Allen Brain Atlas

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ISH Platform Controls Quality control standards for high-throughput RNA in situ hybridization data generation Study: Mouse Brain
Cross Platform Validation Methods for validating the data Study: Mouse Brain
Data Production Processes Processes and procedures used to perform ISH Study: Mouse Brain
Differential gene expression search in Isocortex Adult Mouse Brain differential gene expression search in Isocortex Study: Mouse Brain
Differential gene expression search in Cerebral cortex, layer 2-3 "Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 2-3" Study: Mouse Brain
Differential gene expression search in Cerebral cortex, layer 4 "Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 4" Study: Mouse Brain
Differential gene expression search in Cerebral cortex, layer 5 "Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 5" Study: Mouse Brain
Differential gene expression search in Cerebral cortex, layer 6a "Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 6a" Study: Mouse Brain
Differential gene expression search in Main olfactory bulb Adult Mouse Brain differential gene expression search in Main olfactory bulb Study: Mouse Brain
Differential gene expression search in Accessory olfactory bulb Adult Mouse Brain differential gene expression search in Accessory olfactory bulb Study: Mouse Brain
Differential gene expression search in Piriform area Adult Mouse Brain differential gene expression search in Piriform area Study: Mouse Brain
Differential gene expression search in Hippocampal region Adult Mouse Brain differential gene expression search in Hippocampal region Study: Mouse Brain
Differential gene expression search in Field CA1 Adult Mouse Brain differential gene expression search in Field CA1 Study: Mouse Brain
Differential gene expression search in Field CA3 Adult Mouse Brain differential gene expression search in Field CA3 Study: Mouse Brain
Differential gene expression search in Dentate gyrus Adult Mouse Brain differential gene expression search in Dentate gyrus Study: Mouse Brain
Differential gene expression search in Entorhinal area Adult Mouse Brain differential gene expression search in Entorhinal area Study: Mouse Brain
Differential gene expression search in Striatum Adult Mouse Brain differential gene expression search in Striatum Study: Mouse Brain
Differential gene expression search in Lateral septal complex Adult Mouse Brain differential gene expression search in Lateral septal complex Study: Mouse Brain
Differential gene expression search in Pallidum Adult Mouse Brain differential gene expression search in Pallidum Study: Mouse Brain
Differential gene expression search in Cerebellum Adult Mouse Brain differential gene expression search in Cerebellum Study: Mouse Brain
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ISH Platform Controls

Quality control standards for high-throughput RNA in situ hybridization data generation

Study: Mouse Brain

Cross Platform Validation

Methods for validating the data

Study: Mouse Brain

Data Production Processes

Processes and procedures used to perform ISH

Study: Mouse Brain

Differential gene expression search in Isocortex

Adult Mouse Brain differential gene expression search in Isocortex

Study: Mouse Brain

Differential gene expression search in Cerebral cortex, layer 2-3

"Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 2-3"

Study: Mouse Brain

Differential gene expression search in Cerebral cortex, layer 4

"Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 4"

Study: Mouse Brain

Differential gene expression search in Cerebral cortex, layer 5

"Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 5"

Study: Mouse Brain

Differential gene expression search in Cerebral cortex, layer 6a

"Adult Mouse Brain differential gene expression search in Cerebral cortex, layer 6a"

Study: Mouse Brain

Differential gene expression search in Main olfactory bulb

Adult Mouse Brain differential gene expression search in Main olfactory bulb

Study: Mouse Brain

Differential gene expression search in Accessory olfactory bulb

Adult Mouse Brain differential gene expression search in Accessory olfactory bulb

Study: Mouse Brain

Differential gene expression search in Piriform area

Adult Mouse Brain differential gene expression search in Piriform area

Study: Mouse Brain

Differential gene expression search in Hippocampal region

Adult Mouse Brain differential gene expression search in Hippocampal region

Study: Mouse Brain

Differential gene expression search in Field CA1

Adult Mouse Brain differential gene expression search in Field CA1

Study: Mouse Brain

Differential gene expression search in Field CA3

Adult Mouse Brain differential gene expression search in Field CA3

Study: Mouse Brain

Differential gene expression search in Dentate gyrus

Adult Mouse Brain differential gene expression search in Dentate gyrus

Study: Mouse Brain

Differential gene expression search in Entorhinal area

Adult Mouse Brain differential gene expression search in Entorhinal area

Study: Mouse Brain

Differential gene expression search in Striatum

Adult Mouse Brain differential gene expression search in Striatum

Study: Mouse Brain

Differential gene expression search in Lateral septal complex

Adult Mouse Brain differential gene expression search in Lateral septal complex

Study: Mouse Brain

Differential gene expression search in Pallidum

Adult Mouse Brain differential gene expression search in Pallidum

Study: Mouse Brain

Differential gene expression search in Cerebellum

Adult Mouse Brain differential gene expression search in Cerebellum

Study: Mouse Brain

	Prenatal (9896)
	Juvenile (57411)
	Adult (116514)
	Aged (32659)

