title: No.6_aorta

status: Public on Nov 27 2013

city: TSUKUBA CITY

first: Keiichi

last: Minami

state: IBARAKI

address: 17-2 WADAI

department: Tsukuba Research Institute

country: Japan

institute: Ono pharmaceutical

description: miRNA expression ATLAS

hyb_protocol: Whole volume of Cy3-labelled RNA was incubated at 100°C for 5 minutes in a reaction volume of 45 ul containing 1x Agilent blocking agent and Hybridization Spike-In and Hi-RPM Hybridization Buffer following the manufacturer's instructions. On completion of the incubation,  samples were hybridized to Rat miRNA microarray 8 x 15k, miRBase 16.0 including miRBase 15.0 probes for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 8x16k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and eXtended Dynamic Range Scan Mode;  Hi = 100 %, Lo = 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters.

organism: Rattus norvegicus

source_name: Animal No.6, 52. aorta

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.1 ug RNA using the miRNA Complete Laveling and Hyb Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the miRNeasy kit (QIAGEN, Hilden, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Saline perfusion before tissue collection (Animal No. 4-6), NO treatment (Animal No. 1-3)

value: aorta

value: 10 weeks

tag: strain

value: Sprague-Dawley


title: No.6_vein

type: RNA

description: miRNA expression ATLAS

molecule: total RNA

source_name: Animal No.6, 53. vein

tag: tissue

value: vein

tag: age

tag: gender

value: male


title: 11181 T

status: Public on Feb 19 2014

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

description: Gene expression data from colon tumor and adjacent noncancerous tissue

hyb_protocol: Following fragmentation  cRNA were hybridized using a Affymetrix U133A arrays according to manufacterer's specifications

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

data_processing: The data were imported and normalized using Partek.  Arrays were in two batches and the batch correction function of Partek was used to normalize that difference away.

label: biotin

organism: Homo sapiens

source_name: Colon tissue from patient with colon cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

tag: microarray batch

value: A

tag: rs5995355 genotype

value: AG

value: Tumor


title: No.6_white adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.6, 54. white adipose tissue

value: white adipose tissue


title: 11181 N

value: adjacent nontumor


title: 10167 T

value: GG


title: 11642 T


title: 11148 T


title: 10212 N

value: AA


title: 11275 T


title: 12031 N


title: 11157 N


title: No.6_interseptum

description: miRNA expression ATLAS

source_name: Animal No.6, 50. interseptum

value: interseptum


title: No.6_bone marrow

description: miRNA expression ATLAS

source_name: Animal No.6, 51. bone marrow

value: bone marrow


title: No.6_musculus soleus

description: miRNA expression ATLAS

source_name: Animal No.6, 48. soleus muscle

value: musculus soleus


title: No.6_ischial nerve

description: miRNA expression ATLAS

source_name: Animal No.6, 49. ischial nerve

value: ischial nerve


title: No.6_gastrocnemial muscle

description: miRNA expression ATLAS

source_name: Animal No.6, 47. gastrocnemial muscle

value: gastrocnemial muscle


title: No.6_brown adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.6, 55. brown adipose tissue

value: brown adipose tissue


title: 10515 N


title: 10212 T


title: 10167 N


title: No.6_spinal cord_cervical

description: miRNA expression ATLAS

source_name: Animal No.6, 43. spinal cord_cervical

value: spinal cord_cervical

value: 10 weeks


title: No.6_spinal cord_pectoral

description: miRNA expression ATLAS

source_name: Animal No.6, 44. spinal cord_pectoral

value: spinal cord_pectoral

value: Sprague-Dawley


title: No.6_femoris muscle

description: miRNA expression ATLAS

source_name: Animal No.6, 46. femoris muscle

value: femoris muscle

value: male


title: No.6_spinal cord_pars lumbalis

description: miRNA expression ATLAS

source_name: Animal No.6, 45. spinal cord_pars lumbalis

value: spinal cord_pars lumbalis


title: No.6_cerebellum

description: miRNA expression ATLAS

source_name: Animal No.6, 40. cerebellum

value: cerebellum


title: No.6_Pituitary gland

description: miRNA expression ATLAS

source_name: Animal No.6, 42. pituitary gland

value: Pituitary gland


title: No.6_medulla oblongata

description: miRNA expression ATLAS

source_name: Animal No.6, 41. medulla oblongata

value: medulla oblongata


title: No.6_cerebrum_cerebral cortex

description: miRNA expression ATLAS

source_name: Animal No.6, 37. cerebrum_cerebral cortex

value: cerebrum_cerebral cortex


title: No.6_cerebrum_hippocampus

description: miRNA expression ATLAS

source_name: Animal No.6, 38. cerebrum_hippocampus


title: No.6_optic nerve

description: miRNA expression ATLAS

source_name: Animal No.6, 36. optic nerve

value: optic nerve


title: No.5_vein

description: miRNA expression ATLAS

source_name: Animal No.5, 53. vein

value: vein


title: No.5_aorta

description: miRNA expression ATLAS

source_name: Animal No.5, 52. aorta

value: aorta


title: No.6_eyeball

description: miRNA expression ATLAS

source_name: Animal No.6, 34. eyeball

value: eyeball


title: No.5_brown adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.5, 55. brown adipose tissue


title: No.6_epididymis

description: miRNA expression ATLAS

source_name: Animal No.6, 33. epididymis

value: epididymis


title: No.6_Harderian gland

description: miRNA expression ATLAS

source_name: Animal No.6, 35. harderian gland

value: Harderian gland


title: No.6_prostate_other

description: miRNA expression ATLAS

source_name: Animal No.6, 31. prostate_other


title: No.5_white adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.5, 54. white adipose tissue

value: white adipose tissue


title: No.6_testicle

description: miRNA expression ATLAS

source_name: Animal No.6, 32. testis

value: testicle

value: 10 weeks


title: No.6_cerebrum_Thalamus

description: miRNA expression ATLAS

source_name: Animal No.6, 39. cerebrum_thalamus

value: Sprague-Dawley


title: No.5_femoris muscle

description: miRNA expression ATLAS

source_name: Animal No.6, 46. femoris muscle

value: femoris muscle


title: No.5_gastrocnemial muscle

description: miRNA expression ATLAS

source_name: Animal No.6, 47. gastrocnemial muscle

value: gastrocnemial muscle

value: male


title: No.5_musculus soleus

description: miRNA expression ATLAS

source_name: Animal No.6, 48. soleus muscle

value: musculus soleus


title: No.5_interseptum

description: miRNA expression ATLAS

source_name: Animal No.5, 50. interseptum

value: interseptum


title: No.5_ischial nerve

description: miRNA expression ATLAS

source_name: Animal No.5, 49. ischial nerve

value: ischial nerve


title: No.5_bone marrow

description: miRNA expression ATLAS

source_name: Animal No.5, 51. bone marrow

value: bone marrow


title: No.5_cerebellum

description: miRNA expression ATLAS

source_name: Animal No.5, 40. cerebellum

value: cerebellum


title: No.5_medulla oblongata

description: miRNA expression ATLAS

source_name: Animal No.6, 41. medulla oblongata

value: medulla oblongata


title: No.5_Pituitary gland

description: miRNA expression ATLAS

source_name: Animal No.6, 42. pituitary gland

value: Pituitary gland


title: No.5_spinal cord_pectoral

description: miRNA expression ATLAS

source_name: Animal No.6, 44. spinal cord_pectoral

value: spinal cord_pectoral


title: No.5_cerebrum_Thalamus

description: miRNA expression ATLAS

source_name: Animal No.5, 39. cerebrum_thalamus


title: No.5_spinal cord_cervical

description: miRNA expression ATLAS

source_name: Animal No.6, 43. spinal cord_cervical

value: spinal cord_cervical


title: No.5_spinal cord_pars lumbalis

description: miRNA expression ATLAS

source_name: Animal No.6, 45. spinal cord_pars lumbalis

value: spinal cord_pars lumbalis


title: Flagellin treated nasal mucosa of wild type mouse (C56BL/6)

status: Public on Dec 18 2013

city: Seoul

first: JUNGHEE

last: JOO

address: 134 Shinchon-dong, Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data was normalized using the RMA(Robust Multi-Average)algorithm implemented in Affymetrix expression console version 1.1 software
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

organism: Mus musculus

source_name: nasal mucosa of wild type mouse

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse nasal mucosa were harvested from 8wk mouse

extract_protocol: nasal septum and turbinate’s mucosa from each side was gently elevated off the cartilage and bone and total RNA was isolated from these tissues using TRIzol

treatment_protocol: Flagellin and other inhibitors were administered intranasally. For intranasal (i.n.) instillations, 25 ul of solution were applied drop-wise into each nostril.

tag: genotype/variation

value: wild-type

tag: treatment

value: Flagellin


title: No.5_cerebrum_cerebral cortex

description: miRNA expression ATLAS

source_name: Animal No.5, 37. cerebrum_cerebral cortex

value: cerebrum_cerebral cortex

value: 10 weeks


title: No.5_cerebrum_hippocampus

description: miRNA expression ATLAS

source_name: Animal No.5, 38. cerebrum_hippocampus

value: Sprague-Dawley


title: PBS treated nasal mucosa of Duox2 knockout (Duox2-/-) mouse

source_name: nasal mucosa of Duox2-/- mouse

value: PBS


title: Flagellin treated nasal mucosa of Duox2 knockout (Duox2-/-)  mouse


title: No.4_femoris muscle

description: miRNA expression ATLAS

source_name: Animal No.4, 46. femoris muscle

value: femoris muscle

value: male


title: No.4_bone marrow

description: miRNA expression ATLAS

source_name: Animal No.4, 51. bone marrow


title: No.4_musculus soleus

description: miRNA expression ATLAS

source_name: Animal No.4, 48. soleus muscle

value: musculus soleus


title: No.4_vein

description: miRNA expression ATLAS

source_name: Animal No.4, 53. vein

value: vein


title: No.4_aorta

description: miRNA expression ATLAS

source_name: Animal No.4, 52. aorta

value: aorta


title: No.4_cerebrum_hippocampus

description: miRNA expression ATLAS

source_name: Animal No.4, 38. cerebrum_hippocampus


title: No.4_cerebrum_cerebral cortex

description: miRNA expression ATLAS

source_name: Animal No.4, 37. cerebrum_cerebral cortex


title: No.4_brown adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.4, 55. brown adipose tissue

value: brown adipose tissue


title: No.4_white adipose tissue

description: miRNA expression ATLAS

source_name: Animal No.4, 54. white adipose tissue

value: white adipose tissue


title: No.4_gastrocnemial muscle

description: miRNA expression ATLAS

source_name: Animal No.4, 47. gastrocnemial muscle

value: gastrocnemial muscle


title: PBS treated nasal mucosa of wild type mouse (C56BL/6)


