title: Independent Test Cohort_phchp365v1

first: Dr. Alexander

middle: B.

last: Niculescu

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

description: Sample title format: Participant ID and visit (v) number

hyb_protocol: Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.

scan_protocol: Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values

data_processing: We analyzed the data in two ways: an Absent-Present (AP) approach, and a differential expression (DE) approach, as in previous work by us on suicide biomarkers1-3.  The AP approach may capture turning on and off of genes, and the DE approach may capture gradual changes in expression. We used a powerful within-subject design, then an across-subjects summation score for probesets. Analyses were performed as previously described2-4. In brief, we imported all Affymetrix microarray data as CEL. files into Partek Genomic Suites 6.6 software package (Partek Incorporated, St Louis, MO, USA). Using only the perfect match values, we  ran a robust multi-array analysis (RMA) by gender and diagnosis, background corrected with quantile normalization and a median polish probeset summarization of all chips, to obtain the normalized expression levels of all probesets for each chip. Then, to establish a list of differentially expressed probesets we conducted a within- subject analysis, using a fold change in expression of at least 1.2 between high- and low memory visits within each subject. Probesets that have a 1.2-fold change are then assigned either a 1 (increased in high memory) or a -1 (decreased in high memory) in each comparison. These values were then summed for each probeset across all the comparisons and subjects, yielding a range of raw scores. The probesets  above the 33.3% of scores received an internal score of 2 points, those above 50% 4 points, and those above 80% 6 points2 3 4. We have developed in our labs R scripts to automate and conduct all these large dataset analyses in bulk, checked against human manual scoring4.

label: Biotin

source_name: Whole Blood

label_protocol:
Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps:
1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.
2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA.
3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.
4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step.
5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol: Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

treatment_protocol:
[Cohort protocol]  We used two independent cohorts of psychiatric disorders patients, one for Discovery of candidate biomarkers, and one for Testing of top biomarkers (for predicting memory state, and predicting future positive neuropsychological testing for cognitive impairement ) (Figure 1  Table 1, and Table S1).
[Recruitments protocol] Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a Hopkins Verbal Learning Test (HVLT-R), and the blood was drawn. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing. Whole-blood RNA was extracted for microarray gene expression studies from the PAXgene tubes, as detailed below.

tag: individual

tag: visit (v) number

tag: gender

value: M

tag: diagnosis

value: MDD

tag: hvlt3 memory retention

tag: test cohort memory retention state (hvlt3)

value: Yes

tag: test cohort future neuropsych postitive  testing

tag: number of neuropsych testing

tag: length of follow-up (days)

