title: 1772096139_D12


title: 1772096139_D11

status: Public on Dec 01 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecule counts for each gene and cell. Cells with less than 1500 molecules have been removed from this file.

molecule: polyA RNA

organism: Mus musculus

source_name: hypothalamus

growth_protocol: C57BL/6N mice were housed conventionally (12/12-h light cycle, 55% humidity).

extract_protocol:
Mice were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold pre-oxygenated (95% O2/5% CO2) cutting solution containing (in mM): 90 NaCl, 26 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 10 HEPES-NaOH, 5 Na-ascorbate, 5 Na-pyruvate, 0.5 CaCl2, 8 MgSO4 and 20 glucose. A central column of the mouse hypothalamus spanning the preoptic area-Arc (rostrocaudal axis), paraventricular nucleus (dorsal) and the ventrolateral hypothalamic area (lateral) was microdissected from serial 300-micrometer-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 600-1,000 cells/?microlitre. After mixing C1 suspension reagent (4 microlitre; "C1 reagents", Fluidigm Inc.) to the cell suspension (7 microlitre), this mixture was loaded into a C1-AutoPrep IFC microfluidic chip (Fluidigm Inc.)
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: Formalin stress was induced by injection of 4% PFA into the left paw

tag: strain

tag: age (days postnatal)

tag: Sex

value: F

tag: acute stress

value: N

tag: cell diameter

tag: total molecules

tag: level1 class

value: oligos


title: 1772096140_D02


title: 1772096140_D05


title: 1772096140_C10


title: 1772096139_C12

value: neurons

tag: level2 class (neurons only)

value: Adcyap1;Tac1 (VMH)


title: 1772096139_C11


title: 1772096140_B10

value: astrocytes


title: 1772096139_C10


title: 1772096140_B12

value: endothelial


title: 1772096139_E04


title: 1772096140_B05

value: uc


title: 1772096140_B04


title: 1772096140_A09


title: 1772096140_A06


title: 1772096140_A05


title: 1772096140_A04


title: 1772096139_C04


title: 1772096139_C01


title: 1772096139_B12

value: ependymal


title: 1772096139_B07


title: 1772096140_A02


title: 1772096139_E06


title: 1772096140_A01


title: 1772096139_B05


title: 1772096139_B02


title: 1772096139_B01


title: 1772096139_E02


title: 1772096139_E01


title: 1772096139_D07


title: 1772096139_D06


title: 1772096139_D03


title: 1772096139_C09


title: 1772096139_A07


title: 1772096139_A03

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096138_H11


title: 1772096139_A02


title: 1772096139_C08

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096138_H05


title: 1772096139_C07


title: 1772096138_H04


title: 1772096139_C05


title: 1772096139_B11


title: 1772096138_G05

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096139_B03

value: Crh+/-;Gal-low (PVH)


title: 1772096139_B04


title: 1772096138_F11


title: 1772096138_F08

value: Pomc+/- (ARH)


title: 1772096139_A12


title: 1772096139_A04


title: 1772096139_A08


title: 1772096138_F05


title: 1772096138_H07

value: Hcrt


title: 1772096139_B06


title: 1772096138_H01

value: Vglut2 A


title: 1772096138_H06


title: 1772096138_H02


title: 1772096138_G11


title: 1772096138_G07


title: 1772096138_G06


title: 1772096138_F09


title: 1772096138_G04

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096138_F12

value: F


title: 1772096138_F04

value: N


title: 1772096138_D12

value: oligos


title: 1772096138_F06


title: 1772096138_E08


title: 1772096138_E10

value: neurons


title: 1772096138_E07


title: 1772096138_E12


title: 1772096138_F01


title: 1772096138_E05


title: 1772096138_E06


title: 1772096138_C10


title: 1772096138_D06


title: 1772096138_C11


title: 1772096138_C01


title: 1772096138_G02


title: 1772096138_C09


title: 1772096138_D11


title: 1772096138_D03


title: 1772096138_D02


title: 1772096138_E04

value: Trh-low


title: 1772096138_B11


title: 1772096138_B10

value: astrocytes


title: 1772096138_B06

value: GABA 2


title: 1772096138_E02


title: 1772096138_B02


title: 1772096138_D09


title: 1772096138_B01


title: 1772096138_A12


title: 1772096138_B03


title: 1772096138_A05


title: 1772096138_A09


title: 1772096138_A04


title: 1772096138_A03


title: 1772096138_A07


title: 1772096136_H06

value: M

value: Y


title: 1772096138_A10


title: 1772096138_A02


title: 1772096136_H03


title: 1772096136_H02


title: 1772096136_H04


title: 1772096136_H11


title: 1772096138_B05


title: 1772096136_H07

value: uc


title: 1772096138_B04


title: 1772096136_G04

value: endothelial


title: 1772096136_H01


title: 1772096136_G10

value: vsm


title: 1772096136_F11


title: 1772096136_G03


title: 1772096136_F05


title: 1772096136_G05


title: 1772096136_F04


title: 1772096136_E12


title: 1772096136_F01


title: 1772096136_E07


title: 1772096136_E10


title: 1772096138_A06


title: 1772096138_A08


title: 1772096136_E06


title: 1772096136_G06


title: 1772096136_E05


title: 1772096136_E03


title: 1772096136_D04


title: 1772096136_D12


title: 1772096136_C09


title: 1772096136_C12


title: 1772096136_C11


title: 1772096136_C06


title: 1772096136_B09


title: 1772096136_B11


title: 1772096136_C05


title: 1772096136_C04


title: 1772096136_A12


title: 1772096136_A10


title: 1772096136_A11


title: 1772096136_B01


title: 1772096136_B06


title: 1772096136_A06


title: 1772096136_A09


title: 1772096136_A03


title: 1772096135_H06


title: 1772096136_A05


title: 1772096136_A02


title: 1772096135_H11


title: 1772096136_D11


title: 1772096136_D05


title: 1772096136_D07


title: 1772096135_G04


title: 1772096135_F01


title: 1772096135_E07


title: 1772096135_E08


title: 1772096135_F08


title: 1772096135_E06


title: 1772096135_E10


title: 1772096135_F02


title: 1772096135_G12


title: 1772096135_D12

value: Sst-medium;Cartpt


title: 1772096135_E05


title: 1772096135_D11

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096135_H12


title: 1772096135_D07


title: 1772096135_D10

value: ependymal


title: 1772096135_C09

value: Pomc+/- (ARH)


title: 1772096135_C10


title: 1772096135_C11


title: 1772096135_D06


title: 1772096135_C06


title: 1772096135_B12


title: 1772096135_C08


title: 1772096135_B11


title: 1772096135_C04


title: 1772096135_B09


title: 1772096135_B08


title: 1772096135_B06


title: 1772096135_B05

value: Vglut2;Gpr149 (PVH;VMH)


title: 1772096135_B03


title: 1772096135_B07


title: 1772096135_A04


title: 1772096135_A08


title: 1772096135_A07


title: 1772096135_A03


title: 1772096134_H06


title: 1772096135_A01


title: 1772096134_H10


title: 1772096134_H11


title: 1772096134_F06


title: 1772096134_G05


title: 1772096134_G10


title: 1772096134_G02


title: 1772096134_F05


title: 1772096134_E11


title: 1772096134_E12


title: 1772096134_H01


title: 1772096134_F04


title: 1772096134_E06


title: 1772096134_E07


title: 1772096134_D04


title: 1772096134_D10


title: 1772096134_D07


title: 1772096134_E01


title: 1772096134_E02


title: 1772096134_E04

value: Adcyap1;Tac1 (VMH)


title: 1772096134_C02


title: 1772096134_B12


title: 1772096134_C04


title: 1772096134_A07


title: 1772096134_A06


title: 1772096134_A01


title: 1772096133_H12


title: 1772096134_F03

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096134_B06


title: 1772096134_A09

value: oligos


title: 1772096134_A12

value: neurons

value: Vglut2 A


title: 1772096133_H06


title: 1772096133_G06


title: 1772096133_G10


title: 1772096133_G05

value: astrocytes


title: 1772096133_F12


title: 1772096133_E11


title: 1772096133_H02


title: 1772096133_E08


title: 1772096133_H11


title: 1772096133_D02


title: 1772096133_D10


title: 1772096133_C07


title: 1772096133_D12


title: 1772096133_C09


title: 1772096133_E01


title: 1772096133_C05


title: 1772096133_C11


title: 1772096133_C01


title: 1772096133_B10


title: 1772096133_B12


title: 1772096133_B09


title: 1772096133_B02


title: 1772096133_A12


title: 1772096133_B03


title: 1772096133_F10


title: 1772096133_F06


title: 1772096133_E06


title: 1772096133_A09

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772096133_F01

value: M

value: Trh-low


title: 1772096133_A04

value: Y


title: 1772096133_A10


title: 1772096133_A03


title: 1772096133_D05

value: Hcrt


title: 1772096132_H11


title: 1772096132_H10


title: 1772096133_A02


title: 1772096133_C04


title: 1772096133_E04

value: endothelial


title: 1772096132_H06


title: 1772096132_H04


title: 1772096132_H03


title: 1772096132_G11


title: 1772096132_G05


title: 1772096132_G09


title: 1772096132_G06


title: 1772096132_H05


title: 1772096132_F10


title: 1772096132_G10


title: 1772096132_G01


title: 1772096132_H02

value: uc


title: 1772096132_G04


title: 1772096132_F08

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096132_F11

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096132_F02


title: 1772096132_F12


title: 1772096132_E12

value: ependymal


title: 1772096132_G02


title: 1772096132_E04


title: 1772096132_F09


title: 1772096132_D12


title: 1772096132_E07


title: 1772096132_D11


title: 1772096132_F04


title: 1772096132_D10


title: 1772096132_E09


title: 1772096132_D09


title: 1772096132_D08


title: 1772096132_D06


title: 1772096132_C11


title: 1772096132_C09


title: 1772096132_C05

value: Hmit+/-


title: 1772096132_C12


title: 1772096132_C06


title: 1772096132_C08


title: 1772096132_C04


title: 1772096132_B12


title: 1772096132_C01


title: 1772096132_E08


title: 1772096132_B08


title: 1772096132_B09


title: 1772096132_B11


title: 1772096132_B02


title: 1772096132_B04


title: 1772096132_B06


title: 1772096132_A10


title: 1772096132_B05


title: 1772096132_B01


title: 1772096132_A12


title: 1772096132_A04

value: Vglut2;Col9a2 (PVH)


title: 1772096132_A06


title: 1772096132_A07


title: 1772096132_A09


title: 1772096131_H12


title: 1772096132_A03


title: 1772096132_A02


title: 1772096131_H10


title: 1772096131_H04


title: 1772096131_G12


title: 1772096131_H06


title: 1772096131_H01


title: 1772096131_G04


title: 1772096131_F04


title: 1772096131_E12


title: 1772096131_F01


title: 1772096131_E07


title: 1772096132_A05


title: 1772096131_D06


title: 1772096131_E05


title: 1772096131_C10


title: 1772096131_C11


title: 1772096131_C12


title: 1772096131_C06


title: 1772096131_C05


title: 1772096131_C09


title: 1772096131_C03


title: 1772096131_B11


title: 1772096131_F03


title: 1772096131_B02


title: 1772096131_A08


title: 1772096131_A11


title: 1772096131_B04

value: vsm


title: 1772096131_A12


title: 1772096131_B07

value: microglia


title: 1772096131_F06


title: 1772096131_A06

value: neurons


title: 1772096131_A05


title: 1772096128_H12

value: oligos


title: 1772096131_A01


title: 1772096128_H11

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096131_A02


title: 1772096128_H06


title: 1772096128_G12

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772096131_D12

value: M


title: 1772096128_H02


title: 1772096128_G09


title: 1772096131_B08


title: 1772096128_G08


title: 1772096128_G06


title: 1772096128_F04


title: 1772096128_G02

value: Sst low-medium


title: 1772096128_G05

value: Y


title: 1772096128_F09

value: Galanin


title: 1772096128_F03


title: 1772096128_F11


title: 1772096128_F02


title: 1772096128_E10

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096128_E07

value: uc


title: 1772096128_E12


title: 1772096128_E08

value: Oxt;Avp-low


title: 1772096128_E04


title: 1772096128_E02


title: 1772096128_F01


title: 1772096128_D09


title: 1772096128_D04


title: 1772096128_C11


title: 1772096128_D10

value: Vip;Grp+/-;circadian (SCH)


