title: DH line, CFD12-307


title: DH line, CFD12-310

status: Public on Sep 05 2013

type: genomic

city: Freising

first: Eva

last: Bauer

address: Liesel-Beckmann-Str. 2

department: Plant Breeding

country: Germany

institute: Technical University of Munich

description: Genomic DNA from maize was analyzed with the Illumina MaizeSNP50 BeadChip

hyb_protocol: Array hybridization and raw data processing was performed according to manufacturer’s instructions (Illumina).

data_processing: Data processing was performed using GenomeStudio software 2011.1 (Illumina)(Genotyping Module v 1.9.4) using the clusterfile maizesnp50_b.egt available from Illumina.

label: Cy3, Cy5

molecule: genomic DNA

organism: Zea mays

source_name: leaf

growth_protocol: Plants grown in greenhouse or field.

extract_protocol: DNA was extracted from dried leaves using a modified CTAB protocol (modified from Saghai-Maroof et al. 1984, PNAS)

tag: status

value: DH line

tag: maize population

value: Dent


title: DH line, CFD12-306

scan_protocol: Array hybridization and raw data processing was performed according to manufacturer’s instructions (Illumina).


title: DH line, CFD12-304

label_protocol: Array hybridization and raw data processing was performed according to manufacturer’s instructions (Illumina).