tag: frequency of neuropsych testing positive visits

tag: time to future neuropsych positive visits

value: Whole Blood


title: Independent Test Cohort_phchp364v1

status: Public on Apr 01 2020

type: RNA

city: Indianapolis

state: IN

country: USA

molecule: total RNA

organism: Homo sapiens

value: F

value: PTSD

tag: tissue


title: Independent Test Cohort_phchp360v3

value: BP


title: Independent Test Cohort_phchp357v4


title: Independent Test Cohort_phchp366v1

value: SZ


title: Independent Test Cohort_phchp357v2


title: Independent Test Cohort_phchp368v1


title: Independent Test Cohort_phchp357v5


title: Independent Test Cohort_phchp357v3


title: Independent Test Cohort_phchp357v1


title: Independent Test Cohort_phchp361v3


title: Independent Test Cohort_phchp361v2


title: Independent Test Cohort_phchp360v1


title: Independent Test Cohort_phchp368v2


title: Independent Test Cohort_phchp356v1


title: Independent Test Cohort_phchp353v1


title: Independent Test Cohort_phchp361v1


title: Independent Test Cohort_phchp343v3


title: Independent Test Cohort_phchp341v2


title: Independent Test Cohort_phchp351v1


title: Independent Test Cohort_phchp351v2


title: Independent Test Cohort_phchp343v2


title: Independent Test Cohort_phchp343v1


title: Independent Test Cohort_phchp341v4


title: Independent Test Cohort_phchp341v3


title: Independent Test Cohort_phchp341v5


title: Independent Test Cohort_phchp340v3


title: Independent Test Cohort_phchp340v2


title: Independent Test Cohort_phchp314v2


title: Independent Test Cohort_phchp327v1


title: Independent Test Cohort_phchp336v3


title: Independent Test Cohort_phchp323v3


title: Independent Test Cohort_phchp348v1


title: Independent Test Cohort_phchp307v1


title: Independent Test Cohort_phchp324v1


title: Independent Test Cohort_phchp304v1


title: Independent Test Cohort_phchp314v1


title: Independent Test Cohort_phchp336v2


title: Independent Test Cohort_phchp293v2


title: Independent Test Cohort_phchp331v1


title: Independent Test Cohort_phchp295v1


title: Independent Test Cohort_phchp304v2


title: Independent Test Cohort_phchp296v3


title: Independent Test Cohort_phchp330v1


title: Independent Test Cohort_phchp296v1


title: Independent Test Cohort_phchp291v3


title: Independent Test Cohort_phchp304v3


title: Independent Test Cohort_phchp291v4


title: Independent Test Cohort_phchp315v1


title: Independent Test Cohort_phchp296v2


title: Independent Test Cohort_phchp291v5


title: Independent Test Cohort_phchp293v1


title: Independent Test Cohort_phchp291v2


title: Independent Test Cohort_phchp314v3


title: Independent Test Cohort_phchp289v1

tag: neuropsych test date

tag: neuropsych test results

value: 1 = MCI


title: Independent Test Cohort_phchp291v1


title: Independent Test Cohort_phchp286v3


title: Independent Test Cohort_phchp286v2


title: Independent Test Cohort_phchp285v2


title: Independent Test Cohort_phchp247v1


title: Independent Test Cohort_phchp248v1


title: Independent Test Cohort_phchp266v3

value: MOOD


title: Independent Test Cohort_phchp285v1


title: Independent Test Cohort_phchp243v4


title: Independent Test Cohort_phchp283v1


title: Independent Test Cohort_phchp265v1


title: Independent Test Cohort_phchp248v5


title: Independent Test Cohort_phchp286v1


title: Independent Test Cohort_phchp248v2


title: Independent Test Cohort_phchp266v2


title: Independent Test Cohort_phchp266v1


title: Independent Test Cohort_phchp243v3


title: Independent Test Cohort_phchp248v3


title: Independent Test Cohort_phchp241v1


title: Independent Test Cohort_phchp239v2

value: SZA


title: Independent Test Cohort_phchp237v2


title: Independent Test Cohort_phchp243v1


title: Independent Test Cohort_phchp239v1


title: Independent Test Cohort_phchp234v3


title: Independent Test Cohort_phchp239v3


title: Independent Test Cohort_phchp236v1


title: Independent Test Cohort_phchp234v2


title: Independent Test Cohort_phchp236v2


title: Independent Test Cohort_phchp243v2


title: Independent Test Cohort_phchp234v1


title: Independent Test Cohort_phchp236v3


title: Independent Test Cohort_phchp232v3


title: Independent Test Cohort_phchp237v1


title: Independent Test Cohort_phchp232v2


title: Independent Test Cohort_phchp231v1


title: Independent Test Cohort_phchp228v1


title: Independent Test Cohort_phchp229v1


title: Independent Test Cohort_phchp223v3


title: Independent Test Cohort_phchp212v1


title: Independent Test Cohort_phchp222v3


title: Independent Test Cohort_phchp225v1

value: PSYCH


title: Independent Test Cohort_phchp223v1


title: Independent Test Cohort_phchp224v1


title: Independent Test Cohort_phchp212v2


title: Independent Test Cohort_phchp222v2


title: Independent Test Cohort_phchp207v1


title: Independent Test Cohort_phchp232v1


title: Independent Test Cohort_phchp205v1

value: 3 = other cognitive disorder but not MCI or ADRD


title: Independent Test Cohort_phchp205v2


title: Independent Test Cohort_phchp198v2


title: Independent Test Cohort_phchp203v2


title: Independent Test Cohort_phchp197v4


title: Independent Test Cohort_phchp191v2


title: Independent Test Cohort_phchp198v1


title: Independent Test Cohort_phchp206v1


title: Independent Test Cohort_phchp198v4


title: Independent Test Cohort_phchp197v3


title: Independent Test Cohort_phchp205v3


title: Independent Test Cohort_phchp197v2


title: Independent Test Cohort_phchp191v3


title: Independent Test Cohort_phchp203v1


title: Independent Test Cohort_phchp182v3


title: Independent Test Cohort_phchp223v2


title: Independent Test Cohort_phchp191v1


title: Independent Test Cohort_phchp177v1


title: Independent Test Cohort_phchp180v2


title: Independent Test Cohort_phchp180v1


title: Independent Test Cohort_phchp182v1


title: Independent Test Cohort_phchp177v2


title: Independent Test Cohort_phchp178v1


title: Independent Test Cohort_phchp173v3


title: Independent Test Cohort_phchp171v2


title: Independent Test Cohort_phchp171v1


title: Independent Test Cohort_phchp167v1


title: Independent Test Cohort_phchp180v3


title: Independent Test Cohort_phchp165v3


title: Independent Test Cohort_phchp173v1


title: Independent Test Cohort_phchp175v1


title: Independent Test Cohort_phchp165v2


title: Independent Test Cohort_phchp173v2


title: Independent Test Cohort_phchp174v1


title: Independent Test Cohort_phchp165v1


title: Independent Test Cohort_phchp164v1


title: Independent Test Cohort_phchp152v1


title: Independent Test Cohort_phchp158v1


title: Independent Test Cohort_phchp164v2


title: Independent Test Cohort_phchp169v1


title: Independent Test Cohort_phchp164v3


title: Independent Test Cohort_phchp147v3


title: Independent Test Cohort_phchp143v2


title: Independent Test Cohort_phchp144v1


title: Independent Test Cohort_phchp156v1


title: Independent Test Cohort_phchp143v3


title: Independent Test Cohort_phchp130v2


title: Independent Test Cohort_phchp147v1


title: Independent Test Cohort_phchp148v1


title: Independent Test Cohort_phchp130v3


title: Independent Test Cohort_phchp143v1


title: Independent Test Cohort_phchp130v1


title: Independent Test Cohort_phchp120v3


title: Independent Test Cohort_phchp122v2


title: Independent Test Cohort_phchp147v2


title: Independent Test Cohort_phchp133v1


title: Independent Test Cohort_phchp120v1


title: Independent Test Cohort_phchp116v1


title: Independent Test Cohort_phchp114v1


title: Independent Test Cohort_phchp182v2


title: Independent Test Cohort_phchp139v1


title: Independent Test Cohort_phchp115v2


title: Independent Test Cohort_phchp122v1


title: Independent Test Cohort_phchp103v1


title: Independent Test Cohort_phchp115v3


title: Independent Test Cohort_phchp113v1


title: Independent Test Cohort_phchp102v3


title: Independent Test Cohort_phchp105v1


title: Independent Test Cohort_phchp197v1


title: Independent Test Cohort_phchp115v1


title: Independent Test Cohort_phchp102v2


title: Independent Test Cohort_phchp102v1


title: Independent Test Cohort_phchp100v1


title: Independent Test Cohort_phchp096v1


title: Independent Test Cohort_phchp096v4


title: Independent Test Cohort_phchp081v3


title: Independent Test Cohort_phchp092v2


title: Independent Test Cohort_phchp076v3


title: Independent Test Cohort_phchp081v1


title: Independent Test Cohort_phchp101v1


title: Independent Test Cohort_phchp098v1

value: 2 = ADRD


title: Independent Test Cohort_phchp078v1


title: Independent Test Cohort_phchp096v3


title: Independent Test Cohort_phchp097v3


title: Independent Test Cohort_phchp076v2


title: Independent Test Cohort_phchp068v3


title: Independent Test Cohort_phchp071v1


title: Independent Test Cohort_phchp092v3


title: Independent Test Cohort_phchp076v1


title: Independent Test Cohort_phchp068v2


title: Independent Test Cohort_phchp064v3


title: Independent Test Cohort_phchp092v1


title: Independent Test Cohort_phchp080v1


title: Independent Test Cohort_phchp064v1


title: Independent Test Cohort_phchp060v1


title: Independent Test Cohort_phchp047v1


title: Independent Test Cohort_phchp039v3


title: Independent Test Cohort_phchp039v1


title: Independent Test Cohort_phchp057v1


title: Independent Test Cohort_phchp047v3


title: Independent Test Cohort_phchp047v2


title: Independent Test Cohort_phchp034v1


title: Independent Test Cohort_phchp051v1


title: Independent Test Cohort_phchp120v2


title: Independent Test Cohort_phchp034v3


title: Independent Test Cohort_phchp034v2


title: Independent Test Cohort_phchp027v1


title: Independent Test Cohort_phchp033v1


title: Independent Test Cohort_phchp029v1


title: Independent Test Cohort_phchp030v1


title: Independent Test Cohort_phchp041v1


title: Independent Test Cohort_phchp037v1


title: Independent Test Cohort_phchp024v1


title: Independent Test Cohort_phchp023v3


title: Independent Test Cohort_phchp025v1


title: Independent Test Cohort_phchp023v2


title: Independent Test Cohort_phchp020v3


title: Independent Test Cohort_phchp022v1


title: Independent Test Cohort_phchp022v2


title: Independent Test Cohort_phchp030v3


title: Independent Test Cohort_phchp063v1


title: Independent Test Cohort_phchp068v1


title: Independent Test Cohort_phchp020v2


title: Independent Test Cohort_phchp023v1


title: Independent Test Cohort_phchp020v1


title: Independent Test Cohort_phchp017v2


title: Independent Test Cohort_phchp006v1


title: Independent Test Cohort_phchp014v1


title: Independent Test Cohort_phchp006v2


title: Independent Test Cohort_phchp018v1


title: Independent Discovery Cohort_phchp359v2

description:
Discovery Cohort Blood Gene Expression
Sample title format: Participant ID and visit (v) number


