppl/GSM36419 - RIE-Ras vs RIE-RASTGFb#1.TIF.gz

source_name: RIE-Ras cells

source_name: RIE-Ras cells treated with TGF-beta x 1 hr


title: 131b: brain-lung

description: Normal organ tissue cDNA hybridizations.

source_name: Lung


title: Tumor 5A

description: Tumor

source_name: Neck


title: RIE-Ras vs RIE-Ras TGF-beta x 1 hr; #4

description:
RIE-Ras cells were established by stable transfection of the parental cells with pSV2-H-Ras(12V) which contain human sequences encoding the constitutively active H-Ras(12V) protein. RIE-Ras cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #4 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Keywords = Ras

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36422/suppl/GSM36422 - RIE-Ras vs RIE-RASTGFb#4.TIF.gz


title: RIE-Ras vs RIE-Ras TGF-beta x 1 hr; #2

description:
RIE-Ras cells were established by stable transfection of the parental cells with pSV2-H-Ras(12V) which contain human sequences encoding the constitutively active H-Ras(12V) protein. RIE-Ras cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #2 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Keywords = Ras

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36420/suppl/GSM36420 - RIE-Ras vs RIE-RASTGFb#2.TIF.gz


title: 120a: Lung-Brain

description:
Noraml organ tissue hybridization of Cy3-lung cDNA and Alexa 647-brain cDNA.
Keywords = Lung
Keywords = heart


title: RIE-Ras vs RIE-Ras TGF-beta x 1 hr; #3

description:
RIE-Ras cells were established by stable transfection of the parental cells with pSV2-H-Ras(12V) which contain human sequences encoding the constitutively active H-Ras(12V) protein. RIE-Ras cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #3 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Keywords = Ras

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36421/suppl/GSM36421 - RIE-Ras vs RIE-RASTGFb#3.TIF.gz


title: RIE vs RIE - TGF-beta x 1 hr; #2

description:
RIE (rat intestinal epithelial) cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #2 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Lot batch = Experiment #2/4

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36416/suppl/GSM36416 - RIE vs RIETGFb #2.TIF.gz

source_name: RIE cells treated with TGF-beta


title: CEA_SGF:ABP029.faible

city: Paris

first: Caroline

last: Dubacq

address: 45 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Strain W303a grown in YPD rich medium to DO 0.5 (channel 1) or grown with 200 mM hydroxyurea (HU) during 2 hours (channel 2). Extraction of RNAs with RNeasy kit (Qiagen). Direct labeling. Hybridization on yeast array slide (CEA France).

organism: Saccharomyces cerevisiae

source_name: Strain W303a (wild-type) grown in YPD to DO 0.5. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain W303a (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ABP035.faible

description: Strain W303a grown in YPD rich medium to DO 0.5 (channel 2) or grown with 200 mM hydroxyurea (HU) during 2 hours (channel 1). Extraction of RNAs with RNeasy kit (Qiagen). Direct labeling. Hybridization on yeast array slide (CEA France).


title: LJMJDW21

description: MeOH control--24h--Replicate #3


title: CEA_SGF:ALX038.faible

description: Strains CM3260 wild-type and Y18daft2 (aft1d aft2d) grown in YPD rich medium to DO 0.5 then grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain Y18daft2 (aft1d aft2d) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain CM3260 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ALX038.fort


title: CEA_SGF:ALX034.faible

description: Strains CM3260 wild-type and Y18daft2 (aft1d aft2d) grown in YPD rich medium to DO 0.5 . Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain CM3260 (wild-type) grown in YPD to DO 0.5. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain Y18daft2 (aft1d aft2d) grown in YPD to DO 0.5. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ALX034.fort


title: CEA_SGF:ALX035.faible


title: CEA_SGF:ALX039.faible

description: Strain BY4741 wild-type and BY4741 aft1? grown in YPD rich medium to DO 0.5 then grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain BY4741 aft1d grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain BY4741 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ALX037.fort

description: Strains BY4741 wild-type or BY4741 aft1? grown in YPD rich medium to DO 0.5 then grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).


title: CEA_SGF:ALX037.faible


title: CEA_SGF:ALX035.fort


title: CEA_SGF:ALX036.faible

description: Strains CM3260 wild-type and Y18daft2 (aft1d aft2d) grown in YPD rich medium to DO 0.5. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).


title: CEA_SGF:ALX039.fort


title: RIE vs RIE - TGF-beta x 1 hr

description:
RIE (rat intestinal epithelial) cells treated with 2 ng/ml of TGF-beta-1 for 1 hr were compared to control cells.  Sample #1 of 4.  Fold-change corresponds to (TGF-beta treated probe signal/Control probe signal).
Keywords = TGF-beta
Lot batch = Experiment #1/4