title: DH line, CFD12-305


title: DH line, CFD12-302


title: DH line, CFF01-013

value: Flint


title: DH line, CFD12-303


title: DH line, CFD12-100


title: DH line, CFD12-098


title: DH line, CFD12-099


title: DH line, CFD12-094


title: DH line, CFD12-096


title: DH line, CFD12-092


title: DH line, CFD12-087


title: DH line, CFD12-091


title: DH line, CFD12-090


title: DH line, CFD12-083


title: DH line, CFD12-301


title: DH line, CFD12-081


title: DH line, CFD12-082


title: DH line, CFD12-089


title: DH line, CFD12-093


title: DH line, CFD12-074


title: DH line, CFD12-080


title: DH line, CFD12-084


title: DH line, CFD12-070


title: DH line, CFD12-069


title: DH line, CFD12-068


title: DH line, CFD12-067


title: DH line, CFD12-072


title: DH line, CFD12-063


title: DH line, CFD12-066


title: DH line, CFD12-061


title: DH line, CFD12-064


title: DH line, CFD12-059


title: DH line, CFD12-065


title: DH line, CFD12-097


title: DH line, CFD12-085


title: DH line, CFD12-060


title: DH line, CFD12-050


title: DH line, CFD12-054


title: DH line, CFD12-058


title: DH line, CFD12-052


title: DH line, CFD12-051


title: DH line, CFD12-057


title: DH line, CFD12-048


title: DH line, CFD12-049


title: DH line, CFD12-042


title: DH line, CFD12-040


title: DH line, CFD12-019


title: DH line, CFD12-071


title: DH line, CFD12-020


title: DH line, CFD12-022


title: DH line, CFD12-034


title: DH line, CFD12-038


title: DH line, CFD12-035


title: DH line, CFD12-018


title: DH line, CFD12-033


title: DH line, CFD11-352


title: DH line, CFD12-013


title: DH line, CFD12-003


title: DH line, CFD12-012


title: DH line, CFD11-349


title: DH line, CFD12-017


title: DH line, CFD11-351


title: DH line, CFD11-350


title: DH line, CFD11-348


title: DH line, CFD11-347


title: DH line, CFD11-344


title: DH line, CFD11-346


title: DH line, CFD11-340


title: DH line, CFD11-341


title: DH line, CFD11-345


title: DH line, CFD11-343


title: DH line, CFD11-334


title: DH line, CFD12-041


title: DH line, CFD11-328


title: DH line, CFD11-333


title: DH line, CFD11-339


title: DH line, CFD11-342


title: DH line, CFD11-324


title: DH line, CFD11-329


title: DH line, CFD11-330


title: DH line, CFD11-337


title: DH line, CFD11-325


title: DH line, CFD11-332


title: DH line, CFD11-327


title: DH line, CFD11-326


title: DH line, CFD11-338


title: DH line, CFD11-323


title: DH line, CFD11-335


title: DH line, CFD11-322


title: DH line, CFD11-331


title: DH line, CFD11-314


title: DH line, CFD11-316


title: DH line, CFD11-319


title: DH line, CFD11-308


title: DH line, CFD11-315


title: DH line, CFD11-312


title: DH line, CFD11-306


title: DH line, CFD11-309


title: DH line, CFD11-313


title: DH line, CFD11-305


title: DH line, CFD11-320


title: DH line, CFD11-318


title: DH line, CFD11-303


title: DH line, CFD11-317


title: DH line, CFD11-321


title: DH line, CFD11-069


title: DH line, CFD11-304


title: DH line, CFD11-310


title: DH line, CFD11-307


title: DH line, CFD11-068


title: DH line, CFD11-336


title: DH line, CFD11-067


title: DH line, CFD11-066


title: DH line, CFD11-302


title: DH line, CFD11-065


title: DH line, CFD11-311


title: DH line, CFD11-053


title: DH line, CFD11-050


title: DH line, CFD11-051


title: DH line, CFD11-058


title: DH line, CFD11-057


title: DH line, CFD11-048


title: DH line, CFD11-054


title: DH line, CFD11-047


title: DH line, CFD11-060


title: DH line, CFD12-037


title: DH line, CFD11-062


title: DH line, CFD11-046


title: DH line, CFD11-059


title: DH line, CFD11-045


title: DH line, CFD11-044


title: DH line, CFD11-042


title: DH line, CFD12-047


title: DH line, CFD11-064


title: DH line, CFD11-010


title: DH line, CFD11-008


title: DH line, CFD11-026


title: DH line, CFD11-007


title: DH line, CFD11-029


title: DH line, CFD12-043


title: DH line, CFD11-030


title: DH line, CFD11-040


title: DH line, CFD11-011


title: DH line, CFD11-021


title: DH line, CFD11-009


title: DH line, CFD12-075


title: DH line, CFD10-325


title: DH line, CFD10-323


title: DH line, CFD10-330


title: DH line, CFD10-331


title: DH line, CFD11-004


title: DH line, CFD10-322


title: DH line, CFD10-329


title: DH line, CFD10-324


title: DH line, CFD10-320


title: DH line, CFD10-317


title: DH line, CFD11-005


title: DH line, CFD11-002


title: DH line, CFD10-327


title: DH line, CFD10-326


title: DH line, CFD10-319


title: DH line, CFD10-318


title: DH line, CFD11-006


title: DH line, CFD10-312


title: DH line, CFD10-314


title: DH line, CFD10-313


title: DH line, CFD10-309


title: DH line, CFD10-305


title: DH line, CFD10-307


title: DH line, CFD10-306


title: DH line, CFD10-308


title: DH line, CFD10-310


title: DH line, CFD10-316


title: DH line, CFD10-311


title: DH line, CFD10-315


title: DH line, CFD10-154


title: DH line, CFD10-301


title: DH line, CFD10-149


title: DH line, CFD10-138


title: DH line, CFD10-303


title: DH line, CFD10-302


title: DH line, CFD10-136


title: DH line, CFD10-153


title: DH line, CFD10-147


title: DH line, CFD10-152


title: DH line, CFD10-139


title: DH line, CFD10-133


title: DH line, CFD10-146


title: DH line, CFD10-142


title: DH line, CFD10-132


title: DH line, CFD10-143


title: DH line, CFD10-145


title: DH line, CFD10-130


title: DH line, CFD10-125


title: DH line, CFD10-121


title: DH line, CFD10-131


title: DH line, CFD10-113


title: DH line, CFD10-119


title: DH line, CFD10-118


title: DH line, CFD10-129


title: DH line, CFD10-112


title: DH line, CFD10-117


title: DH line, CFD10-128


title: DH line, CFD10-114


title: DH line, CFD10-120


title: DH line, CFD10-111


title: DH line, CFD10-100


title: DH line, CFD10-080


title: DH line, CFD10-093


title: DH line, CFD10-087


title: DH line, CFD10-092


title: DH line, CFD10-079


title: DH line, CFD10-063


title: DH line, CFD10-105


title: DH line, CFD10-088


title: DH line, CFD10-077


title: DH line, CFD10-072


title: DH line, CFD10-064


title: DH line, CFD10-071


title: DH line, CFD10-090


title: DH line, CFD10-097


title: DH line, CFD10-083


title: DH line, CFD10-101


title: DH line, CFD10-108


title: DH line, CFD10-061


title: DH line, CFD10-050


title: DH line, CFD10-062


title: DH line, CFD10-049


title: DH line, CFD10-059


title: DH line, CFD10-041


title: DH line, CFD10-089


title: DH line, CFD10-045


title: DH line, CFD10-036


title: DH line, CFD10-039


title: DH line, CFD10-099


title: DH line, CFD10-034


title: DH line, CFD10-015


title: DH line, CFD10-021


title: DH line, CFD10-031


title: DH line, CFD10-007


title: DH line, CFD10-033


title: DH line, CFD10-002


title: DH line, CFD10-006


title: DH line, CFD10-018


title: DH line, CFD10-019


title: DH line, CFD09-338


title: DH line, CFD10-008


title: DH line, CFD09-341


title: DH line, CFD09-342


title: DH line, CFD09-335


title: DH line, CFD09-336


title: DH line, CFD09-334


title: DH line, CFD10-001


title: DH line, CFD09-333


title: DH line, CFD09-328


title: DH line, CFD09-339


title: DH line, CFD09-332


title: DH line, CFD10-004


title: DH line, CFD09-329


title: DH line, CFD09-325


title: DH line, CFD09-326


title: DH line, CFD09-324


title: DH line, CFD09-319


title: DH line, CFD09-323


title: DH line, CFD09-317


title: DH line, CFD09-327


title: DH line, CFD09-312


title: DH line, CFD09-307


title: DH line, CFD09-308


title: DH line, CFD09-309


title: DH line, CFD09-320


title: DH line, CFD09-306


title: DH line, CFD09-313


title: DH line, CFD09-314


title: DH line, CFD09-305


title: DH line, CFD09-310


title: DH line, CFD09-322


title: DH line, CFD09-304


title: DH line, CFD09-302


title: DH line, CFD09-316


title: DH line, CFD09-315


title: DH line, CFD09-303


title: DH line, CFD09-311


title: DH line, CFD09-108


title: DH line, CFD09-103


title: DH line, CFD09-110


title: DH line, CFD09-101


title: DH line, CFD09-115


title: DH line, CFD09-102


title: DH line, CFD09-105


title: DH line, CFD09-112


title: DH line, CFD09-097


title: DH line, CFD09-077


title: DH line, CFD09-044


title: DH line, CFD09-054


title: DH line, CFD10-051


title: DH line, CFD09-062


title: DH line, CFD09-086


title: DH line, CFD09-079


title: DH line, CFD09-076


title: DH line, CFD09-046


title: DH line, CFD09-078


title: DH line, CFD09-340


title: DH line, CFD09-080


title: DH line, CFD09-068


title: DH line, CFD09-048


title: DH line, CFD09-012


title: DH line, CFD09-033


title: DH line, CFD07-342


title: DH line, CFD07-334


title: DH line, CFD07-330


title: DH line, CFD07-335


title: DH line, CFD07-329


title: DH line, CFD07-331


title: DH line, CFD09-009


title: DH line, CFD09-001


title: DH line, CFD07-336


title: DH line, CFD07-332


title: DH line, CFD07-327


title: DH line, CFD07-328


title: DH line, CFD07-320


title: DH line, CFD07-333


title: DH line, CFD07-324


title: DH line, CFD07-321


title: DH line, CFD07-325


title: DH line, CFD07-326


title: DH line, CFD07-318


title: DH line, CFD07-312


title: DH line, CFD07-316


title: DH line, CFD07-317


title: DH line, CFD07-322


title: DH line, CFD09-337


title: DH line, CFD07-323


title: DH line, CFD07-313


title: DH line, CFD07-315


title: DH line, CFD07-314


title: DH line, CFD07-311


title: DH line, CFD07-307


title: DH line, CFD07-309


title: DH line, CFD07-319


title: DH line, CFD07-305


title: DH line, CFD07-310


title: DH line, CFD07-308


title: DH line, CFD07-303


title: DH line, CFD07-304


title: DH line, CFD07-306


title: DH line, CFD07-125


title: DH line, CFD09-318


title: DH line, CFD07-113


title: DH line, CFD07-106


title: DH line, CFD07-126


title: DH line, CFD07-124


title: DH line, CFD07-123


title: DH line, CFD07-112


title: DH line, CFD07-120


title: DH line, CFD07-301


title: DH line, CFD07-118


title: DH line, CFD07-107


title: DH line, CFD07-110


title: DH line, CFD07-116


title: DH line, CFD07-108


title: DH line, CFD07-302


title: DH line, CFD07-111


title: DH line, CFD07-121


title: DH line, CFD07-117


title: DH line, CFD07-115


title: DH line, CFD07-119


title: DH line, CFD07-109


title: DH line, CFD07-105


title: DH line, CFD07-100


title: DH line, CFD07-104


title: DH line, CFD07-114


title: DH line, CFD07-099


title: DH line, CFD07-101


title: DH line, CFD07-084


title: DH line, CFD07-095


title: DH line, CFD07-079


title: DH line, CFD07-097


title: DH line, CFD07-085


title: DH line, CFD07-083


title: DH line, CFD07-102


title: DH line, CFD07-074


title: DH line, CFD07-076


title: DH line, CFD07-103


title: DH line, CFD07-077


title: DH line, CFD07-078


title: DH line, CFD07-094


title: DH line, CFD07-090


title: DH line, CFD07-080


title: DH line, CFD07-070


title: DH line, CFD07-086


title: DH line, CFD07-089


title: DH line, CFD07-122


title: DH line, CFD07-068


title: DH line, CFD07-071


title: DH line, CFD07-073


title: DH line, CFD07-098


title: DH line, CFD07-067


title: DH line, CFD07-063


title: DH line, CFD07-069


title: DH line, CFD07-072


title: DH line, CFD07-064


title: DH line, CFD07-061


title: DH line, CFD07-042


title: DH line, CFD07-024


title: DH line, CFD07-047


title: DH line, CFD07-062


title: DH line, CFD07-018


title: DH line, CFD07-015


title: DH line, CFD07-003


title: DH line, CFD06-342


title: DH line, CFD06-346


title: DH line, CFD07-010


title: DH line, CFD07-036


title: DH line, CFD07-014


title: DH line, CFD07-023


title: DH line, CFD07-011


title: DH line, CFD06-340


title: DH line, CFD06-345


title: DH line, CFD07-017


title: DH line, CFD07-005


title: DH line, CFD06-337


title: DH line, CFD07-037


title: DH line, CFD07-002


title: DH line, CFD06-343


title: DH line, CFD06-338


title: DH line, CFD07-029


title: DH line, CFD06-341


title: DH line, CFD06-344


title: DH line, CFD06-347


title: DH line, CFD06-339


title: DH line, CFD06-335


title: DH line, CFD06-336


title: DH line, CFD06-324


title: DH line, CFD06-321


title: DH line, CFD06-327


title: DH line, CFD06-334


title: DH line, CFD06-331


title: DH line, CFD06-330


title: DH line, CFD06-310


title: DH line, CFD06-326


title: DH line, CFD06-322


title: DH line, CFD06-323


title: DH line, CFD06-316


title: DH line, CFD06-317


title: DH line, CFD06-325


title: DH line, CFD06-309


title: DH line, CFD06-320


title: DH line, CFD06-315


title: DH line, CFD06-319


title: DH line, CFD06-314


title: DH line, CFD06-332


title: DH line, CFD06-312


title: DH line, CFD06-306


title: DH line, CFD06-311


title: DH line, CFD06-313


title: DH line, CFD06-307


title: DH line, CFD06-328


title: DH line, CFD06-308


title: DH line, CFD06-333


title: DH line, CFD06-329


title: DH line, CFD06-305


title: DH line, CFD06-318


title: DH line, CFD06-301


title: DH line, CFD06-302


title: DH line, CFD06-085


title: DH line, CFD06-082


title: DH line, CFD06-303


title: DH line, CFD06-070


title: DH line, CFD06-092


title: DH line, CFD06-076


title: DH line, CFD06-073


title: DH line, CFD06-091


title: DH line, CFD06-084


title: DH line, CFD06-066


title: DH line, CFD06-069


title: DH line, CFD06-087


title: DH line, CFD06-064


title: DH line, CFD06-067


title: DH line, CFD06-304


title: DH line, CFD06-083


title: DH line, CFD06-080


title: DH line, CFD06-079


title: DH line, CFD06-074


title: DH line, CFD06-088


title: DH line, CFD06-090


title: DH line, CFD06-065


title: DH line, CFD06-063


title: DH line, CFD06-089


title: DH line, CFD06-077


title: DH line, CFD06-081


title: DH line, CFD06-072


title: DH line, CFD06-062


title: DH line, CFD06-056


title: DH line, CFD06-049


title: DH line, CFD06-042


title: DH line, CFD06-047


title: DH line, CFD06-023


title: DH line, CFD06-054


title: DH line, CFD06-027


title: DH line, CFD06-024


title: DH line, CFD06-058


title: DH line, CFD06-035


title: DH line, CFD06-044


title: DH line, CFD06-051


title: DH line, CFD06-037


title: DH line, CFD06-039


title: DH line, CFD06-026


title: DH line, CFD06-045


title: DH line, CFD06-033


title: DH line, CFD06-021


title: DH line, CFD06-059


title: DH line, CFD06-019


title: DH line, CFD06-022


title: DH line, CFD06-025


title: DH line, CFD06-005


title: DH line, CFD06-018


title: DH line, CFD06-004


title: DH line, CFD06-041


title: DH line, CFD05-324


title: DH line, CFD05-321


title: DH line, CFD05-319


title: DH line, CFD06-013


title: DH line, CFD05-317


title: DH line, CFD05-315


title: DH line, CFD05-312


title: DH line, CFD05-322


title: DH line, CFD06-002


title: DH line, CFD05-318


title: DH line, CFD05-316


title: DH line, CFD05-313


title: DH line, CFD05-304


title: DH line, CFD05-314


title: DH line, CFD05-307


title: DH line, CFD06-011


title: DH line, CFD05-320


title: DH line, CFD06-007


title: DH line, CFD05-309


title: DH line, CFD06-093


title: DH line, CFD05-303


title: DH line, CFD05-311


title: DH line, CFD05-073


title: DH line, CFD05-301


title: DH line, CFD05-310


title: DH line, CFD05-072


title: DH line, CFD05-074


title: DH line, CFD05-069


title: DH line, CFD05-070


title: DH line, CFD05-308


title: DH line, CFD05-058


title: DH line, CFD05-061


title: DH line, CFD05-063


title: DH line, CFD05-071


title: DH line, CFD06-003


title: DH line, CFD05-065


title: DH line, CFD05-067


title: DH line, CFD05-068


title: DH line, CFD05-064


title: DH line, CFD05-306


title: DH line, CFD05-059


title: DH line, CFD05-062


title: DH line, CFD05-060


title: DH line, CFD05-057


title: DH line, CFD05-056


title: DH line, CFD05-054


title: DH line, CFD05-055


title: DH line, CFD05-050


title: DH line, CFD05-049


title: DH line, CFD05-047


title: DH line, CFD05-046


title: DH line, CFD05-066


title: DH line, CFD05-048


title: DH line, CFD05-043


title: DH line, CFD05-045


title: DH line, CFD05-039


title: DH line, CFD05-042


title: DH line, CFD05-040


title: DH line, CFD05-032


title: DH line, CFD05-035


title: DH line, CFD05-044


title: DH line, CFD05-027


title: DH line, CFD05-022


title: DH line, CFD05-026


title: DH line, CFD05-029


title: DH line, CFD05-036


title: DH line, CFD05-024


title: DH line, CFD05-037


title: DH line, CFD05-023


title: DH line, CFD05-019


title: DH line, CFD05-028


title: DH line, CFD05-021


title: DH line, CFD05-025


title: DH line, CFD05-031


title: DH line, CFD05-009


title: DH line, CFD04-351


title: DH line, CFD05-015


title: DH line, CFD05-020


title: DH line, CFD05-016


title: DH line, CFD05-018


title: DH line, CFD05-006


title: DH line, CFD04-349


title: DH line, CFD04-348


title: DH line, CFD04-343


title: DH line, CFD04-350


title: DH line, CFD04-337


title: DH line, CFD04-338


title: DH line, CFD04-344


title: DH line, CFD04-336


title: DH line, CFD04-341


title: DH line, CFD04-340


title: DH line, CFD04-335


title: DH line, CFD04-347


title: DH line, CFD04-345


title: DH line, CFD05-013


title: DH line, CFD04-346


title: DH line, CFD04-342


title: DH line, CFD04-334


title: DH line, CFD04-331


title: DH line, CFD04-333


title: DH line, CFD04-332


title: DH line, CFD04-328


title: DH line, CFD04-330


title: DH line, CFD04-325


title: DH line, CFD04-327


title: DH line, CFD04-326


title: DH line, CFD04-324


title: DH line, CFD04-310


title: DH line, CFD04-315


title: DH line, CFD04-309


title: DH line, CFD04-322


title: DH line, CFD04-320


title: DH line, CFD04-319


title: DH line, CFD04-318


title: DH line, CFD04-321


title: DH line, CFD04-323


title: DH line, CFD04-307


title: DH line, CFD04-314


title: DH line, CFD04-316


title: DH line, CFD04-313


title: DH line, CFD04-311


title: DH line, CFD04-308


title: DH line, CFD04-304


title: DH line, CFD04-117


title: DH line, CFD04-303


title: DH line, CFD04-305


title: DH line, CFD04-104


title: DH line, CFD04-111


title: DH line, CFD04-101


title: DH line, CFD04-306


title: DH line, CFD04-302


title: DH line, CFD04-317


title: DH line, CFD04-312


title: DH line, CFD04-098


title: DH line, CFD04-093


title: DH line, CFD04-107


title: DH line, CFD04-092


title: DH line, CFD04-116


title: DH line, CFD04-108


title: DH line, CFD04-102


title: DH line, CFD05-033


title: DH line, CFD04-088


title: DH line, CFD04-106


title: DH line, CFD05-302


title: DH line, CFD04-100


title: DH line, CFD04-114


title: DH line, CFD04-103


title: DH line, CFD04-099


title: DH line, CFD04-085


title: DH line, CFD04-080


title: DH line, CFD04-095


title: DH line, CFD04-074


title: DH line, CFD04-339


title: DH line, CFD04-084


title: DH line, CFD04-096


title: DH line, CFD04-076


title: DH line, CFD04-094


title: DH line, CFD04-061


title: DH line, CFD04-301


title: DH line, CFD04-073


title: DH line, CFD04-091


title: DH line, CFD04-082


title: DH line, CFD04-060


title: DH line, CFD04-079


title: DH line, CFD04-075


title: DH line, CFD04-087


title: DH line, CFD04-057


title: DH line, CFD04-054


title: DH line, CFD04-063


title: DH line, CFD04-059


title: DH line, CFD04-048


title: DH line, CFD04-058


title: DH line, CFD04-047


title: DH line, CFD04-053


title: DH line, CFD04-046


title: DH line, CFD04-015


title: DH line, CFD04-041


title: DH line, CFD04-049


title: DH line, CFD04-045


title: DH line, CFD04-042


title: DH line, CFD04-007


title: DH line, CFD04-005


title: DH line, CFD04-008


title: DH line, CFD04-013


title: DH line, CFD04-034


title: DH line, CFD04-004


title: DH line, CFD04-003


title: DH line, CFD03-355


title: DH line, CFD04-002


title: DH line, CFD03-354


title: DH line, CFD03-353


title: DH line, CFD03-349


title: DH line, CFD03-345


title: DH line, CFD03-346


title: DH line, CFD03-348


title: DH line, CFD03-351


title: DH line, CFD03-347


title: DH line, CFD03-356


title: DH line, CFD03-341


title: DH line, CFD03-343


title: DH line, CFD03-342


title: DH line, CFD03-337


title: DH line, CFD03-328


title: DH line, CFD03-329


title: DH line, CFD03-339


title: DH line, CFD03-335


title: DH line, CFD03-334


title: DH line, CFD03-338


title: DH line, CFD03-331


title: DH line, CFD03-333


title: DH line, CFD03-327


title: DH line, CFD03-322


title: DH line, CFD03-325


title: DH line, CFD03-323


title: DH line, CFD03-321


title: DH line, CFD03-320


title: DH line, CFD03-330


title: DH line, CFD03-332


title: DH line, CFD03-324


title: DH line, CFD03-318


title: DH line, CFD03-326


title: DH line, CFD03-315


title: Control CD11c_vs_K2 CD11c

type: RNA

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

institute: Miltenyi Biotec GmbH

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays CTID 878 in a dual colour approach using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore ™ microarrays was done with the Agilent's Microarray Scanner System (Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing:
Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Hy5/Hy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using LOWESS.
A ratio was not calculated if the average signal intensities for both channels was below the adjusted threshold value (calculated based on the 50% percentile of the background signal intensities and adjusted by the mean of the calibration oligos):
avg(Cy5-bkg) < adjust_Cy5_default AND avg(Cy3-bkg) < adjust_Cy3_default

molecule: total RNA

organism: Mus musculus

source_name: Control CD11c

label_protocol: 1.5 µg (for 0007090032 - 0007090035) and 2 µg (for 0007090036 and 0007090037) of the respective total RNA were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer.