title: Independent Test Cohort_phchp005v1


title: Independent Discovery Cohort_phchp358v3


title: Independent Discovery Cohort_phchp358v2


title: Independent Test Cohort_phchp017v3


title: Independent Discovery Cohort_phchp363v2


title: Independent Test Cohort_phchp005v2


title: Independent Test Cohort_phchp005v3


title: Independent Discovery Cohort_phchp359v1


title: Independent Discovery Cohort_phchp367v2


title: Independent Discovery Cohort_phchp363v1


title: Independent Discovery Cohort_phchp362v2


title: Independent Discovery Cohort_phchp358v1


title: Independent Discovery Cohort_phchp359v3


title: Independent Discovery Cohort_phchp362v3


title: Independent Discovery Cohort_phchp350v2


title: Independent Discovery Cohort_phchp350v4


title: Independent Discovery Cohort_phchp350v3


title: Independent Discovery Cohort_phchp362v1


title: Independent Discovery Cohort_phchp355v2


title: Independent Discovery Cohort_phchp355v1


title: Independent Discovery Cohort_phchp349v2


title: Independent Discovery Cohort_phchp346v3


title: Independent Discovery Cohort_phchp345v3


title: Independent Test Cohort_phchp094v1


title: Independent Discovery Cohort_phchp346v1


title: Independent Discovery Cohort_phchp342v1


title: Independent Discovery Cohort_phchp345v1


title: Independent Discovery Cohort_phchp342v2


title: Independent Discovery Cohort_phchp349v3


title: Independent Discovery Cohort_phchp342v3


title: Independent Discovery Cohort_phchp349v1


title: Independent Discovery Cohort_phchp333v4


title: Independent Discovery Cohort_phchp333v3


title: Independent Discovery Cohort_phchp334v2


title: Independent Discovery Cohort_phchp345v2


title: Independent Discovery Cohort_phchp338v5


title: Independent Discovery Cohort_phchp334v1


title: Independent Discovery Cohort_phchp334v3


title: Independent Discovery Cohort_phchp338v1


title: Independent Discovery Cohort_phchp338v2


title: Independent Discovery Cohort_phchp338v3


title: Independent Discovery Cohort_phchp367v1


title: Independent Discovery Cohort_phchp329v3


title: Independent Discovery Cohort_phchp329v2


title: Independent Discovery Cohort_phchp333v2


title: Independent Discovery Cohort_phchp332v1


title: Independent Discovery Cohort_phchp332v2


title: Independent Discovery Cohort_phchp325v3


title: Independent Discovery Cohort_phchp333v1


title: Independent Discovery Cohort_phchp328v3


title: Independent Discovery Cohort_phchp325v1


title: Independent Discovery Cohort_phchp325v4


title: Independent Discovery Cohort_phchp320v2


title: Independent Discovery Cohort_phchp320v1


title: Independent Discovery Cohort_phchp328v1


title: Independent Discovery Cohort_phchp319v6


title: Independent Discovery Cohort_phchp319v1


title: Independent Discovery Cohort_phchp316v4


title: Independent Discovery Cohort_phchp319v3


title: Independent Discovery Cohort_phchp312v3


title: Independent Discovery Cohort_phchp316v5


title: Independent Discovery Cohort_phchp318v3


title: Independent Discovery Cohort_phchp319v5


title: Independent Discovery Cohort_phchp313v3


title: Independent Discovery Cohort_phchp316v3


title: Independent Test Cohort_phchp008v1


title: Independent Discovery Cohort_phchp316v6


title: Independent Discovery Cohort_phchp316v1


title: Independent Discovery Cohort_phchp318v2


title: Independent Discovery Cohort_phchp318v1


title: Independent Discovery Cohort_phchp316v2


title: Independent Discovery Cohort_phchp312v1


title: Independent Discovery Cohort_phchp311v3


title: Independent Discovery Cohort_phchp311v2


title: Independent Discovery Cohort_phchp313v1


title: Independent Discovery Cohort_phchp310v2


title: Independent Discovery Cohort_phchp311v1


title: Independent Discovery Cohort_phchp346v2


title: Independent Discovery Cohort_phchp310v3


title: Independent Discovery Cohort_phchp310v1


title: Independent Discovery Cohort_phchp309v2


title: Independent Discovery Cohort_phchp309v3


title: Independent Discovery Cohort_phchp309v1


title: Independent Discovery Cohort_phchp308v3


title: Independent Discovery Cohort_phchp308v1


title: Independent Discovery Cohort_phchp308v4


title: Independent Discovery Cohort_phchp308v2


title: Independent Discovery Cohort_phchp312v2


title: Independent Discovery Cohort_phchp302v6


title: Independent Discovery Cohort_phchp302v2


title: Independent Discovery Cohort_phchp302v5


title: Independent Discovery Cohort_phchp300v5


title: Independent Discovery Cohort_phchp302v1


title: Independent Discovery Cohort_phchp302v3


title: Independent Discovery Cohort_phchp300v3


title: Independent Discovery Cohort_phchp300v2


title: Independent Discovery Cohort_phchp300v6


title: Independent Discovery Cohort_phchp300v4


title: Independent Discovery Cohort_phchp300v1


title: Independent Discovery Cohort_phchp299v2


title: Independent Discovery Cohort_phchp299v1


title: Independent Discovery Cohort_phchp298v3


title: Independent Discovery Cohort_phchp299v5


title: Independent Discovery Cohort_phchp299v4


title: Independent Discovery Cohort_phchp298v2


title: Independent Discovery Cohort_phchp298v1


title: Independent Discovery Cohort_phchp292v3


title: Independent Discovery Cohort_phchp297v4


title: Independent Discovery Cohort_phchp290v2


title: Independent Discovery Cohort_phchp287v3


title: Independent Discovery Cohort_phchp297v1


title: Independent Discovery Cohort_phchp297v2


title: Independent Discovery Cohort_phchp292v2


title: Independent Discovery Cohort_phchp290v3


title: Independent Discovery Cohort_phchp290v1


title: Independent Discovery Cohort_phchp282v4


title: Independent Discovery Cohort_phchp282v3


title: Independent Discovery Cohort_phchp287v1


title: Independent Discovery Cohort_phchp292v1


title: Independent Discovery Cohort_phchp287v2


title: Independent Discovery Cohort_phchp277v5


title: Independent Discovery Cohort_phchp279v1


title: Independent Discovery Cohort_phchp279v2


title: Independent Discovery Cohort_phchp277v4


title: Independent Discovery Cohort_phchp277v3


title: Independent Discovery Cohort_phchp279v4


title: Independent Discovery Cohort_phchp277v2


title: Independent Discovery Cohort_phchp277v1


title: Independent Discovery Cohort_phchp282v1


title: Independent Discovery Cohort_phchp276v4


title: Independent Discovery Cohort_phchp276v2


title: Independent Discovery Cohort_phchp276v1


title: Independent Discovery Cohort_phchp274v4


title: Independent Discovery Cohort_phchp275v3


title: Independent Discovery Cohort_phchp274v3


title: Independent Discovery Cohort_phchp275v1


title: Independent Discovery Cohort_phchp274v2


title: Independent Discovery Cohort_phchp273v2


title: Independent Discovery Cohort_phchp273v1


title: Independent Discovery Cohort_phchp270v6


title: Independent Discovery Cohort_phchp270v3


title: Independent Discovery Cohort_phchp270v5


title: Independent Discovery Cohort_phchp270v2


title: Independent Discovery Cohort_phchp270v4


title: Independent Discovery Cohort_phchp259v3


title: Independent Discovery Cohort_phchp258v2


title: Independent Discovery Cohort_phchp270v1


title: Independent Discovery Cohort_phchp254v3


title: Independent Discovery Cohort_phchp254v2


title: Independent Discovery Cohort_phchp259v1


title: Independent Discovery Cohort_phchp253v1


title: Independent Discovery Cohort_phchp242v3


title: Independent Discovery Cohort_phchp253v2


title: Independent Discovery Cohort_phchp258v3


title: Independent Discovery Cohort_phchp274v1


title: Independent Discovery Cohort_phchp253v3


title: Independent Discovery Cohort_phchp258v1


title: Independent Discovery Cohort_phchp240v1


title: Independent Discovery Cohort_phchp254v1


title: Independent Discovery Cohort_phchp240v3


title: Independent Discovery Cohort_phchp259v2


title: Independent Discovery Cohort_phchp238v1


title: Independent Discovery Cohort_phchp242v2


title: Independent Discovery Cohort_phchp238v2


title: Independent Discovery Cohort_phchp238v3


title: Independent Discovery Cohort_phchp235v2


title: Independent Discovery Cohort_phchp227v3


title: Independent Discovery Cohort_phchp227v2


title: Independent Discovery Cohort_phchp235v1


title: Independent Discovery Cohort_phchp240v2


title: Independent Discovery Cohort_phchp235v3


title: Independent Discovery Cohort_phchp219v2


title: Independent Discovery Cohort_phchp219v1


title: Independent Discovery Cohort_phchp216v1


title: Independent Discovery Cohort_phchp215v3


title: Independent Discovery Cohort_phchp221v1


title: Independent Discovery Cohort_phchp219v3


title: Independent Discovery Cohort_phchp214v1


title: Independent Discovery Cohort_phchp214v3


title: Independent Discovery Cohort_phchp221v3


title: Independent Discovery Cohort_phchp216v2


title: Independent Discovery Cohort_phchp227v1


title: Independent Discovery Cohort_phchp213v2


title: Independent Discovery Cohort_phchp215v2


title: Independent Discovery Cohort_phchp215v1


title: Independent Discovery Cohort_phchp213v1


title: Independent Discovery Cohort_phchp216v3


title: Independent Discovery Cohort_phchp221v2


title: Independent Discovery Cohort_phchp213v3


title: Independent Discovery Cohort_phchp209v2


title: Independent Discovery Cohort_phchp211v2


title: Independent Discovery Cohort_phchp209v3


title: Independent Discovery Cohort_phchp210v3


title: Independent Discovery Cohort_phchp211v1


title: Independent Discovery Cohort_phchp211v3


title: Independent Discovery Cohort_phchp282v5


title: Independent Discovery Cohort_phchp210v1


title: Independent Discovery Cohort_phchp208v3


title: Independent Discovery Cohort_phchp210v2


title: Independent Discovery Cohort_phchp214v2


title: Independent Discovery Cohort_phchp208v1


title: Independent Discovery Cohort_phchp204v1


title: Independent Discovery Cohort_phchp200v3


title: Independent Discovery Cohort_phchp208v2


title: Independent Discovery Cohort_phchp196v3


title: Independent Discovery Cohort_phchp200v2


title: Independent Discovery Cohort_phchp204v3


title: Independent Discovery Cohort_phchp199v2


title: Independent Discovery Cohort_phchp195v3


title: Independent Discovery Cohort_phchp195v2


title: Independent Discovery Cohort_phchp200v1


title: Independent Discovery Cohort_phchp194v2


title: Independent Discovery Cohort_phchp199v3


title: Independent Discovery Cohort_phchp194v1


title: Independent Discovery Cohort_phchp195v1


title: Independent Discovery Cohort_phchp192v1


title: Independent Discovery Cohort_phchp192v2


title: Independent Discovery Cohort_phchp190v2


title: Independent Discovery Cohort_phchp190v3


title: Independent Discovery Cohort_phchp190v1


title: Independent Discovery Cohort_phchp193v1


title: Independent Discovery Cohort_phchp193v4


title: Independent Discovery Cohort_phchp194v3


title: Independent Discovery Cohort_phchp192v3


title: Independent Discovery Cohort_phchp190v4


title: Independent Discovery Cohort_phchp199v1


title: Independent Discovery Cohort_phchp204v2


title: Independent Discovery Cohort_phchp193v3


title: Independent Discovery Cohort_phchp189v1


title: Independent Discovery Cohort_phchp187v1


title: Independent Discovery Cohort_phchp188v2


title: Independent Discovery Cohort_phchp242v1


title: Independent Discovery Cohort_phchp185v1


title: Independent Discovery Cohort_phchp186v2


title: Independent Discovery Cohort_phchp188v3


title: Independent Discovery Cohort_phchp184v1


title: Independent Discovery Cohort_phchp184v3


title: Independent Discovery Cohort_phchp184v2


title: Independent Discovery Cohort_phchp183v2


title: Independent Discovery Cohort_phchp187v2


title: Independent Discovery Cohort_phchp186v5


title: Independent Discovery Cohort_phchp186v1


title: Independent Discovery Cohort_phchp188v1


title: Independent Discovery Cohort_phchp186v3


title: Independent Discovery Cohort_phchp186v4


title: Independent Discovery Cohort_phchp185v2


title: Independent Discovery Cohort_phchp185v3


title: Independent Discovery Cohort_phchp189v3


title: Independent Discovery Cohort_phchp183v1


title: Independent Discovery Cohort_phchp179v1


title: Independent Discovery Cohort_phchp181v1


title: Independent Discovery Cohort_phchp181v4


title: Independent Discovery Cohort_phchp176v2


title: Independent Discovery Cohort_phchp181v3


title: Independent Discovery Cohort_phchp179v4


title: Independent Discovery Cohort_phchp172v3


title: Independent Discovery Cohort_phchp176v1


title: Independent Discovery Cohort_phchp172v1


title: Independent Discovery Cohort_phchp172v2


title: Independent Discovery Cohort_phchp179v2


title: Independent Discovery Cohort_phchp168v3


title: Independent Discovery Cohort_phchp166v1


title: Independent Discovery Cohort_phchp160v2


title: Independent Discovery Cohort_phchp166v4


title: Independent Discovery Cohort_phchp166v5


title: Independent Discovery Cohort_phchp168v1


title: Independent Discovery Cohort_phchp166v2


title: Independent Discovery Cohort_phchp166v6


title: Independent Discovery Cohort_phchp162v1


title: Independent Discovery Cohort_phchp162v2


title: Independent Discovery Cohort_phchp161v2


title: Independent Discovery Cohort_phchp161v1


title: Independent Discovery Cohort_phchp160v1


title: Independent Discovery Cohort_phchp162v3


title: Independent Discovery Cohort_phchp168v2


title: Independent Discovery Cohort_phchp166v3


title: Independent Discovery Cohort_phchp160v3


title: Independent Discovery Cohort_phchp161v3


title: Independent Discovery Cohort_phchp157v3


title: Independent Discovery Cohort_phchp157v1


title: Independent Discovery Cohort_phchp155v2


title: Independent Discovery Cohort_phchp157v2


title: Independent Discovery Cohort_phchp154v3


title: Independent Discovery Cohort_phchp196v1


title: Independent Discovery Cohort_phchp153v6


title: Independent Discovery Cohort_phchp153v3


title: Independent Discovery Cohort_phchp153v1


title: Independent Discovery Cohort_phchp154v1


title: Independent Discovery Cohort_phchp154v2


title: Independent Discovery Cohort_phchp153v4


title: Independent Discovery Cohort_phchp150v3


title: Independent Discovery Cohort_phchp149v2


title: Independent Discovery Cohort_phchp150v2