title: No.4_cerebrum_Thalamus

description: miRNA expression ATLAS

source_name: Animal No.4, 39. cerebrum_thalamus


title: No.4_medulla oblongata

description: miRNA expression ATLAS

source_name: Animal No.4, 41. medulla oblongata

value: medulla oblongata


title: No.4_spinal cord_cervical

description: miRNA expression ATLAS

source_name: Animal No.4, 43. spinal cord_cervical

value: spinal cord_cervical


title: No.4_Pituitary gland

description: miRNA expression ATLAS

source_name: Animal No.4, 42. pituitary gland

value: Pituitary gland


title: No.4_ischial nerve

description: miRNA expression ATLAS

source_name: Animal No.4, 49. ischial nerve

value: ischial nerve


title: No.4_spinal cord_pectoral

description: miRNA expression ATLAS

source_name: Animal No.4, 44. spinal cord_pectoral

value: spinal cord_pectoral


title: No.4_spinal cord_pars lumbalis

description: miRNA expression ATLAS

source_name: Animal No.4, 45. spinal cord_pars lumbalis

value: spinal cord_pars lumbalis


title: No.4_interseptum

description: miRNA expression ATLAS

source_name: Animal No.4, 50. interseptum

value: interseptum

value: 10 weeks


title: No.5_testicle

description: miRNA expression ATLAS

source_name: Animal No.5, 32. testis

value: testicle

value: Sprague-Dawley


title: No.5_epididymis

description: miRNA expression ATLAS

source_name: Animal No.5, 33. epididymis

value: epididymis

value: male


title: No.5_optic nerve

description: miRNA expression ATLAS

source_name: Animal No.5, 36. optic nerve

value: optic nerve


title: No.5_eyeball

description: miRNA expression ATLAS

source_name: Animal No.5, 34. eyeball

value: eyeball


title: No.5_Harderian gland

description: miRNA expression ATLAS

source_name: Animal No.5, 35. harderian gland

value: Harderian gland


title: No.4_Harderian gland

description: miRNA expression ATLAS

source_name: Animal No.4, 35. harderian gland


title: No.4_eyeball

description: miRNA expression ATLAS

source_name: Animal No.4, 34. eyeball


title: No.4_testicle

description: miRNA expression ATLAS

source_name: Animal No.4, 32. testis


title: No.6_prostate_ventral

description: miRNA expression ATLAS

source_name: Animal No.6, 30. prostate_ventral


title: No.4_prostate_other

description: miRNA expression ATLAS

source_name: Animal No.4, 31. prostate_other


title: No.4_epididymis

description: miRNA expression ATLAS

source_name: Animal No.4, 33. epididymis


title: No.6_bladder

description: miRNA expression ATLAS

source_name: Animal No.6, 28. bladder

value: bladder


title: No.6_seminal vesicle

description: miRNA expression ATLAS

source_name: Animal No.6, 29. seminal vesicle

value: seminal vesicle


title: No.6_stomach_glandular

description: miRNA expression ATLAS

source_name: Animal No.6, 18. stomach_glandular


title: No.6_esophagus

description: miRNA expression ATLAS

source_name: Animal No.6, 16. esophagus

value: esophagus


title: No.6_ileum

description: miRNA expression ATLAS

source_name: Animal No.6, 21. ileum

value: ileum


title: No.6_stomach_anterior

description: miRNA expression ATLAS

source_name: Animal No.6, 17. stomach_anterior


title: No.6_colon

description: miRNA expression ATLAS

source_name: Animal No.6, 23. colon

value: colon


title: No.6_spleen

description: miRNA expression ATLAS

source_name: Animal No.6, 26. spleen

value: spleen


title: No.6_adrenal gland

description: miRNA expression ATLAS

source_name: Animal No.6, 27. adrenal gland

value: adrenal gland


title: No.6_rectum

description: miRNA expression ATLAS

source_name: Animal No.6, 24. rectum

value: rectum


title: No.6_pancreas

description: miRNA expression ATLAS

source_name: Animal No.6, 25. pancreas

value: pancreas


title: No.6_lymph node - mesenteric

description: miRNA expression ATLAS

source_name: Animal No.6, 8. lymph node - mesenteric

value: lymph node - mesenteric

value: 10 weeks


title: No.6_trachea

description: miRNA expression ATLAS

source_name: Animal No.6, 13. trachea

value: trachea

value: Sprague-Dawley


title: No.6_mandibular gland

description: miRNA expression ATLAS

source_name: Animal No.6, 10. mandibular gland

value: mandibular gland

value: male


title: No.6_cecum

description: miRNA expression ATLAS

source_name: Animal No.6, 22. cecum

value: cecum


title: No.6_sublingual gland

description: miRNA expression ATLAS

source_name: Animal No.6, 9. sublingual gland

value: sublingual gland


title: No.6_thyroid

description: miRNA expression ATLAS

source_name: Animal No.6, 14. thyroid gland

value: thyroid


title: No.6_thymus

description: miRNA expression ATLAS

source_name: Animal No.6, 12. thymus

value: thymus


title: No.6_lymph node - cervical

description: miRNA expression ATLAS

source_name: Animal No.6, 7. lymph node - cervical

value: lymph node - cervical


title: No.6_parotid gland

description: miRNA expression ATLAS

source_name: Animal No.6, 11. parotid gland

value: parotid gland


title: No.6_tongue

description: miRNA expression ATLAS

source_name: Animal No.6, 15. tongue

value: tongue


title: No.6_skin

description: miRNA expression ATLAS

source_name: Animal No.6, 6. skin

value: skin


title: No.6_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.6, 5. heart_interventricular septum

value: heart_interventricular septum


title: No.6_jejunum

description: miRNA expression ATLAS

source_name: Animal No.6, 20. jejunum

value: jejunum


title: No.6_duodenum

description: miRNA expression ATLAS

source_name: Animal No.6, 19. duodenum

value: duodenum


title: No.6_lung

description: miRNA expression ATLAS

source_name: Animal No.6, 3. lung

value: lung


title: No.6_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.6, 4. heart_atrium

value: 10 weeks


title: No.6_kidney

description: miRNA expression ATLAS

source_name: Animal No.6, 2. kidney

value: kidney


title: No.5_pancreas

description: miRNA expression ATLAS

source_name: Animal No.5, 25. pancreas

value: pancreas

value: Sprague-Dawley


title: No.5_prostate_other

description: miRNA expression ATLAS

source_name: Animal No.5, 31. prostate_other

value: male


title: No.5_seminal vesicle

description: miRNA expression ATLAS

source_name: Animal No.5, 29. seminal vesicle

value: seminal vesicle


title: No.6_liver

description: miRNA expression ATLAS

source_name: Animal No.6, 1. liver

value: liver


title: No.5_adrenal gland

description: miRNA expression ATLAS

source_name: Animal No.5, 27. adrenal gland

value: adrenal gland


title: No.5_bladder

description: miRNA expression ATLAS

source_name: Animal No.5, 28. bladder

value: bladder


title: No.5_spleen

description: miRNA expression ATLAS

source_name: Animal No.5, 26. spleen

value: spleen


title: No.5_prostate_ventral

description: miRNA expression ATLAS

source_name: Animal No.5, 30. prostate_ventral


title: No.4_optic nerve

description: miRNA expression ATLAS

source_name: Animal No.4, 36. optic nerve

value: optic nerve


title: No.5_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.5, 5. heart_interventricular septum


title: No.5_jejunum

description: miRNA expression ATLAS

source_name: Animal No.5, 20. jejunum


title: No.5_ileum

description: miRNA expression ATLAS

source_name: Animal No.5, 21. ileum

value: ileum


title: No.5_duodenum

description: miRNA expression ATLAS

source_name: Animal No.5, 19. duodenum


title: No.5_rectum

description: miRNA expression ATLAS

source_name: Animal No.5, 24. rectum

value: rectum


title: No.4_cerebellum

description: miRNA expression ATLAS

source_name: Animal No.4, 40. cerebellum

value: cerebellum


title: No.5_lymph node - mesenteric

description: miRNA expression ATLAS

source_name: Animal No.5, 8. lymph node - mesenteric

value: lymph node - mesenteric


title: No.5_sublingual gland

description: miRNA expression ATLAS

source_name: Animal No.5, 9. sublingual gland

value: sublingual gland


title: No.5_trachea

description: miRNA expression ATLAS

source_name: Animal No.5, 13. trachea

value: trachea


title: No.5_lymph node - cervical

description: miRNA expression ATLAS

source_name: Animal No.5, 7. lymph node - cervical

value: lymph node - cervical

value: 10 weeks


title: No.5_thymus

description: miRNA expression ATLAS

source_name: Animal No.5, 12. thymus

value: thymus


title: No.5_mandibular gland

description: miRNA expression ATLAS

source_name: Animal No.5, 10. mandibular gland

value: mandibular gland

value: Sprague-Dawley


title: No.5_esophagus

description: miRNA expression ATLAS

source_name: Animal No.5, 16. esophagus

value: esophagus

value: male


title: No.5_parotid gland

description: miRNA expression ATLAS

source_name: Animal No.5, 11. parotid gland

value: parotid gland


title: No.5_cecum

description: miRNA expression ATLAS

source_name: Animal No.5, 22. cecum

value: cecum


title: No.5_colon

description: miRNA expression ATLAS

source_name: Animal No.5, 23. colon

value: colon


title: No.5_thyroid

description: miRNA expression ATLAS

source_name: Animal No.5, 14. thyroid gland

value: thyroid


title: No.5_stomach_anterior

description: miRNA expression ATLAS

source_name: Animal No.5, 17. stomach_anterior


title: No.5_tongue

description: miRNA expression ATLAS

source_name: Animal No.5, 15. tongue

value: tongue


title: No.5_stomach_glandular

description: miRNA expression ATLAS

source_name: Animal No.5, 18. stomach_glandular


title: No.5_skin

description: miRNA expression ATLAS

source_name: Animal No.5, 6. skin

value: skin


title: No.5_lung

description: miRNA expression ATLAS

source_name: Animal No.5, 3. lung

value: lung


title: No.5_kidney

description: miRNA expression ATLAS

source_name: Animal No.5, 2. kidney

value: kidney


title: No.5_liver

description: miRNA expression ATLAS

source_name: Animal No.5, 1. liver

value: liver


title: No.4_seminal vesicle

description: miRNA expression ATLAS

source_name: Animal No.4, 29. seminal vesicle

value: seminal vesicle


title: No.4_pancreas

description: miRNA expression ATLAS

source_name: Animal No.4, 25. pancreas

value: pancreas


title: No.5_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.5, 4. heart_atrium

value: 10 weeks


title: No.4_bladder

description: miRNA expression ATLAS

source_name: Animal No.4, 28. bladder

value: bladder


title: No.4_mandibular gland

description: miRNA expression ATLAS

source_name: Animal No.4, 10. mandibular gland

value: mandibular gland


title: No.4_thymus

description: miRNA expression ATLAS

source_name: Animal No.4, 12. thymus

value: thymus

value: Sprague-Dawley


title: No.4_trachea

description: miRNA expression ATLAS

source_name: Animal No.4, 13. trachea

value: trachea

value: male


title: No.4_thyroid

description: miRNA expression ATLAS

source_name: Animal No.4, 14. thyroid gland


title: No.4_duodenum

description: miRNA expression ATLAS

source_name: Animal No.4, 19. duodenum

value: duodenum


title: No.4_stomach_anterior

description: miRNA expression ATLAS

source_name: Animal No.4, 17. stomach_anterior


title: No.4_tongue

description: miRNA expression ATLAS

source_name: Animal No.4, 15. tongue


title: No.4_lymph node - mesenteric

description: miRNA expression ATLAS

source_name: Animal No.4, 8. lymph node - mesenteric

value: lymph node - mesenteric


title: No.4_esophagus

description: miRNA expression ATLAS

source_name: Animal No.4, 16. esophagus

value: esophagus


title: No.4_sublingual gland

description: miRNA expression ATLAS

source_name: Animal No.4, 9. sublingual gland

value: sublingual gland


title: No.4_parotid gland

description: miRNA expression ATLAS

source_name: Animal No.4, 11. parotid gland

value: parotid gland


title: No.4_colon

description: miRNA expression ATLAS

source_name: Animal No.4, 23. colon

value: colon


title: No.4_jejunum

description: miRNA expression ATLAS

source_name: Animal No.4, 20. jejunum

value: jejunum


title: No.4_ileum

description: miRNA expression ATLAS

source_name: Animal No.4, 21. ileum

value: ileum


title: No.4_cecum

description: miRNA expression ATLAS

source_name: Animal No.4, 22. cecum

value: cecum


title: No.4_spleen

description: miRNA expression ATLAS

source_name: Animal No.4, 26. spleen

value: spleen


title: No.4_skin

description: miRNA expression ATLAS

source_name: Animal No.4, 6. skin

value: skin

value: 10 weeks


title: No.4_kidney

description: miRNA expression ATLAS

source_name: Animal No.4, 2. kidney

value: kidney


title: No.4_lung

description: miRNA expression ATLAS

source_name: Animal No.4, 3. lung

value: lung


title: No.4_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.4, 4. heart_atrium

value: Sprague-Dawley


title: No.4_stomach_glandular

description: miRNA expression ATLAS

source_name: Animal No.4, 18. stomach_glandular


title: No.4_liver

description: miRNA expression ATLAS

source_name: Animal No.4, 1. liver

value: liver


title: No.4_adrenal gland

description: miRNA expression ATLAS

source_name: Animal No.4, 27. adrenal gland

value: adrenal gland

value: male


title: No.4_lymph node - cervical

description: miRNA expression ATLAS

source_name: Animal No.4, 7. lymph node - cervical

value: lymph node - cervical


title: No.4_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.4, 5. heart_interventricular septum