growth_protocol: No additional growth was done.

extract_protocol: RNA was isolated using Trizol.

treatment_protocol: Spleens were dissociated by 40 U/ml of collagenase D. Total splenocytes were stained with antibodies (anti-CD11c, anti-MHC II, anti-CD4, anti-TCRb, and anti-B220) on ice for 15 min. Each population of cells was purified by a cell sorter, spun down and snap frozen by liquid nitrogen until shipping to the company.

tag: strain/background

tag: genotype

value: Blimp-1 flox and CD11c-CRE-

tag: gender

value: female

tag: age

value: 6-10 weeks

tag: tissue

value: spleen

tag: cell type

value: CD11chiMHChi dendritic cells

source_name: KO CD11c

value: Blimp-1 flox and CD11c-CRE+


title: DH line, CFD03-307


title: DH line, CFD03-311


title: DH line, CFD03-312


title: Control CD4_vs_K1 CD4

source_name: Control CD4

value: TCRb+ CD4+ T cells

source_name: KO CD4


title: Control B220_vs_K2 B220

source_name: Control B220

value: B220+ B cells

source_name: KO B220


title: Control CD4_vs_K2 CD4


title: DH line, CFD03-313


title: DH line, CFD03-309


title: Control CD11c_vs_K1 CD11c


title: DH line, CFD03-314


title: DH line, CFD03-317


title: DH line, CFD03-306


title: Control B220_vs_K1 B220


title: DH line, CFD03-310


title: DH line, CFD03-301


title: DH line, CFD03-305


title: DH line, CFD03-302


title: DH line, CFD03-079


title: DH line, CFD03-083


title: DH line, CFD03-081


title: DH line, CFD03-084


title: DH line, CFD03-308


title: DH line, CFD03-303


title: DH line, CFD03-082


title: DH line, CFD03-080


title: DH line, CFD03-304


title: DH line, CFD03-077


title: MADS29 RNAi S3-transgenic-replicate 3

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi, South Campus

description: Gene expression data of transgenic seed 5-10 DAP

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300

data_processing: First-order analysis was performed using Affymetrix® GeneChip® Command Console® 3.0. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5.1 (Stratagene, CA, USA)

label: Biotin

organism: Oryza sativa

source_name: Seed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA

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

tag: variety

tag: genotype/variation

value: MADS29 RNAi (silencing)

value: seed

tag: developmental stage

value: S3 Stage (5-10 Days after pollination)


title: DH line, CFD03-075


title: DH line, CFD03-069


title: DH line, CFD03-068


title: DH line, CFD03-076


title: WTPB1 S3-control-replicate  2

description: Gene expression data of wild type seed 5-10 DAP

value: wild type


title: DH line, CFD03-074


title: DH line, CFD03-071


title: DH line, CFD03-066


title: DH line, CFD03-073


title: MADS29 OX-transgenic-replicate 1

description: Gene expression data of transgenic leaves

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

data_processing: First-order analysis was performed using Affymetrix® GeneChip® Command Console® 3.0. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5 (Stratagene, CA, USA)

source_name: Leaf

value: MADS29 OX (overexpression)

value: leaf

value: 3rd and 4th leaf from flag leaf


title: MADS29 OX-transgenic-replicate 3


title: WTPB1-control-replicate  1

description: Gene expression data of wild type leaves


title: MADS29 RNAi S3-transgenic-replicate 1


title: WTPB1 S3-control-replicate  3


title: DH line, CFD03-070

value: DH line

value: Dent


title: DH line, CFD03-072


title: Keratinocytes SP60125+SB203580+PD98059 48h

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

country: USA

institute: NYU School of Medicine

description: All 3 inhibitors 48h

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5 GCOS, RMAExpress summarized using PLM and log2 transformed

organism: Homo sapiens

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

treatment_protocol: ~70% confluent keratinocytes treated with 5 uM JNK inhibitor SP600125, 15 uM p38 inhibitor SB203580, or 50 um  ERK inhibitor PD98059.

value: Epidermal keratinocytes

tag: treatment

value: All 3 inhibitors

tag: timpe point


title: DH line, CFD03-063


title: DH line, CFD03-067


title: MADS29 RNAi S3-transgenic-replicate 2


title: WTPB1-control-replicate  2


title: WTPB1-control-replicate  3


title: MADS29 OX-transgenic-replicate 2


title: DH line, CFD03-064


title: DH line, CFD03-065


title: WTPB1 S3-control-replicate  1


title: Keratinocytes SP60125+SB203580+PD98059 24h

description: All 3 inhibitors 24h

extract_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.


title: Keratinocytes SP60125+SB203580+PD98059 4h

description: All 3 inhibitors 4h


title: Keratinocytes SB20358-treated 1h

description: p38 inhibitor SB203580-1h

source_name: Keratinocytes SB20358-treated 1h

value: p38 inhibitor SB203580


title: Keratinocytes SP60125+SB203580+PD98059 1h

description: All 3 inhibitors 1h


title: DH line, CFD03-060


title: Keratinocytes SB20358-treated 24h

description: p38 inhibitor SB203580-24h

source_name: Keratinocytes SB20358-treated 24h


title: DH line, CFD03-062


title: DH line, CFD03-052


title: Keratinocytes PD98059-treated 24h

description: ERK inhibitor PD98059-24h

source_name: Keratinocytes PD98059-treated 24h

value: ERK inhibitor PD98059


title: DH line, CFD03-059


title: DH line, CFD03-057


title: Keratinocytes PD98059-treated 48h

description: ERK inhibitor PD98059-48h

source_name: Keratinocytes PD98059-treated 48h


title: DH line, CFD03-053


title: Keratinocytes untreated 48h rep1

description: Ctrl 48hrs-exp I.

source_name: Keratinocytes untreated 48h rep1

value: Untreated control


title: Keratinocytes PD98059-treated 4h

description: ERK inhibitor PD98059-4h

source_name: Keratinocytes PD98059-treated 4h


title: Keratinocytes PD98059-treated 1h

description: ERK inhibitor PD98059-1h

source_name: Keratinocytes PD98059-treated 1h


title: DH line, CFD03-058


title: DH line, CFD03-051


title: Keratinocytes SB20358-treated 48h

description: p38 inhibitor SB203580-48h

source_name: Keratinocytes SB20358-treated 48h


title: DH line, CFD03-050

source_name: leaf


title: DH line, CFD03-048


title: Keratinocytes SB20358-treated 4h

description: p38 inhibitor SB203580-4h

source_name: Keratinocytes SB20358-treated 4h


title: DH line, CFD03-054


title: DH line, CFD03-056


title: Keratinocytes untreated 4h

description: Ctrl-4hrs-exp I

source_name: Keratinocytes untreated 4h


title: DH line, CFD03-049


title: Keratinocytes untreated 24h rep1

description: Ctrl-24hrs-exp I

source_name: Keratinocytes untreated 24h rep1


title: DH line, CFD03-047


title: DH line, CFD03-045


title: Keratinocytes untreated 1h

description: Ctrl-1hr-exp I

source_name: Keratinocytes untreated 1h


title: DH line, CFD03-046


title: DMSO_Macr_1

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalized using cubic spline normalization and background subtraction implemented in Illumina GenomeStudio V2011.1.
Illumina GenomeStudio V2011.1 calculated intensity and detection P value.

source_name: Macrophages, DMSO

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: THP-1 cells were obtained from DSMZ and cultivated at 37 °C (5% CO2, 95% humidity) in RPMI 1640 (Invitrogen) supplemented with 10% FBS Superior (Biochrom). For macrophage generation, differentiation was induced by supplementation of 10-8 M Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) for 48 h.

extract_protocol: Total RNA was purified and isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser or agarose gel electrophoresis.

treatment_protocol: Ligand treatment of macrophages was performed for further 24 h with 10 µM STX4 or 0.1% DMSO as vehicle control.

value: blood cell (leukemic monozyte)

value: male

tag: cell line


title: DMSO_Macr_2

description: replicate 2


title: DMSO_Macr_4

description: replicate 4


title: DH line, CFD03-041


title: DH line, CFD03-044


title: STX4_Macr_4

description: replicate 4

source_name: Macrophages, STX4


title: DH line, CFD03-037


title: DH line, CFD03-022


title: DH line, CFD03-020


title: DH line, CFD03-043


title: DH line, CFD03-040


title: DH line, CFD03-017


title: STX4_Macr_1

description: replicate 1


title: DH line, CFD03-042


title: DMSO_Foam_3

description: replicate 3

source_name: Foam cells, DMSO

growth_protocol: THP-1 cells were obtained from DSMZ and cultivated at 37 °C (5% CO2, 95% humidity) in RPMI 1640 (Invitrogen) supplemented with 10% FBS Superior (Biochrom). For macrophage generation, differentiation was induced by supplementation of 10-8 M Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) for 48 h. To induce foam cell formation macrophages were treated for additional 48 h with 100 µg/mL modified human oxidized low density lipoprotein (oxLDL) obtained from Source BioScience (RP-048).

treatment_protocol: Ligand treatment was performed simultaneously with foam cell formation with 10 µM STX4 or 0.1% DMSO as vehicle control.


title: DH line, CFD03-006


title: DH line, CFD03-021


title: DH line, CFD03-016


title: STX4_Macr_3

description: replicate 3


title: STX4_Foam_2

description: replicate 2

source_name: Foam cells, STX4


title: DMSO_Foam_2

description: replicate 2


title: DH line, CFD03-038


title: STX4_Macr_2

description: replicate 2


title: DH line, CFD03-013


title: STX4_Foam_3

description: replicate 3


title: DMSO_Macr_3

description: replicate 3


title: DMSO_Foam_1

description: replicate 1


title: Myeloma cell line-XG1-CD138-

city: IOWA CITY

first: Fenghuang

last: Zhan

state: IA

address: 285 Newton Rd, 3269A CBRB

institute: University of Iowa

description: Microarray-based gene expression data from XG1-CD138-

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
affymetrix-algorithm-name = rma-gene-default
program-name = Expression Console

label: biotin

source_name: Myeloma cell line-XG1-CD138-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were  cultured in RPMI 1640 containing 2mM L-glutamine, 10% heat-inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100 μg/mL) in a humidified incubator at 37°C in 5% CO2.

treatment_protocol: Cells were incubated with CD138-microbeads for 20mins at 4 degree Celsius, and  autoMACS and CD138 microbeads (Miltenyi Biotec Inc., Auburn, CA) were used for sorting.