title: Independent Discovery Cohort_phchp153v2


title: Independent Discovery Cohort_phchp151v2


title: Independent Discovery Cohort_phchp155v1


title: Independent Discovery Cohort_phchp151v1


title: Independent Discovery Cohort_phchp142v4


title: Independent Discovery Cohort_phchp140v2


title: Independent Discovery Cohort_phchp140v3


title: Independent Discovery Cohort_phchp142v5


title: Independent Discovery Cohort_phchp142v6


title: Independent Discovery Cohort_phchp142v3


title: Independent Discovery Cohort_phchp151v3


title: Independent Discovery Cohort_phchp149v1


title: Independent Discovery Cohort_phchp142v1


title: Independent Discovery Cohort_phchp141v1


title: Independent Discovery Cohort_phchp141v3


title: Independent Discovery Cohort_phchp142v2


title: Independent Discovery Cohort_phchp140v4


title: Independent Discovery Cohort_phchp140v1


title: Independent Discovery Cohort_phchp141v2


title: Independent Discovery Cohort_phchp138v3


title: Independent Discovery Cohort_phchp138v2


title: Independent Discovery Cohort_phchp138v1


title: Independent Discovery Cohort_phchp134v5


title: Independent Discovery Cohort_phchp134v6


title: Independent Discovery Cohort_phchp136v3


title: Independent Discovery Cohort_phchp134v4


title: Independent Discovery Cohort_phchp134v2


title: Independent Discovery Cohort_phchp132v3


title: Independent Discovery Cohort_phchp134v3


title: Independent Discovery Cohort_phchp132v1


title: Independent Discovery Cohort_phchp132v4


title: Independent Discovery Cohort_phchp134v1


title: Independent Discovery Cohort_phchp132v2


title: Independent Discovery Cohort_phchp132v5


title: Independent Discovery Cohort_phchp136v1


title: Independent Discovery Cohort_phchp131v3


title: Independent Discovery Cohort_phchp129v3


title: Independent Discovery Cohort_phchp132v6


title: Independent Discovery Cohort_phchp131v1


title: Independent Discovery Cohort_phchp136v2


title: Independent Discovery Cohort_phchp124v1


title: Independent Discovery Cohort_phchp131v2


title: Independent Discovery Cohort_phchp150v1


title: Independent Discovery Cohort_phchp129v1


title: Independent Discovery Cohort_phchp127v2


title: Independent Discovery Cohort_phchp124v2


title: Independent Discovery Cohort_phchp127v3


title: Independent Discovery Cohort_phchp121v2


title: Independent Discovery Cohort_phchp118v4


title: Independent Discovery Cohort_phchp119v3


title: Independent Discovery Cohort_phchp118v2


title: Independent Discovery Cohort_phchp119v2


title: Independent Discovery Cohort_phchp109v1


title: Independent Discovery Cohort_phchp109v2


title: Independent Discovery Cohort_phchp112v2


title: Independent Discovery Cohort_phchp117v3


title: Independent Discovery Cohort_phchp112v1


title: Independent Discovery Cohort_phchp121v1


title: Independent Discovery Cohort_phchp106v2


title: Independent Discovery Cohort_phchp128v2


title: Independent Discovery Cohort_phchp117v1


title: Independent Discovery Cohort_phchp117v2


title: Independent Discovery Cohort_phchp118v1


title: Independent Discovery Cohort_phchp108v1


title: Independent Discovery Cohort_phchp112v3


title: Independent Discovery Cohort_phchp128v1


title: Independent Discovery Cohort_phchp108v3


title: Independent Discovery Cohort_phchp106v3


title: Independent Discovery Cohort_phchp106v1


title: Independent Discovery Cohort_phchp099v3


title: Independent Discovery Cohort_phchp093v2


title: Independent Discovery Cohort_phchp091v1


title: Independent Discovery Cohort_phchp093v5


title: Independent Discovery Cohort_phchp091v3


title: Independent Discovery Cohort_phchp088v6


title: Independent Discovery Cohort_phchp093v6


title: Independent Discovery Cohort_phchp089v4


title: Independent Discovery Cohort_phchp088v3


title: Independent Discovery Cohort_phchp093v3


title: Independent Discovery Cohort_phchp093v4


title: Independent Discovery Cohort_phchp089v2


title: Independent Discovery Cohort_phchp086v3


title: Independent Discovery Cohort_phchp088v5


title: Independent Discovery Cohort_phchp088v2


title: Independent Discovery Cohort_phchp086v2


title: Independent Discovery Cohort_phchp087v1


title: Independent Discovery Cohort_phchp089v1


title: Independent Discovery Cohort_phchp099v1


title: Independent Discovery Cohort_phchp087v3


title: Independent Discovery Cohort_phchp087v2


title: Independent Discovery Cohort_phchp093v1


title: Independent Discovery Cohort_phchp088v1


title: Independent Discovery Cohort_phchp099v2


title: Independent Discovery Cohort_phchp085v3


title: Independent Discovery Cohort_phchp086v1


title: Independent Discovery Cohort_phchp085v2


title: Independent Discovery Cohort_phchp127v1


title: Independent Discovery Cohort_phchp084v4


title: Independent Discovery Cohort_phchp121v3


title: Independent Discovery Cohort_phchp079v6


title: Independent Discovery Cohort_phchp083v1


title: Independent Discovery Cohort_phchp079v3


title: Independent Discovery Cohort_phchp079v2


title: Independent Discovery Cohort_phchp085v1


title: Independent Discovery Cohort_phchp079v5


title: Independent Discovery Cohort_phchp079v4


title: Independent Discovery Cohort_phchp083v3


title: Independent Discovery Cohort_phchp074v2


title: Independent Discovery Cohort_phchp084v1


title: Independent Discovery Cohort_phchp072v3


title: Independent Discovery Cohort_phchp074v1


title: Independent Discovery Cohort_phchp079v1


title: Independent Discovery Cohort_phchp083v2


title: Independent Discovery Cohort_phchp072v1


title: Independent Discovery Cohort_phchp073v3


title: Independent Discovery Cohort_phchp073v1


title: Independent Discovery Cohort_phchp072v2


title: Independent Discovery Cohort_phchp075v1


title: Independent Discovery Cohort_phchp070v6


title: Independent Discovery Cohort_phchp070v4


title: Independent Discovery Cohort_phchp075v3


title: Independent Discovery Cohort_phchp084v3


title: Independent Discovery Cohort_phchp084v2


title: Independent Discovery Cohort_phchp070v5


title: Independent Discovery Cohort_phchp070v2


title: Independent Discovery Cohort_phchp069v2


title: Independent Discovery Cohort_phchp070v1


title: Independent Discovery Cohort_phchp065v2


title: Independent Discovery Cohort_phchp070v3


title: Independent Discovery Cohort_phchp067v1


title: Independent Discovery Cohort_phchp067v3


title: Independent Discovery Cohort_phchp069v3


title: Independent Discovery Cohort_phchp069v1


title: Independent Discovery Cohort_phchp065v3


title: Independent Discovery Cohort_phchp062v2


title: Independent Discovery Cohort_phchp065v1


title: Independent Discovery Cohort_phchp062v1


title: Independent Discovery Cohort_phchp061v1


title: Independent Discovery Cohort_phchp058v2


title: Independent Discovery Cohort_phchp061v3


title: Independent Discovery Cohort_phchp074v3


title: Independent Discovery Cohort_phchp061v2


title: Independent Discovery Cohort_phchp053v3


title: Independent Discovery Cohort_phchp058v3


title: Independent Discovery Cohort_phchp053v2


title: Independent Discovery Cohort_phchp055v2


title: Independent Discovery Cohort_phchp055v1


title: Independent Discovery Cohort_phchp058v1


title: Independent Discovery Cohort_phchp055v3


title: Independent Discovery Cohort_phchp053v1


title: Independent Discovery Cohort_phchp052v3


title: Independent Discovery Cohort_phchp048v1


title: Independent Discovery Cohort_phchp040v2


title: Independent Discovery Cohort_phchp048v3


title: Independent Discovery Cohort_phchp042v1


title: Independent Discovery Cohort_phchp049v1


title: Independent Discovery Cohort_phchp042v2


title: Independent Discovery Cohort_phchp038v3


title: Independent Discovery Cohort_phchp046v3


title: Independent Discovery Cohort_phchp035v3


title: Independent Discovery Cohort_phchp028v1


title: Independent Discovery Cohort_phchp049v2


title: Independent Discovery Cohort_phchp038v1


title: Independent Discovery Cohort_phchp028v2


title: Independent Discovery Cohort_phchp046v2


title: Independent Discovery Cohort_phchp031v2


title: Independent Discovery Cohort_phchp040v3


title: Independent Discovery Cohort_phchp040v1


title: Independent Discovery Cohort_phchp035v1


title: Independent Discovery Cohort_phchp062v3


title: Independent Discovery Cohort_phchp031v1


title: Independent Discovery Cohort_phchp035v2


title: Independent Discovery Cohort_phchp042v3


title: Independent Discovery Cohort_phchp048v2


title: Independent Discovery Cohort_phchp052v2


title: Independent Discovery Cohort_phchp021v3


title: Independent Discovery Cohort_phchp026v2


title: Independent Discovery Cohort_phchp019v2


title: Independent Discovery Cohort_phchp038v2


title: Independent Discovery Cohort_phchp019v3


title: Independent Discovery Cohort_phchp021v1


title: Independent Discovery Cohort_phchp031v3


title: Independent Discovery Cohort_phchp026v1


title: Independent Discovery Cohort_phchp013v3


title: Independent Discovery Cohort_phchp012v1


title: Independent Discovery Cohort_phchp016v1


title: Independent Discovery Cohort_phchp046v1


title: Independent Discovery Cohort_phchp012v2


title: Independent Discovery Cohort_phchp019v5


title: Independent Discovery Cohort_phchp019v1


title: Independent Discovery Cohort_phchp026v3


title: Independent Discovery Cohort_phchp016v3


title: Independent Discovery Cohort_phchp012v3


title: Independent Discovery Cohort_phchp021v2


title: Independent Discovery Cohort_phchp013v1


title: Independent Discovery Cohort_phchp010v3


title: Independent Discovery Cohort_phchp010v2


title: SMN Knock Out rep1

type: SRA

city: Shanghai

first: Liang

last: Li

address: 300 Fenglin Road

country: China

institute: University of Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapped to dm6 whole genome using Tophat2 with defeault parameters. Reference genome and gene model annotation files were downloaded from FlyBase r6.13.
FeatureCounts was used to count the reads numbers mapped to each gene.
The TPM of each gene was calculated by in-house script.
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .

organism: Drosophila melanogaster

source_name: Larva L3

extract_protocol:
Total RNAs from larvae were isolated by TRIzol (Ambion) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, cDNAs were reverse transcribed using RevertAid Reverse Transcriptase (Thermo) and amplified by Ex-Taq (TaKaRa).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole Larvae

tag: developmental stage

value: Larva L3

tag: genotype

value: Smn-delta/delta


title: sn12 Knock Out rep2

description: Total RNAs from larvae were isolated by TRIzol (Ambion) and treated with RNase-free DNase I (Invitrogen)


title: Wild Type rep2


title: sn12 Knock Out rep1


title: Wild Type rep1


title: sn6 Knock Out rep1


title: SMN Knock Out rep2


title: Independent Discovery Cohort_phchp009v3

value: M


title: Independent Discovery Cohort_phchp016v2


title: leaf_salt_rep2_dsRNase_noprotein

city: Philadelphia

first: Marianne

middle: C

last: Kramer

state: PENNSYLVANIA

address: 433 South University Ave

department: Biology

institute: University of Pennsylvania

data_processing:
Library strategy: PIP-seq
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Trimmed and untrimmed reads were aligned to the Arabidopsis thaliana genome (TAIR10) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
PPS files - PPSs were identified using a modified version of the CSAR software package, as previously described (Silverman et al., 2014; Gosai et al., 2015; Foley et al., 2017a; Shan et al., 2019). Briefly, read coverage is calculated at each nucleotide in the genome and a Poisson test was used to determine an enrichment score for footprint compared to structure-only samples. PPSs were then called with a false discovery rate of 5% as previously described (Silverman et al., 2014; Gosai et al., 2015; Foley et al., 2017a; Shan et al., 2019).
mRNA structure scores - The structure score for every nucleotide of detected mRNAs was calculated using all mapped and spliced reads. We only considered mRNAs with a ≥ 45 nt 5’ UTRs, ≥ 140 nt 3’ UTRs and a minimum coverage of 50 reads across the entire transcript in both conditions. To generate profiles, introns were spliced out and each nucleotide in the spliced transcript was normalized by the average structure score across the entire spliced transcript. At the start and stop codons, the average structure score at each nucleotide was plotted with shading around the line representing the SEM at each nucleotide. For plotting secondary structure across the entire transcript, the 5’ UTR, CDS, and 3’ UTR were each divided into 100 equally sized bins. We then plotted the average structure score across each bin with shading around the line representing the SEM at each nucleotide.
lncRNA structure score : The Araport11 annotation of “lncRNAs”, “antisense lncRNAs”, “antisense RNA”, and “ncRNA” were merged together for all lncRNA analyses. The structure score for every nucleotide of detected lncRNAs was calculated using all mapped and spliced reads. We only considered lncRNAs with a minimum coverage of 5 reads across the entire transcript in both conditions. To generate profiles, each nucleotide in the spliced transcript was normalized by the average structure score across the entire unspliced transcript and introns were spliced out. Each lncRNA was divided into 100 equal sized bins and average structure score was plotted for each bin with shading around the line representing the SEM at each nucleotide.
Genome_build: TAIR10
Supplementary_files_format_and_content: BED format of protein protected sites (PPSs), bed12+1 for structure scores. The 13th column is a comma separated list of the structure score at each nucleotide in that spliced transcript

organism: Arabidopsis thaliana

source_name: 4-week-old rosette leaves

growth_protocol: Control- and salt-treated rosette leaves of UBQ10:NTF/ACT2p:BirA Columbia-0 ecotype were crosslinked in a 1% (vol/vol) formaldehyde solution in 1X PBS under vacuum for 10 minutes followed by a 5 minute quench in 125 mM glycine under vacuum. Crosslinked tissue was then frozen in liquid nitrogen until INTACT purification, as previously described (Deal and Henikoff, 2010; Gosai et al., 2015).

