title: untrained pre 2

status: Public on Oct 31 2023

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

description: Gene expression data from pooled RNA obtained from the blood of animals in the untrained group at the pre-training timepoint.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.62.0), using R version 3.6.0 and the Brainarray mogene20stmmentrezgcdf R package (version 24.0.0).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: blood

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: C57B16/J mice (16 male, 18 female) were maintained on a reverse 12h light/dark cycle.  Surgery was performed at 8-12 weeks of age to head fix, followed by 7d post-op recovery.

extract_protocol: Blood was isolated before and after training, immediately stored in RNAlater. RNA isolated using Mouse Ribopure-Blood RNA Isolation kit (Invitrogen). Samples were pooled in sets of 7 yielding three biological replicates. Each pool had excess globin transcripts depleted using GlobinClear (Ambion).

treatment_protocol: Water-deprived mice were head fixed and on an air-cushioned ball. Trained: learned to respond to visual cue for water reward. Control: same treatment but given water at random intervals.

tag: strain

tag: batch

value: batch 1

tag: timepoint

value: pre-training

tag: training

value: untrained


title: trained pre 1

description: Gene expression data from pooled RNA obtained from the blood of animals in the trained group at the pre-training timepoint.

value: trained


title: trained post 3

description: Gene expression data from pooled RNA obtained from the blood of animals in the trained group at the post-training timepoint.

value: batch 2

value: post-training


title: trained pre 3


title: ACC untrained 3

description: Gene expression data from pooled RNA obtained from the anterior cingulate cortex of untrained animals.

source_name: anterior cingulate cortex

extract_protocol: Brain tissue was dissected in RNAlater (Invitrogen), homogenized with liquid nitrogen and a Qiashredder (Qiagen), and RNA was isolated using an RNeasy kit (Qiagen). Samples were pooled in sets of 7 (HC) or 5 (ACC) yielding three biological replicates.

treatment_protocol: Water-deprived mice were head fixed and on an air-cushioned ball. Trained: learned to respond to visual cue for water reward. Control: same treatment but given water at random intervals.  The average days of training to criterion was 27 ± 2.6.

tag: tissue

value: brain

tag: brain region

value: anterior cingulate cortex


title: untrained post 2

description: Gene expression data from pooled RNA obtained from the blood of animals in the untrained group at the post-training timepoint.


title: trained post 2


title: untrained pre 1


title: HC trained 3

description: Gene expression data from pooled RNA obtained from the hippocampus of trained animals.

source_name: hippocampus

value: hippocampus


title: ACC trained 1

description: Gene expression data from pooled RNA obtained from the anterior cingulate cortex of trained animals.


title: ACC trained 2


title: untrained post 3


title: HC untrained 1

description: Gene expression data from pooled RNA obtained from the hippocampus of untrained animals.


title: ACC untrained 2


title: Subject 36_6days

type: protein

city: Silver Spring

first: Paula

middle: L

last: Hyland

state: MD

address: 10903 New Hampshire Avenue

department: CDER

institute: FDA

description: Plate position: Plate 5,  F3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing: https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

organism: Homo sapiens

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a, pegIFNβ-1a and placebo groups

tag: drug group

tag: delivery

value: IM

tag: dose


title: Subject 36_5days

description: Plate position: Plate 5,  F2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: HC untrained 3


title: Subject 36_4days

description: Plate position: Plate 5,  F1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: ACC trained 3


title: Subject 36_3days

description: Plate position: Plate 5,  E10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: untrained pre 3


title: HC untrained 2


title: trained post 1


title: trained pre 2


title: HC trained 1


title: Subject 36_2days

description: Plate position: Plate 5,  E9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: HC trained 2


title: untrained post 1


title: ACC untrained 1


title: Subject 36_1.33days

description: Plate position: Plate 5,  E8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 36_0.33days

description: Plate position: Plate 5,  E6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_3days

description: Plate position: Plate 5,  D8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.

value: SC


title: Subject 35_13days

description: Plate position: Plate 5,  E3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_9days

description: Plate position: Plate 5,  E2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_6days

description: Plate position: Plate 5,  E1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_4days

description: Plate position: Plate 5,  D9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_5days

description: Plate position: Plate 5,  D10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_5days

description: Plate position: Plate 5,  C8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_4days

description: Plate position: Plate 5,  C7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_0.67days

description: Plate position: Plate 5,  C3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_0.67days

description: Plate position: Plate 5,  D5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_6days

description: Plate position: Plate 5,  C9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_1.33days

description: Plate position: Plate 5,  D6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 36_0days

description: Plate position: Plate 5,  E4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_0.13days

description: Plate position: Plate 5,  D3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 36_0.13days

