title: dlPFC from 6H6 [LID_105193]

city: Tempe

first: Kenneth

last: Chiou

state: AZ

address: 427 E Tyler Mall

department: Center for Evolution and Medicine

institute: Arizona State University

data_processing:
Gene expression counts were quantified from RNA-seq reads using the pseudoalignment method implemented in kallisto.
Estimated counts and transcripts-per-million (TPM) values were then imported into R v4.0.2 and summarized to genes using the tximport package.
Genome_build: rhesus macaque reference genome (Mmul_10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with transcripts per million (TPM) values for every gene and every sample

organism: Macaca mulatta

source_name: dorsolateral prefrontal cortex

growth_protocol: free-ranging population

extract_protocol:
Total RNA was extracted using a TRIzol-chloroform gradient followed by column isolation of RNA using the Quick-RNA Microprep kit (Zymo Research). Briefly, 1 ml of TRIzol (Invitrogen) was added to each 2-ml sample tube, along with a sterile 5-mm stainless steel grinding bead (QIAGEN cat. no. 69989). Samples were then homogenized using the Tissuelyser II system (QIAGEN) at 20 Hz in two sets of 2 minutes each, with rotation in between, and the lysate transferred to a new tube. 200 µl of chloroform were added to each sample, which was then vortexed at full speed for 15 seconds and incubated at room temperature for 2 minutes. The sample was then centrifuged at 12,000 × g for 15 minutes at 4°C. After centrifugation, the aqueous layer was transferred to a new tube and mixed with 600 µl of 70% ethanol to precipitate RNA. The resulting solution was transferred to Quick-RNA Microprep columns (Zymo Research). The remainder of the protocol followed manufacturer instructions for the Quick-RNA Microprep kit. Total RNA was eluted in 60 µl of RNase-free water.
We prepared bulk RNA-seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with an initial mRNA isolation step using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). We followed manufacturer instructions and guidelines for library preparation using these kits. We used 200 ng of starting RNA and set the enzymatic fragmentation time (10 minutes), first-strand synthesis incubation time (50 minutes at 42°C), and bead cleanup volume ratios for a target insert size of 400 bp. Libraries were amplified using 10 cycles of PCR and eluted in a final volume of 20 µl of RNase-free water. Libraries were quantified by Qubit 3 using the Qubit DNA HS Assay kit (Invitrogen) and library quality was assessed using the Fragment Analyzer HS NGS kit (AATI/Agilent). Libraries were pooled in equimolar quantities prior to sequencing.

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

tag: individual id

value: dorsolateral prefrontal cortex

value: female

tag: dominance rank

value: mid


title: dlPFC from 80S [LID_105196]

status: Public on Sep 26 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: age

tag: Sex

value: low


title: dlPFC from 9I5 [LID_105200]


title: dlPFC from 7L0 [LID_105194]


title: dlPFC from 20S [LID_105182]


title: dlPFC from 4J3 [LID_105189]


title: dlPFC from 5B6 [LID_105190]

value: high


title: dlPFC from 2E9 [LID_105185]


title: dlPFC from 94O [LID_105198]

value: male


title: dlPFC from 22H [LID_105183]


title: dlPFC from 48V [LID_105188]


title: dlPFC from 9I7 [LID_105201]


title: dlPFC from 8K7 [LID_105197]


title: dmPFC from 94O [LID_105199]

source_name: dorsomedial prefrontal cortex

value: dorsomedial prefrontal cortex


title: dlPFC from 7L7 [LID_105195]


title: dlPFC from 9N0 [LID_105202]


title: dlPFC from 65Z [LID_105192]


title: aorta_594s_K08

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard Smart-Seq2 protocol

value: aorta

tag: strain

value: 10 weeks

tag: description


title: dlPFC from 5N1 [LID_105191]


title: V1 from 6H6 [LID_105205]

source_name: primary visual cortex

value: primary visual cortex


title: dlPFC from 3A9 [LID_105187]


title: dlPFC from 36O [LID_105186]


title: dlPFC from 1B7 [LID_105181]


title: dlPFC from 2C7 [LID_105184]


title: aorta_594s_K07


title: aorta_594s_K06


title: CA3 from 94O [LID_105159]

source_name: cornu ammonis 3

value: cornu ammonis 3


title: aorta_594s_K05


title: CA3 from 6I4 [LID_105160]


title: aorta_594s_K04


title: ACCg from 6H6 [LID_105157]

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: aorta_594s_J23


title: aorta_594s_J22


title: aorta_594s_K02


title: aorta_594s_J19


title: Pu from 5N1 [LID_105153]

source_name: putamen

value: putamen


title: aorta_594s_J24


title: ACCg from 94O [LID_105155]


title: V1 from 36O [LID_105152]


title: HC15 naiveB

type: RNA

city: Kyoto

first: Kenji

last: Okuma

state: Kyoto

address: 53, Shogoin Kawara-cho, Sakyo-ku, Medical Innovation Center

country: Japan

institute: Astellas Pharma Inc.

hyb_protocol: Labeled samples were hybridized to microarray G4110B Human 1A Microarray (V2) for 17hr, 65 deg C.

scan_protocol: Gene expression pixel intensities were extracted by scanning the microarrays with an Agilent Scanner.

data_processing: Data processing and trimming were performed with GeneSpring ver. 12.6.1.

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Total RNA from a human sample were amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and labeled with Cy3 respectively according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted using RNAqueous Micro Kit (Thermo Fisher Scientific/Ambion, USA) with RNase-Free DNase Set (Qiagen). RNA Integrity Number (RIN) value was measured using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with RIN ≥7.0 were used.

treatment_protocol: Fresh peripheral blood from SLE patients and healthy volunteers was collected and T, B, monocyte, mDC, pDC, naiveB, memoryB and PBMC were isolated at spontaneous state.

tag: diagnosis

value: Healthy control

tag: cell type

value: naiveB

tag: date measured

value: F

tag: sex (1 vs 2)


title: aorta_594s_K03


title: dlPFC from 5H7 [LID_105149]


title: dmPFC from 60T [LID_105154]


title: aorta_594s_J20


title: dmPFC from 8L6 [LID_105148]


title: CN from 36O [LID_105150]

source_name: caudate nucleus

value: caudate nucleus


title: CA3 from 2C7 [LID_105158]


title: ACCg from 6I4 [LID_105156]


title: DG from 22H [LID_105151]

source_name: dentate gyrus

value: dentate gyrus


title: aorta_594s_J18


title: aorta_594s_K01


title: DG from 4C6 [LID_105147]


title: aorta_594s_J17


title: aorta_594s_J16


title: aorta_594s_J15


title: CN from 9I7 [LID_105146]

value: female


title: M1 from 94O [LID_105145]

source_name: primary motor cortex

value: primary motor cortex


title: dmPFC from 4N8 [LID_105144]

value: mid


title: aorta_594s_J14


title: dlPFC from 4J0 [LID_105143]

value: dorsolateral prefrontal cortex


title: M1 from 48V [LID_105142]


title: aorta_594s_J11


title: aorta_594s_J09


title: aorta_594s_J13


title: aorta_594s_J10


title: aorta_594s_J12


title: aorta_594s_J06


title: aorta_594s_J08


title: VMH from 5H7 [LID_105140]

source_name: ventromedial hypothalamus

value: ventromedial hypothalamus

value: male

value: low


title: dmPFC from 2C7 [LID_105141]

value: dorsomedial prefrontal cortex


title: VMH from 65Z [LID_105139]


title: dmPFC from 3A9 [LID_105136]


title: M1 from 4J0 [LID_105137]


title: STS from 3L6 [LID_105135]

source_name: superior temporal sulcus

value: superior temporal sulcus


title: aorta_594s_J04

value: aorta

value: 10 weeks


title: LGN from 7L7 [LID_105134]

source_name: lateral geniculate nucleus

value: lateral geniculate nucleus


title: aorta_594s_J07


title: aorta_594s_J05


title: aorta_594s_J21


title: aorta_594s_J02


title: LGN from 65Z [LID_105132]


title: dlPFC from 3L5 [LID_105138]


title: aorta_594s_I24


title: VMH from 60T [LID_105133]


title: vlPFC from 9I7 [LID_105131]

source_name: ventrolateral prefrontal cortex

value: ventrolateral prefrontal cortex


title: LGN from 4N8 [LID_105130]


title: aorta_594s_J03


title: LGN from 7L0 [LID_105129]


title: aorta_594s_I23


title: M1 from 5B6 [LID_105128]

value: high


title: aorta_594s_I19


title: M1 from 3L6 [LID_105127]


title: vlPFC from 8K7 [LID_105124]


title: aorta_594s_I18


title: aorta_594s_I22


title: aorta_594s_I17


title: aorta_594s_I16


title: vmPFC from 6H6 [LID_105125]

source_name: ventromedial prefrontal cortex

value: ventromedial prefrontal cortex


title: aorta_594s_I21


title: M1 from 36O [LID_105122]


title: aorta_594s_J01


title: vlPFC from 48V [LID_105126]


title: LGN from 0K1 [LID_105121]


title: aorta_594s_I14


title: vlPFC from 36O [LID_105123]


title: Pu from 0K1 [LID_105120]

value: putamen


title: aorta_594s_I13


title: aorta_594s_I15


title: dmPFC from 3L5 [LID_105119]


title: CA3 from 4C6 [LID_105118]

value: cornu ammonis 3


title: aorta_594s_I11


title: aorta_594s_I10


title: aorta_594s_I09


title: Pu from 6H6 [LID_105116]

value: female


title: M1 from 8L6 [LID_105117]

value: primary motor cortex


title: Pu from 2E9 [LID_105115]


title: STS from 22H [LID_105114]

value: mid


title: aorta_594s_I08


title: aorta_594s_I12


title: aorta_594s_I07


title: vlPFC from 80S [LID_105111]


title: aorta_594s_I06


title: aorta_594s_I05


title: STS from 3A6 [LID_105112]


title: aorta_594s_I02


title: CN from 48V [LID_105113]

value: caudate nucleus


title: aorta_594s_I04


title: aorta_594s_H24


title: Pu from 48V [LID_105107]


title: Pu from 4J0 [LID_105109]


title: vlPFC from 4J0 [LID_105105]


title: aorta_594s_I03


title: vlPFC from 2E9 [LID_105108]


title: vlPFC from 20S [LID_105104]


title: aorta_594s_I01


title: aorta_594s_H22


title: aorta_594s_H23


title: vmPFC from 4C6 [LID_105103]


title: aorta_594s_H20


title: aorta_594s_H21


title: aorta_594s_H19


title: vlPFC from 6I4 [LID_105101]


title: M1 from 3L5 [LID_105102]


title: Pu from 9I5 [LID_105100]


title: aorta_594s_H17


title: aorta_594s_H18


title: STS from 9C6 [LID_105106]


title: V1 from 20S [LID_105099]

value: primary visual cortex


title: dmPFC from 49Z [LID_105110]

value: male


title: aorta_594s_H14


title: aorta_594s_H13


title: aorta_594s_H12


title: VMH from 20S [LID_105097]

value: ventromedial hypothalamus


title: aorta_594s_H08


title: M1 from 1B7 [LID_105094]


title: CA3 from 22H [LID_105092]


title: aorta_594s_H10


title: ACCg from 9I7 [LID_105091]

value: anterior cingulate cortex

value: low


title: CA3 from 9I5 [LID_105093]


title: ACCg from 8K7 [LID_105090]


title: ACCg from 20S [LID_105089]


title: aorta_594s_H07

value: aorta


title: aorta_594s_H05

value: 10 weeks


title: AMY from 6H6 [LID_105087]

source_name: amygdala

value: amygdala


title: aorta_594s_H06


title: vlPFC from 3A6 [LID_105086]

value: ventrolateral prefrontal cortex


title: STS from 8K7 [LID_105098]

value: superior temporal sulcus

value: high


title: ACCg from 80S [LID_105088]


title: aorta_594s_H04


title: aorta_594s_H03


title: aorta_594s_H09


title: LGN from 60T [LID_105095]

value: lateral geniculate nucleus


title: aorta_594s_H11


title: aorta_594s_H02


title: AMY from 48V [LID_105085]


title: dmPFC from 3A6 [LID_105083]

value: dorsomedial prefrontal cortex


title: aorta_594s_H01


title: dmPFC from 9N0 [LID_105084]

value: female


title: aorta_594s_G24


title: aorta_594s_G23


title: Pu from 49Z [LID_105082]

value: putamen


title: aorta_594s_G20


title: vmPFC from 94O [LID_105079]

value: ventromedial prefrontal cortex


title: dlPFC from 4N7 [LID_105081]