extract_protocol:
3 grams of rosette leaves from control- and salt-treated conditions were pulverized in liquid nitrogen then resuspended in 30 mL ice-cold nuclei purification buffer (NPB; 20 mM MOPS (pH = 7), 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5mM spermidine, 0.2 mM spermine) with RNase and protease inhibitors (0.5 µL/mL RNase OUT; Invitrogen; Carlsbad, CA, USA;, cOmplete protease inhibitor; Roche, Basel, Switzerland). The solution is then passed over a 70 µM Nylon mesh filter and incubated on ice for at least 10 minutes. Samples were then centrifuged at 1,200 rcf for 10 minutes at 4°C and pelleted nuclei were resuspended in 3 mL (1 mL per gram of tissue) NPB plus inhibitors and separated into 3-1.7 mL tubes containing 1 mL each. Following resuspension, 25 µL streptavidin coated M-280 Dynabeads (Invitrogen; Carlsbad, CA, USA) per gram of tissue were washed twice with NPB before being ultimately resuspended in NPB and added to samples. Samples were incubated for 30 minutes at 4°C with end-over-end rotation, after which they were transferred to 15 mL conical tubes containing 12 mL NPB supplemented with 0.1% (vol/vol) Tween-20 (NPBt). Samples were washed four times for 2 minutes at 4°C with end-over-end rotation. After the last wash, the beads were resuspended in 1 mL NPBt and transferred to 1.7 mL tubes and washed two additional times with 1 mL NPBt for 2 minutes at 4°C. The final samples were resuspended in 20 µL NPB and samples from the same tissue were recombined before being frozen in liquid nitrogen and stored at -80°C until processing.
PIP-seq libraries were constructed as previously described (Kramer and Gregory, 2019). To summarize, INTACT purified nuclei from 3 grams of tissue per replicate were lysed and separated into footprinting and structure-only samples. The footprinting samples were then treated with either dsRNase (ds-P) or ssRNase (ss-P) before protein digestion by proteinase K and reversal of crosslinks. In the structure-only samples, proteins were first digested with proteinase K before treatment with either dsRNase (P-ds) or ssRNase (P-ss). Each sample resulted in 4 libraries: 2 footprinting libraries (ss-P, ds-P) and 2 structure-only libraries (P-ss, P-ds). All libraries were sequenced on an Illumina HiSeq2000 using the standard protocol for 50 base pair single read sequencing.

treatment_protocol: All plants were grown in controlled chambers with a cycle of 16 hours light and 8 hours of dark at 22°C. All experiments were performed using UBQ10:NTF/ACT2p:BirA Columbia-0 ecotype of Arabidopsis thaliana (Deal and Henikoff, 2010). Salt-stress experiments  were carried out as previously described (Anderson et al., 2018).

value: UBQ10:NTF/ACT2p:BirA Columbia-0 ecotype

tag: treatment

value: salt-treated

tag: rnase

value: dsRNase (Rnase V1)

tag: protein-bound

value: no


title: leaf_salt_rep2_ssRNase_protein

value: ssRNase (Rnase ONE)

value: yes


title: leaf_salt_rep2_dsRNase_protein


title: leaf_salt_rep1_ssRNase_protein


title: leaf_ctrl_rep2_ssRNase_noprotein

value: control-treated


title: sn6 Knock Out rep2


title: leaf_ctrl_rep2_ssRNase_protein


title: leaf_salt_rep2_ssRNase_noprotein


title: Independent Discovery Cohort_phchp052v1

tag: individual

tag: visit (v) number

tag: gender

value: SZ

value: Whole Blood


title: leaf_ctrl_rep2_dsRNase_noprotein


title: Independent Discovery Cohort_phchp010v1

tag: diagnosis

value: SZA

tag: hvlt3 memory retention


title: leaf_salt_rep1_ssRNase_noprotein


title: leaf_ctrl_rep1_ssRNase_protein


title: leaf_salt_rep1_dsRNase_protein


title: leaf_ctrl_rep1_dsRNase_noprotein


title: leaf_ctrl_rep2_dsRNase_protein


title: Independent Discovery Cohort_phchp003v5


title: Independent Discovery Cohort_phchp003v3


title: Independent Discovery Cohort_phchp009v1


title: Independent Discovery Cohort_phchp003v2


title: GRO-seq-cisplatin-treated A549cells

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig

molecule: polyA RNA

growth_protocol: The human lung adenocarcinoma A549 cell line (RRID:CVCL_0023) were cultured in Dulbecco’s modified Eagle’s-Glutamax I medium (DMEM-Glutamax I, Gibco, Cat#10566-016) supplemented with 10% FBS (FBS, Omega Scientific, Cat#FB-11) and antibiotics penicillin and streptomycin (100 ug/mL, Gemini Bio, Cat#400-109) at 5% CO2 37ºC, and sub-cultured at 1:5 to 1:6 dilutions after dissociation with 0.25% trypsin. Media was changed every other day, or daily when cells reached >50-60% confluency.

extract_protocol:
GRO-seq analysis was perfromed as previously reported (PMID: 21572438, Wang et al., 2011).
RNA quality was calculated on TapeStation (Agilent Technologies). PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

treatment_protocol: Acute treatments (IC50) were administrated for 3 days, adding fresh media with drug at day 0 and after 2 days again.

tag: cell line

value: cisplatin


title: Independent Discovery Cohort_phchp004v2


title: Independent Discovery Cohort_phchp004v4


title: siRNA-15-3

city: Cambridge

first: Alisa

last: Manning

state: MA

address: 75 Ames Street

department: Metabolism Program

institute: Broad Institute

data_processing:
Data was analyzed using the Broad Picard Pipeline which includes; initial data alignment using STAR aligner and duplicate read marking for downstream interpretation. Data is delivered in BAM format including base calls, quality scores, and alignment data.
Genes were counted using featurecounts from the Rsubread package using a gene model derived from gencode.v19.annotation.gff3.gz with all exons (spanning multiple transcripts) joined into a single representative gene.
Normalized gene counts were obtained with DESeq2, with adjustment for batch effects
Genome_build: hg19
Supplementary_files_format_and_content: Tab deliminated text files with genes in each row and samples in each column

source_name: primary human hepatocyte

growth_protocol: Primary human hepatocytes were plated into collagen-coated 6-well plates and grown in Williams' E complete medium.

extract_protocol:
RNA was prepared using  Qiagen RNeasy Mini Kit  (#74104).
Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. An aliquot of 200ng for each sample was transferred into library preparation which was an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit.  This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample.  It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 500bp cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.  The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing.

treatment_protocol: Cells were transfected with 50 nM siRNA and Lipofectamine® RNAiMAX reagent in a final concentration of 1 mL/well Opti-MEM™. The target sequences in the 3.4 kb LOC157273 lncRNA (NR_040039.1 or Ensembl ENST00000520390.1) were: siRNA09 in the 3’-end of the third exon (GGGAAGGGTTAGAGAGGTC), siRNA11 in the first exon (CAACTTAGCTTCTCCATTTTT), siRNA13 near the 5’-end of the third exon (AGAGAAGGACTGAAGATCATT) and siRNA15 in the second exon (TCAGAGGACTTGACACCAT) where the sequences represent the sense-strand DNA targeted by the siRNAs.

tag: batch

tag: sirna


title: leaf_salt_rep1_dsRNase_noprotein


title: leaf_ctrl_rep1_ssRNase_noprotein


title: siRNA-11-2


title: GRO-seq-vehicle-treated A549cells

value: vehicle


title: Mock_si_-3

value: Mock


title: siRNA-11-3


title: siRNA-11-1


title: leaf_ctrl_rep1_dsRNase_protein


title: scramble-2

value: Scramble


title: siRNA-15-2


title: scramble-3


title: Mock_si_-1


title: Mock_si_-2


title: scramble-1


title: 9-111-2-1_S163

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

source_name: adipose tisue

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 9-111-2-2_S19

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 9-111-2-3_S25

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 9-109-2-1_S159


title: 9-109-2-2_S169


title: 9-107-2-2_S185


title: 9-107-1-2_S110


title: 9-108-2-1_S80


title: 9-108-2-3_S176


title: 9-105-2-1_S78


title: 9-105-1-2_S86


title: 9-104-2-2_S129


title: 9-104-2-1_S184


title: 9-104-2-1_S88


title: 9-103-2-1_S140


title: 9-103-1-3_S1


title: 9-103-1-1_S93


title: 9-111-2-2_S115


title: 9-102-1-1_S137


title: 9-103-2-2_S188


title: 9-099-2-2_S100


title: 9-099-2-1_S157


title: 9-101-1-1_S101


title: 9-100-2-1_S175


title: 9-100-2-2_S29


title: 9-103-2-3_S90


title: 9-098-2-3_S81


title: 9-107-2-2_S200


title: 9-097-2-1_S57


title: 9-097-2-2_S97


title: 9-098-2-3_S177


title: 9-095-2-3_S66


title: 9-094-1-1_S124


title: 9-095-2-1_S117


title: 9-093-2-3_S143


title: 9-093-2-2_S175


title: 9-092-2-3_S84


title: 9-092-1-3_S35


title: 9-092-1-1_S192


title: 9-091-2-3_S173


title: 9-089-2-2_S60


title: 9-091-2-2_S176


title: 9-091-2-3_S77


title: 9-089-2-1_S154


title: 9-091-2-1_S87


title: 9-088-2-1_S174


title: 9-108-2-3_S80


title: 9-086-2-2_S4


title: 9-093-2-1_S147


title: 9-083-2-1_S182


title: 9-086-2-1_S75


title: 9-084-2-2_S20


title: 9-085-2-1_S35


title: 9-084-2-3_S58


title: 9-083-2-2_S93


title: 9-085-2-1_S131


title: 9-092-2-1_S157


title: 9-080-2-2_S120


title: 9-084-2-1_S39


title: 9-081-2-3_S39


title: 9-079-2-1_S76


title: 9-078-2-3_S30


title: 9-078-2-1_S144


title: 9-078-2-2_S140


title: 9-088-2-1_S78


title: 9-076-2-2_S41


title: 9-077-2-1_S97


title: 9-077-1-1_S99


title: 9-073-2-1_S110


title: 9-075-2-3_S17


title: 9-076-2-1_S124


title: 9-071-2-1_S96


title: 9-074-2-1_S145


title: 9-072-2-1_S33


title: 9-075-2-1_S58


title: 9-066-2-1_S179


title: 9-057-2-1_S2


title: 9-057-2-3_S183


title: 9-061-2-1_S180


title: 9-063-2-3_S86


title: 9-063-2-1_S78


title: 9-063-1-2_S60


title: 9-056-2-3_S41


title: 9-070-2-1_S13


title: 9-060-2-1_S167


title: 9-055-2-1_S120


title: 9-057-2-1_S98


title: 9-052-2-1_S126


title: 9-055-2-3_S28


title: 9-097-2-3_S151


title: 9-054-2-1_S85


title: 9-075-2-2_S137


title: 9-050-2-1_S60


title: 9-052-2-1_S30


title: 9-054-2-2_S106


title: 9-049-2-1_S183


title: 9-049-2-1_S87


title: 9-069-2-1_S170


title: 9-049-2-2_S42


title: 9-056-2-1_S8


title: 9-064-2-1_S12


title: 9-050-1-1_S191


title: 9-051-2-1_S54


title: Independent Discovery Cohort_phchp004v3

value: M

tag: tissue


title: 9-050-2-1_S156


title: 9-047-2-1_S25


title: 9-046-2-2_S50


title: 9-046-2-1_S88


title: 9-046-2-2_S146


title: 9-046-1-1_S34


title: N40_N_TgOFF_1

city: Tokyo

first: Seiji

last: Shiozawa

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University, School of Medicine

data_processing:
Poor-quality reads (score < 30) were trimmed using Trim Galore! (ver.0.4.0).
The resulting reads were aligned to the Callithrix jacchus genome (Callithrix_jacchus-3.2.1) using STAR aligner (version 2.5.3a).
The mapped reads were counted by featureCounts (1.5.2)
Genome_build: Callithrix jacchus-3.2

organism: Callithrix jacchus

source_name: marmoset ESC

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit.
Poly(A)+ RNA was selected and converted to a library of cDNA fragments (200–250 bp) with adaptors attached to both ends for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit Set [Illumina] as per the manufacturer’s instructions.