description: Plate position: Plate 5,  E5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_0.33days

description: Plate position: Plate 5,  D4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_9days

description: Plate position: Plate 5,  C10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_2days

description: Plate position: Plate 5,  D7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_13days

description: Plate position: Plate 5,  D1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 35_0days

description: Plate position: Plate 5,  D2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 36_0.67days

description: Plate position: Plate 5,  E7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_3days

description: Plate position: Plate 5,  C6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_2days

description: Plate position: Plate 5,  C5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_1.33days

description: Plate position: Plate 5,  C4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_0.33days

description: Plate position: Plate 5,  C2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_0days

description: Plate position: Plate 5,  B10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 34_0.13days

description: Plate position: Plate 5,  C1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_13days

description: Plate position: Plate 5,  B9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_9days

description: Plate position: Plate 5,  B8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_6days

description: Plate position: Plate 5,  B7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_5days

description: Plate position: Plate 5,  B6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_4days

description: Plate position: Plate 5,  B5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_0.67days_replicate

description: Plate position: Plate 5,  A1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_6days

description: Plate position: Plate 5,  A7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_0.33days

description: Plate position: Plate 4, I4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_0.67days

description: Plate position: Plate 4, I5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_1.33days

description: Plate position: Plate 5,  A2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_0days

description: Plate position: Plate 4, I2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_0days

description: Plate position: Plate 5,  A8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_5days

description: Plate position: Plate 5,  A6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_0.13days

description: Plate position: Plate 4, I3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_2days

description: Plate position: Plate 5,  A3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_3days

description: Plate position: Plate 5,  A4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_0.67days

description: Plate position: Plate 5,  B1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_0.13days

description: Plate position: Plate 5,  A9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 32_4days

description: Plate position: Plate 5,  A5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_1.33days

description: Plate position: Plate 5,  B2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_2days

description: Plate position: Plate 5,  B3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_0.33days

description: Plate position: Plate 5,  A10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_9days

description: Plate position: Plate 4, H10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_1.33days

description: Plate position: Plate 4, H4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_6days

description: Plate position: Plate 4, H9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_3days

description: Plate position: Plate 4, H6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_2days

description: Plate position: Plate 4, H5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_4days

description: Plate position: Plate 4, H7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_13days

description: Plate position: Plate 4, I1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 33_3days

description: Plate position: Plate 5,  B4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_0.33days

description: Plate position: Plate 4, H2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_0.67days

description: Plate position: Plate 4, H3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_5days

description: Plate position: Plate 4, H8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_0days

description: Plate position: Plate 4, G10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 31_0.13days

description: Plate position: Plate 4, H1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_13days

description: Plate position: Plate 4, G9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_4days

description: Plate position: Plate 4, G5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_5days

description: Plate position: Plate 4, G6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_3days

description: Plate position: Plate 4, G4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_0.13days

description: Plate position: Plate 4, F9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_9days

description: Plate position: Plate 4, G8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_6days

description: Plate position: Plate 4, G7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_0days

description: Plate position: Plate 4, F8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_4days

description: Plate position: Plate 4, F5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_3days

description: Plate position: Plate 4, F4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_0.33days

description: Plate position: Plate 4, F10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_0.33days

description: Plate position: Plate 4, E10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_6days

description: Plate position: Plate 4, E5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_5days

description: Plate position: Plate 4, F6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_6days

description: Plate position: Plate 4, F7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_0.67days

description: Plate position: Plate 4, G1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_9days

description: Plate position: Plate 4, E6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_0.67days

description: Plate position: Plate 4, F1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_3days

description: Plate position: Plate 4, E2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_13days

description: Plate position: Plate 4, E7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_2days

description: Plate position: Plate 4, F3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_1.33days

description: Plate position: Plate 4, F2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_0days

description: Plate position: Plate 4, E8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 29_0.13days

description: Plate position: Plate 4, E9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_2days

description: Plate position: Plate 4, G3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_5days

description: Plate position: Plate 4, E4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_4days

description: Plate position: Plate 4, E3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 30_1.33days

description: Plate position: Plate 4, G2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_1.33days

description: Plate position: Plate 4, D10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_2days

description: Plate position: Plate 4, E1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_0.67days

description: Plate position: Plate 4, D9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_0.13days

description: Plate position: Plate 4, D7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_0.33days

description: Plate position: Plate 4, D8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_13days

description: Plate position: Plate 4, D5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_1.33days

description: Plate position: Plate 4, C8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_2days

description: Plate position: Plate 4, C9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_0.67days

description: Plate position: Plate 4, C7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_5days

description: Plate position: Plate 4, D2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_5days

description: Plate position: Plate 4, B10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 28_0days