value: heart_interventricular septum


title: No.4_rectum

description: miRNA expression ATLAS

source_name: Animal No.4, 24. rectum

value: rectum


title: No.3_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.3, 5. heart_interventricular septum_no-perfusion


title: No.3_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.3, 4. heart_atrium_no-perfusion


title: No.2_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.2, 5. heart_interventricular septum_no-perfusion


title: No.1_heart_interventricular septum

description: miRNA expression ATLAS

source_name: Animal No.1, 5. heart_interventricular septum_no-perfusion


title: No.3_lung

description: miRNA expression ATLAS

source_name: Animal No.3, 3. lung_no-perfusion


title: No.2_liver

description: miRNA expression ATLAS

source_name: Animal No.2, 1. liver_no-perfusion


title: No.3_kidney

description: miRNA expression ATLAS

source_name: Animal No.3, 2. kidney_no-perfusion


title: No.2_kidney

description: miRNA expression ATLAS

source_name: Animal No.2, 2. kidney_no-perfusion


title: No.2_lung

description: miRNA expression ATLAS

source_name: Animal No.2, 3. lung_no-perfusion


title: No.1_lung

description: miRNA expression ATLAS

source_name: Animal No.1, 3. lung_no-perfusion


title: patient no -15_T

status: Public on Nov 15 2013

city: Washington DC,

first: Deepak

last: Kumar

state: District of Columbia

address: 4200 Connecticut Avenue, NW

department: Biology

institute: University of the District of Columbia

description:
SAMPLE 7-T
Test
FFPE prostate cancer tissues

data_processing:
U6 was used as normalizing control
Target miRNA signals normalized to normalizing control; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: FAM

source_name: prostate cancer tissues

label_protocol: RNA was converted to cDNA using MegaplexTM Primer pools and High Capacity cDNA Archive Kit (Applied Biosystems)

extract_protocol: RNA extraction from microdissected cells was performed using Ambion® Recover All™ Total Nucleic Acid Isolation isolation kit (Ambion) following the manufacturer’s instructions.

treatment_protocol: Laser capture microdissection was performed to isolate the cells from PCa foci and normal adjacent tissue. Captured cells were immediately frozen until further use.

tag: disease state

value: Prostate Cancer

tag: ethnicity

value: African American

value: prostate cancer


title: patient no -15_N

description:
SAMPLE 7-N
Control
FFPE prostate cancer tissues

source_name: adjacent normal tissues

value: adjacent normal


title: patient no -16_T

description:
SAMPLE 8-T
Test
FFPE prostate cancer tissues


title: patient no -16_N

description:
SAMPLE 8-N
Control
FFPE prostate cancer tissues


title: patient no -18_T

description:
SAMPLE 9-T
Test
FFPE prostate cancer tissues


title: patient no -12_N

description:
SAMPLE 6-N
Control
FFPE prostate cancer tissues


title: No.3_liver

description: miRNA expression ATLAS

source_name: Animal No.3, 1. liver_no-perfusion


title: No.1_kidney

description: miRNA expression ATLAS

source_name: Animal No.1, 2. kidney_no-perfusion


title: patient no -18_N

description:
SAMPLE 9-N
Control
FFPE prostate cancer tissues


title: patient no -09_N

description:
SAMPLE 4-N
Control
FFPE prostate cancer tissues

value: Caucasian American


title: No.1_liver

description: miRNA expression ATLAS

source_name: Animal No.1, 1. liver_no-perfusion


title: patient no -09_T

description:
SAMPLE 4-T
Test
FFPE prostate cancer tissues


title: patient no -12_T

description:
SAMPLE 6-T
Test
FFPE prostate cancer tissues


title: patient no -04_N

description:
SAMPLE 3-N
Control
FFPE prostate cancer tissues


title: patient no -11_N

description:
SAMPLE 5-N
Control
FFPE prostate cancer tissues


title: No.2_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.2, 4. heart_atrium_no-perfusion


title: No.1_heart_atrium

description: miRNA expression ATLAS

source_name: Animal No.1, 4. heart_atrium_no-perfusion


title: patient no -21_N

description:
SAMPLE 10-N
Control
FFPE prostate cancer tissues


title: No.4_prostate_ventral

description: miRNA expression ATLAS

source_name: Animal No.4, 30. prostate_ventral


title: patient no -21_T

description:
SAMPLE 10-T
Test
FFPE prostate cancer tissues


title: patient no -11_T

description:
SAMPLE 5-T
Test
FFPE prostate cancer tissues


title: patient no -04_T

description:
SAMPLE 3-T
Test
FFPE prostate cancer tissues


title: patient no -03_N

description:
SAMPLE 2-N
Control
FFPE prostate cancer tissues


title: patient no -02_T

description:
SAMPLE 1-T
Test
FFPE prostate cancer tissues


title: patient no -02_N

description:
SAMPLE 1-N
Control
FFPE prostate cancer tissues


title: Validation sample -- Pancreas Liver core biopsy 4

status: Public on Oct 19 2013

city: Copenhagen

first: Katharina

middle: Anne

last: Perell

address: Blegdamsvej

department: Dep. of Oncology

country: Denmark

institute: Copenhagen University Hospital

description:
Pancreas(Caput)
C-165-CO-B

data_processing: Data were normalized by centering and scaling the individual samples to mean 0 and variance 1

label: TagMan

source_name: Liver core biopsy

label_protocol: see manufacturer's website

extract_protocol: Total RNA was extracted from FFPE tissue using a combination of ReCover All Total Nucleic Acid Isolation Kit (Ambion, Austin, Tx) and RNAqueous Micro Kit (Ambion).