value: myeloma cell line XG1

tag: cell fraction


title: DH line, CFD03-003


title: Myeloma cell line-XG1-CD138+

description: Microarray-based gene expression data from XG1-CD138+

source_name: Myeloma cell line-XG1-CD138+


title: Myeloma cell line-U266-CD138-

description: Microarray-based gene expression data from U266-CD138-

source_name: Myeloma cell line-U266-CD138-

value: myeloma cell line U266


title: Myeloma cell line-OCI-CD138+

description: Microarray-based gene expression data from OCI-CD138+

source_name: Myeloma cell line-OCI-CD138+

value: myeloma cell line OCI


title: Myeloma cell line-KMS28PE-CD138-

description: Microarray-based gene expression data from KMS28PE-CD138-

source_name: Myeloma cell line-KMS28PE-CD138-

value: myeloma cell line KMS28PE


title: Myeloma cell line-OCI-CD138-

description: Microarray-based gene expression data from OCI-CD138-

source_name: Myeloma cell line-OCI-CD138-


title: DH line, CFD02-320


title: Myeloma cell line-U266-CD138+

description: Microarray-based gene expression data from U266-CD138+

source_name: Myeloma cell line-U266-CD138+


title: STX4_Foam_1

description: replicate 1


title: Myeloma cell line-OPM2-CD138-

description: Microarray-based gene expression data from OPM2-CD138-

source_name: Myeloma cell line-OPM2-CD138-

value: myeloma cell line OPM2


title: Myeloma cell line-ARP1-CD138+

description: Microarray-based gene expression data from ARP1-CD138+

source_name: Myeloma cell line-ARP1-CD138+

value: myeloma cell line ARP1


title: DH line, CFD02-322

source_name: leaf


title: Myeloma cell line-KMS28PE-CD138+

description: Microarray-based gene expression data from KMS28PE-CD138+

source_name: Myeloma cell line-KMS28PE-CD138+


title: DH line, CFD02-318


title: Myeloma cell line-H929-CD138-

description: Microarray-based gene expression data from H929-CD138-

source_name: Myeloma cell line-H929-CD138-

value: myeloma cell line H929


title: Myeloma cell line-H929-CD138+

description: Microarray-based gene expression data from H929-CD138+

source_name: Myeloma cell line-H929-CD138+


title: DH line, CFD03-005

description: Genomic DNA from maize was analyzed with the Illumina MaizeSNP50 BeadChip


title: DH line, CFD03-004


title: DH line, CFD02-312


title: DH line, CFD02-315


title: DH line, CFD02-314


title: DH line, CFD02-319


title: DH line, CFD02-316


title: Myeloma cell line-OPM2-CD138+

description: Microarray-based gene expression data from OPM2-CD138+

source_name: Myeloma cell line-OPM2-CD138+


title: DH line, CFD02-317


title: DH line, CFD02-321


title: DH line, CFD02-313


title: Myeloma cell line-CAG-CD138+

description: Microarray-based gene expression data from CAG-CD138+

source_name: Myeloma cell line-CAG-CD138+

value: myeloma cell line CAG


title: Myeloma cell line-CAG-CD138-

description: Microarray-based gene expression data from CAG-CD138-

source_name: Myeloma cell line-CAG-CD138-


title: Myeloma cell line-ARP1-CD138-

description: Microarray-based gene expression data from ARP1-CD138-

source_name: Myeloma cell line-ARP1-CD138-


title: DH line, CFD02-305

value: DH line


title: DH line, CFD02-102

value: Dent


title: DH line, CFD02-100


title: DH line, CFD02-303


title: DH line, CFD02-104


title: DH line, CFD02-306


title: DH line, CFD02-101


title: DH line, CFD02-304


title: DH line, CFD02-310


title: DH line, CFD02-301


title: DH line, CFD02-308


title: DH line, CFD02-309


title: DH line, CFD02-302


title: DH line, CFD02-307


title: DH line, CFD02-098


title: DH line, CFD02-105


title: DH line, CFD02-099


title: DH line, CFD02-311


title: DH line, CFD02-106


title: DH line, CFD02-082


title: DH line, CFD02-091


title: DH line, CFD02-103


title: DH line, CFD02-095


title: DH line, CFD02-090


title: DH line, CFD02-092


title: DH line, CFD02-097


title: DH line, CFD02-088


title: DH line, CFD02-085


title: DH line, CFD02-086


title: DH line, CFD02-081


title: DH line, CFD02-075


title: DH line, CFD02-063


title: DH line, CFD02-072


title: DH line, CFD02-079


title: DH line, CFD02-073


title: DH line, CFD02-077


title: DH line, CFD02-064


title: DH line, CFD02-078


title: control Luminal, biological rep 3

city: Houston

first: Bingnan

last: Gu

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression from sorted mature luminal population in control mouse

hyb_protocol: 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640)

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

data_processing: These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile

source_name: control mouse

label_protocol: The fragmented single-stranded DNA is labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: 8-12-week old virgin female control and Pygo2 SSKO littermates are hosted in the same cage before analysis

extract_protocol: dissect the mammary gland, chop into paste with blade, then enzymatic digested with collagenase at 37C for 1.5 hr, then cells are labeled with antibodies for  lineage markers (CD31-APC, CD45-APC, TER119-APC) and surface markers (CD24-PE-Cy7, CD29-FTIC, CD61-PE), and sorted for MaSC and luminal populations, then RNA is extracted by RNeasy Mini Kit with on-column DNase treatment according to manufacturer’s protocol (QIAGEN)

value: Mammary gland

value: mature luminal population

value: 8-12 weeks old


title: control Luminal, biological rep 2


title: DH line, CFD02-067


title: DH line, CFD02-076


title: DH line, CFD02-069


title: DH line, CFD02-074


title: SSKO MaSCs, biological rep 1

description: Gene expression from sorted MaSC/basal population in Pygo2 SSKO mouse

source_name: Pygo2 SSKO mouse

value: MaSC/basal population


title: control Luminal, biological rep 1


title: DH line, CFD02-059


title: control MaSCs, biological rep 3

description: Gene expression from sorted MaSC/basal population in control mouse


title: control MaSCs, biological rep 4


title: DH line, CFD02-051


title: DH line, CFD02-048


title: DH line, CFD02-057


title: DH line, CFD02-061


title: DH line, CFD02-053


title: SSKO MaSCs, biological rep 3


title: control MaSCs, biological rep 1


title: SSKO MaSCs, biological rep 2


title: control MaSCs, biological rep 2


title: DH line, CFD02-060


title: DH line, CFD02-058


title: AKI, biological rep3

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

institute: Charité - Universitätsmedizin Berlin

description: rhabdomyolysis induced AKI

hyb_protocol: The biotinylated cDNA was added to a hybridization cocktail for hybridization to the Mouse Gene 1.0ST Array (Hybridization Wash and Stain Kit, Affymetrix). The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16 h, the staining and washing processed in the Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomics Suite 6.4 software. Normalization according to RMA method.
MoGene-1_0-st-v1

source_name: halved kidney

label_protocol: Random-primed cDNA synthesis was performed using the Ambion® WT Expression Kit (Ambion, Austin, Texas, USA). Subsequently, cDNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled using the WT terminal labeling kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: Mice of both sexes (24 to 31 g body weight) were fed a standard rodent chow with 19% protein content (V1534/300, Ssniff, Soest, Germany), and had free access to drinking water unless otherwise specified. Up to 5 mice were housed per cage in 12 h day and night cycles. All experiments were carried out in transgenic mice in which selective renal tubular VHL knockout (VHL-KO) was inducible by doxycycline.

extract_protocol: For each condition, kidneys were harvested after cervical dislocation under isoflurane anaesthesia, and processed for homogenization. Tissue homogenates were performed from transversally sectioned fresh kidney halves which were snap frozen in liquid nitrogen immediately thereafter. Total RNA from halved kidneys was isolated using RNA-Bee (AMS Biotechnology (Europe) Ltd - Germany) according to the manufacturer’s instructions. RNA integrity was checked by analyzing on the 2100 Bioanalyzer (Agilent technologies, PA, USA).

treatment_protocol: Doxycycline (0.1 mg per 10 g body weight SC) was injected 4 days prior to sacrifice (Groups: VHL-KO and VHL-KO/AKI). To induce AKI, 50% glycerol (0.05 ml per 10 g body weight) was injected IM into the left hind limb under isoflurane narcosis (Groups: AKI AND VHL-KO/AKI). Drinking water was withdrawn between 20 h prior and 24 h after glycerol injection.

value: kidney

tag: disease state

value: rhabdomyolysis/AKI

value: wt


title: DH line, CFD02-036


title: DH line, CFD02-043


title: DH line, CFD02-027


title: VHL-KO/AKI, biological rep3

description: VHL-KO & rhabdomyolysis induced AKI

value: doxycycline

value: VHL-KO


title: VHL-KO/AKI, biological rep1

description: VHL-KO & rhabdomyolysis induced AKI


title: VHL-KO/AKI, biological rep5

description: VHL-KO & rhabdomyolysis induced AKI


title: AKI, biological rep5

description: rhabdomyolysis induced AKI


title: AKI, biological rep2

description: rhabdomyolysis induced AKI


title: DH line, CFD02-038


title: DH line, CFD02-047


title: VHL-KO/AKI, biological rep4

description: VHL-KO & rhabdomyolysis induced AKI


title: DH line, CFD02-041


title: DH line, CFD02-024


title: VHL-KO/AKI, biological rep2

description: VHL-KO & rhabdomyolysis induced AKI


title: AKI, biological rep1

description: rhabdomyolysis induced AKI


title: DH line, CFD02-006


title: VHL-KO, biological rep3

description: VHL-KO


title: VHL-KO, biological rep2

description: VHL-KO


title: VHL-KO, biological rep1

description: VHL-KO


title: DH line, CFD01-318


title: DH line, CFD02-003


title: DH line, CFD01-317


title: DH line, CFD02-001


title: Control, biological rep3

description: untreated control


title: Control, biological rep2

description: untreated control


title: DH line, CFD01-316


title: DH line, CFD01-314


title: DH line, CFD01-315


title: DH line, CFD01-310


title: Control, biological rep1

description: untreated control


title: DH line, CFD01-311


title: DH line, CFD01-312


title: DH line, CFD02-010


title: DH line, CFD01-309


title: WT MEF cells 1uM MG132-replicate 4

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: Wild type MEFs treated with proteasome inhibitor MG132 for 8 hours

hyb_protocol: Standard Affymetrix hybridization protocol, hybridization for 17 hours.

scan_protocol: Arrays were scanned by Affymetrix 3000-7G scanner controlled by Affymetrix Genechip Command Console.

data_processing: CEL files were imported into Partek Genomics Suite (Partek, Inc., St. Louis, Mo). RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish

source_name: WT MEF cells 1uM MG132

label_protocol: Samples were labeled using Ambion WT expression kit followed by the Affymetrix WT terminal labeling kit.

growth_protocol: Wildype and ATF5-KD mouse embryonic fibroblasts (MEF) stabily expressing ATF5 shRNA were grown in DMEM

extract_protocol: Total RNA was extracted using the Trizol method following the manufacturers instructions, higher quality RNA was then obtained using an RNeasy clean up kit (Qiagen)

treatment_protocol: 8 plates (10cm)  of WT and and 8 plates (10cm) of ATF5-KD MEF cells were subject to no stress (4 each for a total of 8) or treated for 8 hours with 1uM MG132 (4 each for a total of 8).  Unstressed cells were harvested at the same time as the stressed cells

value: Wildtype, scramble shRNA

value: 1uM MG132, 8h exposure

value: embryonic fibroblasts


title: WT MEF cells 1uM MG132-replicate 3


title: ATF5-KD MEF cells 1uM MG132-replicate 4

description: ATF5-KD MEFs treated with proteasome inhibitor MG132 for 8 hours

source_name: ATF5-KD MEF cells 1uM MG132

value: ATF5-KD shRNA


title: DH line, CFD01-313


title: DH line, CFD01-308


title: ATF5-KD MEF cells 1uM MG132-replicate 3


title: ATF5-KD MEF cells 1uM MG132-replicate 2


title: WT MEF cells 1uM MG132-replicate 2


title: WT MEF cells 1uM MG132-replicate 1


title: ATF5-KD MEF cells 1uM MG132-replicate 1


title: DH line, CFD01-307


title: DH line, CFD01-306


title: ATF5-KD MEF cells untreated-replicate 3

description: ATF5-KD MEFs treated with DMSO as a vehicle control for 8 hours

source_name: ATF5-KD MEF cells untreated

value: sham


title: DH line, CFD01-304


title: DH line, CFD01-305


title: ATF5-KD MEF cells untreated-replicate 4


title: DH line, CFD01-303


title: DH line, CFD01-302


title: DH line, CFD01-301


title: DH line, CFD01-108


title: WT MEF cells untreated-replicate 2

description: Wild type MEFs treated with DMSO as a vehicle control for 8 hours

source_name: WT MEF cells untreated


title: WT MEF cells untreated-replicate 3


title: ATF5-KD MEF cells untreated-replicate 1


title: WT MEF cells untreated-replicate 1


title: AKI, biological rep4

description: rhabdomyolysis induced AKI


title: WT MEF cells untreated-replicate 4


title: DH line, CFD01-106


title: ATF5-KD MEF cells untreated-replicate 2


title: 6hr TPL2-/- Mtb Sample 1 Technical replicate

city: London

first: Fin

last: McNab

address: The Ridgeway, Mill Hill

country: United Kingdom

institute: MRC NIMR

description:
6203221062_F
sample re-run

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using 75th percentile normalisation in GeneSpring 11.5
Background subtracted, normalised and log2 transformed for normalised values and non-normalised values have only had background subtraction