description: Plate position: Plate 4, D6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_6days

description: Plate position: Plate 4, D3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_9days

description: Plate position: Plate 4, C2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_9days

description: Plate position: Plate 4, D4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_3days

description: Plate position: Plate 4, C10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_0.33days

description: Plate position: Plate 4, C6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_0.13days

description: Plate position: Plate 4, C5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_6days

description: Plate position: Plate 4, C1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_9days

description: Plate position: Plate 4, A10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_0days

description: Plate position: Plate 4, C4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_0.33days

description: Plate position: Plate 4, B4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_3days

description: Plate position: Plate 4, B8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_13days

description: Plate position: Plate 4, C3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 27_4days

description: Plate position: Plate 4, D1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_0.13days

description: Plate position: Plate 4, B3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_13days

description: Plate position: Plate 4, B1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_0days

description: Plate position: Plate 4, B2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_0.67days

description: Plate position: Plate 4, B5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_1.33days

description: Plate position: Plate 4, B6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_2days

description: Plate position: Plate 4, B7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 26_4days

description: Plate position: Plate 4, B9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_6days

description: Plate position: Plate 4, A9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_5days

description: Plate position: Plate 4, A8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_4days

description: Plate position: Plate 4, A7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_0.67days

description: Plate position: Plate 4, A3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_1.33days

description: Plate position: Plate 4, A4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_0.13days_replicate

description: Plate position: Plate 4, A1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_3days

description: Plate position: Plate 4, A6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_0.33days

description: Plate position: Plate 4, A2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_1.33days

description: Plate position: Plate 3, H4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_0.33days

description: Plate position: Plate 3, H2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_3days

description: Plate position: Plate 3, H6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_4days

description: Plate position: Plate 3, H7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_4days

description: Plate position: Plate 3, G7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_5days

description: Plate position: Plate 3, H8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_2days

description: Plate position: Plate 3, H5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_6days

description: Plate position: Plate 3, H9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_13days

description: Plate position: Plate 3, I1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 24_0.33days

description: Plate position: Plate 3, I3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_2days

description: Plate position: Plate 4, A5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_6days

description: Plate position: Plate 3, G9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_0days

description: Plate position: Plate 3, G10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_0.13days

description: Plate position: Plate 3, H1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_0days

description: Plate position: Plate 3, I4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_1.33days

description: Plate position: Plate 3, G4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_0.67days

description: Plate position: Plate 3, H3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 23_9days

description: Plate position: Plate 3, H10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_2days

description: Plate position: Plate 3, G5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_5days

description: Plate position: Plate 3, G8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 25_0.13days

description: Plate position: Plate 3, I5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_0.67days

description: Plate position: Plate 3, G3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_0.33days

description: Plate position: Plate 3, G2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 24_0days

description: Plate position: Plate 3, I2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_3days

description: Plate position: Plate 3, G6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_0.13days

description: Plate position: Plate 3, G1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 22_0days

description: Plate position: Plate 3, F10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_1.33days

description: Plate position: Plate 3, F4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_2days

description: Plate position: Plate 3, F5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_4days

description: Plate position: Plate 3, F7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_0.33days

description: Plate position: Plate 3, F2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_5days

description: Plate position: Plate 3, F8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_3days

description: Plate position: Plate 3, F6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_0.67days

description: Plate position: Plate 3, F3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_13days

description: Plate position: Plate 3, E8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 20_0days

description: Plate position: Plate 3, E9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_0.13days

description: Plate position: Plate 3, F1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_0days

description: Plate position: Plate 3, E10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_5days

description: Plate position: Plate 3, E5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_0.67days

description: Plate position: Plate 3, D10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_2days

description: Plate position: Plate 3, E2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_13days

description: Plate position: Plate 3, D6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_1.33days

description: Plate position: Plate 3, E1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_9days

description: Plate position: Plate 3, E7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_3days

description: Plate position: Plate 3, E3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_9days

description: Plate position: Plate 3, D5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_0.13days

description: Plate position: Plate 3, D8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_0.33days

description: Plate position: Plate 3, D9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_6days

description: Plate position: Plate 3, D4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_0days

description: Plate position: Plate 3, D7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_3days

description: Plate position: Plate 3, D1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_6days

description: Plate position: Plate 3, E6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_2days

description: Plate position: Plate 3, C10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 19_4days

description: Plate position: Plate 3, E4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_4days

description: Plate position: Plate 3, D2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_5days

description: Plate position: Plate 3, D3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_1.33days

description: Plate position: Plate 3, C9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_0.13days

description: Plate position: Plate 3, C6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_5days

description: Plate position: Plate 3, C1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_2days