tag: class

value: Pancreas


title: Validation sample -- Squamous Liver core biopsy 2

description:
Esophagus(S)
C-867-DF

value: Squamous


title: Validation sample -- Squamous Liver core biopsy 3

description:
Esophagus(S)
C-919-CU


title: Validation sample -- Squamous Liver core biopsy 4

description:
Cervix(S)
C-780-AT


title: Validation sample -- Squamous Liver core biopsy 1

description:
Esophagus(S)
C-839-AU


title: Validation sample -- Squamous Liver core biopsy 5

description:
Lung(S)
C-462-IQ


title: Validation sample -- Pancreas Liver core biopsy 5

description:
Pancreas(caput)
C-866-CG


title: Validation sample -- Lung Liver core biopsy 4

description:
Lung(A)
C-823-AR

value: Lung


title: Validation sample -- Liver Liver core biopsy 5

description:
Liver(N)
C-247-DC

value: Liver


title: Validation sample -- Pancreas Liver core biopsy 1

description:
Pancreas(caput)
C-885-QR


title: Validation sample -- Lung Liver core biopsy 5

description:
Lung(A)
C-766-US


title: Validation sample -- Lung Liver core biopsy 1

description:
Lung(A)
C-800-VF


title: Validation sample -- Lung Liver core biopsy 2

description:
Lung(A)
C-500-JU


title: Validation sample -- Pancreas Liver core biopsy 3

description:
Pancreas(Cauda)
C-196-BA


title: Validation sample -- Pancreas Liver core biopsy 2

description:
Pancreas(caput)
C-911-QZ


title: Validation sample -- Liver Liver core biopsy 1

description:
Liver(N)
C-789-BG


title: Validation sample -- Liver Liver core biopsy 4

description:
Liver(N)
C-253-BB


title: Validation sample -- Liver Liver core biopsy 3

description:
Liver(N)
D-283-BE


title: patient no -03_T

description:
SAMPLE 2-T_T
Test
FFPE prostate cancer tissues


title: Validation sample -- HCC Liver core biopsy 4

description:
HCC
C-403-KO

value: HCC


title: Validation sample -- Liver Liver core biopsy 2

description:
Liver(N)
C-888-QN


title: Validation sample -- HCC Liver core biopsy 5

description:
HCC
C-492-LH


title: Validation sample -- HCC Liver core biopsy 3

description:
HCC
C-774-VA


title: Validation sample -- HCC Liver core biopsy 2

description:
HCC
C-496-JM


title: Validation sample -- HCC Liver core biopsy 1

description:
HCC
C-752-UB


title: Validation sample -- Lung Liver core biopsy 3

description:
Lung(A)
C-454-KD


title: Validation sample -- GC Liver core biopsy 5

description:
GC(Cardia)
C-880-RZ

value: GC


title: Validation sample -- GC Liver core biopsy 4

description:
GC(Cardia)
C-876-DI


title: Validation sample -- GC Liver core biopsy 3

description:
GC(Stomach)
C-813-AW


title: Validation sample -- GC Liver core biopsy 2

description:
GC(Cardia)
C-175-BG


title: Validation sample -- CRC Liver core biopsy 4

description:
CRC(Transversum)
C-860-RP

value: CRC


title: Validation sample -- CRC Liver core biopsy 2

description:
CRC(Transversum)
C-942-RR


title: Validation sample -- CRC Liver core biopsy 3

description:
CRC(Rectum)
C-300-AO


title: Validation sample -- CRC Liver core biopsy 1

description:
CRC(Coecum)
C-764-AC


title: Validation sample -- Cirrhosis Liver core biopsy 1

description:
Cirrhosis
C-855-RH

value: Cirrhosis


title: Validation sample -- Cirrhosis Liver core biopsy 4

description:
Cirrhosis
C-411-JK


title: Validation sample -- Cirrhosis Liver core biopsy 5

description:
Cirrhosis
C-456-KU


title: Validation sample -- Cirrhosis Liver core biopsy 3

description:
Cirrhosis
C-750-VI


title: Validation sample -- CCA Liver core biopsy 2

description:
CCA
C-772-UQ

value: CCA


title: Validation sample -- Cirrhosis Liver core biopsy 2

description:
Cirrhosis
C-464-JD


title: Validation sample -- Breast Liver core biopsy 5

description:
Breast(Inv duct)
C-788-AD

value: Breast


title: Validation sample -- Breast Liver core biopsy 1

description:
Breast(Karcinom)
C-870-QP


title: Validation sample -- CCA Liver core biopsy 4

description:
CCA
C-438-IP


title: Validation sample -- CCA Liver core biopsy 5

description:
CCA
C-801-BP


title: Validation sample -- CCA Liver core biopsy 3

description:
CCA
C-802-BU


title: Validation sample -- Bladder Liver core biopsy 5

description:
Bladder
C-460-LW

value: Bladder


title: Validation sample -- Breast Liver core biopsy 2

description:
Breast(Inv duct)
C-273-AW


title: Validation sample -- Bladder Liver core biopsy 3

description:
Bladder
C-420-LA


title: Validation sample -- Bladder Liver core biopsy 1

description:
Bladder
C-488-JV


title: Validation sample -- CCA Liver core biopsy 1

description:
CCA
C-796-UX


title: Validation sample -- Breast Liver core biopsy 3

description:
Breast(Inv duct)
C-864-CC


title: Validation sample -- Bladder Liver core biopsy 2

description:
Bladder
C-794-VO


title: Validation sample -- GC Liver core biopsy 1

description:
GC(stomach)
C-828-VQ-B


title: Validation sample -- CRC Liver core biopsy 5

description:
CRC(Rectum)
C-210-DO


title: Training sample -- Cirrhosis Resection 17

description:
Cirrhosis
R-938-CL

source_name: Resection


title: Training sample -- Breast Resection 17

description:
Breast(Inv duct)
R-927-CM


title: Validation sample -- Bladder Liver core biopsy 4

description:
Bladder
C-412-IN


title: Training sample -- Liver Resection 20

description:
Liver(N)
R-923-CQ-B


title: Training sample -- HCC Resection 17

description:
HCC
S-321-FU


title: Validation sample -- Breast Liver core biopsy 4

description:
Breast(Inv duct)
D-290-AU


title: Training sample -- Lung Resection 17

description:
Lung(A)Acinar
R-920-DU


title: Training sample -- Lung Resection 16

description:
Lung(A)Acinar
R-909-DL


title: Training sample -- Cirrhosis Resection 16

description:
Cirrhosis
R-908-DH


title: Training sample -- Liver Resection 19

description:
Liver(N)
R-897-RX


title: Training sample -- Breast Resection 16

description:
Breast(Medullary)
R-882-QU


title: Training sample -- Pancreas Resection 20

description:
Pancreas(Caput)
R-886-QT


title: Training sample -- Liver Resection 16

description:
Liver(N)
R-785-AP


title: Training sample -- Cirrhosis Resection 15

description:
Cirrhosis
R-877-CI


title: Training sample -- HCC Resection 15

description:
HCC
R-878-RG


title: Training sample -- CRC Resection 20

description:
CRC(Sigmoideum)
R-748-TD


title: Training sample -- Liver Resection 17

description:
Liver(N)
R-847-AQ


title: Training sample -- Breast Resection 15

description:
Breast(Medullary)
R-771-AA


title: Training sample -- CCA Resection 20

description:
CCA(I)
R-747-TP


title: Training sample -- Lung Resection 15

description:
Lung(A)Acinar
R-852-QB


title: Training sample -- CCA Resection 19

description:
CCA(I)
R-738-QG


title: Training sample -- CCA Resection 17

description:
CCA(I)
R-711-SF


title: Training sample -- HCC Resection 16

description:
HCC
R-915-RN


title: Training sample -- Pancreas Resection 18

description:
Pancreas(Caput)
R-730-TM


title: Training sample -- GC Resection 17

description:
GC(Stomach)
R-726-SN


title: Training sample -- CRC Resection 19

description:
CRC(Descendens)
R-735-TT


title: Training sample -- Pancreas Resection 17

description:
Pancreas
R-720-RX


title: Training sample -- Pancreas Resection 19

description:
Pancreas(Caput)
R-734-RA


title: Training sample -- Bladder Resection 16

description:
Bladder
R-710-RO


title: Training sample -- CRC Resection 18

description:
CRC(Ascendens)
R-729-QW


title: Training sample -- CRC Resection 17

description:
CRC(Ascendens)
R-725-RH


title: Training sample -- Liver Resection 18

description:
Liver(N)
R-887-RI


title: Training sample -- CCA Resection 18

description:
CCA(I)
R-717-TY


title: Training sample -- GC Resection 18

description:
GC(Stomach)
R-745-RL


title: Training sample -- Bladder Resection 17

description:
Bladder
R-724-SX


title: Training sample -- Bladder Resection 14

description:
Bladder
R-707-QQ


title: Training sample -- GC Resection 16

description:
GC(Stomach)
R-719-QR


title: Training sample -- Pancreas Resection 15

description:
Pancreas(Corpus)
R-706-RF


title: Training sample -- CCA Resection 16

description:
CCA(E)
R-705-QT


title: Training sample -- CRC Resection 16

description:
CRC(Ascendens)
R-702-TF


title: Training sample -- HCC Resection 14

description:
HCC
R-600-PC


title: Training sample -- Pancreas Resection 14

description:
Pancreas(Caput)
R-599-PI


title: Training sample -- CCA Resection 15

description:
CCA(I)
R-595-OV


title: Training sample -- Cirrhosis Resection 14

description:
Cirrhosis
R-594-MI


title: Training sample -- Squamous Resection 14

description:
Cervix Uteri(S)
R-565-NM


title: Training sample -- Squamous Resection 15

description:
Esophagus(S)
R-566-PQ


title: Training sample -- CCA Resection 13

description:
CCA(E)
R-568-OD


title: Training sample -- Bladder Resection 13

description:
Bladder
R-593-NY


title: Training sample -- Squamous Resection 16

description:
HN
R-589-PB


title: Training sample -- Bladder Resection 12

description:
Bladder
R-588-PY


title: Training sample -- Pancreas Resection 13

description:
Pancreas(Caput)
R-570-NZ


title: Training sample -- Cirrhosis Resection 12

description:
Cirrhosis
R-567-OZ


title: Training sample -- Liver Resection 15

description:
Liver(N)
R-577-OG


title: Training sample -- CRC Resection 15

description:
CRC(Rectosigmoideum)
R-578-MX


title: Training sample -- CCA Resection 14

description:
CCA(E)
R-585-NB


title: Training sample -- GC Resection 15

description:
GC(Stomach)
R-584-PN


title: Training sample -- Breast Resection 14

description:
Breast(Lobular)
R-561-MD


title: Training sample -- Cirrhosis Resection 13

description:
Cirrhosis
R-580-NR


title: Training sample -- CCA Resection 12

description:
CCA(I)
R-557-OP


title: Training sample -- Cirrhosis Resection 11

description:
Cirrhosis
R-556-PT


title: Training sample -- Pancreas Resection 16

description:
Pancreas(Caput)
R-708-TS


title: Training sample -- Squamous Resection 13

description:
Lung(S)
R-550-MH


title: Training sample -- HCC Resection 13

description:
HCC
R-592-OB


title: Training sample -- Breast Resection 13

description:
Breast(Lobular)
R-548-MG


title: Training sample -- Lung Resection 14

description:
Lung(A)bronchioloalveolar
R-549-MN


title: Training sample -- GC Resection 14

description:
GC(Stomach)
R-543-OA


title: Training sample -- GC Resection 13

description:
GC(Stomach)
R-542-MB


title: Training sample -- Liver Resection 14

description:
Liver(N)
R-540-OJ


title: Training sample -- Pancreas Resection 12

description:
Pancreas(Cauda)
R-541-OM


title: Training sample -- CRC Resection 14

description:
CRC(Coecum)
R-539-MZ


title: Training sample -- Squamous Resection 12

description:
Esophagus(S)
R-536-PS


title: Training sample -- Pancreas Resection 10

description:
Pancreas(Caput)
R-522-NK


title: Training sample -- Breast Resection 12

description:
Breast(Medullary)
R-535-NN


title: Training sample -- Squamous Resection 11

description:
Lung(S)
R-525-PJ


title: Training sample -- GC Resection 12

description:
GC(Stomach)
R-526-MV


title: Training sample -- Squamous Resection 8

description:
Cervix Uteri(S)
R-391-HV


title: Training sample -- HCC Resection 9

description:
HCC
R-395-HM


title: Training sample -- Squamous Resection 10

description:
Cervix Uteri(S)
R-509-MP


title: Training sample -- HCC Resection 11

description:
HCC
R-516-PK


title: Training sample -- Lung Resection 13

description:
Lung(A)
R-520-NO


title: Training sample -- Bladder Resection 11

description:
Bladder
R-511-OH


title: Training sample -- HCC Resection 8

description:
HCC
R-393-HB


title: Training sample -- CCA Resection 11

description:
CCA(I)
R-389-GA


title: Training sample -- Pancreas Resection 11

description:
Pancreas(Cauda)
R-527-NU


title: Training sample -- HCC Resection 7

description:
HCC
R-385-HK


title: Training sample -- Squamous Resection 7

description:
Lung(S)
R-378-HU


title: Training sample -- Lung Resection 12

description:
Lung(A)Adenopapillary
R-512-OO


title: Training sample -- HCC Resection 10

description:
HCC
R-513-OE


title: Training sample -- Squamous Resection 9

description:
HN
R-508-OL


title: Training sample -- Pancreas Resection 9

description:
Pancreas(Caput)
R-380-EL


title: Training sample -- Bladder Resection 9

description:
Bladder
R-372-HG


title: Training sample -- Lung Resection 11

description:
Lung(A)Acinar
R-386-EV


title: Training sample -- Liver Resection 13

description:
Liver(N)
R-387-EP


title: Training sample -- Bladder Resection 10

description:
Bladder
R-388-GB


title: Training sample -- HCC Resection 12

description:
HCC
R-524-PP


title: Training sample -- Breast Resection 11

description:
Breast(Basal like)
R-371-FO


title: Training sample -- Lung Resection 10

description:
Lung(A)Mixed acinar and solid
R-364-GL


title: Training sample -- Liver Resection 12

description:
Liver(N)
R-368-FY


title: Training sample -- CCA Resection 10

description:
CCA(I)
R-370-GH


title: Training sample -- Lung Resection 9

description:
Lung(A)Large cell
R-358-HN


title: Training sample -- Pancreas Resection 8

description:
Pancreas(Caput)
R-366-ES


title: Training sample -- Cirrhosis Resection 9

description:
Cirrhosis
R-356-FZ


title: Training sample -- CCA Resection 9

description:
CCA(I)
R-365-EW


title: Training sample -- HCC Resection 6

description:
HCC
R-348-HS


title: Training sample -- CRC Resection 13

description:
CRC(Coecum)
R-347-GT


title: Training sample -- CCA Resection 8

description:
CCA(I)
R-346-GM


title: Training sample -- Cirrhosis Resection 10

description:
Cirrhosis
R-360-FA


title: Training sample -- Cirrhosis Resection 8

description:
Cirrhosis
R-354-FS


title: Training sample -- HCC Resection 5

description:
HCC
R-343-HY


title: Training sample -- Cirrhosis Resection 7

description:
Cirrhosis
R-352-GZ


title: Training sample -- Cirrhosis Resection 5

description:
Cirrhosis
R-322-ED


title: Training sample -- Cirrhosis Resection 6

description:
Cirrhosis
R-334-HL


title: Training sample -- CCA Resection 7

description:
CCA(I)
R-345-ER


title: Training sample -- Pancreas Resection 7

description:
Pancreas(Cauda)
R-318-GG