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex


title: aorta_594s_G18


title: DG from 8K7 [LID_105080]

value: dentate gyrus


title: aorta_594s_G22


title: aorta_594s_G19


title: AMY from 36O [LID_105078]


title: aorta_594s_H16


title: DG from 3L6 [LID_105077]

value: male

value: mid


title: VMH from 49Z [LID_105076]

value: ventromedial hypothalamus


title: aorta_594s_G15


title: aorta_594s_G14


title: aorta_594s_G17


title: CN from 80S [LID_105074]

value: caudate nucleus

value: low


title: LGN from 5B6 [LID_105075]


title: aorta_594s_G16

value: aorta

value: 10 weeks


title: vlPFC from 94O [LID_105072]

value: ventrolateral prefrontal cortex


title: M1 from 3A6 [LID_105071]

value: primary motor cortex


title: aorta_594s_G12


title: aorta_594s_G13


title: aorta_594s_G11


title: vlPFC from 4N7 [LID_105069]

value: high


title: STS from 6H6 [LID_105070]

value: superior temporal sulcus


title: aorta_594s_G10


title: aorta_594s_G09


title: aorta_594s_G08


title: vmPFC from 5H7 [LID_105068]


title: dmPFC from 5B6 [LID_105073]

source_name: dorsomedial prefrontal cortex

value: dorsomedial prefrontal cortex


title: dmPFC from 0K1 [LID_105064]


title: LGN from 94S [LID_105063]

value: lateral geniculate nucleus

value: female


title: VMH from 2E9 [LID_105062]


title: aorta_594s_G03

source_name: male mouse


title: aorta_594s_G04


title: aorta_594s_F23


title: aorta_594s_G01


title: aorta_594s_F22


title: VMH from 4N8 [LID_105067]


title: VMH from 48V [LID_105059]


title: V1 from 80S [LID_105057]

source_name: primary visual cortex

value: primary visual cortex


title: VMH from 3L5 [LID_105058]


title: aorta_594s_F21


title: AMY from 6I4 [LID_105056]

value: amygdala


title: AMY from 20S [LID_105066]


title: aorta_594s_G07


title: AMY from 22H [LID_105055]


title: aorta_594s_G06


title: aorta_594s_F20


title: aorta_594s_F24


title: aorta_594s_G02


title: VMH from 7L7 [LID_105060]


title: aorta_594s_F19


title: aorta_594s_F18


title: V1 from 0K1 [LID_105054]


title: aorta_594s_F17


title: VMH from 4J3 [LID_105065]


title: vlPFC from 0K1 [LID_105051]


title: Pu from 4C6 [LID_105061]

value: putamen


title: VMH from 94O [LID_105053]

value: male


title: aorta_594s_F16


title: aorta_594s_F14


title: aorta_594s_F13


title: aorta_594s_F15


title: aorta_594s_F11


title: aorta_594s_F10


title: M1 from 6I4 [LID_105047]

value: mid


title: AMY from 8K7 [LID_105049]


title: M1 from 80S [LID_105050]


title: aorta_594s_F09


title: dmPFC from 6H6 [LID_105045]


title: aorta_594s_F06


title: dmPFC from 9C6 [LID_105044]


title: dmPFC from 7L7 [LID_105048]


title: dmPFC from 4J0 [LID_105042]


title: VMH from 22H [LID_105046]

value: ventromedial hypothalamus


title: CN from 3L6 [LID_105052]

value: caudate nucleus


title: aorta_594s_F05


title: aorta_594s_F07


title: aorta_594s_F08


title: aorta_594s_F12


title: aorta_594s_F03


title: aorta_594s_F01


title: aorta_594s_F04


title: LGN from 1B7 [LID_105043]


title: aorta_594s_E24


title: LGN from 3A9 [LID_105036]

value: low


title: Pu from 94S [LID_105038]


title: vmPFC from 80S [LID_105039]

value: ventromedial prefrontal cortex


title: AMY from 0K1 [LID_105037]


title: vlPFC from 5B6 [LID_105040]


title: VMH from 4C6 [LID_105035]


title: aorta_594s_F02

value: aorta

value: 10 weeks


title: CA3 from 8K7 [LID_105034]

source_name: cornu ammonis 3

value: cornu ammonis 3


title: aorta_594s_E23


title: aorta_594s_E22


title: CN from 22H [LID_105031]


title: DG from 5H7 [LID_105026]

value: dentate gyrus


title: DG from 6H6 [LID_105027]


title: STS from 20S [LID_105030]

value: superior temporal sulcus


title: M1 from 9C6 [LID_105028]

value: primary motor cortex


title: M1 from 9N0 [LID_105032]

value: high


title: Pu from 4N7 [LID_105029]


title: vlPFC from 5H7 [LID_105033]

value: ventrolateral prefrontal cortex


title: aorta_594s_E19


title: aorta_594s_E11


title: aorta_594s_E13


title: aorta_594s_E10


title: aorta_594s_E12


title: aorta_594s_E16


title: aorta_594s_E21


title: aorta_594s_E17


title: aorta_594s_E20


title: aorta_594s_E18


title: aorta_594s_E15


title: aorta_594s_E14


title: aorta_594s_E07


title: aorta_594s_E08


title: aorta_594s_E09


title: aorta_594s_E04


title: aorta_594s_E03


title: aorta_594s_E06


title: Pu from 94O [LID_105020]


title: VMH from 36O [LID_105025]

value: female


title: Pu from 9N0 [LID_105023]


title: M1 from 3A9 [LID_105021]


title: CA3 from 20S [LID_105018]


title: VMH from 4N7 [LID_105022]


title: vlPFC from 22H [LID_105019]


title: M1 from 7L0 [LID_105024]


title: aorta_594s_D22


title: aorta_594s_E02


title: aorta_594s_D24


title: aorta_594s_E01


title: aorta_594s_D23


title: Pu from 60T [LID_105015]


title: CN from 9I5 [LID_105017]


title: CN from 6H6 [LID_105016]


title: aorta_594s_D20


title: aorta_594s_E05


title: dlPFC from 3L6 [LID_105014]

value: dorsolateral prefrontal cortex


title: aorta_594s_D21


title: VMH from 8L6 [LID_105007]


title: aorta_594s_D18


title: LGN from 4C6 [LID_105008]

value: lateral geniculate nucleus


title: M1 from 7L7 [LID_105010]


title: dmPFC from 80S [LID_105009]

value: dorsomedial prefrontal cortex


title: dmPFC from 3L6 [LID_105012]

value: male

value: mid


title: aorta_594s_D16


title: STS from 9N0 [LID_105006]


title: Pu from 5B6 [LID_105013]

value: putamen


title: CN from 6I4 [LID_105011]

value: caudate nucleus


title: aorta_594s_D17


title: aorta_594s_D14


title: aorta_594s_D15


title: VMH from 8K7 [LID_105004]

value: ventromedial hypothalamus


title: CN from 20S [LID_105005]


title: DG from 6I4 [LID_105003]


title: aorta_594s_D12

value: aorta


title: aorta_594s_D13

value: 10 weeks


title: Pu from 3L5 [LID_105000]


title: aorta_594s_C24


title: aorta_594s_D07


title: aorta_594s_D05


title: aorta_594s_D06


title: aorta_594s_D02


title: aorta_594s_D11


title: aorta_594s_D08


title: aorta_594s_D04


title: aorta_594s_D10


title: aorta_594s_D01


title: aorta_594s_D09


title: aorta_594s_C23


title: aorta_594s_D03


title: aorta_594s_C19


title: aorta_594s_C21


title: aorta_594s_C18


title: aorta_594s_C17


title: aorta_594s_C22


title: aorta_594s_C20


title: aorta_594s_C16


title: M1 from 5N1 [LID_104979]


title: vlPFC from 4J3 [LID_104977]


title: STS from 4J3 [LID_104980]


title: vmPFC from 0K1 [LID_104981]

value: ventromedial prefrontal cortex

value: low


title: STS from 5H7 [LID_104983]

value: superior temporal sulcus


title: M1 from 8K7 [LID_104978]

value: primary motor cortex


title: AMY from 4C6 [LID_104982]

value: amygdala


title: AMY from 94O [LID_104989]

value: high


title: LGN from 9I7 [LID_104985]

value: female


title: LGN from 5N1 [LID_104987]


title: dmPFC from 1B7 [LID_104990]


title: CA3 from 3L6 [LID_104996]

value: cornu ammonis 3


title: dlPFC from 9C6 [LID_104986]

value: dorsolateral prefrontal cortex


title: M1 from 9I5 [LID_104988]


title: ACCg from 3L6 [LID_104993]

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: LGN from 5H7 [LID_104999]

value: lateral geniculate nucleus

value: male


title: ACCg from 48V [LID_104995]

value: mid


title: ACCg from 2C7 [LID_104994]


title: vmPFC from 48V [LID_104998]


title: VMH from 4J0 [LID_104991]


title: CA3 from 36O [LID_104997]


title: STS from 48V [LID_104984]


title: VMH from 9I7 [LID_104975]


title: M1 from 5H7 [LID_104976]


title: dmPFC from 65Z [LID_104974]

value: dorsomedial prefrontal cortex


title: aorta_594s_C14


title: vlPFC from 2C7 [LID_104972]

value: ventrolateral prefrontal cortex


title: aorta_594s_C13

value: aorta


title: aorta_594s_C12

value: 10 weeks


title: aorta_594s_C11


title: dlPFC from 3A6 [LID_104971]


title: aorta_594s_C10


title: aorta_594s_C06


title: aorta_594s_C15


title: VMH from 3A6 [LID_104967]

value: ventromedial hypothalamus


title: vlPFC from 9N0 [LID_104965]


title: aorta_594s_C03


title: aorta_594s_C09


title: aorta_594s_C08


title: V1 from 22H [LID_104966]

value: primary visual cortex


title: CN from 94O [LID_104968]

value: caudate nucleus


title: VMH from 5B6 [LID_104963]


title: Pu from 8L6 [LID_104962]

source_name: putamen

value: putamen

value: low


title: vlPFC from 3A9 [LID_104961]


title: VMH from 94S [LID_104964]


title: aorta_594s_C05


title: aorta_594s_C01


title: aorta_594s_B24


title: aorta_594s_C07


title: aorta_594s_C02


title: vlPFC from 9C6 [LID_104959]


title: aorta_594s_B23


title: dmPFC from 20S [LID_104960]


title: dmPFC from 7L0 [LID_104970]


title: aorta_594s_C04


title: dmPFC from 9I7 [LID_104958]


title: aorta_594s_B22


title: DG from 80S [LID_104969]

value: dentate gyrus


title: VMH from 5N1 [LID_104957]

value: female


title: aorta_594s_B20


title: aorta_594s_B21


title: V1 from 3A9 [LID_104956]


title: aorta_594s_B19


title: LGN from 2E9 [LID_104955]


title: aorta_594s_B17


title: aorta_594s_B16


title: dmPFC from 5H7 [LID_104950]


title: aorta_594s_B18


title: AMY from 9I7 [LID_104952]

value: amygdala


title: Pu from 20S [LID_104953]


title: LGN from 9N0 [LID_104954]

value: high


title: dmPFC from 5N1 [LID_104949]