source_name: BMDM_6hr TPL2-/- Mtb

label_protocol: Biotinylated, amplified cRNA were prepared using the Illumina CustomPrep RNA amplification kit

growth_protocol: bone marrow cells were cultured for 6 days in L929-cell conditioned media and rested for 1 further day in normal media prior to infection

extract_protocol: RNA was extracted using the Qiagen RNeasy minikit

treatment_protocol: cells were infected with Mtb H37Rv or not, with or without IFNgamma (5ng/ml) treatment, for indicated times and harvested into RLT buffer

tag: strain background

value: bone marrow derived macrophages (BMDM)

tag: infected with

value: Mtb H37Rv for 6hr

tag: treated with

value: Media (un-treated control)


title: DH line, CFD01-105

tag: status

value: DH line

tag: maize population

value: Dent


title: DH line, CFD01-107


title: DH line, CFD01-099


title: 6hr Wild-type Mtb + IFNg Sample 1 Technical replicate

description:
6203212059_F
sample re-run

source_name: BMDM_6hr Wild-type Mtb + IFNg

value: Wild-type

value: IFNg


title: 6hr IFNabR-/- Mtb + IFNg Sample 1 Technical replicate

description:
6203212102_F
sample re-run

source_name: BMDM_6hr IFNabR-/- Mtb + IFNg

value: IFNabR-/-


title: DH line, CFD01-098

source_name: leaf


title: DH line, CFD01-100


title: DH line, CFD01-102


title: DH line, CFD01-104


title: DH line, CFD01-103


title: DH line, CFD01-101


title: 6hr TPL2-/- Medium Control Sample 1

description:
6203221061_F
sample re-run

source_name: BMDM_6hr TPL2-/- Medium Control

value: none (uninfected) for 6hr


title: 1hr TPL2-/- Mtb Sample 1 Technical replicate

description:
6203221061_E
sample re-run

source_name: BMDM_1hr TPL2-/- Mtb

value: Mtb H37Rv for 1hr


title: 1hr TPL2-/- Medium Control Sample 1

description:
6203212013_F
sample re-run

source_name: BMDM_1hr TPL2-/- Medium Control

value: none (uninfected) for 1hr


title: 6hr Wild-type Mtb Sample 1 Technical replicate

description:
6203212027_F
sample re-run

source_name: BMDM_6hr Wild-type Mtb


title: 1hr TPL2-/-IFNabR-/- Medium Control Sample 1

description:
6203212018_F
sample re-run

source_name: BMDM_1hr TPL2-/-IFNabR-/- Medium Control


title: 6hr IFNabR-/- Mtb Sample 1 Technical replicate

description:
6203212064_F
sample re-run

source_name: BMDM_6hr IFNabR-/- Mtb


title: DH line, CFD01-097


title: DH line, CFD01-095


title: 1hr IFNabR-/- Mtb Sample 1 Technical replicate

description:
6203212064_E
sample re-run

source_name: BMDM_1hr IFNabR-/- Mtb


title: DH line, CFD01-091


title: 1hr IFNabR-/- Mtb + IFNg Sample 1 Technical replicate

description:
6203212102_E
sample re-run

source_name: BMDM_1hr IFNabR-/- Mtb + IFNg


title: 0hr IFNabR-/- Medium Control Sample 1

description:
6203221061_D
sample re-run

source_name: BMDM_0hr IFNabR-/- Medium Control

value: none (uninfected) for 0hr


title: 0hr TPL2-/- Medium Control Sample 1

description:
6203212013_E
sample re-run

source_name: BMDM_0hr TPL2-/- Medium Control


title: DH line, CFD01-093


title: DH line, CFD01-094


title: DH line, CFD01-092


title: 1hr Wild-type IFNg Sample 1 Technical replicate

description:
6203212059_E
sample re-run

source_name: BMDM_1hr Wild-type IFNg


title: 1hr IFNabR-/- IFNg Sample 1 Technical replicate

description:
6203221062_E
sample re-run

source_name: BMDM_1hr IFNabR-/- IFNg


title: 1hr Wild-type Mtb + IFNg Sample 1 Technical replicate

description:
6203212027_E
sample re-run

source_name: BMDM_1hr Wild-type Mtb + IFNg


title: DH line, CFD01-085


title: DH line, CFD01-089


title: 0hr Wild-type Medium Control Sample 1 Technical replicate

description:
6203221062_D
sample re-run

source_name: BMDM_0hr Wild-type Medium Control


title: 6hr IFNabR-/- IFNg Sample 2 Technical replicate

description:
6203212064_D
sample re-run

source_name: BMDM_6hr IFNabR-/- IFNg


title: DH line, CFD01-083


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 1 Technical replicate

description:
6203212027_D
sample re-run

source_name: BMDM_6hr TPL2-/-IFNabR-/- Mtb


title: 6hr IFNabR-/- IFNg Sample 1 Technical replicate

description:
6203212018_D
sample re-run


title: DH line, CFD01-082

source_name: leaf


title: DH line, CFD01-079


title: DH line, CFD01-084


title: 6hr Wild-type IFNg Sample 1 Technical replicate

description:
6203212013_D
sample re-run

source_name: BMDM_6hr Wild-type IFNg


title: DH line, CFD01-080


title: DH line, CFD01-078


title: 6hr Wild-type IFNg Sample 2 Technical replicate

description:
6203212059_D
sample re-run


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 2 Technical replicate

description:
6203212102_D
sample re-run


title: DH line, CFD01-090


title: 1hr Wild-type Mtb Sample 1 Technical replicate

description:
6203212018_E
sample re-run

source_name: BMDM_1hr Wild-type Mtb


title: 6hr Wild-type Medium Control Sample 2 Technical replicate

description:
6203212059_C
sample re-run

source_name: BMDM_6hr Wild-type Medium Control


title: DH line, CFD02-013


title: 6hr Wild-type Medium Control Sample 1 Technical replicate

description:
6203212027_C
sample re-run


title: DH line, CFD01-077


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 3 Technical replicate

description:
6203221061_C
sample re-run


title: 6hr IFNabR-/- IFNg Sample 3 Technical replicate

description:
6203221062_C
sample re-run


title: DH line, CFD01-076


title: DH line, CFD01-073


title: 6hr Wild-type Medium Control Sample 3 Technical replicate

description:
6203212064_C
sample re-run


title: DH line, CFD01-069


title: 6hr IFNabR-/- Medium Control Sample 3

description:
6203212018_C
sample re-run

source_name: BMDM_6hr IFNabR-/- Medium Control


title: 6hr Wild-type IFNg Sample 3 Technical replicate

description:
6203212102_C
sample re-run


title: DH line, CFD01-074


title: DH line, CFD01-067


title: 6hr IFNabR-/- Medium Control Sample 1

description:
6203221061_B
sample re-run


title: DH line, CFD01-066


title: DH line, CFD01-065


title: 1hr TPL2-/-IFNabR-/- Sample 1

description:
6203212018_B
sample re-run

source_name: BMDM_1hr TPL2-/-IFNabR-/-


title: 1hr IFNabR-/- Medium Control Sample 3

description:
6203212013_B
sample re-run

source_name: BMDM_1hr IFNabR-/- Medium Control


title: DH line, CFD01-068


title: 6hr Wild-type Medium Control Sample 2

description:
6203212102_B
sample re-run


title: 1hr TPL2-/-IFNabR-/- Sample 3

description:
6203212059_B
sample re-run


title: 6hr Wild-type Medium Control Sample 3

description:
6203221062_B
sample re-run


title: 6hr IFNabR-/- Medium Control Sample 2

description:
6203212013_C
sample re-run


title: 6hr Wild-type Medium Control Sample 1

description:
6203212064_B
sample re-run


title: DH line, CFD01-062


title: DH line, CFD01-063


title: DH line, CFD01-059


title: 1hr TPL2-/-IFNabR-/- Sample 2

description:
6203212027_B
sample re-run


title: DH line, CFD01-056


title: DH line, CFD01-055


title: 1hr Wild-type Medium Control Sample 2

description:
6203212064_A
sample re-run

source_name: BMDM_1hr Wild-type Medium Control


title: 1hr Wild-type Medium Control Sample 1

description:
6203212059_A
sample re-run


title: DH line, CFD01-052


title: DH line, CFD01-060


title: 1hr IFNabR-/- Medium Control Sample 2

description:
6203221061_A
sample re-run


title: DH line, CFD01-057


title: 1hr IFNabR-/- Medium Control Sample 1

description:
6203221062_A
sample re-run


title: DH line, CFD01-058


title: 1hr Wild-type Medium Control Sample 3

description:
6203212102_A
sample re-run


title: DH line, CFD01-047


title: DH line, CFD01-046


title: DH line, CFD01-051


title: 0hr TPL2-/-IFNabR-/- Sample 3

description:
6203212027_A
sample re-run

source_name: BMDM_0hr TPL2-/-IFNabR-/-


title: 0hr TPL2-/-IFNabR-/- Sample 2

description:
6203212018_A
sample re-run


title: DH line, CFD01-044


title: 0hr TPL2-/-IFNabR-/- Sample 1

description:
6203212013_A
sample re-run


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 2


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 1


title: 6hr TPL2-/-IFNabR-/- Mtb Sample 3


title: DH line, CFD01-028


title: DH line, CFD01-029


title: DH line, CFD01-037


title: 6hr TPL2-/- Media Control Sample 1

source_name: BMDM_6hr TPL2-/- Media Control


title: 6hr TPL2-/- Media Control Sample 2


title: DH line, CFD01-027


title: 6hr TPL2-/-IFNabR-/- Media Control Sample 1

source_name: BMDM_6hr TPL2-/-IFNabR-/- Media Control


title: 6hr TPL2-/-IFNabR-/- Media Control Sample 2


title: DH line, CFD01-030


title: DH line, CFD01-064


title: DH line, CFD01-038


title: DH line, CFD01-036


title: 6hr TPL2-/- Media Control Sample 3


title: 6hr TPL2-/-IFNabR-/- Media Control Sample 3


title: DH line, CFD01-035


title: DH line, CFD01-022


title: 6hr TPL2-/- Mtb Sample 3

source_name: BMDM_6hr TPL2-/- Mtb


title: DH line, CFD01-013


title: DH line, CFD01-011


title: DH line, CFD01-012


title: DH line, CFD01-010


title: 6hr IFNabR-/- Medium Control 3


title: DH line, CFD01-009


title: DH line, CFD01-008


title: 6hr IFNabR-/- Medium Control 2


title: 6hr TPL2-/- Mtb Sample 1


title: 6hr IFNabR-/- IFNg Sample 3


title: 6hr IFNabR-/- IFNg Sample 1


title: 6hr IFNabR-/- IFNg Sample 2


title: 6hr IFNabR-/- Medium Control 1


title: DH line, CFD01-003


title: 6hr IFNabR-/- Mtb + IFNg Sample 3

source_name: BMDM_6hr IFNabR-/- Mtb + IFNg


title: Parental line, UH250

value: parental line, inbred

tag: population information

value: parent 2 of pop. CFD10

tag: seed source

value: University of Hohenheim, Germany


title: DH line, CFD01-072


title: Parental line, UH304

value: parent 2 of pop. CFD11


title: DH line, CFD01-070


title: 6hr IFNabR-/- Mtb + IFNg Sample 2


title: 6hr IFNabR-/- Mtb Sample 3

source_name: BMDM_6hr IFNabR-/- Mtb


title: Parental line, W117

value: parent 2 of pop. CFD12

value: University of Wisconsin, USA (obtained via USDA)


title: Parental line, UH007

value: parent 1 of pop. CFF01, parent 2 of pop. CFD01

value: Flint


title: DH line, CFD01-006

value: DH line


title: Parental line, UH009

value: parent 2 of pop. CFF13


title: 6hr IFNabR-/- Mtb Sample 2

value: bone marrow derived macrophages (BMDM)

value: Mtb H37Rv for 6hr

value: Media (un-treated control)