title: 1772096128_D06


title: 1772096128_D01

value: astrocytes


title: 1772096128_G04

value: ependymal


title: 1772096128_F12


title: 1772096128_C09


title: 1772096128_C08


title: 1772096128_C06


title: 1772096128_C10


title: 1772096128_C03


title: 1772096128_C01

value: endothelial


title: 1772096128_C04


title: 1772096128_B09


title: 1772096128_B10


title: 1772096128_B04


title: 1772096128_B03


title: 1772096128_A10

value: Hmit+/-


title: 1772096128_A09

value: Avp-high;Oxt-low


title: 1772096128_A05

value: neurons


title: 1772096127_H11

value: N


title: 1772096128_B02

value: oligos


title: 1772096127_H05


title: 1772096128_D02

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096127_H03

value: M


title: 1772096128_B01

value: Sst-medium;Cartpt


title: 1772096127_G07

value: Hcrt


title: 1772096127_G10


title: 1772096127_G01

value: Trh-low


title: 1772096127_F12


title: 1772096127_F09


title: 1772096127_F06

value: Pomc+/- (ARH)


title: 1772096127_G06

value: Sst low-medium


title: 1772096128_B12

value: Y

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772096127_E12


title: 1772096127_E11


title: 1772096127_G05


title: 1772096127_G02


title: 1772096127_E09

value: uc


title: 1772096127_E05

value: ependymal


title: 1772096127_D03


title: 1772096128_B11

value: astrocytes


title: 1772096127_F02


title: 1772096127_D12


title: 1772096127_E06


title: 1772096127_D06


title: 1772096127_B12


title: 1772096127_C03

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772096127_B09


title: 1772096127_C01

value: GABA 2


title: 1772096127_B08

value: neurons

value: Pmch


title: 1772096127_B04

value: N

value: endothelial


title: 1772096127_F05

value: M


title: 1772096127_A10


title: 1772096127_B01


title: 1772096127_A09


title: 1772096127_A04

value: Galanin


title: 1772096127_A07


title: 1772096127_A01


title: 1772096126_H11

value: oligos


title: 1772096126_G05

value: Per2;circadian (SCH)


title: 1772096126_H06

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096126_G12


title: 1772096127_B11


title: 1772096126_E02


title: 1772096126_G02


title: 1772096126_F07


title: 1772096126_D10


title: 1772096126_D11


title: 1772096126_F06


title: 1772096127_C12

value: Vglut2 A


title: 1772096126_D09


title: 1772096126_C11


title: 1772096126_D02

value: GABA 1


title: 1772096126_F11

value: Gad-low;Gnrh-/+


title: 1772096126_D05


title: 1772096127_B03

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772096126_D06


title: 1772096126_D08


title: 1772096126_C05


title: 1772096126_H12


title: 1772096126_D07


title: 1772096126_C04


title: 1772096126_H01

value: ependymal


title: 1772096126_C06


title: 1772096126_G10


title: 1772096126_B08


title: 1772096126_B06


title: 1772096126_C01


title: 1772096126_B12


title: 1772096126_A12


title: 1772096126_A09


title: 1772096126_B03


title: 1772096126_A08


title: 1772096126_B01


title: 1772096126_A06

value: Trh-low


title: 1772096126_A05


title: 1772096126_C07


title: 1772096126_A10

value: uc


title: 1772096126_C10


title: 1772096103_F08

value: Y


title: 1772096103_F06


title: 1772096103_H05


title: 1772096103_G11


title: 1772096103_G03


title: 1772096103_G02

value: neurons


title: 1772096103_H12


title: 1772096103_H09


title: 1772096103_F12


title: 1772096103_G09

value: vsm


title: 1772096126_B04

value: N

value: Adcyap1;Tac1 (VMH)


title: 1772096103_E11

value: M


title: 1772096103_G08


title: 1772096103_G01

value: astrocytes


title: 1772096103_E08

value: oligos


title: 1772096103_F07


title: 1772096103_G05

value: endothelial


title: 1772096103_E07


title: 1772096103_E06


title: 1772096103_E03


title: 1772096103_E04


title: 1772096126_A01


title: 1772096103_D11


title: 1772096103_D10


title: 1772096103_D08


title: 1772096103_D07


title: 1772096103_D12


title: 1772096103_D05


title: 1772096103_D09


title: 1772096103_D06

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772096103_D02


title: 1772096103_C06


title: 1772096103_C07


title: 1772096103_C12


title: 1772096103_C09


title: 1772096103_C05


title: 1772096103_C11


title: 1772096103_C04


title: 1772096103_B10

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096103_B06


title: 1772096103_B09


title: 1772096103_B02

value: Hmit+/-


title: 1772096103_B04


title: 1772096103_C08


title: 1772096103_C03


title: 1772096103_B08


title: 1772096103_A09


title: 1772096103_A04


title: 1772096103_B07


title: 1772096103_A05


title: 1772096103_A07


title: 1772096103_B12


title: 1772096102_H04


title: 1772096103_A10


title: 1772096103_A03


title: 1772096102_H07

value: Npvf


title: 1772096102_H06


title: 1772096103_B11


title: 1772096102_H01


title: 1772096102_H02


title: 1772096102_G07


title: 1772096102_G05


title: 1772096102_G01


title: 1772096102_F07


title: 1772096102_F04


title: 1772096102_E04


title: 1772096102_E06


title: 1772096102_E02


title: 1772096102_F01


title: 1772096102_D12


title: 1772096102_B10


title: 1772096102_D06

value: Trh-medium


title: 1772096102_B02


title: 1772096102_A09


title: 1772096102_C06


title: 1772096102_D08


title: 1772096101_H05


title: 1772096101_H10


title: 1772096101_H02


title: 1772096101_H03

value: Avp-high;Gal;Oxt-low


title: 1772096101_G09


title: 1772096101_G10


title: 1772096101_G04


title: 1772096101_G08

value: Galanin


title: 1772096101_G05


title: 1772096101_G03

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096101_F11


title: 1772096102_A06


title: 1772096102_A03


title: 1772096101_F06


title: 1772096102_A01


title: 1772096101_F10


title: 1772096101_F03

value: Avp-medium


title: 1772096101_F05

value: neurons


title: 1772096101_E04


title: 1772096101_E12


title: 1772096101_E02

value: Crh+/-;Gal-low (PVH)


title: 1772096101_E03

value: N


title: 1772096101_H01

value: Vglut2 A


title: 1772096101_D12

value: M


title: 1772096101_D11


title: 1772096101_D08


title: 1772096101_D05


title: 1772096101_D01


title: 1772096101_C12


title: 1772096101_D06

value: astrocytes


title: 1772096101_C05

value: oligos


title: 1772096101_C03


title: 1772096101_C10

value: microglia


title: 1772096101_C07


title: 1772096101_C09


title: 1772096101_B11


title: 1772096101_E06


title: 1772096101_E11


title: 1772096101_E09

value: endothelial


title: 1772096101_E05


title: 1772096101_B07


title: 1772096101_C08


title: 1772096101_B04


title: 1772096101_A04


title: 1772096101_B10


title: 1772096101_A10


title: 1772096101_A05

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096101_A12


title: 1772096101_A03


title: 1772096100_H11


title: 1772096100_H12


title: 1772096100_H10


title: 1772096100_G12

value: vsm


title: 1772096100_G10


title: 1772096101_A01

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772096100_G05


title: 1772096100_G02


title: 1772096100_F10


title: 1772096100_F11


title: 1772096100_F05


title: 1772096100_F01


title: 1772096100_E11


title: 1772096100_F02

value: ependymal


title: 1772096100_E12


title: 1772096100_E06


title: 1772096100_F04


title: 1772096100_E05

value: Trh-medium


title: 1772096100_D08


title: 1772096100_E04


title: 1772096100_D06


title: 1772096100_E03


title: 1772096100_E09


title: 1772096100_D03


title: 1772096100_H05


title: 1772096100_D11


title: 1772096100_C10


title: 1772096100_D05


title: 1772096100_D10


title: 1772096100_C12


title: 1772096100_C09


title: 1772096100_C05


title: 1772096100_E10


title: 1772096100_C02


title: 1772096100_B10


title: 1772096100_C06


title: 1772096100_C03


title: 1772096100_D09


title: 1772096100_B09


title: 1772096100_B08


title: 1772096100_B05


title: 1772096100_B02


title: 1772096100_A10


title: 1772096100_A12


title: 1772096100_B04


title: 1772096100_A05


title: 1772096100_A09


title: 1772096099_H11


title: 1772096099_H12

value: Pomc+/- (ARH)


title: 1772096099_H09


title: 1772096100_A02


title: 1772096099_H04


title: 1772096100_A03

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096099_H10


title: 1772096099_H08


title: 1772096099_H03


title: 1772096099_G10


title: 1772096099_H02

value: GABA 2


title: 1772096099_G03

value: neurons

value: GABA 1


title: 1772096099_G01

value: N

value: Vglut2;Gpr149 (PVH;VMH)


title: 1772096099_F07

value: M


title: 1772096099_E06

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096099_E04

value: oligos


title: 1772096099_E02


title: 1772096099_E12


title: 1772096099_D12


title: 1772096099_D11

value: microglia


title: 1772096099_D10


title: 1772096100_A06


title: 1772096099_D02


title: 1772096099_D04


title: 1772096099_D01

value: uc


title: 1772096099_C11

value: endothelial


title: 1772096099_F11


title: 1772096099_C02


title: 1772096099_C12

value: Trh-low


title: 1772096099_C01


title: 1772096099_F06


title: 1772096099_C10

value: astrocytes


title: 1772096099_C04


title: 1772096099_E11


title: 1772096099_B04


title: 1772096099_B05


title: 1772096099_B02


title: 1772096099_B08


title: 1772096099_B03


title: 1772096099_A11


title: 1772096099_B12


title: 1772096099_A09


title: 1772096099_B10


title: 1772096099_B01


title: 1772096099_A10


title: 1772096099_A04


title: 1772096099_A01


title: 1772096099_A02


title: 1772096099_A03

value: Per2;circadian (SCH)


title: 1772096097_H10

value: Y


title: 1772096099_C07


title: 1772096099_E10


title: 1772096097_H02

value: Vglut2 A


title: 1772096097_G12


title: 1772096097_G06


title: 1772096097_G01


title: 1772096097_F12


title: 1772096097_G08

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096097_F06


title: 1772096099_C06

value: vsm


title: 1772096097_F03


title: 1772096097_F08

value: neurons

value: Hmit+/-


title: 1772096097_E02


title: 1772096097_E04


title: 1772096097_D09


title: 1772096097_D10


title: 1772096097_D08


title: 1772096097_C12


title: 1772096097_E06


title: 1772096097_D05


title: 1772096097_C11


title: 1772096097_B10


title: 1772096097_B05


title: 1772096097_C05


title: 1772096097_C04


title: 1772096097_C09


title: 1772096097_A11

value: Npy;Agrp (ARH)


title: 1772096097_A06

value: Avp-high;Gal;Oxt-low


title: 1772096097_B02

value: M

value: ependymal


title: 1772096097_A02

value: oligos


title: 1772096096_H12


title: 1772096097_F04


title: 1772096096_G06


title: 1772096097_E10


title: 1772096096_F03

value: Pomc+/- (ARH)


title: 1772096096_E10


title: 1772096096_E11


title: 1772096096_F04


title: 1772096096_E06


title: 1772096096_D12


title: 1772096096_D07


title: 1772096096_D06

value: uc


title: 1772096096_E04


title: 1772096096_D10


title: 1772096096_D05

value: Adcyap1;Tac1 (VMH)