value: Naïve ESC


title: N40_N_TgOFF_3


title: 9-028-2-1_S168


title: 9-031-2-1_S16


title: 9-038-2-1_S22


title: 9-029-2-2_S116


title: 9-029-2-1_S100


title: N40_N_TgOFF_2


title: 9-049-2-3_S33


title: N40_P_Tg_3

value: Primed ESC


title: siRNA-15-1


title: DSY-c2_N_TgON_3


title: 9-046-1-1_S130


title: N40_P_Tg_2


title: DSY-c2_N_TgON_2


title: 9-026-2-1_S47


title: 9-024-2-2_S74


title: 9-026-2-2_S177


title: DSY-c2_P_Tg_4


title: N40_P_Tg_1


title: 9-025-2-2_S32


title: 9-025-2-1_S4


title: DSY-c2_N_TgON_1


title: 9-027-2-2_S190


title: 9-024-2-1_S201


title: 9-022-2-1_S122


title: 9-021-1-1_S129


title: No.40_3


title: DSY-c2_P_Tg_2


title: No.40_1


title: 9-020-2-3_S194


title: 9-020-2-3_S15


title: DSY127_2


title: DSY127_1


title: 9-019-2-1_S154


title: 9-025-2-1_S100


title: DSY-c2_P_Tg_5


title: 9-018-2-2_S125


title: Epiblast_2

source_name: marmoset early embryo

value: Postimplantation embryo epiblast


title: Epiblast_3


title: HatchedBlastocyst_3

value: Hatched blastocyst ICM


title: 9-017-2-1_S130


title: Epiblast_1


title: 9-018-2-1_S132


title: 9-016-2-3_S83


title: HatchingBlastocyst_3

value: Hatching blastocyst ICM


title: DSY127_3


title: 9-016-2-2_S63


title: No.40_2


title: 9-016-2-2_S159


title: 9-016-2-1_S181


title: HatchedBlastocyst_1


title: ExpandBlastocyst_3

value: Expanded blastocyst ICM


title: ExpandBlastocyst_2


title: HatchingBlastocyst_1


title: 9-015-2-2_S98


title: 9-020-2-1_S60


title: ExpandBlastocyst_1


title: 9-013-2-1_S24


title: Blastocyst_3

value: Blastocyst ICM


title: 9-017-2-2_S122


title: 9-011-2-3_S75


title: HatchedBlastocyst_2


title: 9-009-2-1_S90


title: 9-011-2-3_S171


title: EarlyBlastocyst_3

value: Early blastocyst ICM


title: Blastocyst_2


title: Blastocyst_1


title: EarlyBlastocyst_2


title: 9-009-2-1_S186


title: HatchingBlastocyst_2


title: Morula_3

value: Morula stage embryo


title: 9-008-1-1_S48


title: 9-006-2-2_S127


title: EarlyBlastocyst_1


title: 9-008-1-1_S144


title: 9-004-2-1_S46


title: Morula_1


title: 9-018-2-3_S95


title: 9-005-1-2_S9


title: 9-015-2-1_S23


title: 9-003-2-3_S107


title: SCV56_PH5_03

city: Bethesda

first: Subhash

last: Verma

state: MD

address: 37 Convent Dr

department: National Cancer Institute

institute: National Institutes of Health

description: Biological replicate 3

data_processing:
The reads were trimmed for adapters and low-quality bases using Cutadapt 1.18
Alignment of the reads to the E. coli K12 MG1655 reference genome and the annotated transcriptome was done using STAR 2.6.1
Transcript abundances were calculated by RSEM 1.2.31
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified using the glmTreat function in edgeR by following the steps outlined in (Chen Y et al  F1000Res. 2016 Jun 20 [revised 2016 Aug 2];5:1438).
Genome_build: ASM584v2 Escherichia coli K12 MG1655
Supplementary_files_format_and_content: tab-delimited output files of rsem_calculate_expression with expected_count, transcript per million (TPM), Fragments Per Kilobase of transcript per Million mapped reads (FPKM)

organism: Escherichia coli

source_name: Cells harvested at OD 600 between 0.2-0.3

growth_protocol: Overnight culture grown in LB was diluted 1:100 in fresh LB of pH 7.0 or pH 5.0

extract_protocol:
For total RNA isolation, a frozen pellet of cells was resuspended in 1 ml TRIzol reagent (Life Technologies) to homogenization and incubated at room temperature for 5 min.  To the resuspension, 0.2 ml chloroform was added and mixed by inverting the tube for 15 seconds. The mixture was incubated at  room temperature for 10 min and then centrifuged at 20,000 g for 10 min at 4°C.  After centrifugation, ~0.6 ml of the upper phase was transferred to a new centrifuge tube containing 0.5 ml isopropanol.  The mixture was incubated at room temperature for 10 min and then centrifuged at 20,000 g for 15 min at 4°C.  After centrifugation, the supernatant was discarded and the pellet was washed twice with 1 ml 75% ethanol, made with Diethyl pyrocarbonate (DEPC) treated water, by centrifugation at 12,000 rpm, for 5 min at 4°C. After the second wash, the tube was left open for 10-15 min at room temperature to dry the pellet. To the pellet, 50 µl DEPC treated water was added and the tube was left at 37°C for 10-15 min and then the pellet was fully resuspended using a pipette.  DNA was removed using TURBO DNA-free™ Kit (Invitrogen). Quality of total RNA was determined by electrophoresis on the TapeStation system (Agilent).
Paired-end sequencing libraries were prepared with 2.5 µg of total RNA using Illumina® TruSeq® Stranded Total RNA library prep workflow with Ribo-Zero according to the manufacturer’s instructions.

treatment_protocol: Strains were grown in LB of pH 7.0 or pH 5.0

tag: background strain

value: Escherichia coli K12  MG1655

value: hupAE34K hupB+

value: Growth in LB broth of pH 5.0


title: 9-003-2-1_S150


title: SCV85_PH5_02

description: Biological replicate 2

value: hupAE34K delta-hupB


title: SCV85_PH5_01

description: Biological replicate 1


title: 9-003-1-3_S112


title: 9-001-2-2_S147


title: SCV56_PH5_02

description: Biological replicate 2


title: 7-093-2-3_S161


title: 7-093-2-2_S144


title: SCV27_PH5_02

description: Biological replicate 2

value: delta-hupA delta-hupB


title: SCV56_PH5_01

description: Biological replicate 1


title: 7-092-2-3_S186


title: SCV27_PH5_01

description: Biological replicate 1


title: SCV85_PH5_03

description: Biological replicate 3


title: SCV18_PH5_03

description: Biological replicate 3

value: delta-hupA


title: Morula_2


title: 7-092-2-1_S76

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 7-091-2-3_S41

value: baseline, cid2 :lcd, cid3 :di):CID3


title: SCV18_PH5_01

description: Biological replicate 1


title: SCV18_PH5_02

description: Biological replicate 2


title: SCV96_PH5_03

description: Biological replicate 3

value: wild-type


title: 7-091-2-2_S117

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 7-091-2-2_S225


title: SCV96_PH5_01

description: Biological replicate 1


title: 7-090-2-1_S142


title: SCV85_PH7_03

description: Biological replicate 3

value: Growth in LB broth of pH 7.0


title: 7-090-2-2_S148


title: SCV85_PH7_02

description: Biological replicate 2


title: SCV56_PH7_02

description: Biological replicate 2


title: SCV56_PH7_03

description: Biological replicate 3


title: SCV56_PH7_01

description: Biological replicate 1


title: 7-089-1-3_S132


title: 7-092-2-2_S82


title: 7-091-2-1_S172


title: 7-089-1-2_S143


title: 7-090-2-3_S72


title: SCV96_PH5_02

description: Biological replicate 2


title: 7-088-2-1_S178


title: 7-089-1-1_S88


title: SCV27_PH7_03

description: Biological replicate 3


title: SCV27_PH7_01

description: Biological replicate 1


title: 7-087-2-2_S65


title: 7-088-2-3_S112


title: SCV85_PH7_01

description: Biological replicate 1


title: 7-086-2-1_S181


title: 7-086-2-3_S1


title: SCV19_PH7_01

description: Biological replicate 1

value: delta-hupB


title: SCV18_PH7_03

description: Biological replicate 3


title: SCV19_PH7_03

description: Biological replicate 3


title: SCV27_PH7_02

description: Biological replicate 2


title: 7-089-1-3_S36


title: 7-085-2-1_S14


title: SCV96_PH7_02

description: Biological replicate 2


title: SCV96_PH7_03

description: Biological replicate 3


title: 7-084-2-3_S92


title: 7-084-2-1_S177


title: 7-084-2-2_S42


title: SCV96_3

description: Biological replicate 3

source_name: Cells harvested at OD 600 between 0.4-0.5


title: SCV96_PH7_01

description: Biological replicate 1


title: SCV96_1

description: Biological replicate 1


title: 7-083-2-1_S62


title: SCV96_2

description: Biological replicate 2


title: SCV18_PH7_02

description: Biological replicate 2


title: SCV19_PH7_02

description: Biological replicate 2


title: 7-081-2-3_S24


title: 7-085-2-2_S27


title: 7-082-2-1_S177


title: 7-081-2-3_S120


title: 7-083-2-3_S91


title: 7-080-2-1_S170


title: 7-079-2-3_S155


title: SCV27_PH5_03

description: Biological replicate 3


title: 7-083-2-2_S215


title: 7-088-2-2_S154


title: 7-082-2-2_S91


title: SCV18_PH7_01

description: Biological replicate 1


title: Striatum_saline_rep2

city: Chengdu

first: Xiaobo

last: Cen

state: Sichuan

address: #28 Gaopeng Street, High Technological Development Zone

department: State Key Lab of Biotherapy

institute: West China Hospital of Sichuan University

description: Gene expression after saline self-administration in striatum

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Axon GenePix 4000B microarray scanner (Molecular Devices, Inc.).