description: Plate position: Plate 3, B8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_6days

description: Plate position: Plate 3, C2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_9days

description: Plate position: Plate 3, C3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_0days

description: Plate position: Plate 3, C5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_13days

description: Plate position: Plate 3, C4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_0.13days

description: Plate position: Plate 3, A4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_0days

description: Plate position: Plate 3, A3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_6days

description: Plate position: Plate 2, I4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_0.33days

description: Plate position: Plate 3, A5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_3days

description: Plate position: Plate 3, B9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_4days

description: Plate position: Plate 3, B10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_0.67days

description: Plate position: Plate 3, A6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_9days_replicate

description: Plate position: Plate 3, A1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_13days

description: Plate position: Plate 3, A2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_9days

description: Plate position: Plate 2, I5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_4days

description: Plate position: Plate 2, I2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_5days

description: Plate position: Plate 2, I3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_1.33days

description: Plate position: Plate 3, A7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_0.33days

description: Plate position: Plate 3, C7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 18_0.67days

description: Plate position: Plate 3, C8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_2days

description: Plate position: Plate 3, A8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_1.33days

description: Plate position: Plate 3, B7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_0.67days

description: Plate position: Plate 3, B6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_3days

description: Plate position: Plate 3, A9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_4days

description: Plate position: Plate 3, A10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_5days

description: Plate position: Plate 3, B1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_3days

description: Plate position: Plate 2, I1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_0.33days

description: Plate position: Plate 3, B5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_0.13days

description: Plate position: Plate 3, B4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 16_6days

description: Plate position: Plate 3, B2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 17_0days

description: Plate position: Plate 3, B3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_1.33days

description: Plate position: Plate 2, H9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_0.13days

description: Plate position: Plate 2, H6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_3days

description: Plate position: Plate 2, G9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_13days

description: Plate position: Plate 2, H4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_0.33days

description: Plate position: Plate 2, H7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_0days

description: Plate position: Plate 2, H5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_4days

description: Plate position: Plate 2, G10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_2days

description: Plate position: Plate 2, H10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_6days

description: Plate position: Plate 2, H2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 15_0.67days

description: Plate position: Plate 2, H8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_5days

description: Plate position: Plate 2, H1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_2days

description: Plate position: Plate 2, G8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_1.33days

description: Plate position: Plate 2, G7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_9days

description: Plate position: Plate 2, G1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_0days

description: Plate position: Plate 2, F1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_3days

description: Plate position: Plate 2, F7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_0.33days

description: Plate position: Plate 2, F3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_9days

description: Plate position: Plate 2, H3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_0.13days

description: Plate position: Plate 2, G4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_6days

description: Plate position: Plate 2, F10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_4days

description: Plate position: Plate 2, F8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_0.67days

description: Plate position: Plate 2, F4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_1.33days

description: Plate position: Plate 2, F5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_0.33days

description: Plate position: Plate 2, G5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 21_6days

description: Plate position: Plate 3, F9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_0.67days

description: Plate position: Plate 2, G6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 14_0days

description: Plate position: Plate 2, G3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_2days

description: Plate position: Plate 2, F6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_6days

description: Plate position: Plate 2, E10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_5days

description: Plate position: Plate 2, F9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_4days

description: Plate position: Plate 2, E8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_5days

description: Plate position: Plate 2, E9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_2days

description: Plate position: Plate 2, E6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_0days

description: Plate position: Plate 2, E1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_0.33days

description: Plate position: Plate 2, E3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_0.67days

description: Plate position: Plate 2, E4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_0.13days

description: Plate position: Plate 2, E2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_5days

description: Plate position: Plate 2, D7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_2days

description: Plate position: Plate 2, D4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_13days

description: Plate position: Plate 2, D10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_6days

description: Plate position: Plate 2, D8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_0days

description: Plate position: Plate 2, C9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_9days

description: Plate position: Plate 2, D9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_0.67days

description: Plate position: Plate 2, D2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_0.33days

description: Plate position: Plate 2, D1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_0.13days

description: Plate position: Plate 2, C10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_1.33days

description: Plate position: Plate 2, D3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_3days

description: Plate position: Plate 2, D5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_1.33days

description: Plate position: Plate 2, E5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_13days

description: Plate position: Plate 2, G2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 12_3days

description: Plate position: Plate 2, E7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_6days

description: Plate position: Plate 1, F6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_3days

description: Plate position: Plate 1, F3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_5days

description: Plate position: Plate 1, F5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_2days

description: Plate position: Plate 1, F2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 11_4days

description: Plate position: Plate 2, D6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_1.33days

description: Plate position: Plate 1, F1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_0.67days

description: Plate position: Plate 1, E10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_0.13days