title: 1772096096_D08

value: Avp-high;Oxt-low


title: 1772096096_C11

value: endothelial


title: 1772096096_C10


title: 1772096096_B12

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096097_A09

value: Y


title: 1772096096_C09


title: 1772096096_B10


title: 1772096096_D11


title: 1772096096_B07

value: Hcrt


title: 1772096096_B05

value: astrocytes


title: 1772096096_B04


title: 1772096096_F06


title: 1772096097_E12

value: vsm


title: 1772096096_H05

value: neurons

value: Gad-low;Gnrh-/+


title: 1772096096_B03

value: microglia


title: 1772096096_B02

value: Vip;Grp+/-;circadian (SCH)


title: 1772096096_B01

value: M


title: 1772092013_H07

value: F

value: N


title: 1772096096_A12

value: oligos


title: 1772092013_G12

value: ependymal


title: 1772096096_D04


title: 1772092013_H02


title: 1772096096_D03


title: 1772092013_G09


title: 1772096096_B09


title: 1772092013_G06


title: 1772092013_F04


title: 1772092013_F02


title: 1772092013_F09


title: 1772092013_F10


title: 1772092013_F08


title: 1772092013_G03


title: 1772092013_E12


title: 1772092013_E10


title: 1772092013_E03


title: 1772092013_E04


title: 1772092013_D11


title: 1772092013_D10


title: 1772092013_E02


title: 1772092013_D04


title: 1772092013_H04


title: 1772092013_C10


title: 1772092013_C12


title: 1772092013_G02


title: 1772092013_B12

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772092013_C05


title: 1772092013_G11


title: 1772092013_F01


title: 1772092013_C02


title: 1772092013_C11


title: 1772092013_B11

value: Sst low-medium


title: 1772092013_B08


title: 1772092013_B03

value: endothelial


title: 1772092013_A05


title: 1772092013_A03


title: 1772092013_C08


title: 1772092013_A09


title: 1772092013_E11


title: 1772092013_A08


title: 1772092013_A10


title: 1772092013_A01


title: 1772092012_H10


title: 1772092012_H12


title: 1772092012_H04


title: 1772092013_C04


title: 1772092012_H05


title: 1772092012_H01


title: 1772092012_G12


title: 1772092012_G10


title: 1772092012_G09


title: 1772092012_G08


title: 1772092013_B02


title: 1772092012_G04


title: 1772092012_G06


title: 1772092012_G03


title: 1772092012_G05


title: 1772092012_F11


title: 1772092012_F06


title: 1772092012_E05


title: 1772092012_F10


title: 1772092012_F01


title: 1772092012_E11


title: 1772092012_E09


title: 1772092012_E08


title: 1772092012_F04


title: 1772092012_E04


title: 1772092012_E06


title: 1772092012_F08


title: 1772092012_D12


title: 1772092012_D11


title: 1772092012_D03


title: 1772092012_C01


title: 1772092012_C09


title: 1772092012_C04


title: 1772092012_B10


title: 1772092012_D07


title: 1772092012_C11


title: 1772092012_B07


title: 1772092012_E07


title: 1772092012_B03


title: 1772092012_B05

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772092012_B06


title: 1772092012_A12


title: 1772092012_B02


title: 1772092012_B01


title: 1772092012_A10

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772092011_H12

value: Y


title: 1772092011_H10


title: 1772092012_A02


title: 1772092012_A04


title: 1772092012_A03


title: 1772092011_G10


title: 1772092011_G06

value: Sst-medium;Cartpt


title: 1772092012_A07

value: uc


title: 1772092011_G09


title: 1772092011_G12


title: 1772092011_G04


title: 1772092011_G05


title: 1772092011_G01

value: neurons


title: 1772092011_F01

value: Pomc+/- (ARH)


title: 1772092011_F03


title: 1772092011_F02


title: 1772092011_F04


title: 1772092011_G02


title: 1772092011_F10


title: 1772092011_E10

value: astrocytes


title: 1772092011_E09


title: 1772092012_D06


title: 1772092011_E03

value: Trh-medium


title: 1772092011_D09

value: M


title: 1772092011_D12


title: 1772092011_C11


title: 1772092011_D01


title: 1772092011_D05


title: 1772092011_C12


title: 1772092011_C03

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772092011_C05


title: 1772092011_B05


title: 1772092011_B07


title: 1772092011_B11


title: 1772092011_B04


title: 1772092011_B09


title: 1772092011_A11


title: 1772092011_A09


title: 1772092011_A08


title: 1772092010_H10


title: 1772092010_H06


title: 1772092010_H12


title: 1772092011_A02


title: 1772092010_H05


title: 1772092010_G05


title: 1772092010_G11

value: Avp-high;Oxt-low


title: 1772092011_C10


title: 1772092011_C06


title: 1772092011_C07

value: Npy;Agrp (ARH)


title: 1772092010_G04

value: ependymal


title: 1772092010_F11


title: 1772092010_E10


title: 1772096096_A05


title: 1772092010_G01

value: vsm


title: 1772092010_E03

value: oligos


title: 1772092010_E01


title: 1772092010_F06


title: 1772092010_D11


title: 1772092010_E08

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772092010_D05


title: 1772092010_D06

value: endothelial


title: 1772092011_A01


title: 1772092010_D03


title: 1772092010_C12


title: 1772092010_C11


title: 1772092010_C07


title: 1772092010_C06


title: 1772092010_C04


title: 1772092010_C05


title: 1772092010_C03


title: 1772092010_H03


title: 1772092010_B07


title: 1772092010_B06


title: 1772092010_B04


title: 1772092010_E07


title: 1772092010_D12


title: 1772092010_A05


title: 1772092009_H01

value: F

value: N


title: 1772092010_A01

value: Y


title: 1772092010_A08


title: 1772092010_A12


title: 1772092010_A03


title: 1772092010_A11


title: 1772092009_G01


title: 1772092009_G05


title: 1772092009_F07


title: 1772092009_E12


title: 1772092009_E06


title: 1772092009_G07


title: 1772092009_F02


title: 1772092009_E04


title: 1772092009_E01


title: 1772092009_E02


title: 1772092009_D10


title: 1772092009_D02


title: 1772092009_D06


title: 1772092010_B12


title: 1772092009_C09


title: 1772092009_D09


title: 1772092010_D04


title: 1772092009_C02


title: 1772092009_B12


title: 1772092009_C05


title: 1772092009_B09

value: Vip;Grp+/-;circadian (SCH)


title: 1772092009_B06


title: 1772092009_F03


title: 1772092009_B01


title: 1772092009_A10


title: 1772092009_A01

value: microglia


title: 1772092009_A02


title: 1772092008_H03

value: neurons

value: GABA 2


title: 1772092009_A12


title: 1772092008_H02


title: 1772092008_H06

value: Crh+/-;Gal-low (PVH)


title: 1772092008_H11


title: 1772092008_H10


title: 1772092008_G10


title: 1772092009_A08

value: Pomc+/- (ARH)


title: 1772092008_G11


title: 1772092008_G02

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772092008_F11


title: 1772092008_G01


title: 1772092008_G04


title: 1772092008_F07


title: 1772092008_F10


title: 1772092008_G03


title: 1772092008_F06


title: 1772092008_F02

value: Avp-high;Gal;Oxt-low


title: 1772092008_E12


title: 1772092008_E11


title: 1772092008_F05


title: 1772092008_F01


title: 1772092008_E08


title: 1772092008_E07


title: 1772092008_G05


title: 1772092008_D06


title: 1772092008_E02


title: 1772092008_G08


title: 1772092008_E03


title: 1772092008_E04


title: 1772092008_D10


title: 1772092008_D03


title: 1772092008_E06

value: astrocytes


title: 1772092008_D11


title: 1772092008_C06

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772092008_E10


title: 1772092008_C07

value: ependymal


title: 1772092008_C04

value: oligos


title: 1772092008_A12


title: 1772092008_B12


title: 1772092008_B05


title: 1772092008_C02


title: 1772092008_B06


title: 1772092008_B07

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772092008_B02


title: 1772092008_A11


title: 1772092008_A10


title: 1772092008_B01

value: endothelial


title: 1772092008_A08

value: F


title: 1772092008_A07

value: N


title: 1772092008_A05


title: 1772092008_A01

value: vsm


title: 1772092005_H12

value: M

value: Y


title: 1772092005_H06


title: 1772092008_C12


title: 1772092005_H03

value: neurons

value: uc


title: 1772092005_G12


title: 1772092005_G05

value: Sst low-medium


title: 1772092005_G01

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772092005_G07


title: 1772092005_F06

value: microglia


title: 1772092005_H04

value: Avp-high;Oxt-low


title: 1772092005_F10


title: 1772092005_F08

value: Trh-low


title: 1772092005_F09


title: 1772092005_F05

value: Pomc+/- (ARH)


title: 1772092005_F04

value: ependymal


title: 1772092005_E12


title: 1772092005_F01


title: 1772092005_E04

value: oligos


title: 1772092005_E02


title: 1772092005_D09


title: 1772092005_D10

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772092005_D03

value: endothelial


title: 1772092005_D05


title: 1772092005_D02

value: Per2;circadian (SCH)


title: 1772092005_B12

value: Crh+/-;Gal-low (PVH)


title: 1772092005_C01


title: 1772092005_B11

value: astrocytes


title: 1772092005_C04

value: M


title: 1772092005_F03

value: Y


title: 1772092005_B10

value: neurons

value: Hmit+/-


title: 1772092005_B02


title: 1772092005_C03


title: 1772092005_B08


title: 1772092005_A09

value: Vglut2;Gpr149 (PVH;VMH)