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM36nnn/GSM36415/suppl/GSM36415 - RIE vs RIETGFb #1.TIF.gz


title: CEA_SGF:ALX036.fort


title: CEA_SGF:AIW013.faible

description: Strain CDY59 (wild-type) grown in YPD rich medium to DO 0.5 or grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain CDY59 (wild-type) grown in YPD to DO 0.5. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain CDY59 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:AIW025.faible

description: Strain CDY59 (wild-type) grown in YPD rich medium to DO 0.5 or grown with 200 mM hydroxyurea (HU) during 1 hour. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain CDY59 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 1 hour. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:AIW013.fort


title: CEA_SGF:AIW022.faible

description: Strain CDY59 (wild-type) grown in YPD rich medium to DO 0.5 or grown with 200 mM hydroxyurea (HU) during 4 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain CDY59 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 4 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:AIW015.fort

description: Strain CDY59 (wild-type) grown in YPD rich medium to DO 0.5 or grown with 200 mM hydroxyurea (HU) during 6 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain CDY59 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 6 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:AIW020.faible


title: CEA_SGF:AIW018.fort


title: CEA_SGF:AIW018.faible


title: CEA_SGF:AIW011.fort


title: CEA_SGF:AIW022.fort


title: CEA_SGF:AIW023.faible


title: CEA_SGF:AIW020.fort


title: CEA_SGF:AIW023.fort


title: CEA_SGF:ABO035.faible


title: CEA_SGF:AIW011.faible


title: CEA_SGF:ABO029.faible


title: CEA_SGF:AIW025.fort


title: CEA_SGF:ALX022_fort

description: Strains BY4742-WT (wild-type) and BY4742-yap1d grown in YPD rich medium to DO 0.5 then grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain BY4742 (wild-type) grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).

source_name: Strain BY4742 yap1d grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ALX021_fort


title: CEA_SGF:ALX021_faible


title: CEA_SGF:ALX019_fort

description: Strains BY4741-WT (wild-type) and BY4741-yap1d grown in YPD rich medium to DO 0.5 then grown with 200 mM hydroxyurea (HU) during 2 hours. Extraction of RNAs with RNeasy kit (Qiagen). Indirect labeling. Hybridization on yeast array slide (CEA France).

source_name: Strain BY4741 yap1d grown in YPD to DO 0.5 then in HU 200 mM for 2 hours. RNA extraction with RNeasy kit (Qiagen).


title: CEA_SGF:ALX020_fort


title: CEA_SGF:ALX020_faible


title: CEA_SGF:ALX019_faible


title: CEA_SGF:ALX022_faible


title: Human colon transversum (HuCo.basl) - mRNA

status: Public on Nov 29 2005

type: MPSS

city: Hayward

first: Lynx

last: Lynx

address: 25861 Industrial Blvd.

institute: Lynx Therapeutics, Inc.

description:
Human colon transversum mRNA (HuCo.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuCo.basl.ful01
Cell type Human colon transversum
Age: unknown
Sex: unknown
number of donors: unknown
Ethnicity: unknown
RNA Source: Lynx
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuCo.basl_ful01.3045F.a	8/4/2002	389658	13066
HuCo.basl_ful01.3045T.f	8/4/2002	320595	11557
HuCo.basl_ful01.3045F.c	8/4/2002	294935	8613
HuCo.basl_ful01.3045T.e	8/4/2002	298802	10817
Run group:
Total Beads successfully sequenced - 1303990
Total Distinct Signatures - 18225
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human colon transversum mRNA


title: Human trachea (HuTr.basl) - mRNA

description:
Human trachea mRNA (HuTr.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuTr.basl.ful01
Cell type Human trachea
Age: 17-70
Sex: male/female
number of donors: 84
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuTr.basl_ful01.3104-7T.a	12/9/2002	556300	25373
HuTr.basl_ful01.3104-6T.b	12/9/2002	303896	17146
HuTr.basl_ful01.3104-7T.b	12/8/2002	501798	25257
HuTr.basl_ful01.3104-6T.c	12/14/2002	325766	18594
HuTr.basl_ful01.3104-7T.c	12/14/2002	502880	24542
HuTr.basl_ful01.3104-6T.d	12/15/2002	370648	19950
HuTr.basl_ful01.3104-7T.d	12/15/2002	303833	20064
HuTr.basl_ful01.3111T.a	12/15/2002	357697	19069
HuTr.basl_ful01.3104-6F.a	12/8/2002	294602	18174
HuTr.basl_ful01.3104-7F.a	12/8/2002	401488	22404
HuTr.basl_ful01.3104-7F.c	12/14/2002	543485	25612
HuTr.basl_ful01.3104-6F.b	12/14/2002	342746	19366
HuTr.basl_ful01.3104-7F.b	12/14/2002	376280	21284
HuTr.basl_ful01.3111F.a	12/15/2002	345430	18750
HuTr.basl_ful01.3111F.b	12/15/2002	474403	22593
Run group:
Total Beads successfully sequenced - 6001252
Total Distinct Signatures - 38615
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human trachea mRNA