title: Training sample -- Lung Resection 7

description:
Lung(A)Acinar
R-337-HO


title: Training sample -- CRC Resection 12

description:
CRC(Sigmoideum)
R-333-EU


title: Training sample -- Squamous Resection 5

description:
Esophagus(S)
R-326-GX


title: Training sample -- Bladder Resection 8

description:
Bladder
R-325-FE


title: Training sample -- CCA Resection 6

description:
CCA(E)
R-316-FI


title: Training sample -- Squamous Resection 6

description:
Lung(S)
R-369-EE


title: Training sample -- Liver Resection 11

description:
Liver(N)
R-339-FH


title: Training sample -- GC Resection 11

description:
GC(Stomach)
R-331-FT


title: Training sample -- Lung Resection 8

description:
Lung(A)Large cell
R-353-GI


title: Training sample -- Breast Resection 10

description:
Breast(Basal like)
R-363-FQ


title: Training sample -- Lung Resection 5

description:
Lung(A)Adenopapillary
R-311-GQ


title: Training sample -- Cirrhosis Resection 4

description:
Cirrhosis
R-309-GY


title: Training sample -- Lung Resection 6

description:
Lung(A)Mixed acinar and bronchioloalveolar
R-314-HD


title: Training sample -- Breast Resection 8

description:
Breast(Inv duct)
R-292-CU


title: Training sample -- CCA Resection 5

description:
CCA(E)
R-308-FB


title: Training sample -- Breast Resection 7

description:
Breast(Inv duct)
R-268-DJ


title: Training sample -- GC Resection 9

description:
GC(Cardia)
R-287-CZ


title: Training sample -- Pancreas Resection 6

description:
Pancreas(Caput)
R-272-BW


title: Training sample -- GC Resection 7

description:
GC(Stomach)
R-270-AZ


title: Training sample -- Bladder Resection 4

description:
Bladder
R-300-HI


title: Training sample -- Breast Resection 9

description:
Breast(Lobular)
R-307-FD


title: Training sample -- Bladder Resection 7

description:
Bladder
R-306-FL


title: Training sample -- Bladder Resection 6

description:
Bladder
R-303-GP


title: Training sample -- Bladder Resection 5

description:
Bladder
R-301-GK


title: Training sample -- CRC Resection 11

description:
CRC(Sigmoideum)
R-266-AP


title: Training sample -- GC Resection 10

description:
GC(Cardia)
R-299-CS


title: Training sample -- Breast Resection 6

description:
Breast(Inv duct)
R-258-BD


title: Training sample -- CRC Resection 10

description:
CRC(Coecum)
R-264-AI


title: Training sample -- GC Resection 6

description:
GC(Stomach)
R-251-BN


title: Training sample -- GC Resection 8

description:
GC(Cardia)
R-281-BU


title: Training sample -- Pancreas Resection 5

description:
Pancreas(Caput)
R-242-CR


title: Training sample -- CRC Resection 9

description:
CRC(Ascendens)
R-223-CD


title: Training sample -- GC Resection 5

description:
GC(Cardia)
R-240-BX


title: Training sample -- Breast Resection 5

description:
Breast(Inv duct)
R-234-DI


title: Training sample -- GC Resection 4

description:
GC(Cardia)
R-215-DX


title: Training sample -- Pancreas Resection 4

description:
Pancreas(Caput)
R-203-CQ


title: Training sample -- CRC Resection 8

description:
CRC(Coecum)
R-220-BV


title: Training sample -- Liver Resection 9

description:
Liver(N)
R-192-DP


title: Training sample -- Liver Resection 8

description:
Liver(N)
R-190-CC


title: Training sample -- Liver Resection 7

description:
Liver(N)
R-186-AF


title: Training sample -- Liver Resection 6

description:
Liver(N)
R-181-BZ


title: Training sample -- Liver Resection 10

description:
Liver(N)
R-208-BJ


title: Training sample -- Pancreas Resection 2

description:
Pancreas(Cauda)
R-164-CF


title: Training sample -- CRC Resection 7

description:
CRC(Rectosigmoideum)
R-168-DH


title: Training sample -- CCA Resection 4

description:
CCA(E)
Q-574-PF


title: Training sample -- Liver Resection 5

description:
Liver(N)
R-172-BP


title: Training sample -- Breast Resection 4

description:
Breast(Inv duct)
R-163-CA


title: Training sample -- Liver Resection 4

description:
Liver(N)
R-151-AG


title: Training sample -- Breast Resection 3

description:
Breast(Inv duct)
R-161-DW


title: Training sample -- Breast Resection 2

description:
Breast(Ductal)
R-147-DA


title: Training sample -- CRC Resection 5

description:
CRC(Rectum)
Q-597-MM


title: Training sample -- Pancreas Resection 3

description:
Pancreas(Caput)
R-170-DS


title: Training sample -- GC Resection 3

description:
GC(Cardia)
Q-340-EN


title: Training sample -- HCC Resection 2

description:
HCC
Q-351-ET


title: Training sample -- HCC Resection 3

description:
HCC
Q-367-EY


title: Training sample -- Squamous Resection 4

description:
Cervix Uteri(S)
Q-355-HE


title: Training sample -- Liver Resection 3

description:
Liver(N)
R-102-DM


title: Training sample -- Lung Resection 4

description:
Lung(A)Mixed acinar, papillary, solid and clear cell
Q-515-PA


title: Training sample -- CCA Resection 2

description:
CCA(E)
Q-349-EO


title: Training sample -- HCC Resection 4

description:
HCC
Q-381-HT


title: Training sample -- CRC Resection 6

description:
CRC(Ascendens)
R-115-DG


title: Training sample -- HCC Resection 1

description:
HCC
Q-344-GC


title: Training sample -- Squamous Resection 3

description:
Lung(S)
Q-335-EB


title: Training sample -- Bladder Resection 15

description:
Bladder
R-709-RZ


title: Training sample -- CRC Resection 4

description:
CRC(Descendens)
Q-336-EG


title: Training sample -- CCA Resection 3

description:
CCA(I)
Q-379-HQ


title: Training sample -- Lung Resection 3

description:
Lung(A)
Q-329-HX


title: Training sample -- Squamous Resection 2

description:
Esophagus(S)
Q-317-HH


title: Training sample -- Pancreas Resection 1

description:
Pancreas(Cauda)
R-129-DF


title: Training sample -- Lung Resection 2

description:
Lung(A)bronchioloalveolar
Q-315-GV


title: Training sample -- Bladder Resection 3

description:
Bladder
Q-382-EA


title: Training sample -- Squamous Resection 1

description:
Esophagus(S)
Q-313-GF


title: Training sample -- Cirrhosis Resection 2

description:
Cirrhosis
Q-310-FF


title: Training sample -- CCA Resection 1

description:
CCA(E)
Q-250-GS


title: Training sample -- GC Resection 2

description:
GC(Cardia)
Q-199-AB


title: Training sample -- Cirrhosis Resection 3

description:
Cirrhosis
Q-327-GR


title: Training sample -- CRC Resection 3

description:
CRC(Transversum)
Q-278-DK


title: Training sample -- Bladder Resection 2

description:
Bladder
P-582-NC


title: Training sample -- CRC Resection 2

description:
CRC(Rectum)
P-590-OU


title: Training sample -- Liver Resection 2

description:
Liver(N)
P-598-PO


title: Training sample -- Bladder Resection 1

description:
Bladder
P-569-PM


title: Training sample -- GC Resection 1

description:
GC(Cardia)
P-559-OI


title: Training sample -- Liver Resection 1

description:
Liver(N)
P-564-MO


title: Training sample -- CRC Liver core biopsy 12

description:
CRC(Sigmoideum)
C-941-RW


title: Training sample -- Pancreas Liver core biopsy 8

description:
Pancreas(caput)
C-928-RD


title: Training sample -- Pancreas Liver core biopsy 9

description:
Pancreas(caput)
C-930-DK


title: Training sample -- Breast Liver core biopsy 6

description:
Breast(Inv duct)
D-112-CV


title: Training sample -- Pancreas Liver core biopsy 10

description:
Pancreas(corpus)
C-946-RQ


title: Training sample -- Lung Resection 1

description:
Lung(A)Acinar
P-528-NX


title: Training sample -- Breast Resection 1

description:
Breast(Medullary)
P-544-ME


title: Training sample -- Liver Liver core biopsy 7

description:
Liver(N)
D-183-AQ


title: Training sample -- Cirrhosis Liver core biopsy 8

description:
Cirrhosis
C-935-CH


title: Training sample -- Squamous Liver core biopsy 12

description:
Cervix(S)
C-918-RO


title: Training sample -- Cirrhosis Resection 1

description:
Cirrhosis
P-554-NW


title: Training sample -- Liver Liver core biopsy 6

description:
Liver(N)
C-914-DC


title: Training sample -- CRC Resection 1

description:
CRC(Ascendens)
P-579-MY


title: Training sample -- GC Liver core biopsy 10

description:
GC(Cardia)
C-913-QH


title: Training sample -- Breast Liver core biopsy 7

description:
Breast(Inv duct)
D-207-BH


title: Training sample -- GC Liver core biopsy 12

description:
GC(Cardia)
C-947-CX


title: Training sample -- Breast Liver core biopsy 5

description:
Breast(Inv duct)
C-905-CP


title: Training sample -- Breast Liver core biopsy 4

description:
Breast(Inv duct)
C-899-QM


title: Training sample -- Squamous Liver core biopsy 11

description:
Esophagus(S)
C-902-CD


title: Training sample -- Cirrhosis Liver core biopsy 7

description:
Cirrhosis
C-906-DA


title: Training sample -- GC Liver core biopsy 9

description:
GC(Cardia)
C-903-DJ


title: Training sample -- GC Liver core biopsy 8

description:
GC(Cardia)
C-890-RY


title: Training sample -- Squamous Liver core biopsy 10

description:
HN
C-894-QJ


title: Training sample -- CRC Liver core biopsy 11

description:
CRC(Coecum)
C-921-RT


title: Training sample -- CRC Liver core biopsy 10

description:
CRC(Sigmoideum)
C-895-CK


title: Training sample -- Liver Liver core biopsy 5

description:
Liver(N)
C-889-CE


title: Training sample -- CRC Liver core biopsy 9

description:
CRC(Coecum)
C-884-QF


title: Training sample -- Squamous Liver core biopsy 8

description:
HN
C-872-RA


title: Training sample -- Squamous Liver core biopsy 9

description:
Esophagus(S)
C-874-DE


title: Training sample -- HCC Liver core biopsy 3

description:
HCC
C-848-AH


title: Training sample -- CRC Liver core biopsy 8

description:
CRC(Sigmoideum)
C-862-RF


title: Training sample -- Cirrhosis Liver core biopsy 5

description:
Cirrhosis
C-836-BD


title: Training sample -- CCA Liver core biopsy 4

description:
CCA
C-844-UP


title: Training sample -- GC Liver core biopsy 6

description:
GC(Stomach)
C-837-VC


title: Training sample -- CRC Liver core biopsy 7

description:
CRC(Sigmoideum)
C-845-BF


title: Training sample -- Pancreas Liver core biopsy 7

description:
Pancreas(Corpus)
C-834-BT


title: Training sample -- Cirrhosis Liver core biopsy 6

description:
Cirrhosis
C-900-RE


title: Training sample -- Pancreas Liver core biopsy 6

description:
Pancreas(Caput)
C-829-UN


title: Training sample -- Liver Liver core biopsy 4

description:
Liver(N)
C-831-AO


title: Training sample -- GC Liver core biopsy 5

description:
GC(Cardia)
C-826-VS


title: Training sample -- Bladder Liver core biopsy 2

description:
Bladder
C-820-UE


title: Training sample -- CRC Liver core biopsy 6

description:
CRC(Sigmoideum)
C-822-VU


title: Training sample -- Breast Liver core biopsy 1

description:
Breast(Inv duct)
C-786-AK


title: Training sample -- Breast Liver core biopsy 3

description:
Breast
C-806-VZ


title: Training sample -- Squamous Liver core biopsy 7

description:
Esophagus(S)
C-816-UM


title: Training sample -- Breast Liver core biopsy 2

description:
Breast(Inv duct)
C-805-AV


title: Training sample -- CRC Liver core biopsy 5

description:
CRC(Ascendens)
C-812-UW-B


title: Training sample -- Pancreas Liver core biopsy 5

description:
Pancreas(Caput)
C-783-BY


title: Training sample -- Squamous Liver core biopsy 6

description:
HN
C-797-UC


title: Training sample -- Pancreas Liver core biopsy 4

description:
Pancreas(Caput)
C-759-UY


title: Training sample -- CCA Liver core biopsy 3

description:
CCA
C-475-IW


title: Training sample -- Liver Liver core biopsy 2

description:
Liver(N)
C-761-BC


title: Training sample -- Squamous Liver core biopsy 5

description:
Anal(S)
C-754-VB


title: Training sample -- GC Liver core biopsy 7

description:
GC(Cardia)
C-843-AF


title: Training sample -- Cirrhosis Liver core biopsy 3

description:
Cirrhosis
C-768-UL


title: Training sample -- Cirrhosis Liver core biopsy 2

description:
Cirrhosis
C-459-JN


title: Training sample -- HCC Liver core biopsy 2

description:
HCC
C-471-LI


title: Training sample -- Squamous Liver core biopsy 4

description:
Anal(S)
C-472-IJ


title: Training sample -- CRC Liver core biopsy 4

description:
CRC(Sigmoideum)
C-803-UG


title: Training sample -- Lung Liver core biopsy 2

description:
Lung(A)
C-451-LY


title: Training sample -- CCA Liver core biopsy 2

description:
CCA
C-455-II


title: Training sample -- Squamous Liver core biopsy 2

description:
Esophagus(S)
C-463-KT


title: Training sample -- Liver Liver core biopsy 3

description:
Liver(N)
C-784-VK


title: Training sample -- HCC Liver core biopsy 1

description:
HCC
C-417-KJ


title: Training sample -- Bladder Liver core biopsy 1

description:
Bladder
C-443-KS


title: Training sample -- CRC Liver core biopsy 2

description:
CRC(Rectum)
C-263-DV


title: Training sample -- GC Liver core biopsy 4

description:
GC(Cardia)
C-277-AS


title: Training sample -- Pancreas Liver core biopsy 3

description:
Pancreas(Cauda)
C-276-CG


title: Training sample -- CCA Liver core biopsy 1

description:
CCA
C-409-LO


title: Training sample -- CRC Liver core biopsy 3

description:
CRC(Ascendens)
C-297-CY


title: Training sample -- Lung Liver core biopsy 1

description:
Lung(A)
C-405-IM


title: Training sample -- GC Liver core biopsy 2

description:
GC(Cardia)
C-146-DB


title: Training sample -- CRC Liver core biopsy 1

description:
CRC(Coecum)
C-243-AY


title: Training sample -- GC Liver core biopsy 1

description:
GC(Stomach)
C-106-AR


title: Training sample -- Liver Liver core biopsy 1

description:
Liver(N)
C-166-AA


title: Training sample -- Pancreas Liver core biopsy 2

description:
Pancreas(Corpus)
C-222-BR


title: Training sample -- GC Liver core biopsy 3

description:
GC(Cardia)
C-191-CB


title: Training sample -- Cirrhosis Liver core biopsy 1

description:
Cirrhosis
C-458-KG


title: Training sample -- Pancreas Liver core biopsy 1

description:
Pancreas(Corpus)
C-158-BO


title: Training sample -- Squamous Liver core biopsy 1

description:
HN(S)Rhinopharynx
C-434-IV


title: DLD1 cells infected  with empty vector, 48 hours

status: Public on May 31 2013

city: Munich

first: Rene

last: Jackstadt

address: Thalkirchnerstrasse 36

country: Germany

institute: Ludwigs maximilians University Munich

hyb_protocol: Arrays were hybridized, washed, stained and scanned according to the manufacturer’s recommendations.