title: 1772092005_B01


title: 1772092005_A10

value: Avp-medium


title: 1772092005_E01

value: microglia


title: 1772092005_B06


title: 1772092004_H10


title: 1772092005_A05


title: 1772092005_A08


title: 1772092005_D11

value: Pmch


title: 1772092005_A02


title: 1772092004_G10


title: 1772092004_F09


title: 1772092005_D01

value: uc


title: 1772092004_G04


title: 1772092004_F02


title: 1772092004_E11


title: 1772092004_F05


title: 1772092004_E12


title: 1772092005_A06

value: Trh-medium


title: 1772092004_E02


title: 1772092004_E01

value: ependymal


title: 1772092004_E09


title: 1772092004_D11

value: oligos


title: 1772092004_D02


title: 1772092004_C08


title: 1772092004_D08


title: 1772092004_H04


title: 1772092004_D04


title: 1772092004_B06


title: 1772092004_D09

value: Trh-low


title: 1772092004_H05


title: 1772092004_B11


title: 1772092004_C02


title: 1772092004_B04


title: 1772092004_B09


title: 1772092004_B03


title: 1772092004_B07


title: 1772092004_A06


title: 1772092004_A05


title: 1772089196_G11

value: endothelial


title: 1772089196_H02


title: 1772089196_G03


title: 1772089196_G02


title: 1772089196_G01


title: 1772089196_F10


title: 1772092004_C04


title: 1772089196_F01


title: 1772089196_E11


title: 1772092004_C01


title: 1772092004_B08


title: 1772089196_E10


title: 1772089196_E09


title: 1772089196_D03


title: 1772089196_D06


title: 1772089196_C04

value: vsm


title: 1772089196_C02


title: 1772089196_E02


title: 1772089196_B01


title: 1772089196_B02


title: 1772089196_A11


title: 1772089196_A05


title: 1772089195_H06


title: 1772089195_H05


title: 1772089195_F02


title: 1772089196_A01


title: 1772089195_G06


title: 1772089196_A09


title: 1772089195_E12


title: 1772089195_F10


title: 1772089195_E06


title: 1772089196_G08


title: 1772089196_F06


title: 1772089195_D09


title: 1772089195_E03


title: 1772089196_E01


title: 1772089195_D12


title: 1772089195_D07


title: 1772089195_E05


title: 1772089196_D02


title: 1772089195_D03


title: 1772089195_C10


title: 1772089195_C09


title: 1772089195_C02


title: 1772089195_B12


title: 1772089195_G10


title: 1772089195_B02


title: 1772089195_B04


title: 1772089195_A07


title: 1772089195_A04


title: 1772089194_H06


title: 1772089195_B10


title: 1772089195_B11


title: 1772089194_H04


title: 1772089195_A12


title: 1772089194_H02


title: 1772089194_G12


title: 1772089194_F11


title: 1772089194_F08


title: 1772089194_F05


title: 1772089194_F04


title: 1772089194_F03


title: 1772089194_E10


title: 1772089194_E05


title: 1772089194_E07


title: 1772089194_E04


title: 1772089194_D08


title: 1772089194_D06


title: 1772089194_D12


title: 1772089194_D03


title: 1772089194_C11


title: 1772089194_C05


title: 1772089194_C09


title: 1772089194_C02


title: 1772089194_B07


title: 1772089194_C03


title: 1772089194_B03


title: 1772089194_B01


title: 1772089194_B09


title: 1772089194_G09


title: 1772089194_A08


title: 1772089194_H03


title: 1772089194_C01


title: 1772089194_A07


title: 1772089194_B08


title: 1772089194_B11


title: 1772089194_A03


title: 1772089194_A02


title: 1772089194_A01


title: 1772089194_A04


title: 1772089190_H10


title: 1772089190_H06


title: 1772089190_G11


title: 1772089190_H04


title: 1772089190_G06


title: 1772089190_G05


title: 1772089190_G02


title: 1772089190_G08

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772089190_F10


title: 1772089190_F12


title: 1772089190_E12


title: 1772089190_F06

value: astrocytes


title: 1772089190_F11

value: M


title: 1772089190_E03

value: Y


title: 1772089190_E04


title: 1772089190_E08


title: 1772089190_D11


title: 1772089190_D01


title: 1772089190_C11


title: 1772089190_C02


title: 1772089190_C12


title: 1772089190_C06


title: 1772089190_C01


title: 1772089190_B07


title: 1772089190_C04


title: 1772089190_B05


title: 1772089190_B06


title: 1772089190_B04


title: 1772089190_B02


title: 1772089190_B03


title: 1772089190_A01


title: 1772089190_A08


title: 1772089190_A11


title: 1772089190_A02


title: 1772089190_A04


title: 1772089188_G12


title: 1772089188_G05


title: 1772089188_G04


title: 1772089188_F07


title: 1772089188_F11


title: 1772089188_E01


title: 1772089188_E10


title: 1772089188_E11


title: 1772089188_D06


title: 1772089188_C06


title: 1772089190_B08


title: 1772089188_B11


title: 1772089188_D10


title: 1772089188_C05

value: neurons

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772089188_E05


title: 1772089188_B10


title: 1772089188_B04


title: 1772089187_H11


title: 1772089187_H10


title: 1772089188_H10


title: 1772089187_F10


title: 1772089187_G05


title: 1772089187_H06


title: 1772089187_G11


title: 1772089187_F05


title: 1772089187_F06


title: 1772089188_G11


title: 1772089188_C12


title: 1772089187_E12


title: 1772089187_E10

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772089187_E05


title: 1772089188_A05


title: 1772089187_E01


title: 1772089187_E04


title: 1772089187_C09


title: 1772089187_D12


title: 1772089187_B10


title: 1772089187_H07


title: 1772089187_D05


title: 1772089187_B06


title: 1772089187_B04


title: 1772089187_B05


title: 1772089187_A12


title: 1772089187_A08


title: 1772089187_A10


title: 1772089188_D02


title: 1772089187_A06


title: 1772089187_A07


title: 1772089187_F04


title: 1772089186_G10


title: 1772089186_H03


title: 1772089186_H10


title: 1772089186_H06


title: 1772089186_G09


title: 1772089187_C04


title: 1772089187_C03


title: 1772089186_G06


title: 1772089186_F12


title: 1772089186_F03


title: 1772089186_E09


title: 1772089186_E10


title: 1772089186_E11


title: 1772089186_F02


title: 1772089186_D12


title: 1772089186_D07


title: 1772089186_D11


title: 1772089186_D02


title: 1772089186_C12


title: 1772089186_D09


title: 1772089186_D04


title: 1772089186_C09


title: 1772089186_C11


title: 1772089186_C08


title: 1772089186_C06


title: 1772089186_C07


title: 1772089186_C02


title: 1772089186_B10


title: 1772089186_C03

value: Npvf


title: 1772089186_B03


title: 1772089186_B01


title: 1772089186_A10


title: 1772089186_G05


title: 1772089186_A05

value: Per2;circadian (SCH)


title: 1772089186_A08


title: 1772084021_H05

value: F

value: N


title: 1772089186_A04


title: 1772089186_B05


title: 1772084021_H12


title: 1772089186_C01


title: 1772084021_H01

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772084021_G12


title: 1772084021_G04


title: 1772084021_G06


title: 1772084021_G10


title: 1772084021_G03

value: Galanin


title: 1772084021_F12


title: 1772084021_G09

value: oligos


title: 1772084021_F11

value: ependymal


title: 1772084021_F10


title: 1772089186_B11


title: 1772089187_D10


title: 1772084021_F09


title: 1772084021_F05

value: Trh-medium


title: 1772084021_F06

value: uc


title: 1772084021_F07


title: 1772084021_F04


title: 1772084021_F01

value: Oxt;Avp-low


title: 1772084021_F02


title: 1772084021_E12


title: 1772084021_E10

value: Trh-low


title: 1772084021_E11


title: 1772084021_H04


title: 1772084021_E04


title: 1772084021_E03


title: 1772084021_E02

value: astrocytes


title: 1772084021_E05


title: 1772084021_E06


title: 1772084021_D12


title: 1772084021_D08


title: 1772084021_D06

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772084021_D07

value: neurons


title: 1772084021_D03


title: 1772084021_C10

value: endothelial


title: 1772084021_D05


title: 1772084021_C11


title: 1772084021_C09

value: Hcrt


title: 1772084021_C08


title: 1772084021_B11


title: 1772084021_C06


title: 1772084021_B08

value: Adcyap1;Tac1 (VMH)


title: 1772084021_B07


title: 1772084021_B10

value: Vglut2;Col9a2 (PVH)


title: 1772084021_B05

value: F


title: 1772084021_B06

value: N


title: 1772084021_B09


title: 1772084021_B03


title: 1772084021_A12


title: 1772084021_A11


title: 1772084021_A08


title: 1772084021_B01


title: 1772084021_B04

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772084021_B02


title: 1772084021_A07


title: 1772084021_E01


title: 1772084020_H12

value: GABA 2


title: 1772084020_G03


title: 1772084020_F08

value: oligos


title: 1772084020_E11


title: 1772084020_E08

value: Pomc+/- (ARH)


title: 1772084020_F06


title: 1772084020_E06


title: 1772084020_C06


title: 1772084020_D04


title: 1772084020_D05


title: 1772084020_C10


title: 1772084020_E02


title: 1772084020_E07


title: 1772084020_B12

value: Avp-high;Gal;Oxt-low


title: 1772084020_B10


title: 1772084020_B02


title: 1772084020_G05


title: 1772084020_H05


title: 1772084020_G12

value: Trh-medium


title: 1772084020_A06


title: 1772084020_A01


title: 1772084017_H11


title: 1772084020_A10


title: 1772084017_H12


title: 1772084017_H10


title: 1772084020_B04


title: 1772084020_F11


title: 1772084020_F12


title: 1772084017_H04


title: 1772084017_H02

value: Oxt;Avp-low


title: 1772084017_G10

value: Per2;circadian (SCH)


title: 1772084017_G12

value: microglia


title: 1772084017_G09


title: 1772084017_G04


title: 1772084020_B05


title: 1772084017_G07

value: Trh-low


title: 1772084017_F09

value: neurons

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772084017_F12

value: ependymal


title: 1772084017_F10

value: Npvf


title: 1772084017_F07


title: 1772084017_F04


title: 1772084017_F03


title: 1772084017_E12


title: 1772084017_E08

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772084017_E11

value: F

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772084017_F05

value: N


title: 1772084017_E06

value: uc


title: 1772084017_H07


title: 1772084017_D05

value: oligos


title: 1772084017_D11

value: endothelial


title: 1772084017_D04


title: 1772084017_D03


title: 1772084017_D08

value: Sst low-medium


title: 1772084017_E05


title: 1772084017_E04

value: Sst-medium;Cartpt


title: 1772084017_C11

value: Crh+/-;Gal-low (PVH)


title: 1772084017_C07


title: 1772084017_C10


title: 1772084017_F11


title: 1772084017_G02


title: 1772084017_C05

value: Hmit+/-


title: 1772084017_C03

value: Avp-high;Gal;Oxt-low


title: 1772084017_C02


title: 1772084017_C01

value: astrocytes


title: 1772084017_B08

value: neurons

value: Adcyap1;Tac1 (VMH)


title: 1772089187_A03

value: M

value: Y


title: 1772084017_B10


title: 1772084017_B04

value: ependymal


title: 1772084017_B03

value: F


title: 1772084017_B01


title: 1772084017_B02


title: 1772084017_C12


title: 1772084017_A07


title: 1772084017_A03


title: 1772084017_A05


title: 1772084017_A04

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772084017_A01

value: N


title: 1772084014_G06

value: Gad-low;Gnrh-/+


title: 1772084014_H10


title: 1772084014_G05

value: Trh-low


title: 1772084014_F08

value: oligos


title: 1772084017_C09

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772084014_E08

value: Npvf


title: 1772084014_H07


title: 1772084014_F07


title: 1772084014_D04

value: Avp-high;Oxt-low


title: 1772084014_D08

value: endothelial


title: 1772084014_D03


title: 1772084014_C11

value: microglia


title: 1772084017_B06

value: uc


title: 1772084014_D01


title: 1772084014_C09


title: 1772084017_A11

value: neurons

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772084014_E02

value: vsm


title: 1772084014_D12


title: 1772084014_C08

value: Hmit+/-


title: 1772084014_C01

value: Galanin


title: 1772084014_C06

value: F

value: astrocytes


title: 1772084014_B12

value: N


title: 1772084014_B10


title: 1772084014_B08

value: Pomc+/- (ARH)


title: 1772084017_B05

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772084014_A08

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772084014_B11

value: oligos


title: 1772084014_B09


title: 1772084014_B05


title: 1772084014_B04


title: 1772084014_B01


title: 1772078031_H11

value: ependymal


title: 1772084014_A10


title: 1772084014_A04

value: Avp-high;Gal;Oxt-low


title: 1772078031_H12


title: 1772078031_H01


title: 1772078031_G11


title: 1772078031_H08


title: 1772078031_H10

value: endothelial


title: 1772078031_H07


title: 1772078031_G12


title: 1772078031_G10


title: 1772078031_G08

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772078031_G02

value: uc


title: 1772078031_G07


title: 1772078031_F06

value: microglia


title: 1772078031_G06

value: neurons

value: Crh+/-;Gal-low (PVH)


title: 1772078031_E10


title: 1772078031_G05


title: 1772078031_G01


title: 1772078031_F10


title: 1772078031_F04

value: Adcyap1;Tac1 (VMH)


title: 1772078031_F11


title: 1772078031_D07


title: 1772078031_D05


title: 1772078031_F03

value: Per2;circadian (SCH)


title: 1772078031_F01

value: F


title: 1772084014_A01

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772078031_E12

value: N


title: 1772078031_E07


title: 1772078031_E05


title: 1772078031_E02


title: 1772078031_D12

value: GABA 2


title: 1772078031_B06


title: 1772078031_A12


title: 1772078031_B05


title: 1772078031_A08


title: 1772078031_D06


title: 1772078031_A06


title: 1772078031_C07


title: 1772078031_C11


title: 1772078031_C06


title: 1772078031_A03


title: 1772078031_A05


title: 1772078031_C03


title: 1772078030_G12

value: Npy;Agrp (ARH)