	FISH (300)
	ISH (137378)
	Microarray (290)
	RNA Sequencing (26216)
	Resource (5)

	Aging Dementia TBI - ISH data (1570)
	Aging Dementia TBI - non-ISH data (109)
	Developing Human Brain ISH (3941)
	Developing Human Prenatal LMD Microarray (243)
	Developing Human Reference Data (163)
	Developing Human Transcriptome (285)
	Developing Mouse Brain (21463)
	Glioblastoma (20203)
	Human Brain ISH Autism Study (528)
	Human Brain ISH Cortex Study (6670)
	Human Brain ISH Neurotransmitter Study (11670)
	Human Brain ISH Schizophrenia Study (3378)
	Human Brain ISH SubCortex Study (462)
	Human Brain Microarray (88)
	Human Glioblastoma RNASeq (26085)
	Mouse Brain (28886)
	Mouse Brain Reference Data (1)
	Mouse Cell Types - transcriptomics data (112)
	Mouse Connectivity Projection (1)
	Mouse Connectivity Transgenic Characterization (1850)
	Mouse Spinal Cord (36698)
	Mouse Strains (1080)
	Non-Human Primate ISH (3057)
	Non-Human Primate Macrodissection Microarray (65)
	Non-Human Primate Microdissection Microarray (82)
	Non-Human Primate Molecular Map (133)
	Sleep (1727)

	129/SvJ (10)
	129S1/SvlmJ (124)
	B6.129 (374)
	B6.129.FVB (39)
	B6.C3H (17)
	B6.FVB (35)
	B6.FVB(ICR) (37)
	B6;CFW (2)
	B6;ICR (2)
	C57BL/6J (85098)
	CAST/EiJ (124)
	DBA/2J (124)
	FVB (23)
	FVB.CD1(ICR) (14)
	FVB/NJ (8)
	PWD/PhJ (93)
	SPRET/EiJ (124)
	WSB/EiJ (93)
	ai2/thcre (1)
	ctgf-cre (2)
	wfs1-creer (2)

	Asian (339)
	Black or African American (8233)
	European (122)
	Hispanic (4125)
	Two or more races (122)
	White or Caucasian (14290)

	Dorsal to Ventral (1096)
	Lateral to Medial (3332)
	Medial to Lateral (5219)
	Ventral to Dorsal (7134)
	coronal (27597)
	sagittal (43609)
	variable (38372)

	autism (258)
	control (26146)
	glioblastoma (32400)
	schizophrenia (1231)
	traumatic brain injury (762)

	Amygdala/Hippocampus (1914)
	Brain (1981)
	Brainstem (43)
	Cerebellum (43)
	Cingulate Cortex (2843)
	Claustrum/Insula (1229)
	Dorsolateral prefrontal cortex (3824)
	Frontal Cortex (4049)
	Parieto-Occipital Cortex (2201)
	Posterior Superior Temporal Cortex (37)
	SubCortex (1144)
	Temporal cortex (3392)
	Ventral Anterior Cingulate (20)
	Ventral striatum (788)
	Visual Cortex (802)
	Visual cortex (3303)
	amygdaloid complex (576)
	brain (173)
	frontal lobe (5823)
	hippocampal cortex (hippocampal formation) (579)
	hippocampus (hippocampal formation) (522)
	medial frontal cortex (areas 24 25 and 32) (576)
	medial prefrontal cortex (715)
	occipital cortex (576)
	occipital lobe (955)
	parietal lobe (7171)
	parietal neocortex (498)
	temporal lobe (5774)
	temporal neocortex (550)
	ventral striatum (576)

	Human (74689)
	Mouse (87459)
	NHP (3204)

	Female (44466)
	Male (141492)

	Passed QC (160928)
	Failed QC (4424)