scan_protocol: Arrays were hybridized, washed, stained and scanned according to the manufacturer’s recommendations with the GeneChip Scanner 3000 7G.

data_processing:
Expression values were derived from CEL files generated from GeneChip Exon 1.0 ST arrays using the Expression Console implemented by Affymetrix. For data processing the genome build hg18 was used and only the core exons were analysed.
probe group file: HuEx-1_0st-v2.r2.pgf
meta-probeset file: HuEx-1_0st-v2.r2.dt1.hg18.core.mps

source_name: DLD-1 cells

label_protocol: cDNA was labeled using the GeneChip WT terminal labeling kit and hybridized to Human Exon ST arrays (Affymetrix) according to the instructions of the manufacturer.

growth_protocol: Mc Coy´s Medium containing 10% FBS; 37°C at 5% CO2

extract_protocol: cDNA was generated from total RNA and amplified using the GeneChip WT cDNA Amplification Kit (Affimetrix). Total RNA was isolated with the RNAeasy kit (Quiagen).

treatment_protocol: DLD-1 were infected with AP4 or GFP coding adenoviruses and harvested after the indicated periods

tag: cell line

tag: infection

value: empty vector

tag: time point

value: 48 hours


title: DLD1 cells infected  with empty vector, 24 hours  rep2

value: 24 hours


title: DLD1 cells infected  with empty vector, 24 hours  rep3


title: DLD1 cells infected  with AP4 coding vector, 12 hours rep3

value: AP4 coding vector

value: 12 hours


title: DLD1 cells infected  with AP4 coding vector, 48 hours rep2


title: DLD1 cells infected  with empty vector, 24 hours  rep1


title: Training sample -- Squamous Liver core biopsy 3

description:
Lung(S)
C-468-JB


title: DLD1 cells infected  with AP4 coding vector, 48 hours rep1


title: DLD1 cells infected  with AP4 coding vector, 12 hours rep2


title: DLD1 cells infected  with empty vector, 12 hours


title: DLD1 cells infected  with AP4 coding vector, 24 hours rep3


title: DLD1 cells not infected rep1


title: DLD1 cells infected  with AP4 coding vector, 24 hours rep1


title: DLD1 cells infected  with AP4 coding vector, 24 hours rep2


title: non receptive endometrium at day 7 of estrous cycle pool1 in vivo

status: Public on Jan 01 2013

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from endometrium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500. The PLIER (Probe Logarithmic Intensity Error) algorithm for normalization was implemented in the Expression Console software (Affymetrix).

organism: Bos taurus

source_name: endometrium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: breed

value: Simmental

value: heifers

tag: state of endometrium

value: non receptive

tag: day of estrous cycle


title: receptive endometrium at day 3 of estrous cycle pool2 in vivo

description: Gene expression data from endometrium

value: receptive


title: receptive endometrium at day 3 of estrous cycle pool1 in vivo

description: Gene expression data from endometrium


title: receptive endometrium at day 3 of estrous cycle pool3 in vivo

description: Gene expression data from endometrium


title: receptive endometrium at day 7 of estrous cycle pool2 in vivo

description: Gene expression data from endometrium


title: DLD1 cells infected  with AP4 coding vector, 48 hours rep3


title: Training sample -- GC Liver core biopsy 11

description:
GC(Cardia)
C-924-RJ


title: DLD1 cells not infected rep2


title: receptive endometrium at day 7 of estrous cycle pool3 in vivo

description: Gene expression data from endometrium


title: receptive endometrium at day 7 of estrous cycle pool1 in vivo

description: Gene expression data from endometrium


title: DLD1 cells not infected rep3


title: receptive endometrium at day 7 of estrous cycle pool3

description: Gene expression data from endometrium

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500. This intensity was used to be processed "by PLIER algorithm". The PLIER (Probe Logarithmic Intensity Error) algorithm for normalization was implemented in the Expression Console software (Affymetrix).


title: DLD1 cells infected with AP4 coding vector, 12 hours rep1


title: non receptive endometrium at day 3 of estrous cycle pool2 in vivo

description: Gene expression data from endometrium


title: non receptive endometrium at day 3 of estrous cycle pool1 in vivo

description: Gene expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle pool2 in vivo

description: Gene expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle pool1

description: Gene expression data from endometrium


title: receptive endometrium at day 7 of estrous cycle pool2

description: Gene expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle pool3 in vivo

description: Gene expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle pool3

description: Gene expression data from endometrium


title: receptive endometrium at day 3 of estrous cycle pool3

description: Gene expression data from endometrium


title: non receptive endometrium at day 3 of estrous cycle pool3 in vivo

description: Gene expression data from endometrium


title: non receptive endometrium at day 7 of estrous cycle pool2

description: Gene expression data from endometrium


title: receptive endometrium at day 7 of estrous cycle pool1

description: Gene expression data from endometrium


title: receptive endometrium at day 3 of estrous cycle pool1

description: Gene expression data from endometrium


title: non receptive endometrium at day 3 of estrous cycle pool2

description: Gene expression data from endometrium


title: Training sample -- Cirrhosis Liver core biopsy 4

description:
Cirrhosis
C-835-UJ


title: Serie I, HepG2 exposed to FU for 48h, biological rep 1

status: Public on Aug 02 2012

city: Maastricht

first: Christina

last: Magkoufopoulou

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Trizol extraction was performed using the miRNAeasy kit from qiagen accoding to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO, 0.5% EtOH or PBS)

tag: compound, dose

value: FU

tag: time


title: non receptive endometrium at day 3 of estrous cycle pool1

description: Gene expression data from endometrium


title: Serie I, HepG2 exposed to DZN for 48h, biological rep 1

value: DZN


title: Serie L, HepG2 exposed to TCE for 48h, biological rep 2

value: TCE


title: receptive endometrium at day 3 of estrous cycle pool2

description: Gene expression data from endometrium


title: Serie I, HepG2 exposed to DZN for 48h, biological rep 3


title: non receptive endometrium at day 3 of estrous cycle pool3

description: Gene expression data from endometrium


title: Serie F, HepG2 exposed to ETOH for 48h, biological rep 3

value: ETOH


title: Serie E, HepG2 exposed to TPA for 48h, biological rep 3

value: TPA


title: Serie I, HepG2 exposed to DZN for 48h, biological rep 2


title: Serie E, HepG2 exposed to TPA for 48h, biological rep 2


title: Serie I, HepG2 exposed to AZA for 48h, biological rep 3

value: AZA


title: Serie L, HepG2 exposed to TCE for 48h, biological rep 1


title: Serie L, HepG2 exposed to TCE for 48h, biological rep 3


title: Serie I, HepG2 exposed to AZA for 48h, biological rep 1


title: Serie I, HepG2 exposed to FU for 48h, biological rep 2


title: Serie I, HepG2 exposed to AZA for 48h, biological rep 2


title: Serie C, HepG2 exposed to PBS for 48h, biological rep 1

value: PBS


title: Serie E, HepG2 exposed to TPA for 48h, biological rep 1


title: Serie C, HepG2 exposed to PBS for 48h, biological rep 2


title: Serie C, HepG2 exposed to Dman for 48h, biological rep 3

value: Dman


title: Serie C, HepG2 exposed to PBS for 48h, biological rep 3


title: Serie F, HepG2 exposed to ETOH for 48h, biological rep 2


title: Serie J, HepG2 exposed to FU for 48h, biological rep 3


title: Serie F, HepG2 exposed to ETOH for 48h, biological rep 1


title: Serie C, HepG2 exposed to Dman for 48h, biological rep 1


title: Serie A, HepG2 exposed to DMSO for 48h, biological rep 2

value: DMSO


title: Serie A, HepG2 exposed to DMSO for 48h, biological rep 3


title: Serie K, HepG2 exposed to TCE for 24h, biological rep 1


title: Serie C, HepG2 exposed to Dman for 48h, biological rep 2


title: Serie A, HepG2 exposed to DMSO for 48h, biological rep 1


title: Serie K, HepG2 exposed to TCE for 24h, biological rep 3


title: Serie I, HepG2 exposed to FU for 24h, biological rep 3


title: Serie H, HepG2 exposed to FU for 24h, biological rep 1


title: Serie H, HepG2 exposed to DZN for 24h, biological rep 1


title: Serie D, HepG2 exposed to TPA for 24h, biological rep 2


title: Serie E, HepG2 exposed to ETOH for 24h, biological rep 1


title: Serie H, HepG2 exposed to AZA for 24h, biological rep 3


title: Serie H, HepG2 exposed to AZA for 24h, biological rep 1


title: Serie C, HepG2 exposed to PBS for 24h, biological rep 1


title: Serie H, HepG2 exposed to DZN for 24h, biological rep 2


title: Serie D, HepG2 exposed to TPA for 24h, biological rep 3


title: Serie C, HepG2 exposed to PBS for 24h, biological rep 3


title: Serie H, HepG2 exposed to FU for 24h, biological rep 2


title: Serie E, HepG2 exposed to ETOH for 24h, biological rep 3


title: Serie H, HepG2 exposed to DZN for 24h, biological rep 3


title: Serie D, HepG2 exposed to TPA for 24h, biological rep 1


title: Serie H, HepG2 exposed to AZA for 24h, biological rep 2


title: Serie C, HepG2 exposed to PBS for 24h, biological rep 2


title: Serie E, HepG2 exposed to ETOH for 24h, biological rep 2


title: Serie C, HepG2 exposed to Dman for 24h, biological rep 3


title: Serie C, HepG2 exposed to Dman for 24h, biological rep 1


title: Serie A, HepG2 exposed to DMSO for 24h, biological rep 3


title: Serie A, HepG2 exposed to DMSO for 24h, biological rep 2


title: Serie K, HepG2 exposed to TCE for 24h, biological rep 2


title: Serie A, HepG2 exposed to DMSO for 24h, biological rep 1


title: pfc_etoh_bxd42

status: Public on Dec 01 2011

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

hyb_protocol: Labeled cRNA and hybridization controls were hybridized to Mouse Genome 430 2.0 microarrays according to the manufacturer’s protocol.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data analysis was conducted using bioconductor’s affy package for R. Array quality was assessed by inspecting the distributions of log-transformed probe intensity values, as well as scanning for outlier chips using a standard battery of quality measurements, including: average background, scaling factor, percentage of probe-sets called present and 3'-5' actin ratios. Expression data from the saline and ethanol treatment groups were background corrected, quantile normalized and summarized using the robust multi-array average (RMA) expression measure.

label_protocol: cRNA was synthesized and biotin labeled using Affymetrix GeneChip IVT labeling kit.

extract_protocol: Total RNA was extracted with Aurum total RNA fatty and fibrous tissue extraction kit (BioRad Cat# 732-6830). RNA concentration was determined by Experion automated electrophoresis system.