title: 1772078030_G11


title: 1772078030_H02


title: 1772078030_G08

value: Trh-medium


title: 1772078031_C08

value: oligos


title: 1772078031_D10

value: ependymal


title: 1772078031_C01


title: 1772078030_G05


title: 1772078031_B09


title: 1772078031_B12

value: vsm


title: 1772078031_B08


title: 1772078031_A11


title: 1772078030_F12


title: 1772078031_B04


title: 1772078030_F11


title: 1772078031_A10


title: 1772078030_F08


title: 1772078030_F07


title: 1772078030_G06


title: 1772078030_H06


title: 1772078030_G01


title: 1772078030_F06


title: 1772078031_A04


title: 1772078030_F05


title: 1772078030_E11


title: 1772078030_E10


title: 1772078030_E08


title: 1772078030_E09


title: 1772078030_D04

value: Hmit+/-


title: 1772078030_D12

value: astrocytes


title: 1772078030_D11


title: 1772078030_D01


title: 1772078030_E04


title: 1772078030_E07


title: 1772078030_C12


title: 1772078030_D03

value: endothelial


title: 1772078030_F01


title: 1772078030_E06


title: 1772078030_E01


title: 1772078030_B12


title: 1772078030_B07

value: uc


title: 1772078030_C11


title: 1772078030_C07


title: 1772078030_C09


title: 1772078030_C05


title: 1772078030_C02


title: 1772078030_B09

value: neurons


title: 1772078030_C01


title: 1772078030_D06


title: 1772078030_B06


title: 1772078030_D08

value: Vglut2 A


title: 1772078030_B04


title: 1772078030_A06


title: 1772078030_A04


title: 1772078030_A09


title: 1772078030_B01


title: 1772078030_B03


title: 1772078029_H07


title: 1772078030_A07


title: 1772078029_H10


title: 1772078030_B08


title: 1772078030_B11


title: 1772078030_C04


title: 1772078029_H06


title: 1772078030_A05


title: 1772078029_G12


title: 1772078029_H04


title: 1772078030_A02


title: 1772078029_F12


title: 1772078029_F11


title: 1772078029_H01

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772078029_F05


title: 1772078029_G08


title: 1772078029_E12


title: 1772078029_F10


title: 1772078030_A01


title: 1772078030_A08


title: 1772078029_H12


title: 1772078030_B05


title: 1772078029_E07

value: Trh-low


title: 1772078029_E08

value: F


title: 1772078029_E11


title: 1772078029_E05

value: Galanin


title: 1772078029_E10

value: N

value: Avp-high;Gal;Oxt-low


title: 1772078029_E04


title: 1772078029_D09

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772078029_D12


title: 1772078029_D11


title: 1772078029_E09


title: 1772078029_D03


title: 1772078029_D10


title: 1772078029_E06


title: 1772078029_D05

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772078029_C08


title: 1772078029_G10

value: oligos


title: 1772078029_G11


title: 1772078029_C05


title: 1772078029_C09

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772078029_C04


title: 1772078029_B06


title: 1772078029_C06


title: 1772078029_B04


title: 1772078029_A12


title: 1772078029_C03


title: 1772078029_B11


title: 1772078029_B08


title: 1772078028_H12

value: microglia


title: 1772078029_B05

value: GABA 2


title: 1772078029_A10


title: 1772078029_B07


title: 1772078028_H10


title: 1772078029_B01


title: 1772078028_H09


title: 1772078028_H03


title: 1772078028_H05


title: 1772078028_H01


title: 1772078028_G03


title: 1772078028_G12


title: 1772078028_G11


title: 1772078028_G08


title: 1772078028_G05


title: 1772078029_A03

value: ependymal


title: 1772078028_F01

value: Sst low-medium


title: 1772078028_G04


title: 1772078028_F12

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772078028_F10

value: endothelial


title: 1772078028_E11

value: neurons

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772078028_H06


title: 1772078028_F04


title: 1772078028_F08

value: Crh+/-;Gal-low (PVH)


title: 1772078028_F06

value: F


title: 1772078028_F11


title: 1772078028_E07


title: 1772078028_F03


title: 1772078028_E09

value: Avp-high;Oxt-low


title: 1772078028_E04

value: N


title: 1772078028_E08

value: astrocytes


title: 1772078028_E12

value: Trh-medium


title: 1772078028_E10

value: Galanin


title: 1772078028_D08


title: 1772078028_E06

value: Qrfp


title: 1772078028_E01


title: 1772078028_E05

value: oligos


title: 1772078028_D12


title: 1772078028_D05

value: uc


title: 1772078028_D11


title: 1772078028_C10


title: 1772078028_D04

value: GABA 1


title: 1772078028_D03

value: Oxt;Avp-low


title: 1772078028_C11


title: 1772078028_C06


title: 1772078028_C08


title: 1772078028_D02


title: 1772078028_D06


title: 1772078028_C04


title: 1772078028_C12

value: Vglut2;Gpr149 (PVH;VMH)


title: 1772078028_C05


title: 1772078028_B09

value: ependymal


title: 1772078028_B06


title: 1772078028_C02

value: Sst low-medium


title: 1772078028_B11


title: 1772078028_B08

value: neurons

value: Adcyap1;Tac1 (VMH)


title: 1772078028_A12


title: 1772078028_A11


title: 1772078028_A09


title: 1772078028_A05


title: 1772078028_A04


title: 1772078023_H11

value: M


title: 1772078023_H10


title: 1772078028_A02

value: F


title: 1772078023_H08

value: Trh-low


title: 1772078023_H06

value: N

value: endothelial


title: 1772078023_G12


title: 1772078028_B10


title: 1772078023_G01


title: 1772078023_F06


title: 1772078023_G03

value: Avp-high;Oxt-low


title: 1772078023_E11


title: 1772078023_E09


title: 1772078023_E06


title: 1772078023_D11


title: 1772078023_E08


title: 1772078023_D10


title: 1772078023_D06

value: Nms;VIP+/-;Avp-low+/-;circadian (SCH)


title: 1772078023_D04


title: 1772078023_E04

value: microglia


title: 1772078023_C05

value: astrocytes


title: 1772078023_C11

value: uc


title: 1772078023_C08


title: 1772078028_B03


title: 1772078023_B10

value: Galanin


title: 1772078028_A07

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772078023_B11

value: oligos


title: 1772078023_B09

value: ependymal


title: 1772078023_B08


title: 1772078023_B07


title: 1772078023_G11


title: 1772078023_F12


title: 1772078023_F05


title: 1772078023_B02


title: 1772078023_A05

value: GABA 1


title: 1772078022_H12

value: neurons


title: 1772078023_A09


title: 1772078023_A04


title: 1772078022_H03


title: 1772078022_H06


title: 1772078022_H02


title: 1772078023_A10


title: 1772078022_G07


title: 1772078022_G12

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772078022_G02

value: M

value: Npy;Agrp (ARH)


title: 1772078022_F11


title: 1772078022_F06


title: 1772078022_F08

value: Gad-low;Gnrh-/+


title: 1772078022_F05

value: N


title: 1772078022_F04


title: 1772078022_F02


title: 1772078022_E06

value: endothelial


title: 1772078022_E04


title: 1772078023_B03


title: 1772078022_E03


title: 1772078022_E11


title: 1772078023_A11


title: 1772078022_D08

value: vsm


title: 1772078022_E01

value: Hcrt


title: 1772078022_D06


title: 1772078022_H05


title: 1772078022_D05


title: 1772078022_G04


title: 1772078022_C11


title: 1772078022_C10


title: 1772078022_C08


title: 1772078022_D01


title: 1772078022_C06


title: 1772078022_D03


title: 1772078022_B08


title: 1772078022_D04


title: 1772078022_D02


title: 1772078022_C05


title: 1772078022_B06


title: 1772078022_B12


title: 1772078022_B03


title: 1772078022_A12

value: Trh-medium


title: 1772078022_B02


title: 1772078022_B10


title: 1772078022_A02


title: 1772078022_A01


title: 1772078019_H05


title: 1772078019_H04


title: 1772078022_A07


title: 1772078019_H01


title: 1772078019_G10

value: microglia


title: 1772078019_G11


title: 1772078022_C03


title: 1772078022_B11


title: 1772078019_G05


title: 1772078019_F09


title: 1772078019_F11

value: astrocytes


title: 1772078019_F08


title: 1772078019_F04


title: 1772078019_E12


title: 1772078019_F01


title: 1772078019_E10


title: 1772078019_E06


title: 1772078022_B01


title: 1772078019_E01


title: 1772078019_E11


title: 1772078019_D01


title: 1772078019_C05


title: 1772078022_A04

value: uc


title: 1772078019_D07


title: 1772078019_D11


title: 1772078019_C12


title: 1772078019_B07


title: 1772078019_C11


title: 1772078019_A12


title: 1772078019_B03


title: 1772078019_C10


title: 1772078019_B04


title: 1772078019_D12


title: 1772078019_C08


title: 1772078019_A05


title: 1772078019_B10


title: 1772078019_A08


title: 1772078019_A01


title: 1772078019_A09


title: 1772078019_B12


title: 1772078018_H03


title: 1772078019_D10


title: 1772078018_H02


title: 1772078019_E02


title: 1772078018_H05


title: 1772078019_A04


title: 1772078019_A03


title: 1772078018_H04


title: 1772078018_G09

value: Avp-high;Gal;Oxt-low


title: 1772078018_H08

value: oligos


title: 1772078018_G04


title: 1772078018_G07


title: 1772078018_G03


title: 1772078019_A07


title: 1772078018_G11


title: 1772078018_G02


title: 1772078018_H01


title: 1772078018_G01

value: ependymal


title: 1772078018_F08


title: 1772078018_F06


title: 1772078018_F05


title: 1772078018_F03


title: 1772078018_E05


title: 1772078018_F04


title: 1772078018_E06


title: 1772078018_E10


title: 1772078018_E04


title: 1772078018_E01

value: Sst low-medium


title: 1772078018_D12


title: 1772078018_E02


title: 1772078018_D10


title: 1772078018_D07


title: 1772078018_D08

value: neurons


title: 1772078018_D03

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772078018_D05

value: M


title: 1772078018_C09


title: 1772078018_C05


title: 1772078018_C06


title: 1772078018_D01

value: Trh-low


title: 1772078018_C04

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772078018_C10

value: N


title: 1772078018_C02


title: 1772078018_B12


title: 1772078018_B10


title: 1772078018_B11

value: Crh+/-;Gal-low (PVH)


title: 1772078018_C01


title: 1772078018_B09


title: 1772078018_B06


title: 1772078018_B04


title: 1772078018_A11


title: 1772078018_B07


title: 1772078018_B02


title: 1772078018_D06


title: 1772078018_A09


title: 1772078018_A06


title: 1772078018_A02


title: 1772078018_B03


title: 1772078028_F05

value: F


title: 1772078018_A07

value: Npy;Agrp (ARH)