title: 6hr Wild-type Medium Control 3

value: Wild-type

value: none (uninfected) for 6hr


title: 6hr IFNabR-/- Mtb + IFNg Sample 1

value: IFNabR-/-

value: IFNg


title: 6hr IFNabR-/- Mtb Sample 1


title: Parental line, UH006

value: parental line, inbred

value: parent 2 of pop. CFF12


title: Parental line, F618

value: parent 2 of pop. CFD07

value: Dent

value: INRA, France


title: 6hr Wild-type Medium Control 1


title: Parental line, F252

value: parent 2 of pop. CFD06


title: 6hr Wild-type Medium Control 2


title: Parental line, Mo17

value: parent 2 of pop. CFD09

value: University of Missouri, USA (obtained via USDA)


title: Parental line, F03802

value: parent 2 of pop. CFF07

value: Flint


title: 6hr Wild-type Mtb + IFNg Sample 2

source_name: BMDM_6hr Wild-type Mtb + IFNg

value: bone marrow derived macrophages (BMDM)


title: Parental line, F2

value: parent 2 of pop. CFF08


title: Parental line, F283

value: parent 2 of pop. CFF09


title: 6hr Wild-type IFNg Sample 2

value: Wild-type


title: Parental line, EC49A

value: parent 2 of pop. CFF04

value: CIAM, Spain


title: Parental line, EZ5

value: parent 2 of pop. CFF06

value: CSIC, Spain


title: Parental line, F353

value: parental line, inbred

value: parent 1 of pop. CFD01, parent 2 of pop. CFF01


title: 6hr Wild-type IFNg Sample 3

value: none (uninfected) for 6hr

value: IFNg


title: 6hr TPL2-/- Mtb Sample 2

value: Mtb H37Rv for 6hr

value: Media (un-treated control)


title: 6hr Wild-type IFNg Sample 1


title: 6hr Wild-type Mtb + IFNg Sample 1


title: Parental line, F64

value: parent 2 of pop. CFF10

value: INRA, France


title: 6hr Wild-type Mtb Sample 3

source_name: BMDM_6hr Wild-type Mtb


title: 6hr Wild-type Mtb Sample 1


title: 1hr TPL2-/-IFNabR-/- Media Control Sample 3

source_name: BMDM_1hr TPL2-/-IFNabR-/- Media Control

value: none (uninfected) for 1hr


title: 6hr Wild-type Mtb + IFNg Sample 3

value: bone marrow derived macrophages (BMDM)


title: Parental line, EC169

source_name: leaf

value: parent 2 of pop. CFD05

value: Flint


title: 6hr Wild-type Mtb Sample 2

value: Wild-type


title: Parental line, EP44

value: parent 2 of pop. CFF05


title: Parental line, D152

value: parent 2 of pop. CFF03

value: University of Hohenheim, Germany


title: mAb 88F7

type: protein

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Purified 10ug/ml of monoclonal antibody is incubated with autoantigen array

hyb_protocol: Autoantigen array  protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX

scan_protocol: Genepix Pro 6.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: All the data is normalized by the positive control human IgG or human IgM after subtracted by the value of PBS (the negative control).

label: Cy3-conjugated anti-human IgG antibody

molecule: protein

source_name: VH4-34 Switched memory B cell generated monoclonal antibody

label_protocol: autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG)

growth_protocol: Single VH4-34 B cells sorted from IgD-CD27+ memory cells of SLE patient

extract_protocol: Monoclonal antibody was obtained by single cell RT-PCR followed by cloning and expressing into 293 cell system. Supernatant was concentrated and quantified by IgG ELISA. Crude was purified by dialysis and 10ug/ml purified monoclonla antibody was used on the autoantigen array

value: SLE

value: VH4-34 Switched memory B cell

tag: purified monoclonal antibody

value: mAb 88F7

tag: concentration


title: Parental line, D09

value: parental line, inbred

value: parent 2 of pop. CFD04

value: Dent


title: 1hr TPL2-/-IFNabR-/- Media Control Sample 1

tag: cell type

value: Media (un-treated control)


title: mAb 88A10

value: mAb 88A10


title: Parental line, DK105

value: parent 2 of pop. CFF15


title: 1hr TPL2-/-IFNabR-/- Media Control Sample 2

tag: genotype/variation

value: none (uninfected) for 1hr


title: 1hr TPL2-/-IFNabR-/- Mtb Sample 3

source_name: BMDM_1hr TPL2-/-IFNabR-/- Mtb

value: bone marrow derived macrophages (BMDM)

value: Mtb H37Rv for 1hr


title: 1hr TPL2-/-IFNabR-/- Mtb Sample 2


title: Parental line, B73

value: parent 2 of pop. CFD02 and parent 2 of pop. CFF02

value: Iowa State University, USA (obtained via USDA)


title: Parental line, D06

value: parent 2 of pop. CFD03


title: 1hr TPL2-/-IFNabR-/- Mtb Sample 1


title: mAb 75G12

value: mAb 75G12


title: 1hr TPL2-/- Media Control Sample 1

source_name: BMDM_1hr TPL2-/- Media Control


title: 1hr TPL2-/- Mtb Sample 2

source_name: BMDM_1hr TPL2-/- Mtb


title: 1hr TPL2-/- Mtb Sample 3


title: 1hr TPL2-/- Media Control Sample 2


title: Pgm- vs. luxS rep4

city: Ames

first: Chris

last: Minion

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: The strain Pgm- is the Y.pestis CO92 pigmentation-negative mutant. The luxS is the Y.pestis CO92 Pgm- luxS::Kan strain.

hyb_protocol: Microarray hybridization and post washes were performed using a Lucidea Slidepro Hybridization Station (GE Healthcare). Corresponding equal amounts (1.5 µg) of Cy3- or Cy5-labelled cDNA targets were mixed and dried using a Thermo Scientific Savant DNA SpeedVac Concentrator (Waltham, MA). Targets were suspended in 225 μl Long Oligo hybridization solution (Corning, Inc., Corning, NY), incubated at 95°C for 5 min, centrifuged (10,000 x g, 4 min), and kept at room temperature until injected into the hybridization station. Hybridization lasted for 16 hours at 42°C and washed in a series of wash buffers (2x saline-sodium citrate (SSC), 0.1% SDS; 1x SSC, and 0.1x SSC) by the hybridization station and dried by centrifugation at 1500 x g for 30 secs.

scan_protocol: Arrays scanned on a ProScanArray HT scanner (Perkin Elmer, Wellesley, MA) three times with varying photomultiplier tube gain and laser power settings.

data_processing:
Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Madsen ML, Nettleton D, Thacker EL, Minion FC. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152:937-944 [PMID 16549658]) excluding slide region and slide-by-region interaction effects. Intensity = mu + trt + dye + slide
Images were quantified using the softWorRx Tracker analysis software package (Applied Precision). Spot-specific mean signals were corrected for local background by subtracting spot-specific median background intensities. The natural logarithms of the background-corrected signals from a single scan were adjusted by an additive constant so that all scans of the same array-by-dye combination would have a common median. The median of these adjusted-log-background-corrected signals across multiple scans was then computed for each spot to obtain one value for each combination of spot, array and dye channel. These data for the two dye channels on any given array were normalized using locally weighted scatterplot smoother (LOWESS) normalization to adjust for intensity-dependent dye bias (Dudoit et al., 2000Down; Yang et al., 2002Down). Following LOWESS adjustment, the data from each channel were adjusted by an additive constant so that the median for any combination of array and dye would be the same for all array-by-dye combinations. The normalized values for triplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples.
A separate mixed linear model analysis was conducted for each probe sequence using the normalized data (Wolfinger et al., 2001Down). Each mixed model included fixed effects for treatment (iron depletion versus control), slide region (upper versus lower) and dye (Alexa 555 versus 647) as well as random effects for slide and slide-by-region interaction. A t-test for differential expression across treatments was conducted for each probe as part of our mixed linear model analyses. The P-values from these t-tests were converted to q-values using the method of Storey & Tibshirani (2003)Down. These q-values can be used to obtain approximate control of the false discovery rate at a specified value. For example, declaring probes with q-values less than or equal to 0·05 to be differentially expressed produces a list of significant results for which the false discovery rate is estimated to be approximately 5 %. Along with q-values, estimates of fold change were computed for each probe by taking the inverse natural log of the mean treatment difference estimated as part of our mixed linear model analyses.

organism: Yersinia pestis

source_name: Pgm-

label_protocol: Target generation and labeling were performed as described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102 [PMID 19473256]).

growth_protocol: An overnight culture was diluted 1:100 and grown at 37°C in BHI broth.

extract_protocol: Cells were pelleted and immediately resuspended in 0.5 ml of RNA Protect Reagent (Qiagen, Valencia, CA). RNA was extracted from frozen cell pellets using the RNeasy Mini kit (Qiagen). The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 30 min to remove the genomic DNA. The RNA was purified and concentrated by Microcon Ultracel/YM 30(Millipore, Billerica, MA).

treatment_protocol: The overnight cultures of wild type and Pgm- luxS::Kan strains were diluted 1:100 in fresh culture medium and incubated at 37°C until the cell density reached OD600 = 1.0, about 10 hours. The cells from each culture were collected. The wild type was considered as treatment and the Pgm- luxS::Kan was considered as control.

tag: strain

tag: variant

value: Pgm-

source_name: luxS

value: luxS


title: Pgm- vs. luxS rep5


title: Pgm- vs. luxS rep3


title: 1hr IFNabR-/- Medium Control 3

source_name: BMDM_1hr IFNabR-/- Medium Control

value: IFNabR-/-


title: 1hr IFNabR-/- Medium Control 2


title: 1hr IFNabR-/- Medium Control 1


title: Pgm- vs. luxS rep2


title: Pgm- vs. luxS rep1


title: AI-2 vs. control rep5

description: The strain Pgm- is pigmentation-negative mutant. The AI-2 is AI-2 added in treatment.The control is the cells grown and treated under the same conditions without added three signals.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 37°C. Purified signal was then added to the cultures at the following concentrations: AI-2 (500 nM final concentration). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.

source_name: control


title: 1hr TPL2-/- Media Control Sample 3


title: Pgm- vs. luxS rep6


title: AI-2 vs. control rep4


title: 1hr TPL2-/- Mtb Sample 1


title: AI-2 vs. control rep6


title: AI-2 vs. control rep2


title: AI-2 vs. control rep1


title: AI-2 vs. control rep3


title: 1hr IFNabR-/- IFNg Sample 2

source_name: BMDM_1hr IFNabR-/- IFNg

value: IFNg


title: 1hr IFNabR-/- IFNg Sample 3


title: 1hr IFNabR-/- IFNg Sample 1


title: 1hr IFNabR-/- Mtb + IFNg Sample 3

source_name: BMDM_1hr IFNabR-/- Mtb + IFNg


title: 1hr IFNabR-/- Mtb + IFNg Sample 2


title: 1hr IFNabR-/- Mtb Sample 2

source_name: BMDM_1hr IFNabR-/- Mtb


title: 3singals vs. control rep6

description: The strain Pgm- is pigmentation-negative mutant. The 3signals are three quorum signals added in treatment.The control are the cells grown and treated under the same conditions without added three signals.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 37°C. Purified signals were then added to the cultures at the following concentrations: AI-2 (500 nM final concentration), AHLs (5 μM N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.


title: 3singals vs. control rep2


title: 1hr IFNabR-/- Mtb Sample 3


title: 1hr IFNabR-/- Mtb + IFNg Sample 1


title: 3singals vs. control rep4


title: 1hr IFNabR-/- Mtb Sample 1


title: 1hr Wild-type Medium Control 2

source_name: BMDM_1hr Wild-type Medium Control

value: Wild-type


title: 3singals vs. control rep3


title: 3singals vs. control rep1


title: 1hr Wild-type Medium Control 3


title: 1hr Wild-type Medium Control 1


title: 3singals vs. control rep5


title: 1hr Wild-type IFNg Sample 2

source_name: BMDM_1hr Wild-type IFNg


title: 1hr Wild-type IFNg Sample 1


title: Pgm- vs. 3XQS, rep3

description: Biological replicate 3 of 6.

data_processing: Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Madsen ML, Nettleton D, Thacker EL, Minion FC. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152:937-944 [PMID 16549658]) excluding slide region and slide-by-region interaction effects. Intensity = mu + trt + dye + slide

growth_protocol: An overnight culture was diluted 1:100 and grown at 37°C in BHI broth until an optical density 600 nm of 1.0 was reached. Two strains, Pgm- as test and 3XQS (luxS::Kan, ΔypslR, ΔytblR) as control.