description: Plate position: Plate 1, E8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_0.33days

description: Plate position: Plate 1, E9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_4days

description: Plate position: Plate 1, F4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_13days

description: Plate position: Plate 1, B2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_6days

description: Plate position: Plate 1, A10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_5days

description: Plate position: Plate 1, A9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 10_0days

description: Plate position: Plate 1, E7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_2days

description: Plate position: Plate 1, A6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_1.33days

description: Plate position: Plate 1, A5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_4days

description: Plate position: Plate 1, A8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_3days

description: Plate position: Plate 1, A7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_0days

description: Plate position: Plate 1, A1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_0.67days

description: Plate position: Plate 1, A4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_13days

description: Plate position: Plate 2, A6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_0.13days

description: Plate position: Plate 1, A2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_4days

description: Plate position: Plate 2, A2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_6days

description: Plate position: Plate 2, A4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_9days

description: Plate position: Plate 1, B1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_9days

description: Plate position: Plate 2, A5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_5days

description: Plate position: Plate 2, A3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 9_0.33days

description: Plate position: Plate 1, A3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_0.67days

description: Plate position: Plate 1, I2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_3days_replicate

description: Plate position: Plate 2, A1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_0.13days

description: Plate position: Plate 1, H10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_0days

description: Plate position: Plate 1, H9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_1.33days

description: Plate position: Plate 1, I3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_3days

description: Plate position: Plate 1, H5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_2days

description: Plate position: Plate 1, I4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_0.33days

description: Plate position: Plate 1, I1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_1.33days

description: Plate position: Plate 1, H3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 8_3days

description: Plate position: Plate 1, I5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_5days

description: Plate position: Plate 1, H7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_4days

description: Plate position: Plate 1, H6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_2days

description: Plate position: Plate 1, H4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_5days

description: Plate position: Plate 1, G5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_13days

description: Plate position: Plate 1, G8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 13_0.13days

description: Plate position: Plate 2, F2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_1.33days

description: Plate position: Plate 1, G1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_6days

description: Plate position: Plate 1, H8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_0days

description: Plate position: Plate 1, F7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_9days

description: Plate position: Plate 1, G7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_0.13days

description: Plate position: Plate 1, F8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_0.67days

description: Plate position: Plate 1, H2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_0.33days

description: Plate position: Plate 1, F9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_0.33days

description: Plate position: Plate 1, H1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_6days

description: Plate position: Plate 2, C8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_3days

description: Plate position: Plate 1, G3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_0.13days

description: Plate position: Plate 1, G10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_2days

description: Plate position: Plate 1, G2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_4days

description: Plate position: Plate 1, G4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_0.67days

description: Plate position: Plate 1, F10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 6_6days

description: Plate position: Plate 1, G6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 7_0days

description: Plate position: Plate 1, G9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_0.33days

description: Plate position: Plate 2, C1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_1.33days

description: Plate position: Plate 2, C3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_0.67days

description: Plate position: Plate 2, C2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_0days

description: Plate position: Plate 2, B9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_3days

description: Plate position: Plate 2, C5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_4days

description: Plate position: Plate 2, C6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_5days

description: Plate position: Plate 2, C7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_0.13days

description: Plate position: Plate 2, B10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_13days

description: Plate position: Plate 1, E6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_9days

description: Plate position: Plate 1, E5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_5days

description: Plate position: Plate 1, E3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_6days

description: Plate position: Plate 1, E4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_1.33days

description: Plate position: Plate 1, D9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_3days

description: Plate position: Plate 1, E1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_2days

description: Plate position: Plate 1, D10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_0.33days

description: Plate position: Plate 1, D7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_0.13days

description: Plate position: Plate 1, D6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 5_2days

description: Plate position: Plate 2, C4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_0.67days

description: Plate position: Plate 1, D8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_13days

description: Plate position: Plate 1, D4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_0days

description: Plate position: Plate 1, D5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_2days

description: Plate position: Plate 1, C8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_9days

description: Plate position: Plate 1, D3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_0.13days

description: Plate position: Plate 1, C4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_5days

description: Plate position: Plate 1, C1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_0days

description: Plate position: Plate 1, C3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_3days

description: Plate position: Plate 1, C9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_0.33days

description: Plate position: Plate 1, C5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_4days

description: Plate position: Plate 1, C10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_6days

description: Plate position: Plate 1, C2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_0.67days

description: Plate position: Plate 1, C6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_1.33days

description: Plate position: Plate 1, C7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_3days

description: Plate position: Plate 1, B9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_0.67days

description: Plate position: Plate 1, B6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_4days

description: Plate position: Plate 1, B10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 4_4days

description: Plate position: Plate 1, E2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_1.33days