title: 1772078017_H12


title: 1772078018_A04

value: Avp-medium


title: 1772078017_H07


title: 1772078017_H05

value: Hmit+/-


title: 1772078017_G12


title: 1772078017_H02


title: 1772078017_H10


title: 1772078017_G06


title: 1772078017_G09

value: astrocytes


title: 1772078017_G04


title: 1772078017_F12


title: 1772078018_C03

value: microglia


title: 1772078017_F10


title: 1772078017_F11


title: 1772078017_F07


title: 1772078017_F03


title: 1772078017_F01


title: 1772078017_E11


title: 1772078017_E09

value: endothelial


title: 1772078017_E06

value: oligos


title: 1772078017_H06


title: 1772078017_E05


title: 1772078017_F04

value: ependymal


title: 1772078017_H04


title: 1772078017_E08


title: 1772078017_E04

value: Trh-medium


title: 1772078017_E02


title: 1772078017_E01


title: 1772078017_D08

value: neurons

value: uc


title: 1772078017_D09

value: M


title: 1772078017_D10

value: Gad-low;Gnrh-/+


title: 1772078017_D12


title: 1772078017_D04


title: 1772078017_D05

value: GABA 1


title: 1772078017_D02

value: N

value: Sst-medium;Cartpt


title: 1772078017_C12


title: 1772078017_F05


title: 1772078017_D01


title: 1772078017_E12


title: 1772078017_E10


title: 1772078017_C11


title: 1772078017_C06


title: 1772078017_B12


title: 1772078017_E07


title: 1772078017_E03


title: 1772078017_B11


title: 1772078017_B09


title: 1772078017_B08

value: GABA 2


title: 1772078017_B07


title: 1772078017_D06


title: 1772078017_B05


title: 1772078017_B01


title: 1772078017_A10


title: 1772078017_A09

value: vsm


title: 1772078017_A06


title: 1772078017_B04


title: 1772078017_A05


title: 1772078016_H12


title: 1772078017_A04


title: 1772078016_H10


title: 1772078017_A02


title: 1772078016_H05


title: 1772078016_G12


title: 1772078016_H11


title: 1772078017_A03


title: 1772078016_H02


title: 1772078016_G08


title: 1772078016_G04


title: 1772078016_H03


title: 1772078016_G03


title: 1772078016_G01


title: 1772078017_C10


title: 1772078016_F06

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772078016_G02


title: 1772078016_F08


title: 1772078016_F10


title: 1772078016_F05


title: 1772078016_F04


title: 1772078016_E12


title: 1772078016_F03


title: 1772078016_E09


title: 1772078016_E11


title: 1772078016_E05


title: 1772078016_E10


title: 1772078016_E03


title: 1772078016_E04


title: 1772078016_D12


title: 1772078016_D11


title: 1772078016_D06


title: 1772078016_D05


title: 1772078016_D09


title: 1772078016_D03


title: 1772078016_D01


title: 1772078016_C12


title: 1772078016_C11


title: 1772078016_C10


title: 1772078016_C08


title: 1772078016_C06


title: 1772078016_C05

value: Oxt;Avp-low


title: 1772078016_F01


title: 1772078016_C03


title: 1772078016_C04


title: 1772078016_C02


title: 1772078016_B10

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772078016_B11


title: 1772078016_B09


title: 1772078016_B08


title: FUS_KO_5

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
RNA-sequencing reads were mapped to the zebrafish genome (Zv10) using the aligner STAR (version 2.4.1d). The command-line parameters for the aligner STAR (version 2.4.1d) were: STAR --runMode alignReads --outBAMsortingThreadN 0 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 2 --alignIntronMin 21 --outSAMtype BAM SortedByCoordinate --sjdbOverhang 99 --outSJfilterReads Unique
Read count table was produced with featureCounts (v. 1.4.6) using Ensembl database gene annotation (release 80). The command-line parameters for the featureCounts (v. 1.4.6) were: -Q 1 -O -T 4 -p -P -s 2
Differential expression was performed using the R/Bioconductor package DESeq2. CollapseReplicates function was used to collapse technical replicates from both sequencing runs.
We followed the GATK (version 3.5) best practices for RNA-seq variant calling which involved a 2-step mapping approach with STAR. Reads were initially mapped with the following command-line parameters: STAR --runMode alignReads --outFilterMismatchNmax 2 --outFilterMultimapNmax 10 --alignIntronMin 21 --outStd SAM --outSAMattributes Standard --outSJfilterReads Unique. Detected splice-junctions were then collected and filtered to generate a new index: STAR   --runMode genomeGenerate   --runThreadN 8   --genomeDir sjdbStarIndex   --sjdbFileChrStartEnd SJ.out.tab.Pass1.sjdb  --sjdbOverhang 100. This new index now contains the splice-junctions identified in any of the samples, and can be used for more accurate mapping ensuring that all samples are mapped to the same index. The second mapping was done with the same parameters as the first with the addition of --outSAMstrandField intronMotif, which adds the XS strand attribute required for isoSCM. Aligned reads were then used to call variants using the suggested GATK best practices parameters. The reference Zebrafish VCF was downloaded from Ensembl (release 83). Briefly, reads groups were added to the alignments and duplicated reads identified and marked with Picard's AddOrReplaceReadGroups and MarkDuplicates respectively. Next, unidentified nucleotides, Ns, were corrected with GenomeAnalysisTK.jar -T SplitNCigarReads -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS, improving intronic exonic assignments in the process. Base call scores were then adjusted for systematic sequencing errors with GenomeAnalysisTK.jar -T BaseRecalibrator -knownSites vcf. Finally, variants were called with GenomeAnalysisTK.jar -T HaplotypeCaller -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 and filtered with GenomeAnalysisTK.jar -T VariantFiltration -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "QD < 2.0".
To identify de novo 3'UTRs and changes occurring between wild-type and Fus knockout, we used IsoSCM v2.0.10.7 This method uses abrupt changes in coverage to identify terminal exon boundaries. IsoSCM does not handle replicates, thus we merged the alignments generated by the second mapping for the biological replicates of Fus knockout and wild-type. New gene models with improved 3'UTRs were generated with the command assemble, and then differential 3'UTR usage quantified with compare command. The top changes were selected with the following criteria: (i) upstream coverage higher than the median (smallest median of either WT or Fus knockout); (ii) differential usage > 0.20; (ii) 3'UTR length > 50; and (iv) confidence score > 0.99.
Genome_build: Zv10
Supplementary_files_format_and_content: Tab-delimited counts table file includes results of the DESeq2 analysis: normalized reads, log2 fold change and statistics. VCF file represents a list of SNPs called by GATK and filtered (see methods). isoSCM text file represents a list of most differentially changed 3'UTRs (see methods).

organism: Danio rerio

source_name: adult female brain

growth_protocol: Zebrafish were maintained in standard conditions. Unless stated otherwise, in all experiments a mix of AB and TU strain was used. All experiments were carried out according to German animal welfare law (licenses 23 177-07/G 13-5-087 (CRISPR-Cas9 knockouts), 23177-07/A 15-5-001 OES (tail fin clips)).

extract_protocol:
Whole brains from young adult individuals were dissected with forceps inside a dish filled with ice-cold PBS. Each brain was immediately transferred to 500µl RNALater (AM7020, Ambion) and stored overnight at 4°C. Subsequently, the brains were homogenized with a plastic pestle on ice in 300µl iCLIP Lysis buffer (50mM Tris-Cl pH 7.5, 100mM NaCl, 1% Igepal CA-630(Sigma I8896), 0.1% SDS, 0.5% sodium deoxycholate, Protease Inhibitors EDTA-free (Roche), anti-RNase (AM2692, Ambion) 1:1000). The lysate was further split in two parts: 250µl of the lysate were immediately transferred to 750µl Trizol LS (10296028, Thermo Fisher) and vigorously mixed. Total RNA for RNA sequencing was isolated from this fraction using standard Trizol LS protocol.
Strand-specific polyadenylated RNA libraries were prepared using the TruSeq Stranded RNA Library Preparation Kit and sequenced on an Illumina HiSeq2000 using the 2x 100bp read protocol.

treatment_protocol: The knockout Zebrafish line was created using CRISPR-Cas9 and a single guide RNA targeting exon 3 of the FUS gene. Primers to clone the single guide RNA sequence for fus into DR274 were 5'-TAGGGGGTTATGGAGGACAGTC-3' and 5'-AAACGACTGTCCTCCATAACCC-3'. Injected fish were raised to adulthood and genotyped via tail fin biopsy.

tag: tissue

value: whole brain

value: AB x TU

tag: developmental stage

value: adult

tag: gender

value: female

tag: genotype

value: FUS KO


title: FUS_KO_2


title: 1772078016_B07

value: neurons


title: FUS_KO_6


title: 1772078016_B05

value: oligos


title: FUS_KO_3


title: 1772078016_B03

value: M


title: WT_6

value: wild type


title: WT_3


title: FUS_KO_1


title: 1772078016_B06

value: Hmit+/-


title: 1772078016_B02

value: N


title: WT_4


title: WT_1


title: 1772078016_A09

value: uc


title: 1772078016_A12


title: 1772078016_D10

value: Galanin


title: 1772078016_A08


title: 1772078016_A06

value: Trh-medium


title: 1772078016_A05

value: endothelial


title: 1772078016_A03

value: GABA 1


title: 1772078014_H11

value: Trh-low


title: 1772078014_H12

value: ependymal


title: 1772078016_A04


title: 1772078014_H03


title: 1772078014_H02


title: 1772078014_H08


title: 1772078014_H04


title: 1772078018_E03

value: vsm


title: 1772078014_G11


title: 1772078014_G08


title: 1772078014_H01

value: Per2;circadian (SCH)


title: 1772078014_F10


title: 1772078014_F12


title: 1772078014_G05


title: 1772078014_G01


title: 1772078014_F04


title: 1772078014_F01

value: microglia


title: 1772078014_E10

value: astrocytes


title: 1772078014_F06

value: neurons


title: 1772078014_E11


title: 1772078014_E03


title: 1772078014_E08


title: 1772078014_E02

value: Pomc+/- (ARH)


title: 1772078014_D10

value: M


title: 1772078014_D04

value: oligos


title: 1772078014_D06


title: KO1-4

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

country: USA

institute: UT MD Anderson Cancer Center

description: from Dr.BertDr. Bert Vogelstein (Johns Hopkins University, Baltimore, MD

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat v2.0.9 with default parameters
Reads per gene were counted with HT-Seq
Read counts were normalized with R package edgeR_3.2.4
Supplementary_files_format_and_content: tab-delimited text files containing the raw counts of sequencing reads for the genes.

molecule: total RNA

organism: Homo sapiens

source_name: colon

growth_protocol: HCT116 and KO1 cells were grown in McCoy’s medium supplemented with 10% fetal bovine serum in 37°C incubator with 5% CO2.

extract_protocol:
HCT116 and KO1 cells were harvested and total RNAs were extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.
Illumina-compatible mRNA libraries were constructed using the TruSeq RNA sample prep kit v2 (Illumina, Inc). Five hundred nanograms of total RNA were enriched for Poly-A mRNA using Oligo-dT magnetic beads. The resulting Poly-A mRNA was fragmented to a median size of 150 bp using divalent cations. Randomly primed first- and second-strand synthesis was then performed to create double-stranded cDNA. The ends of the double-stranded cDNA fragments were repaired, 5′-phosphorylated, and 3′-A tailed, and then the Illumina-specific Y-shaped indexed adapters were ligated. The adaptor-ligated fragments were then purified and enriched by 7 cycles of PCR amplification. The amplified library was then quantified by quantitative PCR using a library quantification kit (KAPA Biosystems) and assessed for size distribution using the Bioanalyzer system (Agilent Technologies). Eight libraries were multiplexed and sequenced on an Illumina HiSeq2000 instrument using the 75-bp paired-end format. After sequencing, BCL files were converted into “.fastq.gz” files, and individual sample libraries were de-multiplexed using CASAVA 1.8.2 with no mismatches.

value: HCT116 with genetic PPARD-KO


title: KO1-3


title: 1772078014_G06

value: N


title: 1772078014_D01


title: KO1-2


title: HCT116-4


title: 1772078014_C11


title: 1772078014_F05


title: 1772078014_F09


title: HCT116-2


title: HCT116-3


title: 1772078014_F02

value: Hmit+/-


title: 1772078014_C10


title: 1772078014_E01


title: 1772078014_C09


title: MMACSF_vem_48h_rep1

city: Boston

first: Mohammad

last: Fallahi-Sichani

state: Massachusetts

address: 200 Longwood Ave.