title: Drosophila_melanogaster_anti-FLAG_RIP_RNA_rep3

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
This sample is total RNA isolated from anti-FLAG (control) RIPs from 0-3 hour GFP-Staufen embryos. It is the third of three biological replicates.
SAMPLE 18

hyb_protocol: Hybridization was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 5.0).

scan_protocol: Arrays were scanned with a GenePix4000B microarray scanner system (Molecular Devices, Inc., Sunnyvale, CA, USA), and scanned images were initially quantified using Nimblescan (Roche), following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 5.0).

data_processing: The raw data (.pair files) were normalized with ArrayStar 3 (DNASTAR) software using the RMA quantile method, and signal intensities were log2-transformed. For normalization, samples were grouped as follows, with each group normalized separately: Samples 1-3, Samples 4-9, Samples 10-12, Samples 13-18.

organism: Drosophila melanogaster

label_protocol: Labelling was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 5.0).

growth_protocol: The following fly strains were used: w1118, w-; stauD3 cn sp / Cyo; GFP-Stau2.2FL / TM3 and TM6B. All stocks were maintained at 25C.

extract_protocol:
For RIPs with synthetic anti-Staufen antibody and synthetic control antibody, synthetic antibodies were expressed and purified as Fabs, as described (Laver et al. 2012). Extract was prepared from embryos collected 0-to-3 hours post-egg-laying and immunoprecipitations were performed as described (Laver et al. 2012), with the following modifications: RNA co-immunoprecipitations were performed using approximately 800 µL of ½ diluted embryo extract (see Laver et al. 2012), extract was incubated with 80 µL of anti-FLAG M2 affinity gel (Sigma) carrying 40 µg of purified FLAG-tagged Fab and blocked with BSA. Fabs with associated protein and RNA were eluted from the beads by three 20 minute elutions at 4˚C with 100 µL of FLAG peptide (Sigma), the three eluates were pooled, and RNA was isolated from the eluate using TRI Reagent (Sigma).
For immunoprecipitation of GFP-Staufen, extract was prepared from 0-to-3 hr embryos as described (Laver et al. 2012), but using a different protease inhibitor cocktail (Roche CAT#11836170001). Extracts were thawed and pooled to create a single replicate of 600-800µL and Triton X-100 was added to a final concentration of 0.1%. A 10µL aliquot of the extract was used to isolate RNA for the input sample (using Invitrogen’s TRIzol reagent, according the manufacturer’s protocol). The remaining extract was divided in half for use in the anti-GFP and control anti-FLAG immunoprecipitations.
For anti-GFP-Staufen immunoprecipitations, protein G magnetic beads were first blocked using a protocol adapted from Ren et al. (Ren et al. 2000): two aliquots of 100 µL of beads (Invitrogen Dynabeads® Protein G CAT#100.04D) were each washed 3 times with 1-1.5 mL of 5 mg/mL PBS/BSA, then blocked overnight in 250µL PBS/BSA at 4C. The immunoprecipitations were then performed using the following protocol, adapted from Invitrogen’s Dynabeads® Protein G protocol and Roche’s immunoprecipitation protocol for anti-GFP (CAT#11814460001), was used: one aliquot of 100µL of beads that was blocked overnight was washed three times with 1.5mL of PBS/BSA and the beads were then divided into two new tubes. Each aliquot of beads was resuspended in an equal volume of embryo extract (300-400µL) and the tubes rotated at 4oC for 1hr. The samples of cleared extract were then transferred to new tubes and 2µg of anti-GFP or anti-FLAG (Sigma-Aldrich CAT#F3165) antibody added to each, for the anti-GFP and mock immunoprecipitations respectively. The samples were then mixed and incubated on ice at 4oC for 1hr. The remaining 100µL aliquot of blocked beads was washed three times with 1.5mL of lysis buffer 150 (150 mM KCl, 20 mM Hepes pH 7.4, 1 mM MgCl2) supplemented with 0.1% Triton X-100. The beads were split into two new tubes, the anti-GFP extract being added to one and the anti-FLAG extract to the other, and each incubated with rotation at 4oC for four hours. The depleted extract was then removed and the beads washed three times with 200µL of lysis buffer 150 with Triton. Finally, the beads were transferred to new tubes where they were resuspended in 500µL of TRIzol for RNA purification according to the manufacturer’s protocol. The RNA retrieved from these extractions was purified and concentrated using the kit and procedure from Zymo Research (CAT#R1015).
Total RNA was extracted by TRIzol according to the manufacturer’s protocol.

tag: developmental stage

value: 0-3 hour embryo

value: GFP-Staufen transgenic

value: w- ; stauD3 cn sp/Cyo;GFP-Stau2.2FL/TM3 and TM6B

tag: rip antibody

value: Anti-Flag M2 mouse monoclonal antibody

tag: rip antibody vendor

value: Sigma Aldrich

tag: rip antibody cat. #

tag: rip antibody lot #


title: Pgm- vs. 3XQS, rep6

description: Biological replicate 6 of 6.


title: 1hr Wild-type IFNg Sample 3

tag: strain background

tag: infected with

value: none (uninfected) for 1hr


title: Pgm- vs. 3XQS, rep4

description: Biological replicate 4 of 6.


title: Drosophila_melanogaster_anti-FLAG_RIP_RNA_rep2

description:
This sample is total RNA isolated from anti-FLAG (control) RIPs from 0-3 hour GFP-Staufen embryos. It is the second of three biological replicates.
SAMPLE 17


title: Pgm- vs. 3XQS, rep1

description: Biological replicate 1 of 6.


title: Pgm- vs. 3XQS, rep5

description: Biological replicate 5 of 6.


title: 1hr Wild-type Mtb Sample 3

source_name: BMDM_1hr Wild-type Mtb

value: bone marrow derived macrophages (BMDM)

tag: treated with

value: Media (un-treated control)


title: Pgm- vs. 3XQS, rep2

description: Biological replicate 2 of 6.


title: 1hr Wild-type Mtb Sample 1

value: Mtb H37Rv for 1hr


title: 1hr Wild-type Mtb Sample 2


title: 1hr Wild-type Mtb + IFNg Sample 2

source_name: BMDM_1hr Wild-type Mtb + IFNg


title: Drosophila_melanogaster_anti-FLAG_RIP_RNA_rep1

description:
This sample is total RNA isolated from anti-FLAG (control) RIPs from 0-3 hour GFP-Staufen embryos. It is the first of three biological replicates.
SAMPLE 16


title: 1hr Wild-type Mtb + IFNg Sample 3


title: 0hr TPL2-/-IFNabR-/- Medium Control Sample 12

source_name: BMDM_0hr TPL2-/-IFNabR-/- Medium Control

value: none (uninfected) for 0hr


title: 1hr Wild-type Mtb + IFNg Sample 1


title: 0hr TPL2-/-IFNabR-/- Medium Control Sample 11


title: 0hr TPL2-/-IFNabR-/- Medium Control Sample 10


title: Drosophila_melanogaster_anti-GFP_RIP_RNA_rep3

description:
This sample is total RNA isolated from anti-GFP RIPs from 0-3 hour GFP-Staufen embryos. It is the third of three biological replicates.
SAMPLE 15

value: anti-GFP antibody

value: Roche


title: 0hr TPL2-/- Medium Control Sample 8

source_name: BMDM_0hr TPL2-/- Medium Control


title: 0hr TPL2-/- Medium Control Sample 9


title: Drosophila_melanogaster_GFP-Staufen_0-3h_embryo_total_RNA_rep2

description:
This sample is total RNA isolated from 0-3 hour GFP-Staufen transgenic embryos. It is the second of three biological replicates.
SAMPLE 11


title: Drosophila_melanogaster_synthetic_control_RIP_RNA_rep3

description:
This sample is total RNA isolated from control synthetic antibody RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.
SAMPLE 9

value: wild type

value: control synthetic antibody

tag: rip antibody information


title: Drosophila_melanogaster_anti-GFP_RIP_RNA_rep2

description:
This sample is total RNA isolated from anti-GFP RIPs from 0-3 hour GFP-Staufen embryos. It is the second of three biological replicates.
SAMPLE 14


title: Drosophila_melanogaster_GFP-Staufen_0-3h_embryo_total_RNA_rep1

description:
This sample is total RNA isolated from 0-3 hour GFP-Staufen transgenic embryos. It is the first of three biological replicates.
SAMPLE 10


title: Drosophila_melanogaster_synthetic_control_RIP_RNA_rep2

description:
This sample is total RNA isolated from control synthetic antibody RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.
SAMPLE 8


title: 0hr IFNabR-/- Medium Control Sample 5

source_name: BMDM_0hr IFNabR-/- Medium Control

value: IFNabR-/-


title: Drosophila_melanogaster_GFP-Staufen_0-3h_embryo_total_RNA_rep3

description:
This sample is total RNA isolated from 0-3 hour GFP-Staufen transgenic embryos. It is the third of three biological replicates.
SAMPLE 12


title: Drosophila_melanogaster_synthetic_control_RIP_RNA_rep1

description:
This sample is total RNA isolated from control synthetic antibody RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.
SAMPLE 7


title: Drosophila_melanogaster_synthetic_anti-Staufen_RIP_RNA_rep3

description:
This sample is total isolated from synthetic anti-Staufen RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.
SAMPLE 6

value: synthetic anti-Staufen antibody


title: 0hr Wild-type Medium Control Sample 2

source_name: BMDM_0hr Wild-type Medium Control

value: Wild-type


title: Drosophila_melanogaster_synthetic_anti-Staufen_RIP_RNA_rep2

description:
This sample is total RNA isolated from synthetic anti-Staufen RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.
SAMPLE 5

value: 0-3 hour embryo


title: 0hr IFNabR-/- Medium Control Sample 6


title: 0hr Wild-type Medium Control Sample 3


title: Drosophila_melanogaster_anti-GFP_RIP_RNA_rep1

description:
This sample is total RNA isolated from anti-GFP RIPs from 0-3 hour GFP-Staufen embryos. It is the first of three biological replicates.
SAMPLE 13

value: GFP-Staufen transgenic


title: Drosophila_melanogaster_w1118_0-3h_embryo_total_RNA_rep2

description:
This sample is total RNA isolated from 0-3 hour w1118 embryos. It is the second of three biological replicates.
SAMPLE 2


title: Drosophila_melanogaster_w1118_0-3h_embryo_total_RNA_rep3

description:
This sample is total RNA isolated from 0-3 hour w1118 embryos. It is the third of three biological replicates.
SAMPLE 3


title: Drosophila_melanogaster_synthetic_anti-Staufen_RIP_RNA_rep1

description:
This sample is total RNA isolated from synthetic anti-Staufen RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.
SAMPLE 4


title: 0hr IFNabR-/- Medium Control Sample 4


title: 0hr TPL2-/- Medium Control Sample 7


title: H37Rv Uninfected 30 min rep2

data_processing: The data were normalised using 75th percentile normalisation in GeneSpring 11.5

source_name: BMDM

treatment_protocol: cells were infected with Mtb H37Rv or not for indicated times and harvested into RLT buffer

value: none (uninfected) for 30 min


title: H37Rv Uninfected 0 min rep2

value: none (uninfected) for 0 min


title: H37Rv Uninfected 15 min rep2

value: none (uninfected) for 15 min


title: 0hr Wild-type Medium Control Sample 1


title: H37Rv Uninfected 30 min rep1


title: H37Rv infected 15 min rep2

value: Mtb H37Rv for 15 min


title: H37Rv infected 360 min rep2

value: bone marrow derived macrophages (BMDM)

value: Mtb H37Rv for 360 min


title: Drosophila_melanogaster_w1118_0-3h_embryo_total_RNA_rep1

description:
This sample is total RNA isolated from 0-3 hour w1118 embryos. It is the first of three biological replicates.
SAMPLE 1


title: H37Rv Uninfected 1440 min rep2

value: none (uninfected) for 1440 min


title: H37Rv Uninfected 180 min rep2

value: none (uninfected) for 180 min


title: H37Rv Uninfected 60 min rep2

value: none (uninfected) for 60 min


title: H37Rv infected 1440 min rep2

value: Mtb H37Rv for 1440 min


title: H37Rv infected 60 min rep2

value: wild type

value: Mtb H37Rv for 60 min


title: H37Rv infected 15 min rep1


title: H37Rv infected 30 min rep2

value: Mtb H37Rv for 30 min


title: H37Rv Uninfected 180 min rep1


title: H37Rv Uninfected 1440 min rep1


title: H37Rv infected 360 min rep1


title: H37Rv infected 180 min rep2

value: Mtb H37Rv for 180 min


title: H37Rv Uninfected 15 min rep1


title: H37Rv Uninfected 360 min rep2

value: none (uninfected) for 360 min


title: H37Rv infected 60 min rep1


title: H37Rv Uninfected 360 min rep1


title: H37Rv Uninfected 60 min rep1


title: H37Rv Uninfected 0 min rep1


title: H37Rv infected 30 min rep1


title: H37Rv infected 1440 min  rep1


title: H37Rv infected 180 min rep1


title: WAT_HFD_RSG_2

description: replicate 2

data_processing: The data were normalized using cubic spline normalization implemented in Illumina GenomeStudio V2011.1.