description: Plate position: Plate 1, B7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_2days

description: Plate position: Plate 1, B8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_5days

description: Plate position: Plate 1, D1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 3_6days

description: Plate position: Plate 1, D2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_0.13days

description: Plate position: Plate 1, B4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_0.33days

description: Plate position: Plate 1, B5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_13days

description: Plate position: Plate 2, B8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 2_0days

description: Plate position: Plate 1, B3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_9days

description: Plate position: Plate 2, B7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_4days

description: Plate position: Plate 2, B4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_5days

description: Plate position: Plate 2, B5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: PCR negative_COVID-19 covalescent plasma (Bio-IVT: HMN373533)

description: Plate position: Plate 5,  F5.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.

value: Covid-19 covalescent plasma


title: Control 1

type: SRA

city: Louisville

first: David

middle: Albert

last: Scott

state: KY

address: 501 S Preston St

department: OIID

institute: University of Louisville

library_source: transcriptomic

data_processing:
Downloaded Treponema_denticola_ATCC_35405 GenBank and FASTA files from NCBI. Generated PTT and RNT files using gbkToPttAnd Rnt. Removed genes with incomplete coordinates
Read QC. Assessed raw read quality using FastQC v0.11.7 [2] and MultiQC v1.1 [3]. FastQC revealed adaptor contamination across the libraries. Removed potential adapter contamination using Trimmomatic v0.39; Ran FastQC and MultiQC again to make sure adapters were removed.
Read alignment and counting. Aligned the trimmed reads against the reference using EDGE-Pro v1.3.1. EDGE-Pro also counted reads on each gene included in the PTT and RNT files
Differential expression analysis was performed using DESeq2 v1.32.0 and normalized based on (rlog) expression values
Preliminary, alignment-derived annotations were augmented using the prokaryote-specific BlastX functions of the KEGG genes database (www.genome.jp/tools/blast/) and/or NCBI (blast.ncbi.nlm.nih.gov)
Assembly: NC_002967.9
Supplementary files format and content: tab-delimited text files containing raw gene counts per sample

organism: Treponema denticola ATCC 35405

source_name: Culture

extract_protocol:
Pellet under anaerobic conditions. Resuspend in Qiagen RLT and lyse in MP fast prep. Supernatant prepared with Qiagen Rneasy kit
NEBNext Ultra II Directional RNA kit (#7760) and NEB UDI plate 1 adapters (#6440) using 220 ng input and 11 cycle PCR

value: Culture

tag: treatment

value: Control


title: CBD 3

value: CBD 5 ug/ml


title: Control 2


title: CBD 1


title: Control 3


title: M1_Meadow (Multiome Gene Expression)

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
M1_Meadow_barcodes.tsv.gz
M1_Meadow_features.tsv.gz
M1_Meadow_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene.
Cells were filtered for low quality nuclei by requiring ≥1000 ATAC fragments and ≥500 genes detected per nuclei.
Genes were annotated with hg38 Gencode v33 for human, mm10 Gencode vM22 for mouse, ensembl release 104 (and Refseq GCF_003339765.1 for 10x multiome) for macaque, and GCA_009663435.2 for marmoset. To maximize the number of orthologous protein-coding quantified in macaque 10x multiome RNA data, we supplemented any missing protein coding genes in GCF_003339765.1 gtf with annotations present in Ensembl release 104.
Assembly: hg38 GRCh38
Assembly: mm10 GRCm38
Assembly: Mmul_10 (rheMac10)
Assembly: cj1700_1.1 (calJac4)
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.   Files provided in tar archives.

organism: Callithrix jacchus

source_name: primary motor cortex

extract_protocol:
[nuclei preparation protocol]  Brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS).
120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading and libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).
10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.

value: primary motor cortex

tag: species

value: Marmoset

tag: donor id

value: Meadow

tag: age

tag: Sex

value: M

tag: library type

value: 10x Genomics Multiome Gene Expression


title: Subject 1_0.13days

description: Plate position: Plate 2, A8.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: M1_Webster (Multiome Gene Expression)

description:
M1_Webster_barcodes.tsv.gz
M1_Webster_features.tsv.gz
M1_Webster_matrix.mtx.gz

value: Webster


title: PCR negative_COVID-19 covalescent plasma (Bio-IVT: HMB373532)

description: Plate position: Plate 5,  F4.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: CBD 2


title: Subject 1_0.33days

description: Plate position: Plate 2, A9.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: M1_Peregrine_rep2 (Multiome Gene Expression)

description:
replication of M1_Peregrine sample
M1_Peregrine_rep2_barcodes.tsv.gz
M1_Peregrine_rep2_features.tsv.gz
M1_Peregrine_rep2_matrix.mtx.gz