title: aorta_594s_B15


title: V1 from 48V [LID_104948]


title: aorta_594s_B14


title: aorta_594s_B12


title: aorta_594s_B13


title: LGN from 3A6 [LID_104946]


title: dlPFC from 6I4 [LID_104947]

value: dorsolateral prefrontal cortex


title: aorta_594s_B10


title: M1 from 4C6 [LID_104945]

value: primary motor cortex


title: aorta_594s_B11


title: Pu from 5H7 [LID_104944]

value: male


title: aorta_594s_B09


title: aorta_594s_B07


title: M1 from 0K1 [LID_104951]


title: aorta_594s_B06


title: VMH from 9I5 [LID_104941]

value: mid


title: Pu from 6I4 [LID_104942]


title: Pu from 3L6 [LID_104943]


title: LGN from 6I4 [LID_104940]

value: lateral geniculate nucleus


title: CA3 from 6H6 [LID_104939]

value: cornu ammonis 3


title: aorta_594s_B05

value: aorta


title: aorta_594s_B04

value: 10 weeks


title: aorta_594s_B03


title: aorta_594s_B02


title: aorta_594s_A22


title: aorta_594s_A23


title: aorta_594s_A21


title: DG from 9I5 [LID_104937]


title: aorta_594s_A19


title: LGN from 22H [LID_104934]


title: Pu from 8K7 [LID_104936]


title: Pu from 3A6 [LID_104933]


title: Pu from 1B7 [LID_104938]


title: aorta_594s_A20


title: M1 from 4J3 [LID_104931]


title: vlPFC from 5N1 [LID_104935]

value: ventrolateral prefrontal cortex


title: aorta_594s_A18


title: AMY from 80S [LID_104932]


title: aorta_594s_B08


title: Pu from 2C7 [LID_104930]


title: aorta_594s_A16


title: VMH from 6H6 [LID_104929]

value: ventromedial hypothalamus


title: aorta_594s_A15


title: dmPFC from 36O [LID_104928]

value: dorsomedial prefrontal cortex


title: aorta_594s_A13


title: dmPFC from 2E9 [LID_104927]


title: aorta_594s_A17


title: DG from 20S [LID_104926]


title: aorta_594s_A12


title: aorta_594s_A08


title: M1 from 22H [LID_104924]


title: M1 from 2C7 [LID_104925]


title: aorta_594s_A11


title: M1 from 9I7 [LID_104918]


title: aorta_594s_A04


title: vlPFC from 9I5 [LID_104919]


title: aorta_594s_A05


title: aorta_594s_A06


title: aorta_594s_A09


title: aorta_594s_A14


title: VMH from 7L0 [LID_104917]


title: dlPFC from 4C6 [LID_104915]


title: aorta_594s_A03


title: dmPFC from 94S [LID_104922]


title: AMY from 9I5 [LID_104914]


title: aorta_594s_A02


title: aorta_594s_A10


title: aorta_594s_A07


title: aorta_594s_D19


title: vlPFC from 7L7 [LID_104913]


title: LGN from 3L6 [LID_104923]


title: Pu from 22H [LID_104916]

value: putamen


title: Pu from 9I7 [LID_104912]

value: low


title: dmPFC from 8K7 [LID_104911]


title: LGN from 8L6 [LID_104910]


title: 8_4_MMmANmF1C6

city: Madrid

first: Maria Jesus

last: Garcia Garcia

state: Madrid

address: Arzobispo Morcillo, sn

country: Spain

institute: Autonoma University of Madrid

description:
Illumina platform
C6_Fe_YES_1

data_processing:
Overall reads quality, total bases, total reads,  GC (%) and basic statistics are calculated.
Artifacts such as low quality reads, adaptor sequence,contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie.
Transcript abundances are measured with mapped read count within gene region.
Expression profiles are represented as read count and normalization values which are calculated  based on transcript length and depth of coverage. Normalization values are provided as FPKM  (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of  transcript per Million mapped reads)
Assembly: M.tuberculosis H37Rv ASM19595v2
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: Minimal media+Glycerol+AN+Fe,Stationary phase,biol rep1

extract_protocol:
RNA was harvested using KIT ZYMO (ZYMO RESEARCH).
1) Isolate the Total RNA from Sample of interest (Cell or Tissue).  2) Eliminate DNA contamination using DNase.  3) Choose an appropriate kit for library prep process depending on the types of RNA. For mRNA with  poly-A tail, use mRNA purification kit; for non-coding RNAs, such as lincRNA, use ribo-zero RNA  removal Kit to purify RNA of interest.  4) Randomly fragment purified RNA for short read sequencing.  5) Reverse transcribe fragmented RNA into cDNA.  6) Ligate adapters onto both ends of the cDNA fragments.  7) After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For  paired-end sequencing, both ends of the cDNA is sequenced by the read length.

tag: treatment

value: iron

tag: phase

value: Stationary


title: 8_4_MMmAN_F1C6

description:
Illumina platform
C6_Fe_NO_1

source_name: Minimal media+Glycerol+AN-Fe,Stationary phase,biol rep1

value: iron-free


title: 8_4_MMmAN_F2C6

description:
Illumina platform
C6_Fe_NO_2

source_name: Minimal media+Glycerol+AN-Fe,Stationary phase,biol rep2


title: Sample 14_Petals Col-0  ZT16 biol rep 2

city: Sevilla

first: Federico

last: Valverde

address: c/Americo Vespucio 49

institute: CSIC

data_processing:
The quality analysis was carried out using FASTQC.
Mapping against the reference genome TAIR10 from A. thaliana with HISAT2.
For transcript assembly and gene expression estimation in FPKM (fragments per exon kilobase and million mapped reads) the Stringtie2 software and R bioconductor package Ballgown v2.20 were used.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Petals

growth_protocol: Plants were grown in controlled cabinets on peat-based compost. Seeds were previously incubated for 4 days at 4°C in the dark before sowing under LD (16 h light, 8 h dark) cycles with temperatures ranging from 22°C (day) to 18°C (night).

extract_protocol:
Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega) from 10-day-old whole seedlings or petals following the manufacturer ́s instructions.
Libraries were prepared using 250 ng of total RNA with wit the Illumina TruSeq Stranded mRNA protocol according to the manufacturer’s instructions.

treatment_protocol: All plants were subjected to LD cycles, and samples collected at either ZT4 or ZT16.

value: Petals

tag: genotype

value: WT Col-0

value: LD ZT16


title: Sample 13_Petals co-10 ZT4 biol rep 2

value: LD ZT4


title: Sample 15_Petals 35S:CO ZT16 biol rep 2


title: 19_4_MMmANmF1C5

description:
Illumina platform
C5_Fe_YES_1

source_name: Minimal media+Glycerol+AN+Fe,Exponential phase,biol rep1

value: Exponential


title: 19_4_MMmAN_F2C5

description:
Illumina platform
C5_Fe_NO_1

source_name: Minimal media+Glycerol+AN-Fe,Exponential phase,biol rep2


title: 8_4_MMmANmF2C6

description:
Illumina platform
C6_Fe_YES_2

source_name: Minimal media+Glycerol+AN+Fe,Stationary phase,biol rep2


title: 19_4_MMmANmF2C5

description:
Illumina platform
C5_Fe_YES_2

source_name: Minimal media+Glycerol+AN+Fe,Exponential phase,biol rep2


title: 19_4_MMmAN_F1C5

description:
Illumina platform
C5_Fe_NO_2

source_name: Minimal media+Glycerol+AN-Fe,Exponential phase,biol rep1


title: Pu from 4J3 [LID_104902]

value: female

value: mid


title: VMH from 3A9 [LID_104907]

source_name: ventromedial hypothalamus


title: VMH from 3L6 [LID_104905]

value: male


title: CN from 2C7 [LID_104904]

source_name: caudate nucleus

value: caudate nucleus


title: Sample 16_Petals co-10 ZT16 biol rep 2


title: Sample 11_Petals Col-0  ZT4 biol rep 2


title: M1 from 2E9 [LID_104906]

source_name: primary motor cortex

value: primary motor cortex


title: ACCg from 36O [LID_104898]

value: anterior cingulate cortex


title: CA3 from 48V [LID_104901]

value: cornu ammonis 3


title: M1 from 4N8 [LID_104903]


title: ACCg from 22H [LID_104897]


title: ACCg from 5H7 [LID_104899]


title: Sample 12_Petals 35S:CO ZT4 biol rep 2


title: Sample 10_Petals co-10 ZT16 biol rep 1


title: Sample 8_Petals Col-0  ZT16 biol rep 1


title: Sample 9_Petals 35S:CO ZT16 biol rep 1


title: dlPFC from 8L6 [LID_104895]

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex


title: AMY from 2C7 [LID_104909]

source_name: amygdala

value: amygdala

value: low


title: STS from 3A9 [LID_104894]

source_name: superior temporal sulcus

value: superior temporal sulcus


title: CA3 from 5H7 [LID_104900]

source_name: cornu ammonis 3


title: ACCg from 0K1 [LID_104896]

source_name: anterior cingulate cortex


title: LGN from 2C7 [LID_104893]

source_name: lateral geniculate nucleus

value: lateral geniculate nucleus


title: Sample 6_Petals 35S:CO ZT4 biol rep 1

value: Petals


title: vmPFC from 20S [LID_104890]

source_name: ventromedial prefrontal cortex

value: ventromedial prefrontal cortex


title: Sample 3_Seedlings 35S:CO biol rep 1

source_name: 10 day-old seedlings

value: 10 day-old seedlings

value: LD ZT16


title: VMH from 2C7 [LID_104891]

value: ventromedial hypothalamus


title: Sample 2_Seedlings Col-0 biol rep 2

value: WT Col-0


title: Sample 4_Seedlings 35S:CO biol rep 2


title: vmPFC from 3L6 [LID_104889]

value: mid


title: Sample 1_Seedlings Col-0 biol rep 1


title: dmPFC from 6I4 [LID_104885]

source_name: dorsomedial prefrontal cortex

value: dorsomedial prefrontal cortex

value: male


title: AMY from 3L6 [LID_104884]


title: Sample29 (med14-2-27C-Rep1)

city: University

first: Yongjian

last: Qiu

state: MS

address: 30 University Ave

department: Biology

institute: University of Mississippi

data_processing:
Base calling was performed using the RTA v2.11.3 software built into the NextSeq 500 instrument.
Demultiplexing and FASTQ file generation was performed with Illumina’s Basespace informatics platform.
Data analysis was performed using the Qiagen CLC Genomics Workbench (CLCGxWB) version 21 software. Sequencing reads were mapped to the A. thaliana reference genome (TAIR10/Araport11 genome release) using default parameters with a strand-specific alignment protocol. The “Differential Expression for RNA-Seq” tool in CLCGxWB software was used, using default parameters, to identify differentially expressed genes across samples.
Genome_build: TAIR10/Araport11 genome release
Supplementary_files_format_and_content: Excel file showing FPKM values for each Sample.

source_name: Seedlings

growth_protocol: Seeds were briefly rinsed with 70% ethanol and surface sterilized with bleach (3% sodium hypochlorite) for 10 min before being plated on half-strength Murashige and Skoog media supplemented with Gamborg’s vitamins, 0.5 mM MES (pH 5.7), and 0.8% agar. Seeds were stratified in the dark at 4 °C for 3-5 days to synchronize germination before treatment under specific light and temperature conditions in LED chambers.

extract_protocol:
Total RNA was extracted from 50-100 mg seedlings using the Zymo Research Quick-RNA Miniprep Kit with on-column DNase I digestion. RNA quality was assessed on the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated with 300 ng to 1 µg of RNA using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. The libraries were assessed for size and purity using the Agilent 2100 Bioanalyzer, and quantitated by qPCR using a KAPA Biosystems Library Quantitation kit. Libraries were normalized, pooled, and diluted to a loading concentration of 1.8 pM, loaded on an Illumina High-Output Flow Cell, and sequenced on the Illumina NextSeq 500 instrument.