institute: Harvard Medical School

data_processing:
The reads were mapped to the human genome (build hg19) using Tophat (Kim et al, 2013) with default settings.
Differential expression analysis was performed using Cuffdiff (Trapnell et al, 2010) running on the web-based Galaxy platform (https://usegalaxy.org/).
Genome_build: hg19
Supplementary_files_format_and_content: text files including normalized abundance measurements (FPKM values) for each sample

source_name: melanoma

growth_protocol: Melanoma cell lines used in this study were obtained from the Massachusetts General Hospital Cancer Center with the following primary sources: COLO858 (ECACC) and MMACSF (RIKEN BioResource Center). MMACSF cells were grown in DMEM/F12 (Invitrogen) supplemented with 5% fetal bovine serum (FBS) and 1% sodium pyruvate (Invitrogen). COLO858 cells were grown in RMPI 1640 (Corning cellgro) supplemented with 5% FBS and 1% sodium pyruvate (Invitrogen). We added penicillin (50 U/ml) and streptomycin (50 μg/ml) to all growth media. All cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
At the time of harvest for RNA, cells were washed once with PBS, then lysed in the dish with RLT buffer (Qiagen). Samples were immediately processed with Qiashredder and RNeasy kits (Qiagen) and frozen until further use. 10 μg of RNA was DNAse-treated and cleaned up with RNeasy MinElute kit (Qiagen). RNA quality was assessed by Bioanalyzer (Agilent) and all samples had RINs of 9.0 or higher.
RNA-seq libraries were constructed using Illumina’s TruSeq stranded mRNA library prep kit and protocol with minor modifications. Briefly, 1 μg of RNA was mixed with 2 μl of a 1:100 dilution of ERCC spike in control Mix2 (Life Technologies) before mRNA purification. Elution and fragmentation was done for 6 min at 94oC. cDNA was synthesized and cleaned up with Ampure beads (Agencourt). Fragments were end-modified and adaptors ligated before another Ampure bead cleanup. Final library amplification was done at 13 cycles and again cleaned up with Ampure beads. The resulting libraries were roughly 380 bp in length as assessed by Bioanalyzer. RAN-seq was performed at the Harvard University Sequencing Facility (FAS Division of Science) on Illumina HiSeq 2000 machines using the standard single-read (1 × 50 bp) protocol.

treatment_protocol: COLO858 and MMACSF cells were seeded in 20% (for COLO858) or 33% (for MMACSF) confluency in 10-cm plates in two replicates. The next day media were replaced with fresh growth media containing either DMSO or 0.2 μM vemurafenib and cells were cultured for a further 24 or 48 h.

tag: cell line

value: MMACSF

tag: cell type

value: melanoma cell line

tag: origin

value: cells in vitro

tag: treatment


title: 1772078014_C08

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: MMACSF_vem_24h_rep1


title: 1772078014_C05

value: Npy;Agrp (ARH)


title: MMACSF_DMSO_rep2

value: DMSO (vehicle)


title: MMACSF_DMSO_rep1


title: COLO858_vem_48h_rep1


title: COLO858_vem_48h_rep2


title: 1772078014_C01


title: KO1-1


title: COLO858_vem_24h_rep2


title: COLO858_DMSO_rep2


title: 1772078014_B09

value: Hcrt


title: COLO858_DMSO_rep1


title: Pat5_p11

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

institute: NIH

data_processing:
Illumina bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 repeat-masked  genome using tophat v2.0.13 with parameters  -p 4 --coverage-search --library-type fr-unstranded
Gene expression level was calculated by cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: text file with Expression matrix

extract_protocol:
Sorted cells were lysed and total RNA was extracted using RNAzol RT (Molecular Research Center Inc., Cincinnati, OH). Poly-adenylated RNA was purified using Dynabeads oligo (dT)25 (Invitrogen, Carlsbad, CA) and fragmented
cDNA was synthesized and Illumina-ready libraries were generated using a modified Illumina TruSeq mRNA Library preparation protocol (paired end HiSeq 2x75 reads)

value: Lymph Node

tag: disease status

value: HIV+

tag: sorting phenotype


title: COLO858_vem_24h_rep1


title: Pat1_p11


title: Pat2_p11


title: 1772078014_B06

tag: strain

tag: age (days postnatal)


title: 1772078014_B10

tag: Sex

tag: acute stress


title: T1_p11

source_name: Tonsil 1

value: Tonsil

value: HIV-


title: HCT116-1


title: MMACSF_vem_48h_rep2


title: Pat4_p11


title: 1772078014_B04

tag: cell diameter

tag: total molecules


title: Pat5_p8


title: Pat3_p8


title: Pat4_p8


title: Pat1_p8


title: 1772078014_B05

tag: level1 class

value: endothelial


title: 1772078014_C06

value: M

value: astrocytes


title: MMACSF_vem_24h_rep2


title: 1772078014_A12

value: ependymal


title: Pat5_p7

tag: tissue


title: T2_p8

source_name: Tonsil 2


title: Pat4_p7


title: Pat1_p7


title: 1772078014_A10

value: N


title: T2_p7


title: T1_p7


title: 1772078014_A09

value: neurons

tag: level2 class (neurons only)


title: 1772078014_A08

value: oligos


title: 1772078014_A05


title: 1772078014_B01


title: 1772078014_A01

value: vsm


title: MDAMB453_10_24h

city: Portland

first: Rosalie

last: Sears

state: OR

address: 3720 SW Moody Ave

department: MMG

institute: Oregon Health & Science University

data_processing:
Base calling using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
All reads were trimmed to 44 bases and aligned to mm19 with Bowtie version 1.0.0 (allowing up to 3 mismatches, but requiring unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with un-normalized tag counts for each RefSeq gene model (suitable for count based tools such as DESeq2).

source_name: MDA-MB-453 cell line

growth_protocol: Cells maintained prior to the experiment in DMEM with 10% serum, then plated for 24 hours on growth factor reduced matrigel in the presence or absence of serum as noted above.

extract_protocol:
Total RNA was extracted with Trizol according to manufacturer's protocol.
Sequencing libraries were constructed using an Illumina TruSeq RNAseq kit. Briefly, poly(A)+ RNA was isolated from 1ug of total RNA (per sample) using oligo-dT coated magnetic beads. The recovered RNA was then chemically fragmented. First strand cDNA was generated using random hexamers as primers for reverse transcriptase. Following second strand synthesis, the ends of the double stranded fragments were repaired and then a single “A” nucleotide was added to each end. Illumina adaptors were ligated to the cDNAs. Limited round (11-cycle) PCR was used to amplify the material to yield the final libraries. Library concentration was determined using real time PCR with primers complementary to the Illumina adaptors. Sample libraries were diluted and applied to an Illumina single read flow cell at a concentration appropriate to generate about 180 million reads per lane. All  libraries were prepared with indexing barcodes to permit multiplexing in a single lane. 100 cycle single read sequencing was used to generate base call files. Illumina’s CASAVA package was used to assemble the reads into standard fastq formatted data.

tag: plated on

value: matrigel

tag: percent serum


title: NSC 103n2

city: Miami

first: Marco

last: Magistri

state: FL

address: 1501 NW 10th Ave

department: Psychiatry

institute: University of Miami

data_processing:
Paired-ends reads generated from sequencing on the Illumina Hiseq2000 were trimmed off the adaptor sequences using a custom script.
Trimmed reads were aligned to the human genome reference GRCh37 using TopHat 2.0.9.
Transcriptome for each sample was assembled using Cufflinks, which also provided transcripts abundance in fragments per kilobase of exon per million fragments mapped (FPKM)
Transcripts assemblies were merged using Cuffmerge.
Genes were annotated according to the ENSEMBL classification, and genes that were not annotated as protein coding genes, lincRNA or antisense RNA were filtered out.
Differential gene expression analysis was performed using Cuffdiff.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file including RPKM values for each Sample

source_name: Fetal brain

growth_protocol: NPCs were isolated from five human fetal brains collected from second trimester-aborted fetuses, which we received from the Birth Defects Research Laboratory at the University of Washington in Seattle. Briefly, fetal brains were mechanically dissociated into single cells and seeded in 75-mm tissue culture flasks in Neurobasal Media supplemented with EGF (20ng/ml), FGF (10ng/ml), B27, Glutamax and Heparin (2μg/ml). After 7–10 days of culture, NSCs cells form neurospheres colonies that can be cultured in suspension for several months.

extract_protocol:
RNA was extracted and purified using a combination of TRIzol reagent and QUIAGEN RNeasy columns. RNA extraction was performed from each NPCs line at the time cells were seeded for differentiation and after 1 week of culture in the differentiation media (FBS or CNTF/BMP4).
1mg of RNA was used to prepare poly-A selected directional libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs)

treatment_protocol: To induce differentiation, neurospheres were disaggregated into single cells using accutase and plated for 1 week in 6-well plates previously coated with poly-L-Ornythine (PLO) for 3 hours and laminin overnight. The differentiation media used consisted of DMEM/F12 supplemented with N2 and Glutamax and containing either 2.5% FBS or CNTF (20ng/ml) and BMP4 (10ng/ml).

tag: developmental stage

value: progeniotor cells

tag: age of the fetus

value: 103 days


title: MDAMB231_10_24h

source_name: MDA-MB-231 cell line

tag: cell line


title: CNTF/BMP4 103

value: CNTF/BMP4 differentiated cells


title: CNTF/BMP4 103n2


title: CNTF/BMP4 110

value: 110 days


title: FBS 110

value: FBS differentiated cells


title: 1772078013_H11


title: FBS 114

value: 114 days


title: NSC 103_2


title: 1772078013_H07


title: MDAMB231_0_24h


title: T1_p8

value: Tonsil


title: NSC 110_2


title: 1772078013_H06

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: FBS 103


title: FBS 91

value: 91 days


title: 1772078013_H05

value: M

value: microglia


title: NSC 114


title: NSC 110


title: NSC 103


title: 1772078013_H04

value: ependymal


title: MDAMB453_0_24h


title: 1772078014_A02

value: N

value: uc


title: 1772078013_H02

value: endothelial


title: RNA-seq of differentiated SH-SY5Y cells (Replicate #2)

city: Palo Alto

first: Jingjing

last: Li

address: 3165 Porter Drive

institute: Stanford University

data_processing:
FASTQ alignment using TopHat v2.0.8 aginst the human RefSeq transcriptome downloaded from UCSC Table Browser.
Gene expression quantification using CUFFLINKS V2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: the FPKM values for gene and each sample were listed in the final excel table

source_name: differentiated SH-SY5Y cells Rep2

growth_protocol: SH-SY5Y cells (ECACC, Sigma-Aldrich) in 1:1 DMEM-F12 medium (Life technologies) supplemented with 10% fetal bovine serum (FBS), penicillin (50 u/mL), streptomycin (50 µg/mL), and L-glutamine (2 mM) were maintained at 37 °C in a saturated humidity atmosphere containing 95% air and 5% CO2. The SH-SY5Y cells were then differentiated into neuron-like cells by the addition of retinoic acid (RA, Sigma-Aldrich; R2625) and brain-derived neurotrophic factor (BDNF, eBioscience) essentially as previously described with minor modifications(Encinas et al., 2000). Briefly, for differentiation, cells were plated at a density of 4 x 104 / cm2 in medium containing 5% FBS along with aforementioned components. On the next day, medium containing 5% FBS and 10 µM RA was added to the cells and the medium was changed every day for a total of 7 days. On the 8th day, the medium was replaced with DMEM supplemented with penicillin (50 u/mL), streptomycin (50 µg/mL), L-glutamine (2 mM), and BDNF (20 ng/mL) but without FBS addition. Again the medium was changed every 2-3 days for an additional 9 days. The differentiated cells were detached by incubating the cells with versene at 37 °C for 10-15 min, followed by phosphate buffer saline wash, and centrifugation (twice) at 190 xg for 10 min. We analyzed the complexes isolated from differentiated SH-SY5Y neuron-like cells on day 16 (starting with undifferentiated cells on day 0).

extract_protocol:
Then the total RNA was treated with RNase-Free DNase (Qiagen) followed by purification with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s instructions.
2 µg of total RNA each sample was subject to RNA-seq library preparation with ScriptSeq™ Complete Gold Kit from Epicentre (Cat. # SCL24EP, Madison, WI) following the manufacturer’s instructions. In brief, ribosomal RNA was depleted from total RNA using Ribo-Zero magnetic beads, then the ribosomal RNA depleted RNA was purified and fragmented. Random primer tailed with Illumina adaptor was used to perform reverse transcription to get cDNA library. Adaptor sequence was added to the other end of cDNA library with a Terminal-Tagging step. cDNA library was amplified with Illumina primers provided with this kit. The product was size selected (350~500 bp) from 2% agarose E-gels (Invitrogen) and sequenced in 1 lane per sample on Illumina’s HiSeq 2000 platform.