source_name: WAT_HFD_rosiglitazone posttreatment

extract_protocol: White adipose tissue was first lysed and homogenized in RLT buffer (QIAGEN) with 5 mm steel beads at 20 Hz for 4 min (TissueLyser, QIAGEN). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

tag: gender

value: male

tag: age

value: 21 weeks

tag: tissue

value: visceral white adipose tissue

tag: pre-treated with

value: high-fat diet (HFD) for 12 wks

value: HFD with 4 mg/kg/d rosiglitazone (RGS) for 3 wks


title: WAT_HFD+A1prev_2

description: replicate 2

source_name: WAT_HFD_amorfrutin 1 cotreatment

value: HFD with 37 mg/kg/d amorfrutin 1 (A1) for 15 wks


title: WAT_HFD_A1_2

description: replicate 2

source_name: WAT_HFD_amorfrutin 1 posttreatment

value: HFD with 100 mg/kg/d amorfrutin 1 (A1) for 3 wks


title: WAT_HFD_3

description: replicate 3

value: HFD without compound for 3wks


title: WAT_HFD_A1_3

description: replicate 3


title: WAT_HFD+A1prev_1

description: replicate 1


title: WAT_HFD_RSG_3

description: replicate 3


title: WAT_LFD_2

description: replicate 2

value: low-fat diet (LFD) for 15 wks


title: WAT_LFD_3

description: replicate 3


title: WAT_HFD_RSG_1

description: replicate 1


title: WAT_HFD_RSG_4

description: replicate 4


title: WAT_HFD_1

description: replicate 1


title: WAT_HFD_A1_1

description: replicate 1


title: WAT_LFD_1

description: replicate 1


title: WAT_HFD_2

description: replicate 2


title: N/Tert-92E6 cell line, 2ug/ml MMC for 18h, replicate 2

city: Philadelphia

first: Elizabeth

middle: A

last: White

state: PA

address: 3610 Hamilton Walk

department: Otorhinolaryngology

institute: University of Pennsylvania

description: gene expression data from mitomycin C N/Tert cells

hyb_protocol: Hybridization was performed by injecting the hybridization cocktail containing fragmented aRNA into Array and incubated at 45oC for about 16 hours with 60 rpm rotation in GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: The image was acquired by scanning the arrays using GeneChip 7G Plus Scanner (Affymetrix).

data_processing: Raw data (.cel files) from individual gene chips were compiled and normalized using Affymetrix Power Tools using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization) then filtered to exclude expression values <80 using the preprocessDataset module in GenePattern software (Broad Institute).

source_name: N/Tert-92E6 cells treated with mitomycin C

label_protocol: Biotin-labeled aRNA was synthesized using GeneChip 3’ IVT Express Kit (Affymetrix P/N: 901229-A, 901229-D) in GeneAmp PCR System 9700 (Applied Biosystems)

growth_protocol: N/Tert-1 cells stably harboring empty or E6 expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 4 ug/ml hygromycin and 0.5 ug/ml puromycin

extract_protocol: RNA was extracted with the Qiagen RNeasy mini kit according to the manufacturer's protocol

treatment_protocol: Cells were treated with 2ug/ml mitomycin C or vehicle control (water) in K-SFM protio to harvest by trypsinization and freezing of cell pellets.

tag: cell line

tag: cell type

value: human foreskin keratinocytes immortalized with hTert

tag: retroviral vector

value: MSCV-IP N HAonly 92E6


title: N/Tert-92E6 cell line, no MMC treatment, replicate 2

description: gene expression data from untreated N/Tert cells

source_name: N/Tert-92E6 cells treated with vehicle control


title: N/Tert-92E6 cell line, no MMC treatment, replicate 3


title: N/Tert-92E6 cell line, 2ug/ml MMC for 18h, replicate 3


title: liver_HFD_A1prev_2

description: replicate 2

source_name: liver_HFD_amorfrutin 1 pretreatment

extract_protocol: Liver tissue was first lysed and homogenized in RLT buffer (QIAGEN) with 5 mm steel beads at 20 Hz for 4 min (TissueLyser, QIAGEN). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

tag: strain

value: liver


title: N/Tert-8E6 cell line, no MMC treatment, replicate 3

source_name: N/Tert-8E6 cells treated with vehicle control

value: MSCV-IP N HAonly 8E6


title: N/Tert-8E6 cell line, 2ug/ml MMC for 18h, replicate 3

source_name: N/Tert-8E6 cells treated with mitomycin C


title: N/Tert-92E6 cell line, 2ug/ml MMC for 18h, replicate 1


title: liver_HFD_A1prev_3

description: replicate 3


title: liver_HFD_A1prev_4

description: replicate 4


title: N/Tert-8E6 cell line, 2ug/ml MMC for 18h, replicate 1


title: N/Tert-92E6 cell line, no MMC treatment, replicate 1


title: N/Tert-8E6 cell line, no MMC treatment, replicate 2


title: liver_HFD_3B

description: replicate 3


title: liver_HFD_2B

description: replicate 2


title: N/Tert-8E6 cell line, 2ug/ml MMC for 18h, replicate 2


title: liver_HFD_A1prev_1

description: replicate 1


title: liver_HFD_1B

description: replicate 1


title: N/Tert-6bE6 cell line, 2ug/ml MMC for 18h, replicate 3

source_name: N/Tert-6bE6 cells treated with mitomycin C

value: MSCV-IP N HAonly 6bE6


title: N/Tert-6bE6 cell line, 2ug/ml MMC for 18h, replicate 1


title: liver_LFD_3

description: replicate 3


title: liver_LFD_2

description: replicate 2


title: N/Tert-8E6 cell line, no MMC treatment, replicate 1


title: N/Tert-6bE6 cell line, 2ug/ml MMC for 18h, replicate 2


title: liver_LFD_1

description: replicate 1


title: N/Tert-6bE6 cell line, no MMC treatment, replicate 2

source_name: N/Tert-6bE6 cells treated with vehicle control


title: liver_HFD_A1_2

description: replicate 2

source_name: liver_HFD_amorfrutin 1 posttreatment


title: liver_LFD_4

description: replicate 4


title: liver_HFD_A1_3

description: replicate 3


title: N/Tert-6bE6 cell line, no MMC treatment, replicate 1


title: N/Tert-16E6 cell line #1, 2ug/ml MMC for 18h, replicate 3

source_name: N/Tert-16E6 cells treated with mitomycin C

value: MSCV-IP N HAonly 16E6


title: N/Tert-6bE6 cell line, no MMC treatment, replicate 3


title: N/Tert-16E6 cell line #1, 2ug/ml MMC for 18h, replicate 1


title: liver_HFD_RSG_1

description: replicate 1

source_name: liver_HFD_rosiglitazone posttreatment


title: N/Tert-16E6 cell line #1, no MMC treatment, replicate 5

source_name: N/Tert-16E6 cells treated with vehicle control


title: liver_HFD_A1_1

description: replicate 1


title: liver_HFD_RSG_3

description: replicate 3


title: N/Tert-empty vector cell line #3, 2ug/ml MMC for 18h, replicate 3

source_name: N/Tert-empty vector cells treated with mitomycin C

value: MSCV-IP N HAonly emptyV2


title: N/Tert-16E6 cell line #1, no MMC treatment, replicate 3


title: heart_HFD_A1_3

description: replicate 3

source_name: Heart_HFD_amorfrutin 1 posttreatment

extract_protocol: Heart tissue was first lysed and homogenized in RLT buffer (QIAGEN) with 5 mm steel beads at 20 Hz for 4 min (TissueLyser, QIAGEN). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

value: 21 wks

value: heart


title: N/Tert-16E6 cell line #1, 2ug/ml MMC for 18h, replicate 2


title: N/Tert-16E6 cell line #1, no MMC treatment, replicate 4


title: liver_HFD_RSG_4

description: replicate 4

value: male

value: 21 weeks


title: liver_HFD_3A

description: replicate 3

value: high-fat diet (HFD) for 12 wks


title: liver_HFD_2A

description: replicate 2


title: N/Tert-16E6 cell line #1, no MMC treatment, replicate 1


title: liver_HFD_RSG_2

description: replicate 2

value: HFD with 4 mg/kg/d rosiglitazone (RGS) for 3 wks


title: heart_HFD_A1_1

description: replicate 1


title: heart_HFD_A1_2

description: replicate 2


title: heart_HFD_RSG_2

description: replicate 2

source_name: Heart_HFD_rosiglitazone posttreatment


title: heart_HFD_RSG_3

description: replicate 3


title: N/Tert-empty vector cell line #3, 2ug/ml MMC for 18h, replicate 2


title: liver_HFD_1A

description: replicate 1


title: N/Tert-16E6 cell line #1, no MMC treatment, replicate 2


title: N/Tert-empty vector cell line #1, no MMC treatment, replicate 3

source_name: N/Tert-empty vector cells treated with vehicle control


title: N/Tert-empty vector cell line #2, no MMC treatment, replicate 1


title: N/Tert-empty vector cell line #3, no MMC treatment, replicate 1


title: N/Tert-empty vector cell line #3, 2ug/ml MMC for 18h, replicate 1


title: BA treated H4Ac, replicate #2

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

description: ChIP-chip H4Ac Benzyl alcohol-treated Drosophila heads.

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

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

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H4Ac ChIP DNA from BA-treated Drosophila heads

label_protocol: 1 µg amplified ChIP DNA prepared from fly heads was labeled by Klenow random priming with Cy5 or Cy3 nonamers per manufacturer's protocol, by Nimblegen personnel (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Adult Drosophila were raised on standard cornmeal agar medium in a 12/12 h light/dark cycle for 3-5 days.

extract_protocol: 500 wild-type flies were sedated with either ethanol, benzyl alcohol or mock sedated for 15 min and then were allowed to recover in a drug-free environment for 6 hours. After recovery, flies were collected, frozen in liquid nitrogen, and vortex decapitated, and then heads were collected by sieving. Heads were cross-linked with 2% formaldehyde for 5 min, and chromatin was solubilized and sonicated on ice 6x30 s, followed by 1 min cooling on ice to produce fragments of approximately 500 bp with a sonic Dismembrator 250 (Fisher Scientific). Chromatin samples (2 ug) were immunoprecipitated using a 1:200 dilution of ChIP grade antibody against acetylated histone H4 at lysine 5, 8, 12 and 16 (catalog # 06-866; EMD Millipore Corporation, Billerica, MA). A fraction (1/10) of the chromatin sample was left unprecipitated for use as input control. DNA from immunoprecipitated (ChIP) and input samples was washed, reversed cross-linked, and purified and subsequently amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO) following the manufacturer's protocol. Approximately 1 ug of amplified ChIP and input DNA from each sample was sent to NimbleGen (Roche NimbleGen, Inc. Madison, WI) for two-color hybridization to Drosophila ChIP-chip 2.1M Whole-Genome Tiling Arrays.

treatment_protocol: Benzyl alcohol exposure for 15 minutes, 6 hrs before chromatin extraction.

tag: genotype/variation

value: wild-type

tag: developmental stage

value: adult

value: head

tag: treatment

value: benzyl alcohol

tag: chip antibody

source_name: H4Ac ChIP DNA from untreated Drosophila heads

treatment_protocol: Control: No benzyl alcohol exposure, 6 hrs before chromatin extraction.


title: BA treated H4Ac, replicate #1


title: heart_HFD_4

description: replicate 4

value: HFD without compound for 3wks


title: Basal H4Ac, replicate #2

description: ChIP-chip H4Ac Drosophila heads.

treatment_protocol: None.

source_name: Input DNA from untreated Drosophila heads


title: Basal H4Ac, replicate #1

description: ChIP-chip H4Ac Drosophila heads.