treatment_protocol: Seedlings were grown at either 20 °C or 27 °C under continuous R light (50 µmol m-2 s-1) for 96 hours.  In all experiments, four biological replicate samples were used for each treatment, and RNA from each replicate was used to generate sequencing libraries.

tag: ecotype

value: 27 degrees for 96 h


title: vlPFC from 6H6 [LID_104886]

source_name: ventrolateral prefrontal cortex

value: ventrolateral prefrontal cortex

value: female


title: vlPFC from 94S [LID_104887]


title: M1 from 60T [LID_104888]

value: primary motor cortex


title: Sample31 (med14-2-27C-Rep3)


title: Sample32 (med14-2-27C-Rep4)


title: dlPFC from 4N8 [LID_104881]

value: dorsolateral prefrontal cortex


title: M1 from 65Z [LID_104880]

value: low


title: dmPFC from 48V [LID_104882]


title: Sample27 (med14-2-20C-Rep3)

value: 20 degrees for 96 h


title: vlPFC from 3L5 [LID_104892]


title: Sample24 (pif4-2-27C-Rep4)


title: Pu from 7L7 [LID_104883]

source_name: putamen

value: putamen


title: Sample26 (med14-2-20C-Rep2)


title: Sample 5_Petals Col-0  ZT4 biol rep 1

source_name: Petals

value: Petals

value: LD ZT4


title: Sample28 (med14-2-20C-Rep4)


title: Sample30 (med14-2-27C-Rep2)


title: Sample 7_Petals co-10 ZT4 biol rep 1


title: Sample25 (med14-2-20C-Rep1)


title: vlPFC from 8L6 [LID_104879]


title: vmPFC from 22H [LID_104878]

value: ventromedial prefrontal cortex


title: Sample23 (pif4-2-27C-Rep3)


title: LGN from 94O [LID_104877]

value: lateral geniculate nucleus

value: high


title: Sample19 (pif4-2-20C-Rep3)


title: Sample20 (pif4-2-20C-Rep4)


title: Sample21 (pif4-2-27C-Rep1)


title: Sample17 (pif4-2-20C-Rep1)


title: vlPFC from 3L6 [LID_104874]


title: Sample18 (pif4-2-20C-Rep2)


title: LGN from 9C6 [LID_104876]


title: Sample15 (Col-0-27C-Rep3)

value: WT


title: vlPFC from 4N8 [LID_104870]

value: mid


title: Sample16 (Col-0-27C-Rep4)


title: Pu from 3A9 [LID_104873]


title: Sample14 (Col-0-27C-Rep2)


title: LGN from 4J0 [LID_104868]


title: Sample12 (Col-0-20C-Rep4)


title: Sample13 (Col-0-27C-Rep1)


title: vmPFC from 6I4 [LID_104866]


title: Sample11 (Col-0-20C-Rep3)


title: Sample10 (Col-0-20C-Rep2)


title: Sample22 (pif4-2-27C-Rep2)


title: vmPFC from 2C7 [LID_104867]


title: M1 from 49Z [LID_104865]


title: Sample9 (Col-0-20C-Rep1)


title: LGN from 6H6 [LID_104875]


title: dmPFC from 22H [LID_104864]

value: dorsomedial prefrontal cortex


title: CN from 8K7 [LID_104872]

value: caudate nucleus


title: dlPFC from 60T [LID_104863]

value: male


title: M1 from 20S [LID_104871]


title: Pu from 80S [LID_104869]


title: CN from 0K1 [LID_104862]


title: Sample5 (hmr-22-27C-Rep1)

value: 27 degrees for 96 h


title: Sample3 (hmr-22-20C-Rep3)


title: Sample7 (hmr-22-27C-Rep3)


title: CA3 from 80S [LID_104859]

value: cornu ammonis 3

value: female


title: vlPFC from 65Z [LID_104860]

value: ventrolateral prefrontal cortex


title: Sample1 (hmr-22-20C-Rep1)


title: Sample4 (hmr-22-20C-Rep4)


title: Sample2 (hmr-22-20C-Rep2)


title: DG from 2C7 [LID_104857]

source_name: dentate gyrus

value: dentate gyrus

value: low


title: M1 from 94S [LID_104856]

value: primary motor cortex


title: Sample8 (hmr-22-27C-Rep4)


title: Diabetic treated with Simvastatin2_rep4_Ampliseq

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: Read counts_Diabetic.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg19 whole genome using bowtie2
Peaks were called against sequenced input chromatin using MACS2
Differences in peaks between conditions were detected by using Manorm2
Genome_build: hg19
Supplementary_files_format_and_content: Peaks in bigWig format
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: hiPSC-ECs

extract_protocol:
hiPSC-ECs RNA was harvested using Trizol reagent. ATAC-seq DNA was extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218). Genomic DNA was clarified from sonicated nuclei and YAP-DNA complexes were isolated with antibody.
RNA Libraries prepared from 10ng RNA, Sequencing data was un-stranded, ERCC spike-in (Ambion) used for data normalization.  ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (Illumina). ChIP-seq libaries were prepared following Zymo Spin-ChIP kit protocol from Zymo Research.

value: hiPSC-ECs

value: diabetic modeling plus simvastatin


title: vmPFC from 9I7 [LID_104858]

value: ventromedial prefrontal cortex


title: Sample6 (hmr-22-27C-Rep2)


title: M1 from 4N7 [LID_104855]


title: Diabetic treated with Simvastatin2_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: vmPFC from 9I5 [LID_104853]


title: VMH from 9C6 [LID_104861]

source_name: ventromedial hypothalamus

value: ventromedial hypothalamus


title: DG from 9C6 [LID_104854]


title: AMY from 5H7 [LID_104851]

value: amygdala


title: VMH from 9N0 [LID_104852]

value: high


title: Diabetic treated with Simvastatin2_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic treated with Simvastatin1_rep3_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic treated with Simvastatin2_rep3_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic treated with Simvastatin1_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic treated with Simvastatin1_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: DG from 9N0 [LID_104848]


title: dmPFC from 4N7 [LID_104849]


title: Diabetic treated with Simvastatin1_rep4_Ampliseq

description: Read counts_Diabetic.txt


title: LGN from 4N7 [LID_104850]

value: lateral geniculate nucleus


title: Diabetic2_rep4_Ampliseq

description: Read counts_Diabetic.txt

value: diabetic modeling


title: Diabetic2_rep3_Ampliseq

description: Read counts_Diabetic.txt


title: VMH from 0K1 [LID_104847]


title: STS from 80S [LID_104846]

value: superior temporal sulcus


title: Diabetic2_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic2_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic1_rep4_Ampliseq

description: Read counts_Diabetic.txt


title: Diabetic1_rep3_Ampliseq

description: Read counts_Diabetic.txt


title: LGN from 20S [LID_104843]

value: mid


title: Diabetic1_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: dmPFC from 9I5 [LID_104841]

value: dorsomedial prefrontal cortex


title: Diabetic1_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: DG from 48V [LID_104842]


title: Healthy Control2_rep3_Ampliseq

description: Read counts_Diabetic.txt

value: no treatment


title: Healthy Control2_rep4_Ampliseq

description: Read counts_Diabetic.txt


title: vlPFC from 7L0 [LID_104845]

value: female


title: CN from 5H7 [LID_104838]

source_name: caudate nucleus

value: caudate nucleus

value: male


title: LGN from 4J3 [LID_104840]


title: dmPFC from 4J3 [LID_104834]


title: VMH from 6I4 [LID_104839]


title: M1 from 6H6 [LID_104837]

source_name: primary motor cortex


title: dlPFC from 49Z [LID_104836]

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex

value: low


title: Healthy Control1_rep3_Ampliseq

description: Read counts_Diabetic.txt

value: hiPSC-ECs


title: Healthy Control1_rep4_Ampliseq

description: Read counts_Diabetic.txt


title: Pu from 7L0 [LID_104844]

value: putamen


title: Healthy Control1_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: Pu from 4N8 [LID_104832]


title: Healthy Control2_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: Healthy Control1_rep1_Ampliseq

description: Read counts_Diabetic.txt


title: V1 from 8K7 [LID_104831]

source_name: primary visual cortex

value: primary visual cortex


title: Simvastatin3_rep4_Ampliseq

description: Read counts_Simvastatin.txt

value: simvastatin


title: VMH from 80S [LID_104833]

value: ventromedial hypothalamus


title: Simvastatin3_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: vlPFC from 1B7 [LID_104830]

value: ventrolateral prefrontal cortex

value: high


title: vlPFC from 4C6 [LID_104829]


title: Healthy Control2_rep2_Ampliseq

description: Read counts_Diabetic.txt


title: Simvastatin3_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: Pu from 36O [LID_104828]


title: Simvastatin3_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: STS from 4J0 [LID_104827]

source_name: superior temporal sulcus


title: vmPFC from 36O [LID_104826]

value: ventromedial prefrontal cortex


title: Simvastatin2_rep4_Ampliseq

description: Read counts_Simvastatin.txt


title: Simvastatin2_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: Simvastatin2_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: vlPFC from 49Z [LID_104825]


title: Simvastatin1_rep4_Ampliseq

description: Read counts_Simvastatin.txt


title: V1 from 5H7 [LID_104822]


title: Simvastatin1_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: Simvastatin2_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: Pu from 65Z [LID_104824]


title: ACCg from 4C6 [LID_104821]

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: Simvastatin1_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: vmPFC from 8K7 [LID_104823]


title: Control3_rep4_Ampliseq

description: Read counts_Simvastatin.txt

value: DMSO


title: dlPFC from 0K1 [LID_104819]


title: VMH from 1B7 [LID_104818]


title: LGN from 49Z [LID_104820]

source_name: lateral geniculate nucleus

value: lateral geniculate nucleus


title: Control3_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: Simvastatin1_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: Control3_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: Control3_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: CN from 4C6 [LID_104816]

value: mid


title: dmPFC from 4C6 [LID_104817]

value: dorsomedial prefrontal cortex


title: Control2_rep4_Ampliseq

description: Read counts_Simvastatin.txt


title: Control2_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: V1 from 9I7 [LID_104814]

value: female


title: Control2_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: V1 from 94O [LID_104815]

value: male


title: Control2_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: STS from 4N8 [LID_104812]

value: superior temporal sulcus


title: V1 from 4N8 [LID_104813]


title: V1 from 3A6 [LID_104810]

value: low


title: STS from 2E9 [LID_104811]


title: DG from 4N8 [LID_104808]

value: dentate gyrus


title: CA3 from 0K1 [LID_104809]

source_name: cornu ammonis 3

value: cornu ammonis 3


title: Control1_rep4_Ampliseq

description: Read counts_Simvastatin.txt

value: hiPSC-ECs


title: Control1_rep2_Ampliseq

description: Read counts_Simvastatin.txt


title: Control1_rep1_Ampliseq

description: Read counts_Simvastatin.txt


title: Control1_rep3_Ampliseq

description: Read counts_Simvastatin.txt


title: V1 from 6I4 [LID_100820]

value: primary visual cortex


title: CA3 from 9I7 [LID_104807]


title: DG from 2E9 [LID_104806]


title: V1 from 4C6 [LID_100818]


title: DG from 36O [LID_100819]


title: CN from 65Z [LID_100817]

value: caudate nucleus


title: V1 from 2C7 [LID_100816]


title: Exosc3 fl/fl Cre- 2

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned to the genome using STAR v2.5.3a
Gene abundances were estimated using RSEM v1.3.0 with parameters "--star --forward-prob 0 --paired-end"
Assembly: mm39/GRCm39, GENCODE M28 annotation with GFP sequences added
Supplementary files format and content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file

organism: Mus musculus domesticus

source_name: liver

extract_protocol:
E14.5 embryos were harvested, and fetal liver cells were dissociated in single cell suspension. Cells were stained with antibodies, and GFP+ Lin- Kit+ CD24/71 10%low BFU-Es were sorted for RNA-seq analyses. Cell pellet was resuspended in RLT buffer 1% 𝛃-mercaptoethanol and RNA was extracted using Qiagen RNeasy Micro kit (#74004).
Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Library Prep

value: Exosc3-floxed and Vav1-Cre

tag: age id

value: liver

tag: tissue id

value: BFU-E

tag: cell type_id

value: Exosc3 fl/fl Cre-


title: Exosc3 fl/fl Cre+ 2

value: Exosc3 fl/fl Cre+


title: Exosc3 fl/fl Cre- 3


title: Exosc3 fl/fl Cre- 1


title: Exosc3 fl/fl Cre+ 3


title: Exosc3 fl/fl Cre+ 1


title: CN from 49Z [LID_100815]

tag: individual id

tag: dominance rank


title: STS from 94O [LID_100814]

tag: tissue

tag: age

value: high


title: CA3 from 49Z [LID_100813]

tag: Sex


title: VX_KJ_LATS-S9-3

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

description: Gene expression data from EYFP+ cells isolated from LATS1/2f/f;Sox9f/f;lsl-EYFP;K8CreERT2  mice.