value: Peregrine


title: M1_Meadow (Multiome ATAC)

library_source: genomic single cell

molecule: genomic DNA

value: 10x Genomics Multiome ATAC


title: M1_Webster (Multiome ATAC)


title: Subject 1_0.67days

description: Plate position: Plate 2, A10.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: M1_Peregrine_rep2 (Multiome ATAC)


title: Subject 1_3days

description: Plate position: Plate 2, B3.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: M1_Peregrine_rep1 (Multiome Gene Expression)

description:
M1_Peregrine_rep1_barcodes.tsv.gz
M1_Peregrine_rep1_features.tsv.gz
M1_Peregrine_rep1_matrix.mtx.gz


title: Subject 1_6days

description: Plate position: Plate 2, B6.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: M1_Peregrine_rep1 (Multiome ATAC)


title: Subject 1_1.33days

description: Plate position: Plate 2, B1.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_2days

description: Plate position: Plate 2, B2.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: Subject 1_0days

description: Plate position: Plate 2, A7.Buffers (n=18), Calibrators (n=25) and QC (n=15) are also included on the array across the 5 plates.


title: RNA_HS18_del_rep2

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

source_name: cortex

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.

value: cortex

tag: cell line

value: cortex-neuron

tag: cell type

value: neuron

tag: genotype

value: HS18 del -/-


title: RNA_HS18_del_rep4


title: RNA_HS18_del_rep3


title: RNA_HS18_del_rep1


title: cerebellar endothelial cells - chronic model - Ccm3 knock-out 5

city: Uppsala

first: Ross

last: Smith

address: Skrindvägen 20

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
The quality control and prepossessing of the raw reads were done using Trim Galore.
Reads were mapped to the mm10 mouse genome using default settings of STAR (version 2.5.3a)for both the acute model and chronic models.
The number of reads per gene were counted while mapping by STAR.
Reads normalization was done using the DESeq2 Bioconductor package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with normalized counts for each acute model sample
Supplementary files format and content: tab-delimited text files with normalized counts for each chronic model sample

source_name: brain

extract_protocol:
For acute disease model: Endothelial cells were isolated from the cerebella of 3 wild-type and 3 Ccm3 knock-out mice with the Adult Brain Dissociation kit (130-107-677; MiltenyiBiotech), CD45 MicroBeads (30-052-301; MiltenyiBiotech) and CD31 MicroBeads (30-097-418; MiltenyiBiotech) according to the manufacturer’s instructions. Total RNA was extracted from each sample with the RNeasy Micro Kit (Qiagen) in the automated QIACube (Qiagen) platform. For chronic disease model: Endothelial cells were similarly isolated from the cerebella of 5 wild-type and 5 Ccm3 knock-out mice.
For acute model: RNA sequencing libraries were prepared with SMARTer Stranded Total RNA Sample Prep kit - Mammalian kit (Clontech), according to the manufacturer’s instructions. This kit includes depletion of ribosomal RNA prior to library synthesis, barcoding and amplification. 1 μl of each library was analyzed in the Agilent 2100 bioanalyzer for validation of fragment size and quality control of the amplified RNA-seq library, using the High Sensitivity DNA kit (Agilent).  For chronic model: Libraries were prepared with the stranded RNA library prep kits (Collibri; for Illumina), with rRNA depletion kits used according to the manufacturer instructions (#A39003024, A39003096; Invitrogen)

value: brain

value: Ccm3 knock-out


title: cerebellar endothelial cells - chronic model - Ccm3 knock-out 3


title: cerebellar endothelial cells - chronic model - wild-type 1

value: WT


title: cerebellar endothelial cells - chronic model - Ccm3 knock-out 1


title: B_1

city: chengdu

first: Huali

last: Fan

email: hanmingyy@126.com, hwari_f@163.com

address: West China School of Pharmacy, Sichuan University, No. 17, Section 3, Southern Renmin Road. Wuhou District, Chengdu 610041, China

institute: Sichcuan University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38

source_name: glioma

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: BIF

tag: strain

value: glioma

value: post tumor implantation 30 days


title: cerebellar endothelial cells - chronic model - wild-type 3


title: cerebellar endothelial cells - chronic model - wild-type 4


title: cerebellar endothelial cells - chronic model - wild-type 5


title: G_3


title: cerebellar endothelial cells - chronic model - Ccm3 knock-out 4


title: G_4


title: B_2


title: G_2


title: B_4


title: G_1


title: B_3


title: Liver, plko-shBicd2, ConA 6h, rep1

city: Beijing

first: Wenyu

last: Tian

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000

treatment_protocol: 25ug of plko-scramble or shBicd2 plasmid were dissolved in 2.5ml saline and hydrodynamic injected into 8w wild-type male mice. On day 3, mice were injected with 15mg/kg ConA i.v and 6 hours later livers were collected to perform RNA sequecing.