data_processing: Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 4 out of 8 samples have flag expressed(greater than 2 times background standard deviation) were retained for further analyses.

organism: Mus musculus

label_protocol: CircRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The dorsal striatum from both hemispheres was snap-frozen in liquid nitrogen, and then stored at 80°C.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions, including a DNase digestion step. The purity and concentrations of the RNA samples were measured by NanoDrop ND-1000 instrument. The integrity of RNA was assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Cocaine was dissolved in 0.9% saline at a concentration of 1.25 mg /ml for intravenous infusion. The self-administration procedures are as follows: FR1, 0.75 mg/kg/infusion, infusions of 15 µl were delivered over a 2-second time period). Mice of cocaine group continued on a cocaine self-administration schedule until they displayed stable responding (usually 10~12 days). Immediately after the last self-administration session, mice were killed by rapid decapitation without anesthesia, brains were removed.

tag: strain

value: C57BL/6J mice

value: Striatum

value: Male

tag: age

value: 8 weeks


title: Striatum_cocaine_rep4

description: Gene expression after cocaine self-administration in striatum


title: Striatum_saline_rep4


title: Striatum_saline_rep3


title: 7-078-1-2_S152


title: 7-078-1-1_S132


title: 7-078-1-3_S54


title: Striatum_cocaine_rep2


title: 7-077-2-3_S214


title: 7-077-2-3_S147


title: TC-797_DMSO_RNApolII_input_replicate2 (ChIP-seq)

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using bowtie2 v2.3.1 with option --very-sensitive.
Reads with a MAPQ ≥ 30 were retained using samtools v1.3.1.
PCR duplicates were removed with picard MarkDuplicates v2.9.2.
MACS2 (Zhang et al., 2008) was used to compute signal tracks by first running macs2 callpeak with parameters -B --SPMR --keep-dup all -g hs -f BAM and then running macs2 bdgcmp with parameter -m FE.
Histone H3K27ac ChIP-seq profiles were calibrated using spike-in normalization with D. melanogaster as the calibration genome, as previously described (Hu et al., 2015). As the NUT epitope is not expressed in Drosophila Kc167 cells, BRD4-NUT ChIP-seq profiles were not spike-in normalized.
The epic v0.2.12 implementation of the SICER algorithm (Xu et al., 2014) was used to identify broadly enriched domains from histone H3K27ac ChIP-seq data setting the window size to 2500 bp and gap size to 1 with parameters -w 2500 -g 1, respectively. Input libraries were used as controls for domain annotation.
Often, we observed closely spaced enriched regions and to span these regions and capture the entire domain, SICER/epic-identified domains within 25 kb of one another were combined using bedtools v2.27.1 with command bedtools merge.
To identify megadomains, the list of called domains was filtered by signal strength and by domain size. Signal strength was determined by subtracting the rpm normalized input reads from rpm normalized sample reads for each called domain and subsequently ranked in increasing order of counts. The ROSE algorithm (Rank Ordering of Super-Enhancers) (Whyte et al., 2013) was applied to the ranked dataset to determine the cutoff threshold for signal strength by sliding a diagonal line and finding the point along the abscissa where the diagonal line was tangent to the rank-ordered curve. The cutoff for feature size was determined in a similar manner by ranking the domain length in base pairs and applying ROSE. Domains that exceeded both the signal cutoff and the size threshold were retained using bedtools intersect with default parameters.
The above was performed for each biological replicate, and, then, to create the highest confidence domain list, domains identified in both replicates were merged using bedtools intersect with default parameters. The resulting domains were considered “megadomains”.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.bw file of ChIP-seq track in bigWig format.
Supplementary_files_format_and_content: *.bed file of megadomain locations in bed format.

molecule: genomic DNA

source_name: TC-797 cultured cells

growth_protocol: 293TRex-Flag-BRD4-NUT-HA cells were a kind gift from Christopher A. French (Brigham and Women’s Hospital, Boston, MA). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 15 µg/mL blasticidin (Gibco #A1113903) + 100 µg/mL hygromycin (Corning #30240CR) at 37° C with 5% CO2. TC-797 cells were a kind gift from Jeffrey A. Toretsky (Georgetown University, Washington, DC). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) at 37° C with 5% CO2. Kc167 cells were obtained from the Drosophila Genomics Resource Center (#1; Bloomington, IN). Cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde. Cells were lysed with detergent and chromatin solubilized by shearing (for H3K27ac IP) or shearing and enzymatic digestion (for BRD4-NUT IP). An aliquot was removed as the input control and the samples then immunoprecipitated with the respective antibody. DNA-protein cross-links were reversed and the DNA then purified.
DNA was prepared for next-generation sequencing using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO. Triptolide (TPL; Cayman Chemical #11973) was solubilized in DMSO. TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) or 500 nM triptolide (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

tag: cell type

value: NUT carcinoma

tag: chip antibody

value: none (input control)

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: TC-797_Triptolide_RNApolII_replicate2 (ChIP-seq)

value: Rpb1 NTD (D8L4Y) rabbit monoclonal antibody (Cell Signaling Technology #14858S; RRID:AB_2687876)


title: TC-797_Triptolide_RNApolII_replicate1 (ChIP-seq)


title: Striatum_cocaine_rep1


title: TC-797_Triptolide_RNApolII_input_replicate1 (ChIP-seq)


title: TC-797_Triptolide_RNApolII_input_replicate2 (ChIP-seq)


title: Striatum_cocaine_rep3


title: 7-077-2-2_S66


title: 7-079-2-2_S131


title: 7-077-2-2_S162


title: 7-077-1-3_S227


title: TC-797_DMSO_RNApolII_replicate1 (ChIP-seq)


title: 7-077-1-3_S106


title: TC-797_Triptolide_H3K27ac_input_replicate4 (ChIP-seq)

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using using bowtie2 v2.3.1 with option --very-sensitive.
Reads with a MAPQ ≥ 30 were retained using samtools v1.3.1.
PCR duplicates were removed with picard MarkDuplicates v2.9.2.
MACS2 (Zhang et al., 2008) was used to compute signal tracks by first running macs2 callpeak with parameters -B --SPMR --keep-dup all -g hs -f BAM and then running macs2 bdgcmp with parameter -m FE.
Histone H3K27ac ChIP-seq profiles were calibrated using spike-in normalization with D. melanogaster as the calibration genome, as previously described (Hu et al., 2015). As the NUT epitope is not expressed in Drosophila Kc167 cells, BRD4-NUT ChIP-seq profiles were not spike-in normalized.
The epic v0.2.12 implementation of the SICER algorithm (Xu et al., 2014) was used to identify broadly enriched domains from histone H3K27ac ChIP-seq data setting the window size to 2500 bp and gap size to 1 with parameters -w 2500 -g 1, respectively. Input libraries were used as controls for domain annotation.
Often, we observed closely spaced enriched regions and to span these regions and capture the entire domain, SICER/epic-identified domains within 25 kb of one another were combined using bedtools v2.27.1 with command bedtools merge.
To identify megadomains, the list of called domains was filtered by signal strength and by domain size. Signal strength was determined by subtracting the rpm normalized input reads from rpm normalized sample reads for each called domain and subsequently ranked in increasing order of counts. The ROSE algorithm (Rank Ordering of Super-Enhancers) (Whyte et al., 2013) was applied to the ranked dataset to determine the cutoff threshold for signal strength by sliding a diagonal line and finding the point along the abscissa where the diagonal line was tangent to the rank-ordered curve. The cutoff for feature size was determined in a similar manner by ranking the domain length in base pairs and applying ROSE. Domains that exceeded both the signal cutoff and the size threshold were retained using bedtools intersect with default parameters.
The above was performed for each biological replicate, and, then, to create the highest confidence domain list, domains identified in both replicates were merged using bedtools intersect with default parameters. The resulting domains were considered “megadomains”.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.bw file of ChIP-seq track in bigWig format.
Supplementary_files_format_and_content: *.bed file of megadomain locations in bed format.


title: 7-077-1-2_S103


title: TC-797_Triptolide_H3K27ac_input_replicate3 (ChIP-seq)


title: 7-077-1-1_S61


title: Striatum_saline_rep1


title: TC-797_DMSO_H3K27ac_input_replicate4 (ChIP-seq)


title: TC-797_Triptolide_H3K27ac_replicate3 (ChIP-seq)

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173S, lot 6 RRID:AB_10949503)


title: 7-076-2-1_S119


title: TC-797_DMSO_H3K27ac_input_replicate3 (ChIP-seq)


title: TC-797_Triptolide_H3K27ac_replicate4 (ChIP-seq)


title: 7-075-2-3_S221


title: 7-075-2-3_S149


title: TC-797_Triptolide_replicate4 (TT-seq)

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using STAR v2.5.2b.
Duplicate and multimapper reads were marked with STAR with option --bamRemoveDuplicatesType UniqueIdentical and then removed with samtools v1.3.1 with option -F 1024.
STAR was used to compute signal tracks with options --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM.
TT-seq profiles were calibrated using spike-in normalization with D. melanogaster as the calibration genome, as previously described (Lugowski et al., 2018).
Reads overlapping genes were counted using htseq-count v0.9.1 (Anders et al., 2015) with parameters -f bam -r pos -s reverse -t gene -i gene_id. The gene set used consisted of protein-coding genes and lincRNAs from human GENCODE v24 (gtf column “transcript_type” either “protein_coding” or “lincRNA”) concatenated with those from FlyBase release 6.21.
Expression levels (fpkm) and differentially expressed genes were determined using DESeq2 v1.18.1 (Love et al., 2014), excluding genes with less than 10 counts in all samples, using size factors determined from the D. melanogaster gene counts, and calling significance at a Benjamini-Hochberg adjusted p-value < 0.01.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *_plus.bw file of plus-strand TT-seq track in bigWig format.
Supplementary_files_format_and_content: *_minus.bw file of minus-strand TT-seq track in bigWig format.
Supplementary_files_format_and_content: *_FPKM.bed file of per gene expression levels as FPKM values.
Supplementary_files_format_and_content: *_DESeq2.csv file of differential gene expression analysis between indicated conditions.

growth_protocol: TC-797 cells were a kind gift from Jeffrey A. Toretsky (Georgetown University, Washington, DC). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) at 37° C with 5% CO2. Kc167 cells were obtained from the Drosophila Genomics Resource Center (#1; Bloomington, IN). Cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Cells were lysed with TRIzol (Thermo Fisher #15596018) and total RNA was isolated essentially following the manufacturer’s instructions. Based on the yield of total RNA  the amount of total RNA per 10 million cells was determined and 400 ng of 4-thiouridine labelled total Drosophila Kc167 cell RNA was added/spiked-in to an aliquot of total RNA corresponding to 10 million TC-797 cells. RNA was fragmented using a NEBNext RNA Fragmentation Module and then labelled with MTSEA-biotin-XX. Labelled RNA was enriched using streptavidin Dynabeads.
rRNA was depleted from the sample using a NEBNext rRNA Depletion Kit (New England Biolabs #E6310). A DNA library (from reverse transcribed RNA) was prepared for high-throughput sequencing following chapter 5 in the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs #E7760).