data_processing:
FASTQ files were generated and demultiplexed using the Illumina BaseSpace platform.
FASTQ files were aligned to the mouse genome (mm10) using STAR v2.6.0c.
Quality control was performed using FastQC v0.11.7 and RSeQC v3.0.0
Transcript and gene level counts were generated using featureCounts from Subread R package v1.6.2 with Ensembl annotation build 100
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Mice mammary gland EYFP+ cells

growth_protocol: Adult nulliparous mice of the indicated genotypes were used.

extract_protocol:
EYFP+ live cells were isolated using FACS. Calcein blue AM (Invitrogen) was used as a live cell marker at a concentration of 1 µM.
FACS-sorted cells were lysed using Trizol LS. RNA was extracted using MaXtract high density columns (Qiagen) and the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the Illumina® TruSeq® RNA Sample Preparation Kit v2 according to the manufacturer's protocol.

treatment_protocol: Mice were treated with 2 mg of Tamoxifen (Sigma) diluted in corn oil (Sigma) via intraperitoneal injection on five consecutive days to induce Cre activity. Seven days after the last Tamoxifen dose, the third, fourth, and fifth pairs of mammary glands were excised and dissociated for FACS.

value: Mammary gland


title: VX_KJ_LATS-S9-1


title: VX_KJ_LATS-S9-2


title: VX_KJ_LATS-3

description: Gene expression data from EYFP+ cells isolated from LATS1/2f/f;lsl-EYFP;K8CreERT2 mice.


title: MYB52R2

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

data_processing:
FASTQ files were imported in pairs in CLC genomics workbench v8.0.1 discarding poor-quality reads (<Q30). For each library, reads were trimmed and filtered using the following criteria: sequence quality <0.01, no ambiguous nucleotides, minimum read length >35 nucleotides, trimming against the Illumina adaptor sequence, and finally a hard trim of 10 nucleotides at the 5’ end and 2 nucleotides at the 3’ end. The filtered reads were mapped to the N. benthamiana transcriptome v5-primary transcript (Nakasugi et al., 2014) obtained from the N. benthamiana genome and transcriptome website (http://benthgenome.qut.edu.au/) with the following criteria: a mismatch, gap and insertion cost on the maximum settings (3=stringent mapping), reads should have 80% identity and 90% coverage to the reference transcriptome. An additional annotation of the transcriptome was performed against the A. thaliana database using BLAST2GO Pro v3.0. Expression values were calculated using the RPKM (Reads per kilobase transcript per million reads) method (Mortazavi et al., 2008). In order to determine the differentially expressed genes between the tobacco leaves infiltrated with p103::MD05G1011100/pBIN61-p19 and p103-empty/pBIN61-P19, a Baggerley’s ‘on proportions’ weighted test (Baggerly et al., 2003) combined with a false discovery rate correction (Benjamini-Hotchberg) set at 0.05 was used. Expression cut-off values were set at 2-fold increase/decrease and 10 RPKM difference, respectively.
Assembly: N. benthamiana transcriptome v5-primary and alternate transcript (Nakasuki et al. 2014)
Supplementary files format and content: tab-delimited text files include, unique and toal hit reads, RPKM values for each Sample fold change for each contig.

organism: Nicotiana benthamiana

source_name: Leaves

growth_protocol: Three A. tumefaciens GV3101-pMP90 strains (p103::MD05G1011100, p103-empty and pBIN61-p19) were grown in 50 mL of LB liquid medium supplemented with gentamycin (30 mg/L), rifampicin (10 mg/L), kanamycin (50 mg/L), and acetosyringone (30 mg/L). As A. tumefaciens is not sensitive to the CcdB protein, we used the p103-empty vector as control in the present work (Traore and Zhao, 2011).  The cultures in 100 mL Erlenmeyer flasks were agitated at 130 rpm/28°C for 48 h. After centrifugation (1000 g/10 min), cultures were re-suspended in infiltration buffer (20 mM MES, 20 mM MgSO4, 150 mg/L acetosyringone). After 3 hours, p103::MD05G1011100, p103-empty and pBIN61-p19 A. tumefaciens cultures were mixed and adjusted to OD600=0.8, 0.8 and 1, respectively.

extract_protocol:
total RNA were extracted from two groups (p103::MD05G1011100/pBIN61-p19 (overexpression) and P103 (empty vector)/pBIN61-p19 (control)) of agroinfiltrated leaves. Three and 4 biological replicates were used for RT-qPCR and RNA-Seq, respectively. Each biological replicate was comprised of a pool of 3 plants with 4 agroinfiltrated leaves per plant. Total RNA extracts were obtained using the RNeasy plant mini kit (QIAGEN, Leusden, The Netherlands) coupled with on-column DNase I treatment, following the manufacturer’s guidelines.  Total RNA integrity (RIN>8) and purity were assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a Nanodrop ND1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France), respectively. Total RNA was quantified using a Qubit RNA assay kit (Life technologies, Carlsbad, CA, USA). For gene isolation and RT-qPCR, reverse transcription was carried out as described in our previous work (Legay et al., 2015).
cDNA libraries were prepared from 20 ng mRNA using the SMARTer Stranded RNA-Seq kit according to the manufacturer’s guidelines (ClonTech laboratories, Mountain View, CA, USA). Libraries were analyzed and quantified as described in Legay et al. (2016). The pooled libraries were sequenced on an Illumina MiSeq using 4 consecutive runs (Illumina MiSeq reagent V3-150 cycles) to generate 76 base-pairs paired-end reads

treatment_protocol: Transient expression were performed using four-weeks old N. benthamiana plants. Each biological replicate was constituted by a pool of 3 plants where the four first leaves were infiltrated with 0.5 mL infiltration buffer using a 1 mL needleless syringe. For the RNA-Seq experiment, plants were divided into two groups, p103::MD05G1011100/pBIN61-p19 (overexpression) and p103-empty/pBIN61-P19 (control) with 4 biological replicates each and were collected 4 days after infiltration. All samples were flash frozen in liquid nitrogen directly after collection.

value: Leaves

tag: cell line

value: 4-week old


title: MYB52R3


title: MYB52R4


title: VX_KJ_LATS-2


title: VX_KJ_LATS-1


title: EMPTYR4

value: Infiltration with EmptyVector/pBIN(p19)


title: VX_KJ_CTL-3

description: Gene expression data from EYFP+ cells isolated from lsl-EYFP;K8CreERT2 control mice.

value: lsl-EYFP;K8CreERT2 + Tamoxifen


title: MYB52R1


title: CA3 from 65Z [LID_100811]

value: female

value: low


title: EMPTYR3


title: STS from 36O [LID_100812]

value: superior temporal sulcus


title: NPE-RMS-Tumor-11-030

city: Memphis

first: Alessandra

last: d'Azzo

state: TN

address: 262 Danny Thomas Place

department: Genetics

institute: St Jude Children's Research Hospital

description: Gene Expression from NPE RMS tumor

hyb_protocol: Five micrograms of cDNA was hybridized for 16 hours at 45ºC on a Clariom S Mouse GeneChip array.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: RMS tumor from  Neu1+/−/Ptch1+/−/ETV7 TG+/−  mouse

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: RMS tumors developed in the trunk and limb of Neu1+/−/Ptch1+/−/ETV7 TG+/− (NPE) and Ptch1+/−/ETV7 TG+/− (PE) mice

extract_protocol: Total RNA was isolated from mouse RMS tumors using the PureLink RNA Kit (Life Technologies) and DNA contaminants were removed on column with deoxyribonuclease I (Life Technologies), according to the manufacturer’s protocol.

treatment_protocol: Tumors were dissected and flash frozen in liquid nitrogen.

value: NPE RMS tumor


title: EMPTYR2


title: PE-RMS-Tumor-1-023

description: Gene Expression from PE RMS tumor

source_name: RMS tumor from Ptch1+/−/ETV7 TG+/−  mouse

value: PE RMS tumor


title: NPE-RMS-Tumor-12-031

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-9-010

description: Gene Expression from NPE RMS tumor


title: VX_KJ_CTL-2


title: VX_KJ_CTL-1


title: PE-RMS-Tumor-5-020

description: Gene Expression from PE RMS tumor


title: KO1

city: beijing

first: ZHANG

last: Tongjia

address: xueyuan Road 38

country: China

institute: peking university

data_processing:
HISAT2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using HISAT2
Read count extraction and normalization were performed using sequence using HISAT2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® mRNA Isolation Master Kit following manufacturer's protocols.

tag: strain


title: STS from 4C6 [LID_100809]

value: male

value: mid


title: KO2

value: liver


title: KO3


title: PE-RMS-Tumor-2-021

description: Gene Expression from PE RMS tumor


title: PE-RMS-Tumor-6-034

description: Gene Expression from PE RMS tumor


title: NPE-RMS-Tumor-13-005

description: Gene Expression from NPE RMS tumor


title: CN from 3A6 [LID_100810]

value: caudate nucleus


title: EMPTYR1


title: ACCg from 1B7 [LID_100808]

value: anterior cingulate cortex


title: WT3

value: WT


title: PE-RMS-Tumor-3-018

description: Gene Expression from PE RMS tumor


title: WT2


title: PE-RMS-Tumor-7-035

description: Gene Expression from PE RMS tumor


title: AMY from 9N0 [LID_100807]

source_name: amygdala

value: amygdala

value: high


title: K326-8h-rep3

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

data_processing:
the quality of raw read was processed using FastQC
Adapter contamination and poor-quality bases were removed using Trimmomatic
Hisat2  was used to align clean reads to the tobacco reference genome.
FeatureCounts was used for counting number of reads and FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values, representing gene expression levels.
Assembly: Nitab-v4.5
Supplementary files format and content: tobacco_FPKM.txt( FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values)

organism: Nicotiana tabacum

source_name: Seeds of K326,drought 8 hour,rep3

growth_protocol: Seeds of K326 and its derived EMS mutant, M28 with enhanced drought resistance, were sterilized and pretreated in 4℃ for 2 days. The pretreated seeds were put in pot with nutrient soil for germination. The germinated seedlings with fully expanded cotyledons were transferred into small pots. Each pot contained the exact same amount (120g) of nutrient soil, 10 seedlings per pot for each replicate, total three replicates for K326 or M28. All pots were randomly put in the incubator to grow under 22±1℃,16h/8h light-dark cycle and 70% humidity.

extract_protocol:
Total RNA was extracted using collected leaves with ND and SD at 0, 1, 2, 4 and 8h. After completely removal of genomic DNA contamination, mRNA was enriched for RNA-seq library preparation following the kit instruction.
After completely removal of genomic DNA contamination, mRNA was enriched for RNA-seq library preparation following the kit instruction.