title: Human Uterus (HuUt.basl) -

description:
Human Uterus   (HuUt.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuUt.basl.ful01
Cell type Human Uterus
Age: 21-60
Sex: female
number of donors: 8
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuUt.basl_ful01.3373T.b	12/21/2002	346918	21014
HuUt.basl_ful01.3361T.b	12/21/2002	477597	31748
HuUt.basl_ful01.3361F.c	12/21/2002	484448	34254
HuUt.basl_ful01.3361T.a	12/21/2002	549328	33191
HuUt.basl_ful01.3361F.a	12/19/2002	692997	37609
HuUt.basl_ful01.3373T.a	12/15/2002	371710	22204
HuUt.basl_ful01.3054F.c	12/9/2002	340011	18883
HuUt.basl_ful01.3054F.f	12/9/2002	321742	21308
HuUt.basl_ful01.3054F.b	12/8/2002	315789	18359
HuUt.basl_ful01.3054F.d	12/8/2002	318277	17703
HuUt.basl_ful01.3054F.a	12/5/2002	301654	17872
HuUt.basl_ful01.3054F.e	12/3/2002	333240	18246
Run group:
Total Beads successfully sequenced - 4853711
Total Distinct Signatures - 49993
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Uterus


title: Human thymus (HuTm.basl) - mRNA

description:
Human thymus mRNA (HuTm.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuTm.basl.ful01
Cell type Human thymus
Age: 18-32
Sex: male/female
number of donors: 9
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuTm.basl_ful01.3322T.a	12/19/2002	636266	33167
HuTm.basl_ful01.3322T.b	12/19/2002	837729	37574
HuTm.basl_ful01.3322T.c	12/19/2002	835881	35247
HuTm.basl_ful01.3322T.d	12/20/2002	338873	22776
HuTm.basl_ful01.3101-RF.b	12/25/2002	510883	30853
HuTm.basl_ful01.3101-TF.b	12/25/2002	435461	29551
HuTm.basl_ful01.3101-RF.c	12/14/2002	497400	30744
HuTm.basl_ful01.3101-TF.c	12/14/2002	477622	30244
HuTm.basl_ful01.3101-RF.a	12/15/2002	461361	29108
HuTm.basl_ful01.3101-TF.a	12/15/2002	493879	29905
Run group:
Total Beads successfully sequenced - 5525355
Total Distinct Signatures - 54492
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human thymus mRNA


title: Human Stomach (HuSt.basl) -

description:
Human Stomach   (HuSt.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuSt.basl.ful01
Cell type Human Stomach
Age: 28-56
Sex: male/female
number of donors: 7
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuSt.basl_ful01.1244T.a	11/25/2002	283504	9748
HuSt.basl_ful01.1244T.b	12/3/2002	293314	10340
HuSt.basl_ful01.1244T.c	12/3/2002	271690	10393
HuSt.basl_ful01.1244T.d	12/5/2002	407683	8446
HuSt.basl_ful01.1244T.e	12/4/2002	379827	8019
HuSt.basl_ful01.1245F.a	12/2/2002	266074	10013
HuSt.basl_ful01.1245F.b	12/2/2002	258546	9025
HuSt.basl_ful01.1245F.c	12/3/2002	248682	8698
HuSt.basl_ful01.1245F.d	12/4/2002	330825	8367
HuSt.basl_ful01.1245F.e	12/14/2002	341230	8947
Run group:
Total Beads successfully sequenced - 3081375
Total Distinct Signatures - 18679
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Stomach


title: CEA_SGF:AIW015.faible


title: Human thyroid (HuTy.basl) - mRNA

description:
Human thyroid mRNA (HuTy.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuTy.basl.ful01
Cell type Human thyroid
Age: 8-78
Sex: male/female
number of donors: 47
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuTy.basl_ful01.1148T.f	11/23/2002	290867	17392
HuTy.basl_ful01.3439T.a	12/14/2002	459936	23532
HuTy.basl_ful01.3439T.b	12/25/2002	434482	24333
HuTy.basl_ful01.1149F.d	11/22/2002	337857	19232
HuTy.basl_ful01.1149F.f	11/25/2002	313988	18578
HuTy.basl_ful01.3439F.a	12/24/2002	635051	29729
HuTy.basl_ful01.3439F.b	12/15/2002	496073	25679
Run group:
Total Beads successfully sequenced - 2968254
Total Distinct Signatures - 40487
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human thyroid mRNA