tag: strain

value: male

tag: age

value: 10-12 weeks

tag: tissue

value: Medial prefrontal cortex


title: pfc_etoh_bxd32

tag: gender


title: Serie C, HepG2 exposed to Dman for 24h, biological rep 2


title: pfc_etoh_bxd33


title: pfc_etoh_bxd21


title: pfc_etoh_bxd39


title: pfc_etoh_bxd31


title: pfc_etoh_bxd23


title: pfc_etoh_bxd27


title: pfc_etoh_bxd34


title: pfc_etoh_bxd16


title: pfc_etoh_bxd11


title: pfc_etoh_bxd15


title: pfc_etoh_bxd19


title: pfc_etoh_bxd36


title: pfc_etoh_bxd12


title: pfc_etoh_bxd08


title: pfc_etoh_bxd06


title: pfc_etoh_bxd20


title: pfc_etoh_bxd22


title: pfc_etoh_bxd14


title: pfc_etoh_bxd28


title: pfc_etoh_bxd38


title: pfc_etoh_bxd09


title: pfc_etoh_bxd18


title: pfc_etoh_bxd05


title: pfc_etoh_dba_rep3


title: pfc_etoh_bxd01


title: pfc_etoh_bxd02


title: pfc_etoh_dba_rep2


title: pfc_etoh_dba_rep1


title: pfc_sal_bxd42


title: pfc_etoh_c57_rep3


title: pfc_sal_bxd32


title: pfc_etoh_c57_rep2


title: pfc_sal_bxd33


title: pfc_sal_bxd22


title: pfc_sal_bxd34


title: pfc_sal_bxd36


title: pfc_sal_bxd14


title: pfc_sal_bxd31


title: pfc_sal_bxd15


title: pfc_sal_bxd19


title: pfc_sal_bxd38


title: pfc_sal_bxd28


title: pfc_etoh_c57_rep1


title: pfc_sal_bxd23


title: pfc_sal_bxd39


title: pfc_sal_bxd18


title: pfc_sal_bxd11


title: pfc_sal_bxd21


title: pfc_sal_bxd20


title: pfc_sal_bxd12


title: pfc_sal_bxd27


title: pfc_sal_bxd08


title: pfc_sal_bxd05


title: pfc_sal_bxd09


title: pfc_sal_bxd06


title: pfc_sal_bxd02


title: pfc_sal_c57_rep3


title: pfc_sal_dba_rep3


title: pfc_sal_c57_rep2


title: pfc_sal_bxd01


title: pfc_sal_bxd16


title: pfc_sal_dba_rep2


title: pfc_sal_c57_rep1


title: pfc_sal_dba_rep1


title: ctherm_ct7_cellobiose_158

status: Public on Dec 15 2010

city: Madison

first: Brian

middle: G

last: Fox

state: WI

address: 141b Biochemistry

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellobiose at the dilution rate of 0.158 h^-1.

22126802

hyb_protocol: Hybridization steps were performed by NimbleGen using standard procedures.

scan_protocol: The single color NimbleGen arrays were scanned with a GenePix 4000B microarray scanner.

data_processing: The data was extracted from scanned images using NimbleScan software.  Expression values were generated using quantile normalization and the Robust Multichip Average algorithm. The calls file contained 8 replicate intensities for each probe set. These were log2 transformed and further summarized by taking the means of the log-transformed values.

organism: Acetivibrio thermocellus ATCC 27405

source_name: Clostridium thermocellum, cellobiose, growth rate 0.158

label_protocol: Cy-3 labeling was performed by NimbleGen using standard procedures.

growth_protocol: C. thermocellum ATCC 27405 was grown on Sigmacell 50 microcrystalline cellulose (equivalent to Avicel PH101) and used as an inoculum for chemostat studies. Cells were grown at 55°C in chemostat culture with continuous stirring. Modified Dehority medium containing (per liter) 3.0 g of cellobiose or 2.7 to 3.1 g of Sigmacell 20 microcrystalline cellulose (Sigma) was delivered to the reactor as segmented slurry. Chemostats were operated to steady state (minimum turnover of three reactor volumes) prior to sampling.

extract_protocol: Total RNA was isolated from freshly collected cells. cDNA was synthesized from isolated RNA and stored at -80˚C prior to use. Total DNA was isolated using the Promega Wizard genomic DNA kit (Promega, Madison, WI) and treated with DNase-free RNase ONE (Promega) following DNA extraction.

treatment_protocol: For cellobiose, the following dilution rates were studied (h-1, calculated from the mass flow rate of the collected effluent): 0.025; 0.048; 0.064; 0.0129 and 0.158. For cellulose, the following dilution rates were studied (h-1): 0.013; 0.032; 0.061; 0.084; 0.105; 0.129; 0.159 and 0.206. The dilution rate (D) is synonymous with the growth rate of the organism at steady-state operation.

tag: substrate

value: cellobiose

tag: growth rate

tag: chemostat


title: ctherm_ct16_cellulose_013

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.013 h^-1.

22102702

source_name: Clostridium thermocellum, cellulose, growth rate 0.013

value: cellulose


title: ctherm_ct6_cellobiose_129

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellobiose at the dilution rate of 0.129 h^-1.

22116702

source_name: Clostridium thermocellum, cellobiose, growth rate 0.129


title: ctherm_ct11_cellulose_206

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.206 h^-1.

22088702

source_name: Clostridium thermocellum, cellulose, growth rate 0.206


title: ctherm_ct13_cellulose_129

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.129 h^-1.

22118802

source_name: Clostridium thermocellum, cellulose, growth rate 0.129


title: ctherm_ct14_cellulose_084

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.084 h^-1.

22110702

source_name: Clostridium thermocellum, cellulose, growth rate 0.084


title: ctherm_ct9_cellulose_105

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.105 h^-1.

22105702

source_name: Clostridium thermocellum, cellulose, growth rate 0.105


title: ctherm_ct12_cellulose_159

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellulose at the dilution rate of 0.159 h^-1.

22120702

source_name: Clostridium thermocellum, cellulose, growth rate 0.159


title: ctherm_ct4_cellobiose_064

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellobiose at the dilution rate of 0.064 h^-1.

22377502

source_name: Clostridium thermocellum, cellobiose, growth rate 0.064


title: ctherm_ct2_cellobiose_048

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellobiose at the dilution rate of 0.048 h^-1.

22122702

source_name: Clostridium thermocellum, cellobiose, growth rate 0.048


title: ctherm_ct1_cellobiose_025

description:
This sample is of Clostridium thermocellum ATCC 27405 grown on cellobiose at the dilution rate of 0.025 h^-1.

22110602

source_name: Clostridium thermocellum, cellobiose, growth rate 0.025


title: chlamydospore sample 3 (Cy3) vs. yeast sample 3 (Cy5)

status: Public on Sep 01 2010

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description:
Candida dubliniensis incubated in YNB containing 0.025% (w/v) galactose and 20 mg/L methionine pH 3.7 (chlamydospore induction) VS. C. dubliniensis incubated in YNB containing 0.5% (w/v) galactose and 20 mg/L methionine pH 3.7 (no chlamydospore induction).

Biological replicate 3 of 3. Technical replicate 1 of 2.

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according to the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX10 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log2 fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

organism: Candida dubliniensis

source_name: Candida dubliniensis, 0.025% (w/v) galactose

label_protocol: Total RNA was labelled with Cy5 or Cy3 using the Agilent Two-Color Low RNA input Linear Amplification Kit PLUS.

growth_protocol: To induce chlamydospores, C. dubliniensis was cultured in YNB containing 0.025% (w/v) galactose and 20 mg/L methionine pH 3.7 (CIM) for 4 days. As the amount of the chlamydospores produced is strongly dependent on the galactose concentration of the incubation medium and from the starting inoculum, parallel cultures in CIM were set up: one control culture containing a 20-fold higher galactose concentration (0.5% w/v) than standard CIM and a starting inoculum of 1x10^7 cells, incubated at room temperature, a condition that did not induce chlamydospore formation, and a second culture with standard galactose-poor CIM (0.025% w/v) and a starting inoculum 1x10^2 cells,  which induced abundant chlamydospores production.

extract_protocol: Total RNA was extracted using Tri-reagent (Sigma) using a microdismembrator (Braun, Melsungen,Germany).

treatment_protocol: Cells were spun down at 2,500 x g for 5 min and flash frozen in liquid N2.

tag: cell type

value: chlamydospore

source_name: Candida dubliniensis, 0.5% (w/v) galactose

value: yeast


title: chlamydospore sample 1 (Cy3) vs. yeast sample 1 (Cy5)

description:
Candida dubliniensis incubated in YNB containing 0.025% (w/v) galactose and 20 mg/L methionine pH 3.7 (chlamydospore induction) VS. C. dubliniensis incubated in YNB containing 0.5% (w/v) galactose and 20 mg/L methionine pH 3.7 (no chlamydospore induction).

Biological replicate 1 of 3.


title: chlamydospore sample 3 (Cy5) vs. yeast sample 3 (Cy3)

description:
Candida dubliniensis incubated in YNB containing 0.025% (w/v) galactose and 20 mg/L methionine pH 3.7 (chlamydospore induction) VS. C. dubliniensis incubated in YNB containing 0.5% (w/v) galactose and 20 mg/L methionine pH 3.7 (no chlamydospore induction).

Biological replicate 3 of 3. Technical replicate 2 of 2.


title: Healthy control 13

status: Public on Mar 13 2010

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

description: Gene expression data from bone marrow CD34+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were pre-processed using Robust MultiChip Analysis (RMA) using GeneSpring 7.3.1.

label: Biotin

source_name: Bone marrow CD34+ cells

label_protocol: 50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using TRIZOL following the manufacturer’s protocol

treatment_protocol: Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.

tag: tissue type

value: bone marrow

value: CD34+ hematopoietic stem cells (HSC)

tag: disease status

value: healthy control


title: Healthy control 15


title: chlamydospore sample 2 (Cy5) vs. yeast sample 2 (Cy3)

description:
Candida dubliniensis incubated in YNB containing 0.025% (w/v) galactose and 20 mg/L methionine pH 3.7 (chlamydospore induction) VS. C. dubliniensis incubated in YNB containing 0.5% (w/v) galactose and 20 mg/L methionine pH 3.7 (no chlamydospore induction).

Biological replicate 2 of 3.


title: Healthy control 14


title: Healthy control 16


title: Healthy control 17


title: Healthy control 8


title: Healthy control 10


title: Healthy control 11


title: Healthy control 6


title: Healthy control 9


title: Healthy control 5


title: Healthy control 3


title: Healthy control 4


title: Healthy control 2


title: Healthy control 7


title: Healthy control 12


title: MDS patient 183

value: myelodysplastic syndromes (MDS)

tag: disease subtype

value: refractory anemia with ringed sideroblasts (RARS)

tag: genome/variation

value: normal


title: Rpb3_IP_1

status: Public on Oct 18 2010

type: genomic

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

hyb_protocol: Hybridization and washing were performed as described in the NimbleChip Array User’s Guide.

scan_protocol: Arrays were scanned with an Agilent G2565CA scanner at 5 µm resolution, two-pass scanning, with manually adjusted gain settings.

data_processing: Data were processed using Nimblescan software (Nimblegen) according to the manufacturer's instructions. For presentation, log2 ratios were converted to fold-enrichment values with fold enrichment of 1 representing the genome-wide average.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: DGRC Drosophila S2 cells, Pol II (Rpb3) IP DNA

label_protocol: 25 ng immunoprecipitated or input DNA was amplified using the Sigma WGA2 Kit. Sample labeling was performed as described in the NimbleChip Array User’s Guide, except immediately following labeling samples were subjected to a second round of labeling consisting of incubation at 98° C for 10 minutes, 2 minute incubation on ice, addition of 2 µl Klenow exo- (NEB), and subsequent 2 hour incubation at 37° C.