treatment_protocol: At the five full leaves stage, each pot with 3 similar sized seedlings was fully watered, and then all pots for K326 or M28 were randomly divided into 3 parts for drought treatment, natural drought (ND) treatment and 200 mM mannitol for simulated drought (SD) treatment.Total RNA was extracted using collected leaves with ND and SD at 0, 1, 2, 4 and 8h.

value: leaf

value: drought 8h


title: K326-8h-rep2

source_name: Seeds of K326,drought 8 hour,rep2


title: STS from 2C7 [LID_100806]


title: 7-META

city: Taipei

first: Ying Chih

last: Chang

state: Taipei City

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description:
the cell line derived from the lung metastasized tumors which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample10

data_processing:
HISAT2 (v2.1.0) for mapping reads to the mouse genome (GRCm38.96)
StringTie (v2.0.3) for transcript assembly
DESeq2 (v1.26.0) for data normalization
Genome_build: GRCm38.96
Supplementary_files_format_and_content: bam

source_name: lung metastasis

extract_protocol: The library was prepared using illumine Truseq standard total RNA library preparation kit and followed by paired-end RNA sequencing using illumina HiSeq 2500 system.

value: NOD-SCID-GAMMA

value: lung metastasis


title: NPE-RMS-Tumor-3-002

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-5-001

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-6-003

description: Gene Expression from NPE RMS tumor


title: K326-4h-rep3

source_name: Seeds of K326,drought 4 hour,rep3

value: drought 4h


title: ACCg from 65Z [LID_100805]

value: female

value: low


title: NPE-RMS-Tumor-7-028

description: Gene Expression from NPE RMS tumor

value: NPE RMS tumor


title: 3-META

description:
the cell line derived from the lung metastasized tumors which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample9


title: NPE-RMS-Tumor-2-007

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-1-004

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-4-032

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-10-022

description: Gene Expression from NPE RMS tumor


title: NPE-RMS-Tumor-8-029

description: Gene Expression from NPE RMS tumor


title: V1 from 9I5 [LID_100804]

value: primary visual cortex


title: NPE-RMS-Tumor-14-009

description: Gene Expression from NPE RMS tumor


title: K326-4h-rep2

source_name: Seeds of K326,drought 4 hour,rep2


title: PE-RMS-Tumor-4-019

description: Gene Expression from PE RMS tumor

value: PE RMS tumor


title: K326-8h-rep1

source_name: Seeds of K326,drought 8 hour,rep1


title: WT1


title: DG from 94O [LID_100803]

source_name: dentate gyrus

value: dentate gyrus

value: male


title: 6-CTC

description:
the cell line derived from the CTCs which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample7

source_name: circulating tumor cell

value: circulating tumor cell


title: ACCg from 3A6 [LID_100802]

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: 5-META

description:
the cell line derived from the lung metastasized tumors which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample8


title: Hepatocyte_48h_rep1

city: Hang Zhou

first: jiang

last: zhengyi

state: State...

address: Qingchun  79 Road

institute: Zhejiang University

description: Gene expression at 48h in replicate1 of primary hepatocytes

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Rat lncRNA Microarray V3  for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1(Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan setting  for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction software using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Rat primary hepatocyte, 48h, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer's instructions, followed by  RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with theNanoDrop ND-2000  Spectrophotometer.

growth_protocol: Primary hepatocytes isolated from rat liver were resuspended in William's E medium supplemented with 10% FBS (GBICO), 1% ITS, dexamethasone, 1 X L-glutamine/ penicillin /streptomycin and plated onto collagen-I-coated plate at the density of 6× 105 cells/ml.   After 3 hours, non-attached cells were washed away and the medium was replaced with William's E free of FBS.

extract_protocol: RNA was prepared using the RNasey Mini Kit (Qiagen p/n 74104) following the manufacturer's recommendations.

treatment_protocol: The treatment in our study in the different length of in vitro culture.

tag: cell

value: primary hepatocyte

tag: gender

tag: weight


title: 3-CTC

description:
the cell line derived from the CTCs which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample6


title: K326-4h-rep1

source_name: Seeds of K326,drought 4 hour,rep1

tag: treatment


title: 1-CTC

description:
the cell line derived from the CTCs which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample5


title: K326-2h-rep3

source_name: Seeds of K326,drought 2 hour,rep3

value: drought 2h


title: K326-2h-rep2

source_name: Seeds of K326,drought 2 hour,rep2


title: K326-2h-rep1

source_name: Seeds of K326,drought 2 hour,rep1


title: ACCg from 4N7 [LID_100800]

value: high


title: ACCg from 5B6 [LID_100801]


title: K326-1h-rep3

source_name: Seeds of K326,drought 1 hour,rep3

value: leaf

value: drought 1h


title: 8-PRI

description:
the cell line derived from the primary tumor xenograft which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample4

source_name: fat pad xenograft

value: NOD-SCID-GAMMA

value: fat pad xenograft


title: Hepatocyte_24h_rep2

description: Gene expression at 24h in replicate2 of primary hepatocytes

source_name: Rat primary hepatocyte, 24h, replicate2


title: 7-PRI

description:
the cell line derived from the primary tumor xenograft which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample3


title: ACCg from 9N0 [LID_100798]


title: Hepatocyte_48h_rep2

description: Gene expression at 48h in replicate2 of primary hepatocytes

source_name: Rat primary hepatocyte, 48h, replicate2


title: Hepatocyte_24h_rep3

description: Gene expression at 24h in replicate3 of primary hepatocytes

source_name: Rat primary hepatocyte, 24h, replicate3


title: Hepatocyte_48h_rep3

description: Gene expression at 48h in replicate3 of primary hepatocytes

source_name: Rat primary hepatocyte, 48h, replicate3


title: K326-1h-rep2

source_name: Seeds of K326,drought 1 hour,rep2


title: 5-PRI

description:
the cell line derived from the primary tumor xenograft which was originated from the CTCs isolated from orthotopically inoculated spontaneous metastasized 4T1-hHER2-Luc-derived NSG mice
Sample2


title: ACCg from 49Z [LID_100797]


title: Hepatocyte_24h_rep1

description: Gene expression at 24h in replicate1 of primary hepatocytes

source_name: Rat primary hepatocyte, 24h, replicate1


title: Hepatocyte_12h_rep3

description: Gene expression at 12h in replicate3 of primary hepatocytes

source_name: Rat primary hepatocyte, 12h, replicate3


title: Hepatocyte_12h_rep2

description: Gene expression at 12h in replicate2 of primary hepatocytes

source_name: Rat primary hepatocyte, 12h, replicate2


title: Hepatocyte_12h_rep1

description: Gene expression at 12h in replicate1 of primary hepatocytes

source_name: Rat primary hepatocyte, 12h, replicate1


title: 4T1-hHER2

description:
lentivirus infection with stable human-HER2-Luciferase expression
Sample1

source_name: mammary gland

value: mammary gland


title: V1 from 4J3 [LID_100799]

source_name: primary visual cortex

value: female

value: mid


title: Hepatocyte_6h_rep2

description: Gene expression at 6h in replicate2 of primary hepatocytes

source_name: Rat primary hepatocyte, 6h, replicate2


title: V1 from 49Z [LID_100795]

value: low


title: V1 from 5B6 [LID_100796]

value: primary visual cortex


title: Hepatocyte_6h_rep3

description: Gene expression at 6h in replicate3 of primary hepatocytes

source_name: Rat primary hepatocyte, 6h, replicate3


title: K326-0h-rep3

source_name: Seeds of K326,Control,rep3

value: drought 0h


title: Fructose diet Rbfox2 knockout liver_sample3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm10 whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome Ensembl GRCm38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Liver

extract_protocol:
Livers were removed from fasted mice and flash frozen in liquid nitrogen RNA was harvested using the Qiagen RNAeasy kit with Dnase treatment. RNA was quanified by Agilent 2100 bioanalsyer.
PolyA enrichment was performed using NEBNext Poly(A) mRNA magnetic Isolation and libraries prepared using NEBNext Ultra II RNA Library Prep kit for Illumina

value: Rbfox2 knockout

value: Liver

tag: weeks on diet

value: 30% (w/v) Fructose supplemented water


title: Fructose diet Rbfox2 knockout liver_sample2

tag: genotype


title: K326-0h-rep2

source_name: Seeds of K326,Control,rep2


title: Fructose diet Rbfox2 knockout liver_sample1


title: K326-0h-rep1

source_name: Seeds of K326,Control,rep1


title: V1 from 2E9 [LID_100793]


title: K326-1h-rep1

source_name: Seeds of K326,drought 1 hour,rep1


title: V1 from 7L7 [LID_100794]


title: M28-8h-rep3

source_name: Seeds of M28,drought 8 hour,rep3

value: EMS mutant

value: drought 8h


title: Fructose diet wild-type liver_sample5

value: wild-type


title: Fructose diet wild-type liver_sample4


title: M28-8h-rep2

source_name: Seeds of M28,drought 8 hour,rep2


title: V1 from 9C6 [LID_100791]

value: male


title: M28-8h-rep1

source_name: Seeds of M28,drought 8 hour,rep1

value: leaf


title: DG from 49Z [LID_100790]

source_name: dentate gyrus

value: dentate gyrus


title: Swap3-iRFP-Low

city: New York

first: Hani

last: Shayya

state: New York

address: 3227 Broadway

department: Biochemistry and Mol Biophysics

institute: Columbia University

data_processing:
Transcript annotations were downloaded from Ensembl (GRCm38, Ensembl version 92). Extended OR gene models were included from Ibarra-Soria et al., PLOS Genetics, 2014. The coding sequence for each extended OR gene model was annotated based on the Ensembl annotations for that OR. Only transcripts from a localized contig and containing an annotated coding sequence were retained in the final transcript set.
A fasta file of transcript sequences was generated using the GRCm38 (mm10) sequence, the above annotation set and custom python scripts. Sequences were indexed using salmon (version 0.13.1, -k 31).
Demultiplexed fastq files were quantified against the reference transcriptome using Salmon (version 0.13.1, --libType A, --seqBias, --gcBias, --validateMappings).
Assembly: mm10
Supplementary files format and content: Tab-delimited quant.sf files generated by Salmon. Each row is a transcript (ENSMUST = Ensembl transcripts, CUFFORT = extended OR gene models, egfp/tdtomato/lacZ as above). Columns indicate Length (nt), EffectiveLength (as modeled by Salmon), TPM (abundance in transcripts per million) and NumReads (expected number of reads originating from each transcript).

source_name: Olfactory epithelium

extract_protocol:
For experiments on OSN developmental populations (INPs, iOSNs, mOSNs), cells were sorted across multiple days, pelleted (10 minutes at 800g) and frozen at -80 until the day of extraction. Lysates were prepared from roughly 1e6 cells per condition using a lysis buffer (20mM Tris pH=7.5, 150mM NaCl, 5mM MgCl2, 1mM DTT, 100ug/mL cycloheximide, 1%(v/v) Triton X-100 and 25U/mL TURBO DNase), RNA was quantified by Quant-iT RiboGreen assay (Thermo Fisher) and lysate containing 100ng of RNA was mixed with 300uL of Trizol (Invitrogen). In all other experiments, 10-20k cells were sorted directly into 500uL of Trizol LS (Sigma). RNA was recovered from Trizol using the Direct-Zol RNA Miniprep kit (Zymo), precipitated overnight with 300mM sodium acetate and 1.5 volumes of isopropanol, digested for 30min at 37°C with TURBO DNase (Invitrogen) and cleaned up on 1.8x Ampure Beads (Beckman Coulter). <10ng RNA was used for library prep, as measured by Quant-iT RiboGreen assay.
Libraries were prepared using the SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio) and the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed by decapitation (if younger than postnatal day 14) or CO2 followed by cervical dislocation, and the main olfactory epithelium (MOE) was isolated by dissection into ice-cold 1xPBS without calcium or magnesium. Single-cell suspensions were prepared using a papain dissociation system (Worthington) following a modified version of the manufacturer’s protocol. Dissociations were for 30-45 minutes at 37°C, centrifugation steps for 5min at 400g and the discontinuous density gradient was not performed. Cells were re-suspended for FACS in a buffer containing 2%FBS (Gibco), 5mM MgCl2, DAPI (1:10k, Invitrogen) and the remaining DNase I from the dissociation kit. For experiments where iRFP intensity was measured to determine stress levels in mice containing the Atf5-reporter allele, cycloheximide (Sigma, 100µg/mL) was added to all solutions during dissociation and cytometry to block new protein synthesis and minimize the effects of dissociation or sorting-related stress on these measurements. Dissociated cells were filtered through a 40µm cell strainer and analyzed on a Beckman Coulter MoFlo Astrios EQ sorter.