title: Human Testis (HuTe.basl) -

description:
Human Testis   (HuTe.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuTe.basl.ful01
Cell type Human Testis
Age: 28-64
Sex: male
number of donors: 25
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuTe.basl_ful01.1263T.a	11/20/2002	251658	24925
HuTe.basl_ful01.1263T.b	11/25/2002	220925	18237
HuTe.basl_ful01.3052T.b	12/8/2002	386249	38437
HuTe.basl_ful01.3052T.a	12/9/2002	426304	40974
HuTe.basl_ful01.3052T.c	12/10/2002	416732	38630
HuTe.basl_ful01.3052F.a	12/9/2002	431688	39852
HuTe.basl_ful01.3052F.b	12/9/2002	449586	41210
HuTe.basl_ful01.3052F.c	12/10/2002	425433	36687
HuTe.basl_ful01.3052F.d	12/14/2002	342235	37069
Run group:
Total Beads successfully sequenced - 3350810
Total Distinct Signatures - 65706
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Testis


title: Human Spinal Cord (HuSC.basl) -

description:
Human Spinal Cord   (HuSC.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuSC.basl.ful01
Cell type Human Spinal Cord
Age: 25-59
Sex: male/female
number of donors: 22
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuSC.basl_ful01.3075T.a	12/8/2002	239249	11896
HuSC.basl_ful01.3382T.b	12/22/2002	462221	27356
HuSC.basl_ful01.3382T.c	12/22/2002	822895	31904
HuSC.basl_ful01.3382F.a	12/21/2002	566298	27220
HuSC.basl_ful01.3382F.b	12/14/2002	586348	28462
HuSC.basl_ful01.3382F.c	12/23/2002	904328	31675
Run group:
Total Beads successfully sequenced - 3581339
Total Distinct Signatures - 42852
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Spinal Cord


title: Human Small Intestine (HuSI.basl) -

description:
Human Small Intestine   (HuSI.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuSI.basl.ful01
Cell type Human Small Intestine
Age: 15-60
Sex: male/female
number of donors: 11
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuSI.basl_ful01.1242T.c	12/3/2002	332357	14482
HuSI.basl_ful01.1242T.d	12/3/2002	350397	15162
HuSI.basl_ful01.1242T.a	12/3/2002	237411	12068
HuSI.basl_ful01.1242T.b	12/3/2002	232174	11837
HuSI.basl_ful01.3354T.b	12/23/2002	523214	27448
HuSI.basl_ful01.3354T.a	12/26/2002	532194	27633
HuSI.basl_ful01.3354T.c	12/24/2002	530231	27873
HuSI.basl_ful01.3354F.b	12/23/2002	518788	26371
HuSI.basl_ful01.3354F.a	12/23/2002	607788	28285
HuSI.basl_ful01.3354F.c	12/24/2002	382954	23438
Run group:
Total Beads successfully sequenced - 4247508
Total Distinct Signatures - 40072
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Small Intestine


title: Human Salivary Gland (HuSG.basl) -

description:
Human Salivary Gland   (HuSG.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuSG.basl.ful01
Cell type Human Salivary Gland
Age: 13-78
Sex: male/female
number of donors: 43
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuSG.basl_ful01.3355T.a	12/20/2002	559722	13853
HuSG.basl_ful01.3355T.b	12/20/2002	573410	14620
HuSG.basl_ful01.3355T.d	12/19/2002	592203	14153
HuSG.basl_ful01.3355T.e	12/20/2002	435846	12535
HuSG.basl_ful01.3355T.c	12/21/2002	614603	14058
HuSG.basl_ful01.3355F.a	12/20/2002	542725	12650
HuSG.basl_ful01.3355F.b	12/20/2002	638574	13302
HuSG.basl_ful01.3355F.c	12/19/2002	521126	12528
HuSG.basl_ful01.3355F.d	12/19/2002	524833	13367
Run group:
Total Beads successfully sequenced - 5003042
Total Distinct Signatures - 23729
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Salivary Gland


title: Human retina (HuRe.basl) - mRNA

description:
Human retina mRNA (HuRe.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuRe.basl.ful01
Cell type Human retina
Age: 16-75
Sex: male/female
number of donors: 76
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuRe.basl_ful01.3074T.b	12/9/2002	302285	19981
HuRe.basl_ful01.3074T.a	12/9/2002	334256	21355
HuRe.basl_ful01.3074T.d	12/14/2002	312143	18703
HuRe.basl_ful01.3074T.e	12/15/2002	405138	22562
HuRe.basl_ful01.3074T.f	12/15/2002	397098	22373
HuRe.basl_ful01.3074T.g	12/15/2002	384977	21857
HuRe.basl_ful01.3074F.b	12/10/2002	373376	19614
HuRe.basl_ful01.3074F.a	12/9/2002	383423	22431
HuRe.basl_ful01.3074F.c	12/10/2002	374069	20078
HuRe.basl_ful01.3074F.e	12/15/2002	398294	22758
HuRe.basl_ful01.3074F.f	12/15/2002	264756	19512
HuRe.basl_ful01.3074F.g	12/15/2002	321629	21074
Run group:
Total Beads successfully sequenced - 4251444
Total Distinct Signatures - 37188
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human retina mRNA