title: RNA-seq of undifferentiated SH-SY5Y cells (Replicate #2)

source_name: undifferentiated SH-SY5Y cells Rep2

treatment_protocol: Briefly, for differentiation, cells were plated at a density of 4 x 104 / cm2 in medium containing 5% FBS along with aforementioned components. On the next day, medium containing 5% FBS and 10 µM RA was added to the cells and the medium was changed every day for a total of 7 days. On the 8th day, the medium was replaced with DMEM supplemented with penicillin (50 u/mL), streptomycin (50 µg/mL), L-glutamine (2 mM), and BDNF (20 ng/mL) but without FBS addition. Again the medium was changed every 2-3 days for an additional 9 days. The differentiated cells were detached by incubating the cells with versene at 37 °C for 10-15 min, followed by phosphate buffer saline wash, and centrifugation (twice) at 190 xg for 10 min.


title: 1772078013_G06


title: 1772078013_G07

value: oligos


title: 1772078013_G02


title: 1772078013_F08

value: vsm


title: 1772078013_E11


title: 1772078013_E10


title: RNA-seq of undifferentiated SH-SY5Y cells (Replicate #1)

source_name: undifferentiated SH-SY5Y cells Rep1


title: 1772078013_E04


title: RNA-seq of differentiated SH-SY5Y cells (Replicate #1)

source_name: differentiated SH-SY5Y cells Rep1


title: 1772078013_F07

value: neurons

value: Sst-medium;Cartpt


title: 1772078013_E09


title: 1772078013_D12


title: 1772078013_D03


title: 1772078013_D09


title: AET_degradome

city: Nanjing

first: zhou

last: rong

address: Nanjing

country: China

institute: Nanjing Agricultural University (NAU)

description: degradome

data_processing:
After sequencing, the raw reads were further analysed using the ACGT101-miR program (LC Sciences, Houston, Texas, USA). After the junk reads and sequences < 19 nt and > 24 nt were removed, the remaining sequences were aligned using Rfam (http://rfam.janelia.org), Solanaceae Genome Network database (http://sgn.cornell.edu/) and repeat database (http://www.girinst.org/repbase). The sequences that matched Rfam, mRNA, rRNA, tRNA, snoRNA, snRNA, other non-coding RNAs and repeat sequences were filtered out. MiRBase is the central online repository for miRNA data50. To identify the miRNAs that are conserved among plants, the valid sequences were analysed by blasting against the reported mature miRNAs and pre-miRNAs in plants from miRBase 21.0 (ftp://mirbase.org/pub/mirbase/CURRENT/). A maximum of one mismatch between the target miRNAs and the known miRNAs from miRBase database was allowed. As described by Meyers et al. (2008)51, specific criteria were applied for miRNA annotation, and a stable hairpin structure was an important indicator. The secondary structures of the pre-miRNAs were predicted using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi)14. Only the pre-miRNAs with stable hairpin structures were considered. Minimal folding free index (MFEI) is an important factor for miRNA identification52. Novel miRNAs were only considered when the MEFIs of their pre-miRNAs were ≥ 0.80 in this study. Moreover, the normalised copy number of the novel miRNAs in at least one sample was required to be ≥ 10.
CleaveLand 3.0 software was used for data analysis after degradome sequencing54. Using the Tomato Genomics Database (ftp.solgenomics.net/unigene_builds/Tomato_current.seq.gz) as reference data, the degradome sequences were matched to mRNAs using the Oligomap short reads aligner55. A penalty score (alignment score) criterion was introduced based on the alignment between each miRNA and its potential target. Mismatched pairs were scored as 1, and G:U pairs were scored as 0.5. If the mismatches were located between the second base and the thirteenth base inclusive counting from the 5’ end of the miRNA sequence the score was doubled. The targets were classified into five categories according to the results of degradome sequencing and the abundance of the cleavage sequences. Category 0 comprised the targets whose scores were equal to the maximum. There was only one maximum position. Category 1 comprised the most abundant targets, in which more than one degradome tag had been detected. Category 2 comprised the targets present at abundances between the median and the maximum. Category 3 comprised the targets with scores below or equal to the median. Category 4 comprised the sequences that included only one raw read.
To clarify the functions of the target genes, GO functional annotation and KEGG pathway analysis of the miRNA targets were performed based on the GO database (http://www.geneontology.org/) and KEGG database (http://www.genome.jp/kegg/), respectively. The network between the miRNAs and their targets was derived according to the GO functional annotation.
To compare the expression levels of the miRNAs or the target genes in tomatoes at normal temperature (NT), the moderately elevated temperature (MET) and the acutely elevated temperature (AET), a chi-square test and Fisher’s exact test were performed after the raw data were normalised from high-throughput sequencing. The log2 ratio was used as the threshold to detect differences in miRNA expression levels or the changes in target genes degradation. The miRNAs or target genes were considered to be significantly up-regulated or significantly down-regulated when the p values of both the chi-square test and Fisher’s exact test were ≤ 0.05 and the |log2 ratio| was ≥ 1.
Genome_build: (http://sgn.cornell.edu/),Solanum_lycopersicum.SL2.40.21
Supplementary_files_format_and_content: expression data of miRNAs and targets of miRNAs,.xls

organism: Solanum pimpinellifolium

source_name: leaf

growth_protocol: The heat-tolerant wild tomato LA2093 (Solanum pimpinellifolium L.), provided by Tomato Genetics Resource Center, University of California, was the plant material for sequencing. Single seeds were sown in a plug tray after soaking and pregermination and then cultured in climate chambers (RDN-560E-4, Dongnan Instrument Co, Ltd, Ningbo, China) at an air temperature of 26/18°C (14 h/10 h, day/night), a light intensity of 280±20 µmol m–2 s–1 and 50±10% relative humidity. On the twentieth day after sowing, healthy and uniform seedlings were transferred to plastic plots (11 cm diameter, 9 cm height) and cultured in the climate chambers with the same environmental parameters. The seedlings were irrigated by flooding the bench for 10 min two times per day with 1/2 nutrient solution, according to the Japanese Garden test formula.

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen, CA, USA), and the quantity and purity of the total RNA were detected using a Bioanalyser 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).Leaf samples from LA2093 exposed to 26/18°C, 33/33°C and 40/40°C for 8 h were used to construct three sRNA libraries, which we called the NT, MET and AET libraries, respectively. The three sRNA samples were extracted using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). The sRNAs were reverse transcribed to cDNAs after isolation and ligation. The purified cDNAs from three sRNA libraries were sequenced with Illumina Hiseq2500 (LC-BIO, Hangzhou, China).All samples were assigned RNA integrity number (RIN) values of at least seven. Approximately 20 µg of total RNAs were used to construct the degradome libraries. The NT, MET and AET degradome libraries were constructed according to the methods described by Addo-Quaye et al. (2008)23 and Ma et al. (2010)53, with minor modifications. The mRNA was mixed with biotinylated random primers, and then the RNA containing the biotinylated random primers was captured by beads and ligated to 5’ adaptors. First-strand cDNA was generated from the ligated sequence after reverse transcription. A number of DNA products were produced by PCR amplification. Following purification, digestion, ligation and repurification, the cDNA library was sequenced with an Illumina Hiseq2500 (LC-BIO, Hangzhou, China).

treatment_protocol: The seedlings were randomly divided into three groups for temperature treatments on the seventh day after transfer. The first group was kept at a normal temperature and used as a control (26/18°C, NT); the second group was exposed to a moderately elevated temperature (33/33°C, MET); and the third group was exposed to an acutely elevated temperature (40/40°C, AET). The temperature reached 33°C in half an hour and 40°C in an hour in the climate chamber. According to the preliminary experiment, the soil moisture and electrical conductivity (EC) during the temperature treatments were in the normal ranges of 40−55% and 260−380 mS/m, as measured by WET Sensor (Delta-T Ltd, Burwell, England), when the seedlings were irrigated in the same way as before but with one more irrigation with water. Therefore, to keep the soil moisture and EC in a normal range and eliminate the effects of water deficit and drought stress, the experimental groups were subjected to an additional irrigation with water once per day during the temperature treatments.

value: seedlings

value: leaf

tag: treatment


title: AET_miRNA

value: acutely elevated temperature (40/40°C, AET)


title: 1772078013_F04

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772078013_D04


title: 1772078013_D11


title: NSC 91

value: progeniotor cells


title: 1772078013_C12

value: astrocytes


title: MET_degradome

description: degradome

value: moderately elevated temperature (33/33°C, MET)


title: 1772078013_C09

value: M


title: 1772078013_G10


title: 1772078013_E08


title: 1772078013_C08


title: MET_miRNA


title: 1772078013_F03


title: 1772078013_E02


title: 1772078013_C06


title: NT_degradome

description: degradome

value: control (26/18°C, NT)


title: NT_miRNA


title: 1772078013_C04


title: 1772078013_C02


title: 1772078013_C07


title: 1772078013_B04


title: 1772078013_B09

value: microglia


title: 1772078013_B08

value: N


title: 1772078013_C05


title: Kdm5C Day 2 exp. 2

city: Odense M

first: Ann-Sofie

middle: Bøgh

last: Brier

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark, Odense

description: processed data file: KDM5C_all_peaks_tags.txt

library_source: genomic

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
KDM5C ChIP-seq and matching Input tag counts were normalized to 10M reads using HOMER.
Regions enriched for KDM5C in the individual libraries were called using HOMER with the ‘-style histone’ and '-F 10' settings. For the individual KDM5C region files, overlapping peak regions were merged into one region and KDM5C peaks at day 2 were identified as having 4-fold more normalized tags in both replicates relative to the input control. Promoter proximal regions were identified as being within ±1kb of transcriptional start site (TSS) and distal binding sites between 5 and 50 kb away from TSS.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph formatted file that can then be uploaded as a custom track to the UCSC genome browser
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A replicate libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C replicate libraries

molecule: genomic DNA

source_name: 3T3-L1_Kdm5C Day 2

extract_protocol:
ChIP experiments were performed in 3T3-L1 cells essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Two days post confluency (day 0), 3T3-L1 cells were induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation. For knock down experiments, pre-confluent 3T3-L1 cells were transduced 4 days before induction of differentiation by incubation for 24 hours at 37°C with medium containing lentiviral constructs (shKDM5A/B/C or control shLuc) and 6 μg/mL polybrene (Sigma). After 24 hours the medium was changed to normal growth medium.

tag: cell type

value: Preadipocyte cell line

tag: time point

value: Two days post induction (day 2)

tag: chip antibody

value: JARID1C/Kdm5C Antibody (A301-034A; Bethyl lab)


title: 1772078013_B05

tag: strain

tag: age (days postnatal)

value: ependymal


title: 1772078013_B03

tag: Sex

tag: acute stress

value: oligos


title: Kdm5A Day 2 exp. 2

description: processed data file: KDM5A_all_peaks_tags.txt

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
KDM5A ChIP-seq and matching Input tag counts were normalized to 10M reads using HOMER.
Regions enriched for KDM5A in the individual libraries were called using HOMER with the ‘-style histone’ and '-F 10' settings. For the individual KDM5A region files, overlapping peak regions were merged into one region and KDM5A peaks at each time point were identified as having 10-fold more average normalized tags over two replicates relative to the input control. Promoter proximal regions were identified as being within ±1kb of transcriptional start site (TSS) and distal binding sites between 5 and 50 kb away from TSS.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph formatted file that can then be uploaded as a custom track to the UCSC genome browser
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A replicate libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C replicate libraries

source_name: 3T3-L1_Kdm5A Day 2

value: KDM5A antibody (ab70892; Abcam)


title: 1772078013_B02

tag: cell diameter

tag: total molecules


title: 1772078013_B01

tag: level1 class

value: vsm


title: 1772078013_A12

value: neurons

tag: level2 class (neurons only)


title: Kdm5C Day 2 exp. 1


title: 1772078013_A10


title: Kdm5A 4 hour exp. 2

source_name: 3T3-L1_Kdm5A 4 hour

value: 4 hours post induction


title: Kdm5A Day 0 exp. 2

source_name: 3T3-L1_Kdm5A Day 0

value: Two days post confluency (day 0)


title: 1772078013_A09

source_name: hypothalamus

value: Gad-low;Gnrh-/+


title: 1772078013_A08


title: Kdm5A 4 hour exp. 1


title: Kdm5A Day 0 exp. 1


title: 1772078013_A05