value: Olfactory epithelium

tag: cell type

value: iOSN


title: Swap3-iRFPGFP-High

value: mOSN


title: Swap3-iRFP-High


title: Swap3-iRFPGFP-Low


title: M28-4h-rep3

source_name: Seeds of M28,drought 4 hour,rep3

value: drought 4h


title: Fructose diet wild-type liver_sample2


title: V1 from 3L5 [LID_100792]

city: Tempe

first: Kenneth

last: Chiou

address: 427 E Tyler Mall

institute: Arizona State University

data_processing:
Gene expression counts were quantified from RNA-seq reads using the pseudoalignment method implemented in kallisto.
Estimated counts and transcripts-per-million (TPM) values were then imported into R v4.0.2 and summarized to genes using the tximport package.
Genome_build: rhesus macaque reference genome (Mmul_10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with transcripts per million (TPM) values for every gene and every sample

extract_protocol:
Total RNA was extracted using a TRIzol-chloroform gradient followed by column isolation of RNA using the Quick-RNA Microprep kit (Zymo Research). Briefly, 1 ml of TRIzol (Invitrogen) was added to each 2-ml sample tube, along with a sterile 5-mm stainless steel grinding bead (QIAGEN cat. no. 69989). Samples were then homogenized using the Tissuelyser II system (QIAGEN) at 20 Hz in two sets of 2 minutes each, with rotation in between, and the lysate transferred to a new tube. 200 µl of chloroform were added to each sample, which was then vortexed at full speed for 15 seconds and incubated at room temperature for 2 minutes. The sample was then centrifuged at 12,000 × g for 15 minutes at 4°C. After centrifugation, the aqueous layer was transferred to a new tube and mixed with 600 µl of 70% ethanol to precipitate RNA. The resulting solution was transferred to Quick-RNA Microprep columns (Zymo Research). The remainder of the protocol followed manufacturer instructions for the Quick-RNA Microprep kit. Total RNA was eluted in 60 µl of RNase-free water.
We prepared bulk RNA-seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with an initial mRNA isolation step using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). We followed manufacturer instructions and guidelines for library preparation using these kits. We used 200 ng of starting RNA and set the enzymatic fragmentation time (10 minutes), first-strand synthesis incubation time (50 minutes at 42°C), and bead cleanup volume ratios for a target insert size of 400 bp. Libraries were amplified using 10 cycles of PCR and eluted in a final volume of 20 µl of RNase-free water. Libraries were quantified by Qubit 3 using the Qubit DNA HS Assay kit (Invitrogen) and library quality was assessed using the Fragment Analyzer HS NGS kit (AATI/Agilent). Libraries were pooled in equimolar quantities prior to sequencing.

value: mid


title: V1 from 4J0 [LID_100789]


title: Fructose diet wild-type liver_sample1


title: V1 from 8L6 [LID_100788]

value: low


title: DG from 0K1 [LID_100787]


title: Fructose diet wild-type liver_sample3


title: M28-2h-rep3

source_name: Seeds of M28,drought 2 hour,rep3

value: drought 2h


title: M28-2h-rep2

source_name: Seeds of M28,drought 2 hour,rep2


title: M28-4h-rep2

source_name: Seeds of M28,drought 4 hour,rep2


title: V1 from 7L0 [LID_100785]

source_name: primary visual cortex

value: primary visual cortex

value: female


title: High fat diet fed (ad libitum) liver_sample2

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm10 whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome GRCm38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

extract_protocol:
Livers were removed and flash frozen in liquid nitrogen RNA was harvested using TRIzol and the Qiagen RNAeasy kit with Dnase treatment. RNA was quanified by Agilent 2100 bioanalsyer.
PolyA enrichment was performed using NEBNext Poly(A) mRNA magnetic Isolation and libraries prepared using NEBNext Ultra II RNA Library Prep kit for Illumina

value: Liver

value: High fat diet fed (ad libitum)


title: High fat diet fed (ad libitum) liver_sample4


title: High fat diet fed (ad libitum) liver_sample3


title: OmpCreDdit3-WT2


title: High fat diet fed (ad libitum) liver_sample1


title: M28-2h-rep1

source_name: Seeds of M28,drought 2 hour,rep1

value: EMS mutant


title: M28-1h-rep3

source_name: Seeds of M28,drought 1 hour,rep3

value: drought 1h


title: High fat diet fasted (16h) liver_sample4

value: High fat diet fasted (16h)


title: OmpCreDdit3-WT1


title: OmpCreDdit3-WT3


title: DG from 4J0 [LID_100784]

value: male


title: ACCg from 5N1 [LID_100783]

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: OmpCreDdit3-Het4


title: M28-4h-rep1

source_name: Seeds of M28,drought 4 hour,rep1

value: leaf


title: OmpCreDdit3-WT4

value: Olfactory epithelium


title: High fat diet fasted (16h) liver_sample3

source_name: Liver


title: V1 from 4N7 [LID_100786]

value: high


title: M28-1h-rep1

source_name: Seeds of M28,drought 1 hour,rep1


title: M28-1h-rep2

source_name: Seeds of M28,drought 1 hour,rep2


title: Hepatocyte_6h _rep1

description: Gene expression at 6h in replicate1 of primary hepatocytes

source_name: Rat primary hepatocyte, 6h, replicate1

value: primary hepatocyte


title: V1 from 1B7 [LID_100782]


title: High fat diet fasted (16h) liver_sample2


title: OmpCreDdit3-Het5

value: mOSN


title: DG from 7L0 [LID_100781]

value: dentate gyrus


title: OmpCreDdit3-cKO5


title: Ctrl6-iRFPGFP-High

value: Atf5(rep/+); Omp(iresGFP/+)


title: M28-0h-rep2

source_name: Seeds of M28,Control,rep2

value: drought 0h


title: M28-0h-rep3

source_name: Seeds of M28,Control,rep3


title: Ctrl6-iRFP-Low

value: iOSN


title: Ctrl6-iRFPGFP-Low


title: M28-0h-rep1

source_name: Seeds of M28,Control,rep1


title: Ctrl6-iRFP-High

source_name: Olfactory epithelium


title: Ctrl5-iRFPGFP-Low


title: DHA teratment3

city: Chengdu

first: dunshui

last: liao

address: chengdu

institute: West China Hospital,sichuan University,Chengdu,China

data_processing:
use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts,V2.1.0) to compare the transcriptome sequencing Reads to the reference genome.
the differential expression genes (DEGs) between treatment groups and control gorups were calculated using the DESeq2(v1.18.1) and edegR(v3.20.9)
Supplementary files format and content: execel file include RPKM values and reads counts for each Sample
Supplementary files format and content: different expresion for each sample

growth_protocol: SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
NEBNext ® Poly (A) mRNA Magnetic Isolation Module kit was used to isolate mRNA
RNA libraries for RNA-seq were prepared using NEBNext ® Ultra ™ II mRNA Library Prep Kit for Illumina ®  following manufacturer's protocols.

treatment_protocol: DHA 20ug/mL  4 hours

value: dihydroartemisinin 20ug/mL  4 h


title: DG from 9I7 [LID_100778]

source_name: dentate gyrus

value: female

value: low


title: ACCg from 8L6 [LID_100777]


title: ACCg from 3L5 [LID_100780]

value: mid


title: DNA teratment2


title: Control diet fed (ad libitum) liver_sample4

value: Liver

value: Control diet fed (ad libitum)


title: Control diet fed (ad libitum) liver_sample3


title: High  fat diet fasted (16h) liver_sample1

value: High  fat diet fasted (16h)


title: Control diet fed (ad libitum) liver_sample1


title: Hepatocyte_0h_rep1

description: Gene expression at 0h in replicate1 of primary hepatocytes

source_name: Rat primary hepatocyte, 0h, replicate1

value: male


title: Hepatocyte_0h_rep2

description: Gene expression at 0h in replicate2 of primary hepatocytes

source_name: Rat primary hepatocyte, 0h, replicate2


title: Hepatocyte_0h_rep3

description: Gene expression at 0h in replicate3 of primary hepatocytes

source_name: Rat primary hepatocyte, 0h, replicate3


title: Control diet fed (ad libitum) liver_sample2


title: ACCg from 60T [LID_100776]

value: anterior cingulate cortex


title: V1 from 5N1 [LID_100779]

source_name: primary visual cortex

value: primary visual cortex


title: Control diet fasted (16h) liver_sample4

value: Control diet fasted (16h)


title: Ctrl5-iRFPGFP-High

value: Olfactory epithelium


title: DHA teratment1


title: Ctrl5-iRFP-Low


title: DG from 3L5 [LID_100775]


title: Control diet fasted (16h) liver_sample3


title: control3

value: control


title: control2


title: Control diet fasted (16h) liver_sample2


title: 4wkM28Ddit3-WT3-tdtomato

value: mOSN


title: control1


title: Ctrl5-iRFP-High

value: Atf5(rep/+); Omp(iresGFP/+)


title: ACCg from 7L0 [LID_100774]


title: DG from 4N7 [LID_100772]

value: dentate gyrus

value: high


title: 4wkM28Ddit3-WT2-tdtomato


title: Control diet Rbfox2 knockout liver_sample4

value: Rbfox2 knockout

value: Chow diet


title: Control diet Rbfox2 knockout liver_sample2


title: ACCg from 3A9 [LID_100770]

value: female

value: low


title: Control diet Rbfox2 knockout liver_sample3

value: Liver


title: shRRM2, rep2

city: Shanghai

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

institute: Department of Plastic and Reconstructive Surgery

data_processing:
The raw paired-end reads were filtered to remove low quality reads and reads containing adapter sequence before performing the assembly using the software TrimGalore
Paired-end reads were mapped to the reference transcriptome using HISAT2, followed by transcriptome assembly and gene expression quantification using StringTie.
Differentially expressed genes were identified by DEseq2 with a cut-off value of log2|fold-change|>1 and p-adjust <0.05.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Count and TPM values for each Sample

growth_protocol: S462TY cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extractibn kit, which yielded > 2 μg of total RNA per sample.
High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing. Illumina HiSeq library construction was performed according to the manufacturer's instructions (Illumina,USA).

value: schwann cell

value: RRM2 knockdown


title: DG from 1B7 [LID_100769]

value: male


title: 4wkM28Ddit3-Het5-tdtomato


title: shRRM2, rep1


title: shRRM2, rep3


title: shNC, con3

value: WT


title: Control diet Rbfox2 knockout liver_sample1


title: 4wkM28Ddit3-Het5-GFP


title: Control diet fasted (16h) liver_sample1


title: Control diet wild-type liver_sample4

value: wild-type


title: DG from 65Z [LID_100767]


title: 4wkM28Ddit3-Het4-tdtomato


title: ACCg from 4J3 [LID_100768]

value: anterior cingulate cortex

value: mid


title: shNC, con2


title: shNC, con1


title: 4wkM28Ddit3-Het4-GFP

value: Olfactory epithelium


title: ACCg from 9C6 [LID_100771]


title: Control diet wild-type liver_sample3


title: 4wkM28Ddit3-WT2-GFP

value: mOSN


title: DG from 3A6 [LID_100766]


title: ACCg from 7L7 [LID_100765]


title: IMT+venetoclax treated xenograft cells_3

city: Gothenburg

first: Cleas

middle: M.