title: Human pancreas (HuPn.basl) -

description:
Human pancreas   (HuPn.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuPn.basl.ful01
Cell type Human pancreas
Age: 25-59
Sex: male/female
number of donors: 20
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuPn.basl_ful01.1224T.a	11/23/2002	304739	6577
HuPn.basl_ful01.3055T.a	12/5/2002	388063	4926
HuPn.basl_ful01.3055T.b	12/8/2002	411868	5053
HuPn.basl_ful01.3055T.c	12/7/2002	396092	4601
HuPn.basl_ful01.3424T.a	12/23/2002	701976	13644
HuPn.basl_ful01.3424T.b	12/25/2002	594078	12450
HuPn.basl_ful01.1225F.b	11/26/2002	303632	5567
HuPn.basl_ful01.3055F.a	12/8/2002	299961	3350
HuPn.basl_ful01.3055F.b	12/7/2002	285890	3031
HuPn.basl_ful01.3055F.c	12/7/2002	355559	3327
HuPn.basl_ful01.3055F.d	12/7/2002	336441	3220
HuPn.basl_ful01.3424F.b	12/23/2002	518866	10272
HuPn.basl_ful01.3424F.a	12/23/2002	426952	9089
Run group:
Total Beads successfully sequenced - 5324117
Total Distinct Signatures - 16238
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human pancreas


title: Human Spleen (HuSp.basl) -

description:
Human Spleen   (HuSp.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuSp.basl.ful01
Cell type Human Spleen
Age: 24-61
Sex: male/female
number of donors: 6
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuSp.basl_ful01.3332T.a	12/19/2002	660778	34936
HuSp.basl_ful01.3332T.b	12/19/2002	674214	35652
HuSp.basl_ful01.3332T.c	12/19/2002	351659	26438
HuSp.basl_ful01.3332F.a	12/20/2002	738376	36241
HuSp.basl_ful01.3332F.b	12/20/2002	722998	34163
Run group:
Total Beads successfully sequenced - 3148025
Total Distinct Signatures - 52274
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Spleen


title: Human Mammary Gland (HuMG.basl) -

description:
Human Mammary Gland   (HuMG.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuMG.basl.ful01
Cell type Human Mammary Gland
Age: 24-43
Sex: female
number of donors: 2
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuMG.basl_ful01.3046T.a	7/31/2002	373380	14111
HuMG.basl_ful01.3046T.b	7/31/2002	373794	14386
HuMG.basl_ful01.3046T.c	7/31/2002	313669	12939
HuMG.basl_ful01.3046T.d	7/31/2002	333681	13182
HuMG.basl_ful01.3046T.e	7/31/2002	236924	16831
HuMG.basl_ful01.3046T.f	7/31/2002	287488	18294
HuMG.basl_ful01.3046F.c	7/31/2002	331361	13028
HuMG.basl_ful01.3046F.d	7/31/2002	343455	12837
Run group:
Total Beads successfully sequenced - 2593752
Total Distinct Signatures - 26029
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Mammary Gland


title: Human monocytes (HuMo.basl) - mRNA

description:
Human monocytes mRNA (HuMo.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuMo.basl.ful03
Cell type Human monocytes
Age: unknown
Sex: unknown
number of donors: 4
Ethnicity: unknown
RNA Source: Lynx
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuMo.basl_ful03.3388T.a	5/22/2002	342164	16982
HuMo.basl_ful03.3388T.d	5/22/2002	394692	19772
HuMo.basl_ful03.3390F.a	5/22/2002	520525	22213
HuMo.basl_ful03.3388T.c	5/22/2002	438940	19998
HuMo.basl_ful03.3390F.c	5/22/2002	412660	20241
HuMo.basl_ful03.3388T.b	5/22/2002	326051	16955
HuMo.basl_ful03.3390F.b	5/22/2002	445530	21316
Run group:
Total Beads successfully sequenced - 2880562
Total Distinct Signatures - 32688
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human monocytes mRNA


title: Human Lung (HuLu.basl) -

description:
Human Lung   (HuLu.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuLu.basl.ful01
Cell type Human Lung
Age: 25-40
Sex: male
number of donors: 5
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuLu.basl_ful01.3379T.a	12/14/2002	360909	21690
HuLu.basl_ful01.3379T.b	12/21/2002	350931	20859
HuLu.basl_ful01.3379T.c	12/23/2002	643980	26947
HuLu.basl_ful01.1266F.b	11/25/2002	285302	13542
HuLu.basl_ful01.3379F.b	12/14/2002	490064	25923
HuLu.basl_ful01.3379F.a	12/21/2002	511580	26841
HuLu.basl_ful01.3379F.c	12/22/2002	588928	27513
Run group:
Total Beads successfully sequenced - 3231694
Total Distinct Signatures - 40829
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Lung