treatment_protocol: MZ1 (Cayman Chemical #21622) was solubilized in DMSO. Triptolide (TPL; Cayman Chemical #11973) was solubilized in DMSO. TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) or 500 nM triptolide (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

value: Drosophila melanogaster Kc167 cell 4-thiouridine-labelled total RNA


title: 9-003-2-1_S54


title: TC-797_DMSO_H3K27ac_replicate3 (ChIP-seq)


title: TC-797_Triptolide_replicate5 (TT-seq)


title: TC-797_DMSO_RNApolII_input_replicate1 (ChIP-seq)


title: 7-075-2-1_S30


title: 7-076-2-2_S33


title: 7-074-2-2_S169


title: 7-074-2-1_S119


title: TC-797_DMSO_RNApolII_replicate2 (ChIP-seq)


title: TC-797_DMSO_replicate5 (TT-seq)


title: 7-073-2-3_S7


title: TC-797_DMSO_replicate4 (TT-seq)


title: 7-073-2-3_S103


title: TC-797_washout_replicate3 (TT-seq)

treatment_protocol: MZ1 (Cayman Chemical #21622) was solubilized in DMSO.  TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.  After each of the above treatments, media was removed from the cells and replaced with media (with or without DMSO or MZ1, as necessary) containing 500 µM 4-thiouridine (Sigma-Aldrich #T4509) prewarmed to 37° C. Cells were incubated for 5 minutes at 37° C with 5% CO2.


title: 7-075-2-2_S86


title: 7-073-2-2_S127


title: 7-073-1-1_S106


title: TC-797_washout_replicate2 (TT-seq)


title: TC-797_DMSO_H3K27ac_replicate4 (ChIP-seq)


title: TC-797_MZ1_replicate3 (TT-seq)


title: 7-073-1-2_S158


title: TC-797_washout_replicate1 (TT-seq)


title: 7-072-2-1_S13


title: 7-071-2-2_S170


title: TC-797_MZ1_replicate2 (TT-seq)


title: TC-797_MZ1_replicate1 (TT-seq)


title: TC-797_DMSO_replicate3 (TT-seq)


title: TC-797_DMSO_replicate2 (TT-seq)


title: TC-797_DMSO_replicate1 (TT-seq)


title: 7-071-1-3_S157


title: 7-073-2-1_S29


title: 7-070-2-3_S191


title: 7-071-1-1_S133


title: 7-071-1-2_S61


title: TC-797_DMSO_replicate1 (HiC)

data_processing:
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using BWA-MEM v0.7.15-r1140.
Reads were then assigned to MboI restriction fragments, duplicates removed, reads with a MAPQ ≥ 30 were retained, and intra restriction fragment reads removed.
The genome was divided into equally spaced, non-overlapping bins and the number of reads counted in each pair of bins gave the number of contacts, generating a Hi-C contact map.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014) using Juicer Tools v1.8.9.
Biological replicates were combined after filtering and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
Loops were identified using the previously described HiCCUPs algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Megadomain-megadomain interactions were identified using a model that accounted for enrichment relative to local background based on Poisson statistics.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_TADs.bedpe file of TAD coordinates in Juicebox format.
Supplementary_files_format_and_content: *_loops.bedpe file of loop coordinates in Juicebox format.
Supplementary_files_format_and_content: *_mega-mega.bedpe file of megadomain-megadomain interactions in Juicebox format.

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde.  Intact nuclei were crudely isolated using detergent lysis.  DNA was digested with MboI (prior to digestion an aliquot was saved as an input control), DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together in situ. DNA-protein cross-links were reversed and the DNA then purified.
DNA sheared to a size of approximately 500 bp.  DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).  The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO.  TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.


title: 293TRex_induced_replicate2 (HiC)

source_name: 293TRex-Flag-BRD4-NUT-HA cultured cells

value: Human embryonic kidney


title: TC-797_washout_replicate1 (HiC)


title: 7-070-2-2_S5


title: TC-797_MZ1_replicate1 (HiC)


title: 7-070-2-1_S65

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 7-069-2-3_S19

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 293TRex_uninduced_replicate2 (HiC)


title: 7-069-2-2_S220


title: 293TRex_induced_replicate1 (HiC)


title: donor 4, liver

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

description: Single-cell RNAseq data

data_processing:
The Cell Ranger Software Suite (Version 2.2.0) was used to perform sample demultiplexing, barcode processing and single-cell 3’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count. Since our samples contain a mix of cell populations, we reanalyzed the data with the force-cells option based on the barcode rank plot. Finally, gene-barcode matrix of all donors was aggregated with cellranger aggr with mapped depth normalization method.
The filtered gene-barcode matrix was analyzed by PCA. Then t-SNE (t-Stochastic Neighbor Embedding) was performed on the top 10 principal components for visualizing the cells. Meanwhile, graph-based clustering  and k-means clustering was performed on the PCA-reduced data for clustering analysis. For different cell types, we used Seurat R Package to find most variable genes (1,123 genes for B cell, 1,164 genes for Monocyte, 1,813 genes for ASC cells, 989 genes for NK&T cells) based on their mean and dispersion. And gene-barcode matrix of these genes for each cell type was analyzed by PCA and 50 PCs were selected for t-SNE analysis and clustering analysis.
Read 1: barcode (16 bp), UMI (10 bp), Poly(dT)VN; Read 2: sample index i7 (8 bp), cDNA fragment
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix. Supplementary files include key to cell types for barcodes.

source_name: liver

extract_protocol: Immune cells from human samples were isolated according to the previous protocols. In brief, peripheral blood mononuclear cells (PBMCs) and bone marrow cells were isolated by ficoll-hypaque density gradient centrifugation from heparinized blood of enrolled subjects. Spleen was first grinded on ice and the cells were then collected and filtered. Liver perfusion was directly filtered and concentrated by centrifugation (750 g, 15 min, 20°C), and were layered onto Ficoll. Upon isolation, human CD45+ cells were isolated with the anti-CD45 magnetic-activated cell sorting (MACS) kit. Then the cells were counted three times by three individuals independently and the mean 22, 000-24, 000 live cells were used for 10x genomics. The left cells were cryopreserved in 90% fetal calf serum plus 10% of DMSO for subsequent assay. Single cells were lysed in droplets using the 10X Chromium instrument Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A.

tag: organ

value: liver

tag: cell subsets


title: 7-071-2-3_S182

tag: individual


title: 293TRex_uninduced_replicate1 (HiC)


title: 7-069-2-2_S105

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 7-069-2-1_S95


title: 7-069-2-1_S247


title: donor 3, spleen

description: Single-cell RNAseq data

source_name: spleen

value: spleen


title: donor 3, blood

description: Single-cell RNAseq data

source_name: blood

value: blood


title: 7-067-2-3_S158


title: donor 2, liver

description: Single-cell RNAseq data


title: donor 2, spleen

description: Single-cell RNAseq data


title: 7-066-1-3_S145


title: 7-067-2-2_S88


title: 7-067-2-1_S138


title: donor 1, liver

description: Single-cell RNAseq data


title: donor 2, blood

description: Single-cell RNAseq data


title: 7-066-1-2_S42


title: 7-066-1-1_S74


title: 7-065-1-2_S56


title: donor 1, spleen

description: Single-cell RNAseq data


title: donor 1, blood

description: Single-cell RNAseq data


title: 7-064-1-1_S86


title: 7-064-1-1_S182


title: 7-062-2-2_S39


title: 7-062-2-1_S43


title: 7-062-2-3_S163


title: 7-061-2-3_S82


title: 7-061-2-1_S79


title: 7-061-2-3_S178


title: 7-061-2-2_S109


title: 7-065-1-1_S74


title: 7-060-1-1_S44


title: 7-064-1-2_S132


title: 7-060-1-2_S190


title: 7-059-2-3_S22


title: P2004KO

city: beijing

first: pengbo

last: lou

address: 2 west Winter Palace road

institute: Agricultural University

description: Gene expression

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: BAT

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: brown adipose tissue

tag: gender

value: male

tag: genotype/variation

value: miR-22 knockout


title: 7-059-2-2_S91


title: Sublingual_Fr3_rep2

first: Yue

last: Yang

state: Tokyo

institute: Tokyo medical and dental university

description: Gene expression of Sublingual mucosa F4/80+CD206hi cells

hyb_protocol: For each hybridization, 2μg of Cy3 labeled cDNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (Design ID: 074809).

scan_protocol: microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 11.7.1.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated, and population outliers (Compromised and Not Detected flags).

source_name: Sublingual mucosa,  F4/80+CD206hi,replicate 2

label_protocol: Total RNA was amplified using Ovation Pico WTA System V2 (NuGEN Technologies, Inc.) following the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using SureTag DNA Labeling Kit (Agilent Technologies) following the manufacturer's instructions. After amplification and labeling, cDNA quantity and cyanine incorporation were determined using a Nanodrop One spectrophometer and an Agilent Bioanalyzer.

extract_protocol: Total RNA was extracted from each sample by using NucleoSpin RNA XS (Macherey-Nagel, Duren, Germany) according to the manufacturer’s instructions. RNA quantity and quality were determined using a Nanodrop One spectrophometer (Thermo Fisher Scientific Inc.).

treatment_protocol: Dorsal site of tongues from repeatedly FITC-painted mice were minced and digested in PBS with collagenase type I (400U/ml; Sigma) and DNase I (1000 U/ml, Wako) followed by incubating in a 37℃ shaker for 30 min. Fr1,Fr2 and Fr3 cells were sorted by cell sorter (MoFlo XDP, Beckman Coulter).

value: sublingual mucosa

value: BALB/c

tag: cell popluation


title: 7-085-2-3_S81


title: Sublingual_Fr3_rep1

source_name: Sublingual mucosa, F4/80+CD206hi,replicate 1


title: P1901WT

description: Gene expression

value: wildtype


title: 7-060-1-3_S178


title: 7-059-2-1_S12


title: Sublingual_Fr2_rep2

description: Gene expression of Sublingual mucosa CD11c-F4/80+CD206- cells

source_name: Sublingual mucosa, CD11c-F4/80+CD206-,replicate 2


title: P2003KO

description: Gene expression


title: 7-059-1-3_S182


title: P1902WT

description: Gene expression


title: Sublingual_Fr1_rep2

description: Gene expression of Sublingual mucosa CD11c+CD206- cells

source_name: Sublingual mucosa, CD11c+CD206-,replicate 2


title: Sublingual_Fr1_rep1

source_name: Sublingual mucosa, CD11c+CD206-,replicate 1


title: P2000KO

description: Gene expression


title: P1900WT

description: Gene expression