last: Gustafsson

address: Medicinaregatan 9A

department: medical biochemistry and cell biology

institute: university of Gothenburg

data_processing:
Reads were aligned to hg38 genome using Hisat2 version 2.2.1.
Number of reads mapping to each feacher were calculated using htseq-count version 0.12.4.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files including raw counts for each sample.

source_name: IMT+venetoclax treated xenograft cells

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). RNA was processed as per manufacturer’s instructions.
RNAseq library preparation and RNA-sequencing was done using the SMARTer Total Stranded RNA pico kit.

value: bone marrow

value: leukemic

value: TP53 mutant

value: combination (POLRMT and BCL-2 inhibitors)


title: Control diet wild-type liver_sample2

value: Chow diet


title: 4wkM28Ddit3-cKO4-tdtomato


title: ACCg from 4J0 [LID_100773]


title: 4wkM28Ddit3-cKO4-GFP


title: 4wkM28Ddit3-WT3-GFP


title: Control diet wild-type liver_sample1


title: IMT+venetoclax treated xenograft cells_2


title: venetoclax treated xenograft cells_2

source_name: venetoclax treated xenograft cells

value: BCL-2 inhibitor


title: ACCg from 2E9 [LID_100762]

source_name: anterior cingulate cortex

value: female

value: low


title: DG from 7L7 [LID_100764]

value: dentate gyrus


title: OmpCreDdit3-cKO3

data_processing:
Transcript annotations were downloaded from Ensembl (GRCm38, Ensembl version 92). Extended OR gene models were included from Ibarra-Soria et al., PLOS Genetics, 2014. The coding sequence for each extended OR gene model was annotated based on the Ensembl annotations for that OR. Only transcripts from a localized contig and containing an annotated coding sequence were retained in the final transcript set.
A fasta file of transcript sequences was generated using the GRCm38 (mm10) sequence, the above annotation set and custom python scripts. Sequences were indexed using salmon (verson 0.13.1, -k 31).
Demultiplexed fastq files were quantified against the reference transcriptome using Salmon (version 0.13.1, --libType A, --seqBias, --gcBias, --validateMappings).
Assembly: mm10
Supplementary files format and content: Tab-delimited quant.sf files generated by Salmon. Each row is a transcript (ENSMUST = Ensembl transcripts, CUFFORT = extended OR gene models, egfp/tdtomato/lacZ as above). Columns indicate Length (nt), EffectiveLength (as modeled by Salmon), TPM (abundance in transcripts per million) and NumReads (expected number of reads originating from each transcript).

extract_protocol:
For experiments on OSN developmental populations (INPs, iOSNs, mOSNs), cells were sorted across multiple days, pelleted (10 minutes at 800g) and frozen at -80 until the day of extraction. Lysates were prepared from roughly 1e6 cells per condition using a lysis buffer (20mM Tris pH=7.5, 150mM NaCl, 5mM MgCl2, 1mM DTT, 100ug/mL cycloheximide, 1%(v/v) Triton X-100 and 25U/mL TURBO DNAse), RNA was quantified by Quant-iT RiboGreen assay (Thermo Fisher) and lysate containing 100ng of RNA was mixed with 300uL of Trizol (Invitrogen). In all other experiments, 10-20k cells were sorted directly into 500uL of Trizol LS (Sigma). RNA was recovered from Trizol using the Direct-Zol RNA Miniprep kit (Zymo), precipitated overnight with 300mM sodium acetate and 1.5 volumes of isopropanol, digested for 30min at 37°C with TURBO DNAse (Invitrogen) and cleaned up on 1.8x Ampure Beads (Beckman Coulter). <10ng RNA was used for library prep, as measured by Quant-iT RiboGreen assay.
Libraries were prepared using the SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio) and the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed by decapitation (if younger than postnatal day 14) or CO2 followed by cervical dislocation, and the main olfactory epithelium (MOE) was isolated by dissection into ice-cold 1xPBS without calcium or magnesium. Single-cell suspensions were prepared using a papain dissociation system (Worthington) following a modified version of the manufacturer’s protocol. Dissociations were for 30-45 minutes at 37°C, centrifugation steps for 5min at 400g and the discontinuous density gradient was not performed. Cells were re-suspended for FACS in a buffer containing 2%FBS (Gibco), 5mM MgCl2, DAPI (1:10k, Invitrogen) and the remaining DNAase I from the dissociation kit. For experiments where iRFP intensity was measured to determine stress levels in mice containing the Atf5-reporter allele, cycloheximide (Sigma, 100µg/mL) was added to all solutions during dissociation and cytometry to block new protein synthesis and minimize the effects of dissociation or sorting-related stress on these measurements. Dissociated cells were filtered through a 40µm cell strainer and analyzed on a Beckman Coulter MoFlo Astrios EQ sorter.


title: DG from 94S [LID_100761]


title: DG from 60T [LID_100763]


title: TLK1_rep2

city: San Francisco

first: Jingjing

last: Li

address: 35 Medical Center Way

institute: UCSF

data_processing:
The original reads were mapped to human genome (GRCh37) with STAR 2.7.3a with default settings, then reads with MAPQ > 20 were collected for further analysis.
FeatureCounts was applied to count the number of reads mapping to genomic feature.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample.

source_name: TLK1 knockout iPSC-CMs

growth_protocol: All induced pluripotent stem cell (iPSC) lines were reprogrammed by the Sendai virus expressing 4 Yamanaka factors (CytoTune®-iPS Sendai Reprogramming Kit, Invitrogen). Protocols in the study were approved by Human Subjects Research Institutional Review Board (IRB) at Stanford University. Human iPSCs were maintained in Essential 8™ Medium (Gibco®, Life Technology). For passaging, iPSC culture was dissociated with Accutase (Innovative Cell Technologies) at 37˚C for 15-20 min, and suspended iPSCs were reseeded on Matrigel-coated plates (BD Biosciences, San Jose, CA) at a density of 500 K cells per well in 6-well plates.

extract_protocol:
The cells were dissociated using TrypLE express 1x (Thermo Fisher Scientific) and GFP+ cells were sorted by flow cytometry 24 hr post-transfection. GFP+ cells were seeded at a density of 1,000 cells per well in a 6-well plate to generate clonal isolates.
NEBNext Ultra II RNA kit with PolyA Selection was used to construct RNA library.

value: iPSC-CMs

tag: genotype/variation

value: TLK1 knockout


title: OmpCreDdit3-cKO2


title: venetoclax treated xenograft cells_3


title: Adapt-NK, mRNA-derived cDNA

city: Oslo

first: Karl-Johan

last: Malmberg

address: Ullernchausseen 70

country: Norway

institute: Oslo University Hospital

description: 3' mRNA library: count matrices of gene expression

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT sequences were treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: NK cells

extract_protocol:
CD3/CD19-depleted PBMC were co-cultured with 100 or 200 gy irradiated K562 feeder cells transfected with lentiviral construct to express high levels of HLA-E with a G-leader-derived peptide (Fate Therapeutics, details in ‘Genetic cell engineering’) in G-Rex24 (Wilson Wolf) at a 1:2 ratio with a total cell number of 0.5x106/cm2. Cells were cultured in GMP-grade Stem Cell Growth Medium (SCGM, CellGenix) supplemented with 100 IU/mL human recombinant IL-2 (Proleukin) for 11 days with 60% medium exchange on day 7, and IL-2 replenishment days 4, 7, and 10.
Standard 10X Genomics library preparation.
To distinguish day 0 and day 11 cells, streptavidin-PE conjugated to different oligos were used, and equal number of sorted viable CD56+ cells from the two cell preparations were pooled as one sample

value: NK cells


title: Adapt-NK, ADT-derived cDNA

description: Antibody-derived oligonucleotide library: read and UMI count matrices

library_source: other

molecule: protein


title: TLK1_rep1


title: venetoclax treated xenograft cells_1


title: DG from 3A9 [LID_100760]


title: mOSN-2

value: Atf5(rep/+); Omp(iresGFP/+)


title: TEAD2_rep2

source_name: TEAD2 knockout iPSC-CMs

value: TEAD2 knockout


title: IMT treated xenograft cells_3

source_name: IMT treated xenograft cells

value: POLRMT inhibitor


title: ACCg from 4N8 [LID_100759]

value: anterior cingulate cortex

value: male

value: mid


title: TEAD2_rep1


title: IMT treated xenograft cells_2

value: bone marrow

value: leukemic


title: DG from 8L6 [LID_100758]


title: mOSN-1

value: Olfactory epithelium

value: mOSN


title: IMT+venetoclax treated xenograft cells_1

value: TP53 mutant

value: combination (POLRMT and BCL-2 inhibitors)


title: OmpCreDdit3-cKO4


title: IMT treated xenograft cells_1


title: OmpCreDdit3-Het3


title: iOSN-2

value: iOSN


title: iOSN-1


title: RBBP5_rep2

source_name: RBBP5 knockout iPSC-CMs

value: RBBP5 knockout


title: RBBP5_rep1

value: iPSC-CMs


title: vehicle treated xenograft cells_3

source_name: vehicle treated xenograft cells

value: placebo


title: ACCg from 94S [LID_100756]

value: female

value: low


title: DG from 4J3 [LID_100754]

value: dentate gyrus


title: ASH2L_rep1

source_name: ASH2L knockout iPSC-CMs

value: ASH2L knockout


title: ASH2L_rep2


title: vehicle treated xenograft cells_1


title: INP-1

value: INP

value: Ngn-GFP(tg/0); Atf5(rep/+)


title: HepG2 spheroid, NaBut treated, day 10, replicate 3

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1925 Eastchester Road, Apt 20D, Apt 208

institute: Albert Einstein College of Medicine

data_processing:
Raw reads were trimmed to remove low quality base calls and Illumina universal adapters using Trim Galore! (Version 0.6.5) with default parameters and then assessed using fastQC (version 0.11.4) and multiqc (version 1.10.1).
Reads were then aligned to the human genome (GRCh38) using STAR with default parameters. Alignment quality control was performed using RSeQC and Qualimap.
Quantification was performed using RSEM. Quantification quality control was performed using EDASeq (version 2.3) and NOISeq (version 2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include length effective_length, expected_count, TPM, and FPKM for each sample

source_name: HepG2 spheroid

growth_protocol: HepG2 spheroids were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, containing 4.5g/L glucose) supplemented with 10% Fetal Bovine Serum (FBS), 1% Non-Essential Amino Acids, 1% GlutaMAX and 0.5% Penicillin/Streptomycin (all Corning). Spheroids were kept in a controlled atmosphere (5% CO2 incubator at 37C) in ClinoReactors. Optimal growth conditions were achieved by exchanging media three times a week and adjusting rotation speed according to spheroids growth.

extract_protocol:
5 spheroids stored at -80C were thawed on ice and then mechanically homogenized. RNA was extracted using an RNeasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared by Novogene lncRNA seqeucning service

treatment_protocol: After 24 h, growth media was replaced by growth media containing 20 mM of NaBut for the treatment group while the non-treated group received growth media only. Spheroids and flat cells were treated for 3 days and, after collection, the treatment media was replaced by the standard growth media and spheroids were maintained for additional 7 days, until the last collection on day 10.

value: HepG2 spheroid

value: hepatocellular carcinoma

value: WT

value: NaBut

tag: time

value: day 10


title: Ctrl2-iRFPGFP-Low

source_name: Olfactory epithelium

value: Olfactory epithelium

value: mOSN

value: Atf5(rep/+); Omp(iresGFP/+)


title: CA3 from 9C6 [LID_100753]

source_name: cornu ammonis 3

value: cornu ammonis 3

value: male


title: Ctrl_rep2

source_name: WT iPSC-CMs

value: iPSC-CMs


title: HepG2 spheroid, NaBut treated, day 10, replicate 2


title: Ctrl_rep1


title: Ctrl2-iRFPGFP-High


title: INP-2


title: CA3 from 4J0 [LID_100752]

value: mid