title: Human Prostate (HuPr.basl) -

description:
Human Prostate   (HuPr.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuPr.basl.ful01
Cell type Human Prostate
Age: 14-57
Sex: male
number of donors: 47
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuPr.basl_ful01.3032T.c	12/3/2002	265772	15788
HuPr.basl_ful01.3032F.a	12/2/2002	299421	20814
HuPr.basl_ful01.3032F.c	12/3/2002	282595	18003
HuPr.basl_ful01.3032F.b	12/3/2002	300018	19070
HuPr.basl_ful01.3032F.d	12/3/2002	363133	18338
HuPr.basl_ful01.3032F.e	12/3/2002	361865	18004
HuPr.basl_ful01.3064F.a	12/7/2002	421587	19013
HuPr.basl_ful01.3064F.b	12/6/2002	379256	18428
HuPr.basl_ful01.3064F.d	12/7/2002	346550	20186
HuPr.basl_ful01.3064F.e	12/9/2002	157864	14627
Run group:
Total Beads successfully sequenced - 3178061
Total Distinct Signatures - 31743
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human Prostate


title: Human heart (HuHe.basl) - mRNA

description:
Human heart mRNA (HuHe.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuHe.basl.ful01
Cell type Human heart
Age: 19-54
Sex: male
number of donors: 4
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuHe.basl_ful01.3384T.a	12/21/2002	507965	24754
HuHe.basl_ful01.3384T.b	12/21/2002	487520	24547
HuHe.basl_ful01.1183F.a	11/20/2002	321393	16797
HuHe.basl_ful01.1183F.b	12/14/2002	264536	15447
HuHe.basl_ful01.3384F.a	12/20/2002	567954	25444
HuHe.basl_ful01.3384F.b	12/21/2002	592511	26097
HuHe.basl_ful01.3384F.c	12/22/2002	900751	30519
Run group:
Total Beads successfully sequenced - 3642630
Total Distinct Signatures - 40414
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human heart mRNA


title: Human pituitary gland (HuPG.basl) -

description:
Human pituitary gland   (HuPG.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuPG.basl.ful01
Cell type Human pituitary gland
Age: 15-75
Sex: male/female
number of donors: 87
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuPG.basl_ful01.3056T.a	12/4/2002	289004	16071
HuPG.basl_ful01.3056T.b	12/8/2002	290604	15964
HuPG.basl_ful01.3056T.c	12/7/2002	287701	15691
HuPG.basl_ful01.3056T.h	12/14/2002	325022	24519
HuPG.basl_ful01.3056F.e	12/8/2002	299331	19370
HuPG.basl_ful01.3056F.a	12/6/2002	302701	17593
HuPG.basl_ful01.3056F.b	12/6/2002	321376	18806
HuPG.basl_ful01.3056F.d	12/7/2002	306498	19701
Run group:
Total Beads successfully sequenced - 2422237
Total Distinct Signatures - 37075
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human pituitary gland


title: Human placenta (HuPl.basl) - mRNA

description:
Human placenta mRNA (HuPl.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuPl.basl.ful01
Cell type Human placenta
Age: 23-35
Sex: female
number of donors: 4
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuPl.basl_ful01.1134T.d	11/19/2002	353869	12906
HuPl.basl_ful01.1134T.c	11/19/2002	328537	10442
HuPl.basl_ful01.1134T.e	11/25/2002	314346	15431
HuPl.basl_ful01.1135F.a	11/22/2002	376200	13030
HuPl.basl_ful01.1135F.c	11/19/2002	405457	14450
HuPl.basl_ful01.1135F.d	11/20/2002	439634	13763
Run group:
Total Beads successfully sequenced - 2218043
Total Distinct Signatures - 23101
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human placenta mRNA


title: Human fetal brain (HuFB.basl) - mRNA

description:
Human fetal brain mRNA (HuFB.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuFB.basl.ful35
Cell type Human fetal brain
Age: 6-32weeks
Sex: male/female
number of donors: 24
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuFB.basl_ful35.3451T.c	12/25/2002	360202	25248
HuFB.basl_ful35.3451F.a	12/25/2002	299116	24284
HuFB.basl_ful35.3451F.b	12/26/2002	334872	21527
HuFB.basl_ful35.3451F.c	12/25/2002	474373	25791
Run group:
Total Beads successfully sequenced - 1468563
Total Distinct Signatures - 35980
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human fetal brain mRNA