growth_protocol: Cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS (GIBCO)

extract_protocol: DGRC S2 cells were grown to a density of ~5E6 cells/ml, diluted 1:2 in M3 media lacking serum, crosslinked with 1% formaldehyde for 10 minutes, then quenched with glycine at a final concentration of 125 mM. Crosslinked cells were washed once with cold PBS, resuspended in 1 ml cold Sonication buffer (0.5% SDS, 20 mM Tris pH8.0, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, protease inhibitors) per 108 cells, incubated on ice for 10 minutes, then sonicated in a Diagenode Bioruptor with 12 30-second pulses, each pulse followed by a 2.5-minute rest, to obtain fragments of 200-600 bp. Sonicated material was spun in a 4° C micro-centrifuge at maximum speed for 10 minutes, and the supernatant (ChIP-material) was stored at -80° C. For each sample, 75 µl ChIP-material was diluted into 1 ml IP buffer (0.5% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl, 10% glycerol), pre-cleared with Protein-A agarose for 90 minutes, immuno-precipitated overnight with a concentration of antibody titrated to maximize signal:noise ratio, and incubated for 90 minutes with Protein-A agarose beads. Beads were washed extensively, bound material was eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3), crosslinks were reversed, precipitated DNA was extracted once with phenol:chloroform:isoamyl alcohol and then ethanol precipitation. Precipitated DNA from 6-10 IPs was resuspended in water and pooled. RNA was degraded by 30 minute treatment with RNAse cocktail (Ambion), and DNA further purified by QIAquick PCR purification kit (QIAGEN). Invitrogen S2 cells treated with 1 µM 20-hydroxyecdysone were grown to a density of ~2E6 cells/ml, challenged with bacteria or mock-challenged with PBS, and subjected to an identical extraction protocol.

value: S2 cells

source_name: DGRC Drosophila S2 cells, Input DNA


title: MDS patient 178

value: other


title: Healthy control 1


title: MDS patient 180

value: refractory anemia (RA)


title: TFIIA_2_Adelman

description: Chromatin immunoprecipitated with antibody raised against TFIIA

source_name: Drosophila S2 cells (DGRC), TFIIA IP DNA

extract_protocol: For ecdysone treatment experiments, Invitrogen S2 cells were diluted to a density of ~1E6 cells/ml and were grown in the presence of 1 µM 20-hyrodxyecdysone or vehicle for 24 hours. Cells were then resuspended by scraping, diluted 1:2 in M3 media lacking serum, crosslinked with 1% formaldehyde for 10 minutes, then quenched with glycine at a final concentration of 125 mM. Crosslinked cells were washed once with cold PBS, resuspended in 1 ml cold Sonication buffer (0.5% SDS, 20 mM Tris pH8.0, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, protease inhibitors) per 108 cells, incubated on ice for 10 minutes, then sonicated in a Diagenode Bioruptor with 12 30-second pulses, each pulse followed by a 2.5-minute rest, to obtain fragments of 200-600 bp. Sonicated material was spun in a 4° C micro-centrifuge at maximum speed for 10 minutes, and the supernatant (ChIP-material) was stored at -80° C. For each sample, 75 µl ChIP-material was diluted into 1 ml IP buffer (0.5% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl, 10% glycerol), pre-cleared with Protein-A agarose for 90 minutes, immuno-precipitated overnight with a concentration of antibody titrated to maximize signal:noise ratio, and incubated for 90 minutes with Protein-A agarose beads. Beads were washed extensively, bound material was eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3), crosslinks were reversed, precipitated DNA was extracted once with phenol:chloroform:isoamyl alcohol and then ethanol precipitation. Precipitated DNA from 6-10 IPs was resuspended in water and pooled. RNA was degraded by 30 minute treatment with RNAse cocktail (Ambion), and DNA further purified by QIAquick PCR purification kit (QIAGEN). For TFIIA experiments, DGRC S2 cells were grown to a density of ~5E6 cells/ml, then processed as described above except that cells were crosslinked for 30 minutes before quenching.

value: Drosophila S2 Cells (DGRC)

tag: fraction

value: TFIIA IP DNA

tag: agent

source_name: Drosophila S2 cells (DGRC), Input DNA

value: input


title: MDS patient 181


title: Pol_II_Embryo_016hours_IP_1

description: Chromatin immunoprecipitated with antibody raised against Rpb3

source_name: Drosophila 0-16 hour embryos, Pol II (Rpb3) IP DNA

growth_protocol: Embryos were collected on grape agar plates from 5 g of Oregon R wild type adults over the course of 16 hours at 25oC.

extract_protocol: Approximately 500 mg of embryos were collected on grape agar plates from 5 g of Oregon R wild type adults over the course of 16 hours at 25oC. Embryos were dechorionated in 50% bleach for 90 seconds, rinsed thoroughly with distilled water, rinsed with 10ml of isopropanol then immediately plunged into a two-phase mixture of 30 ml n-heptane and 10 ml fixation buffer (50 mM HEPES pH 7.6, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1.8% formaldehyde). Embryos were fixed for 15 minutes with vigorous agitation, centrifuged 1 minute at 500 rcf (25° C) to pellet, quenched for 1 minute with 125 mM Glycine (in PBS), then washed once with 50 ml PBT (PBS with 0.1% Triton X-100). The dry embryo cake was weighed, flash frozen and stored at -80° C. Fixed embryos were Dounce homogenized in 10 volumes of PBT using 20 strokes with a loose fitting pestle. The lysate was centrifuged for 1 minute at 400 rcf (4° C) to pellet unbroken embryos, and the supernatant was transferred to a new tube and centrifuged for 10 minutes at 1100 rcf (4° C) to obtain a crude nuclear pellet. The crude nuclear pellet was resuspended in 10 ml of cold Cell Lysis Buffer (50 mM HEPES pH7.6, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, protease inhibitors) per mg of starting frozen fixed embryos, then Dounce homogenized using 20 strokes with a tight-fitting pestle. This homogenate was centrifuged for 4 minutes at 2000 rcf (4° C), resuspended in 1 ml cold Nuclear Lysis Buffer (50 mM Hepes pH 7.6, 10 mM EDTA, 0.5% N-lauroylsarcosine, 1 mM PMSF, protease inhibitors) per 750 mg starting frozen fixed embryos, and incubated at room temperature for 20 minutes. The nuclear lysate was diluted with an additional volume of cold Nuclear Lysis Buffer, then sonicated in a Diagenode Bioruptor with 8 30-second pulses at the medium intensity setting (2 minute rest between pulses) to obtain fragments of 200-600bp. Sonicated material was spun in a 4° C micro-centrifuge at maximum speed for 10 minutes, and the supernatant (ChIP-material) was stored at -80° C. For each sample, 75 µl ChIP-material was diluted into 1 ml IP buffer (0.5% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl, 10% glycerol), pre-cleared with Protein-A agarose for 90 minutes, immuno-precipitated overnight with a concentration of antibody titrated to maximize signal:noise ratio, and incubated for 90 minutes with Protein-A agarose beads. Beads were washed extensively, bound material was eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3), crosslinks were reversed, precipitated DNA was extracted once with phenol:chloroform:isoamyl alcohol and then ethanol precipitation. Precipitated DNA from 6-10 IPs was resuspended in water and pooled. RNA was degraded by 30 minute treatment with RNAse cocktail (Ambion), and DNA further purified by QIAquick PCR purification kit (QIAGEN).

tag: developmental stage

value: embryo 0-16 hours

source_name: Drosophila 0-16 hour embryos, Input DNA


title: MDS patient 179


title: Pol_II_(-)Ecdysone_2_Adelman

source_name: Drosophila S2 cells (Invitrogen), Pol II (Rpb3) IP DNA

growth_protocol: Drosophila S2 cells ( Invitrogen) were grown in Schneider’s media +10% FBS without additional supplementation.

treatment_protocol: Cells were treated for 24 hours with vehicle before crosslinking and sonication.

value: Drosophila S2 Cells (Invitrogen)

value: Pol II (Rpb3) IP DNA

value: vehicle

source_name: Drosophila S2 cells (Invitrogen), Input DNA


title: MDS patient 173


title: Pol_II_Embryo_016hours_IP_2


title: Rpb3_NELF_RNAi_IP_2

treatment_protocol: Cells were crosslinked 96 hours after addition of dsRNA targeting NELF-B and NELF-E.


title: MDS patient 169

value: refractory anemia with excess blasts 1 (RAEB1)


title: Pol_II_(-)Ecdysone_1_Adelman


title: Rpb3_Untreated_RNAi_IP_1


title: Pol_II_(Ser2-P)_IP_2

source_name: DGRC Drosophila S2 cells, Pol II (Ser2-P) IP DNA


title: MDS patient 176

value: bone marrow


title: Pol_II_+Ecdysone_1_Adelman

treatment_protocol: Cells were treated for 24 hours with 1 µM 20-hydroxyecdysone before crosslinking and sonication.

value: 1 µM 20-hydroxyecdysone


title: MDS patient 171

value: CD34+ hematopoietic stem cells (HSC)


title: MDS patient 167

value: myelodysplastic syndromes (MDS)

value: refractory anemia with excess blasts 2 (RAEB2)


title: MDS patient 166


title: DSIF_(Spt5)_IP_2

source_name: DGRC Drosophila S2 cells, DSIF (Spt5) IP DNA


title: NELF-B_IP_2

source_name: DGRC Drosophila S2 cells, NELF-B IP DNA


title: Rpb3_NELF_RNAi_IP_1


title: MDS patient 165

value: normal


title: Pol_II_(Ser2-P)_IP_1

value: S2 cells


title: Pol_II_+Ecdysone_2_Adelman


title: MDS patient 174


title: Rpb3_Mock_RNAi_IP_1

treatment_protocol: Cells were crosslinked 96 hours after addition of dsRNA targeting β-galactosidase.


title: MDS patient 163


title: Rpb3_Untreated_RNAi_IP_2


title: MDS patient 170

value: other


title: NELF-B_IP_1


title: MDS patient 161

value: refractory anemia with ringed sideroblasts (RARS)

value: del5q plus other


title: TFIIA_1_Adelman

value: Drosophila S2 Cells (DGRC)

value: TFIIA IP DNA


title: MDS patient 164


title: MDS patient 172

value: refractory anemia (RA)


title: MDS patient 160


title: MDS patient 159


title: MDS patient 153


title: MDS patient 158

value: del5q plus monosomy7/del7q plus other


title: DSIF_(Spt5)_IP_1


title: Rpb3_IP_2


title: MDS patient 156


title: MDS patient 155


title: MDS patient 157


title: MDS patient 162


title: MDS patient 168


title: MDS patient 151


title: MDS patient 127


title: MDS patient 152


title: MDS patient 141


title: MDS patient 150


title: MDS patient 130


title: MDS patient 147


title: MDS patient 144


title: MDS patient 139


title: MDS patient 134


title: MDS patient 133


title: MDS patient 123


title: MDS patient 149


title: MDS patient 136


title: MDS patient 125


title: MDS patient 135


title: MDS patient 128


title: MDS patient 131


title: MDS patient 146


title: MDS patient 138


title: MDS patient 142


title: MDS patient 140


title: MDS patient 148


title: MDS patient 120


title: MDS patient 124


title: MDS patient 121


title: MDS patient 132


title: MDS patient 116


title: MDS patient 114


title: MDS patient 117


title: MDS patient 113


title: MDS patient 143


title: MDS patient 104


title: MDS patient 115


title: MDS patient 106


title: MDS patient 118


title: MDS patient 102


title: MDS patient 129


title: MDS patient 108


title: MDS patient 103


title: MDS patient 107


title: MDS patient 101


title: MDS patient 99


title: MDS patient 97


title: MDS patient 98


title: MDS patient 89


title: MDS patient 88


title: MDS patient 91


title: MDS patient 81


title: MDS patient 84


title: MDS patient 87


title: MDS patient 90


title: MDS patient 75


title: MDS patient 74


title: MDS patient 85


title: MDS patient 68


title: MDS patient 80


title: MDS patient 76


title: MDS patient 82


title: MDS patient 79


title: MDS patient 92


title: MDS patient 71


title: MDS patient 67


title: MDS patient 63


title: MDS patient 59


title: MDS patient 62


title: MDS patient 72


title: MDS patient 61


title: MDS patient 58


title: MDS patient 57


title: MDS patient 96


title: MDS patient 53


title: MDS patient 55


title: MDS patient 29


title: MDS patient 27


title: MDS patient 52


title: MDS patient 54


title: MDS patient 43


title: MDS patient 25


title: MDS patient 50


title: MDS patient 12


title: MDS patient 15


title: MDS patient 94


title: MDS patient 14


title: MDS patient 9


title: MDS patient 10


title: MDS patient 33