title: Human brain - cerebellum (HuBr.cere) - mRNA

description:
Human brain - cerebellum mRNA (HuBr.cere) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBr.cere.ful01
Cell type Human brain - cerebellum
Age:  16-70
Sex: male/female
number of donors: 24
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBr.cere_ful01.3060T.f	12/16/2002	218066	16757
HuBr.cere_ful01.3060T.g	12/16/2002	227641	17015
HuBr.cere_ful01.3060F.b	12/4/2002	295775	18847
HuBr.cere_ful01.3060F.c	12/3/2002	313696	19458
HuBr.cere_ful01.3060F.f	12/5/2002	228033	14840
HuBr.cere_ful01.3060F.g	12/15/2002	472155	35686
Run group:
Total Beads successfully sequenced - 1755366
Total Distinct Signatures - 38556
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human brain - cerebellum mRNA


title: Human brain - hypothalmus (HuBr.hypo) - mRNA

description:
Human brain - hypothalmus mRNA (HuBr.hypo) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBr.hypo.ful01
Cell type Human brain - hypothalmus
Age: 22-70
Sex: male/female
number of donors: 63
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBr.hypo_ful01.3076T.a	12/9/2002	352460	20285
HuBr.hypo_ful01.3076T.d	12/16/2002	303997	19748
HuBr.hypo_ful01.3076T.f	12/15/2002	402514	21509
HuBr.hypo_ful01.3076T.g	12/15/2002	411517	21188
HuBr.hypo_ful01.3076T.h	12/15/2002	314890	20355
HuBr.hypo_ful01.3076F.b	12/16/2002	675451	26509
HuBr.hypo_ful01.3076F.a	12/9/2002	511577	23829
HuBr.hypo_ful01.3076F.c	12/14/2002	452342	23069
HuBr.hypo_ful01.3076F.d	12/14/2002	352686	21169
HuBr.hypo_ful01.3076F.g	12/15/2002	517667	23550
HuBr.hypo_ful01.3076F.f	12/15/2002	438460	23027
Run group:
Total Beads successfully sequenced - 4733561
Total Distinct Signatures - 37930
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human brain - hypothalmus mRNA


title: Human brain - thalamus (HuBr.thal) - mRNA

description:
Human brain - thalamus mRNA (HuBr.thal) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBr.thal.ful01
Cell type Human brain - thalamus
Age: 32-75
Sex: male/female
number of donors: 10
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBr.thal_ful01.3065T.a	12/17/2002	343474	19149
HuBr.thal_ful01.3403T.a	12/24/2002	194247	15718
HuBr.thal_ful01.3403T.b	12/25/2002	359238	22072
HuBr.thal_ful01.3065F.c	12/17/2002	265533	16469
HuBr.thal_ful01.3065F.d	12/17/2002	302795	17221
HuBr.thal_ful01.3403F.b	12/23/2002	361844	20583
HuBr.thal_ful01.3403F.a	12/23/2002	415148	21938
Run group:
Total Beads successfully sequenced - 2242279
Total Distinct Signatures - 33606
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human brain - thalamus mRNA


title: Human kidney (HuKi.basl) - mRNA

description:
Human kidney mRNA (HuKi.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuKi.basl.ful01
Cell type Human kidney
Age: 32-75
Sex: male/female
number of donors: 10
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuKi.basl_ful01.1184T.a	11/22/2002	244808	11351
HuKi.basl_ful01.1184T.c	11/19/2002	184622	10650
HuKi.basl_ful01.1184T.d	11/19/2002	141295	9774
HuKi.basl_ful01.1184T.e	11/22/2002	227357	13674
HuKi.basl_ful01.1185F.b	11/20/2002	274063	10761
HuKi.basl_ful01.1185F.c	11/19/2002	202287	15883
HuKi.basl_ful01.1185F.d	11/19/2002	246552	17419
HuKi.basl_ful01.1185F.a	11/20/2002	298885	12749
HuKi.basl_ful01.1185F.e	11/25/2002	326833	20563
HuKi.basl_ful01.1185F.f	11/26/2002	352668	19631
Run group:
Total Beads successfully sequenced - 2499370
Total Distinct Signatures - 30716
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human kidney mRNA


title: Human peripheral blood lymphocytes (HuPB.ctrl) - mRNA

description:
Human peripheral blood lymphocytes mRNA (HuPB.ctrl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuPB.ctrl.ful01
Cell type Human peripheral blood lymphocytes
Age: unknown
Sex: unknown
number of donors: 4
Ethnicity: unknown
RNA Source: Lynx
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuPB.ctrl_ful01.3809F.a	8/9/2002	668308	17834
HuPB.ctrl_ful01.3809T.a	8/9/2002	392964	13540
HuPB.ctrl_ful01.3809T.b	8/7/2002	457394	14445
HuPB.ctrl_ful01.3809F.b	8/7/2002	502387	15895
Run group:
Total Beads successfully sequenced - 2021053
Total Distinct Signatures - 23921
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human peripheral blood lymphocytes mRNA


title: Human bone marrow (HuBM.basl) - mRNA

description:
Human bone marrow mRNA (HuBM.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBM.basl.ful01
Cell type Human bone marrow
Age: 22-70
Sex: male/female
number of donors: 51
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBM.basl_ful01.995T.a	11/19/2002	344908	12047
HuBM.basl_ful01.995T.b	11/19/2002	379892	9937
HuBM.basl_ful01.939T.b	11/21/2002	310541	9401
HuBM.basl_ful01.939T.c	11/19/2002	282082	9108
HuBM.basl_ful01.995F.a	11/19/2002	481711	26523
HuBM.basl_ful01.940F.b	11/19/2002	468522	23053
HuBM.basl_ful01.995F.d	12/9/2002	232618	14985
Run group:
Total Beads successfully sequenced - 2500274
Total Distinct Signatures - 30704
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human bone marrow mRNA


title: Human brain - corpus callosum (HuBr.CoCa) - mRNA

description:
Human brain - corpus callosum mRNA (HuBr.CoCa) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBr.CoCa.ful01
Cell type Human brain - corpus callosum
Age: 19-76
Sex: male/female
number of donors: 46
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBr.CoCa_ful01.3441T.a	12/24/2002	471456	28775
HuBr.CoCa_ful01.3441T.b	12/25/2002	416200	26263
HuBr.CoCa_ful01.3441T.c	12/25/2002	409429	24422
HuBr.CoCa_ful01.3071F.a	12/7/2002	274764	15922
HuBr.CoCa_ful01.3071F.e	12/15/2002	370411	28720
HuBr.CoCa_ful01.3441F.a	12/24/2002	513943	28705
HuBr.CoCa_ful01.3441F.b	12/25/2002	472806	25361
HuBr.CoCa_ful01.3441F.c	12/26/2002	536651	25527
Run group:
Total Beads successfully sequenced - 3465660
Total Distinct Signatures - 44341
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human brain - corpus callosum mRNA


title: 1wB6_MB3

status: Public on Nov 28 2005

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Age and sex related differences in C57BL/6 brain were explored in 1w and 8w mice

source_name: 1 week male brain#3-C57BL/6


title: 8wB6_FB2

source_name: 8 week female brain#2-C57BL/6


title: 1wB6_MB1

source_name: 1 week male brain#1-C57BL/6


title: 8wB6_MB2

source_name: 8 week male brain#2-C57BL/6


title: 1wB6_FB3

source_name: 1 week female brain#3-C57BL/6


title: 1wB6_FB2

source_name: 1week female brain#2-C57BL/6


title: Human brain - caudate nucleus (HuBr.CaNu) - mRNA

description:
Human brain - caudate nucleus mRNA (HuBr.CaNu) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBr.CaNu.ful01
Cell type Human brain - caudate nucleus
Age: 18-78
Sex: male/female
number of donors: 57
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBr.CaNu_ful01.3377T.d	12/22/2002	574080	24534
HuBr.CaNu_ful01.3377T.e	12/23/2002	606910	26118
HuBr.CaNu_ful01.3377F.a	12/19/2002	559050	26648
HuBr.CaNu_ful01.3377F.b	12/19/2002	605586	26345
HuBr.CaNu_ful01.3377F.c	12/22/2002	650119	29130
Run group:
Total Beads successfully sequenced - 2995745
Total Distinct Signatures - 40475
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human brain - caudate nucleus mRNA


title: 1wB6_FB1

source_name: 1 week brain-female#1 C57BL/6


title: Human bladder (HuBl.basl) -

description:
Human bladder   (HuBl.basl) The mRNA was analyzed using Agilent's Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library HuBl.basl.ful01
Cell type Human bladder
Age: 22-70
Sex: male/female
number of donors: 26
Ethnicity: Caucasian
RNA Source: Clontech
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
HuBl.basl_ful01.1230T.b	12/2/2002	268190	18388
HuBl.basl_ful01.1230T.a	12/2/2002	277629	20383
HuBl.basl_ful01.1230T.c	12/3/2002	269676	18276
HuBl.basl_ful01.1230T.e	12/16/2002	326097	20726
HuBl.basl_ful01.1230T.f	12/16/2002	247641	14161
HuBl.basl_ful01.1231F.a	12/3/2002	352897	22039
HuBl.basl_ful01.1231F.b	12/3/2002	325285	20995
HuBl.basl_ful01.1231F.c	12/4/2002	471174	20261
Run group:
Total Beads successfully sequenced - 2538589
Total Distinct Signatures - 35314
This data is also available on our signature genome browser at http://SGB.lynxgen.com
and is described in details in 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004
Keywords = MPSS

source_name: Human bladder