value: Liver

value: hydrodynamic injection of plko-shBicd2, ConA (i.v)


title: Liver, plko-scramble, ConA 6h, rep2

value: hydrodynamic injection of plko-scramble, ConA (i.v)


title: Liver, plko-scramble, ConA 6h, rep3


title: Liver, plko-shBicd2, ConA 6h, rep2


title: cerebellar endothelial cells - chronic model - wild-type 2


title: Liver, plko-scramble, ConA 6h, rep1


title: Liver, plko-shBicd2, ConA 6h, rep3


title: KD 10 wk CD45 neg GFP pos

city: Denver

first: Susan

middle: M

last: Majka

email: majkas@njhealth.org, susanmajka@mac.com

state: co

address: 1400 Jackson St, Goodman Bldg K810a

department: Medicine

institute: NJH

description: n=4 pooled

data_processing:
50,000 reads/cell
ScRNA sequencing was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit (v 3.1 10xGenomics, Pleasanton, CA) and the Chromium X. Libraries were sequenced on an Illumina Novaseq 6000. Sequencing guidelines for scRNA-seq include producing at least 50,000 sequencing reads per cell to ensure adequate depth of coverage for comparative analysis as we previously reported(9). Demultiplexing, alignment to the mm10 transcriptome, and UMI-collapsing was performed using the Cellranger toolkit (v5.0, 10X Genomics, Pleasanton, CA). Data were collected on 95,037 cells from 12 samples (WT and Tsc2KD 2 days post tamoxifen induction: CD45neg GFPpos(5885cells WT; 3456cells KD), CD45neg, CD45pos; WT and Tsc2KD 10wk post tamoxifen induction: CD45neg GFPpos(6406cells WT; 6019cells KD), CD45neg, CD45pos. All post-quantification quality control, normalization, integration, clustering, and marker finding were performed in Seurat (v3.1, Satija Lab(104)).
We filtered out low quality cells with less than 200 genes detected or with greater than 7% of mapped reads originating from the mitochondrial genome. We also removed cells with a UMI count greater than the 98th percentile of UMI counts for each sample to limit doublets. Prior to downstream analysis, select mitochondrial and ribosomal genes (genes beginning with MT-, MRPL, MRPS, RPL, or RPS) were removed. The quality-controlled dataset consisted of 91,308 cells. UMI counts were normalized using the SCTransform method based on GLM (v1) in the Seurat R package(104, 105).
In addition to adjusting for sequencing depth, we also adjusted for the proportion of mitochondrial reads and doublets using the scds R package. We did not find clusters enriched for high doublet scores. Data from the 12 samples were combined using single cell integration implemented in Seurat, which identifies mutual nearest neighbor (MNN) cells across pairwise subjects to use as “anchors” to perform batch correction. Integration was carried out using the top 30 dimensions from a canonical correlation analysis (CCA) based on SCTransform-normalized expression of the top 3,000 genes, defined by gene dispersion using the Seurat’s SelectIntegrationFeatures function. Integrated data were then clustered and visualized using the top 25 principal components.
For visualization, we reduced variation to two dimensions using Uniform Manifold Approximation and Projection(106) (UMAP; n.neighbors = 50, min.dist = 0.3). Unsupervised clustering was performed using a shared nearest neighbor (SNN) graph based on 20-nearest neighbors and then determining the number and composition of clusters using a smart local moving (SLM) algorithm (resolution = 0.6).  This algorithm identified 28 clusters. To identify cluster markers, we carried out pairwise differential expression analysis comparing SCTransform-normalized expression in each cluster to all others using a Wilcoxon rank sum test. Markers were identified as genes exhibiting significant upregulation when compared against all other clusters, defined by having a Bonferroni adjusted p-value < 0.05, a log fold change > 0.25, and >10% of cells with detectable expression. This analysis was then performed separately for each subject using Seurat’s FindConservedMarkers function to determine if marker genes were consistent across samples.
Assembly: Mouse reference, mm10 (Ensembl 93)
Supplementary files format and content: H5 file with all samples

source_name: Lung

growth_protocol: Isolated cells were dropped at the CU AMC Genomica core https://medschool.cuanschutz.edu/colorado-cancer-center

extract_protocol:
10x genomics
Chromium Single Cell 3’ Library and Gel Bead Kit (v 3.1 10xGenomics, Pleasanton, CA) and the Chromium X

value: Lung

tag: time

value: 10 weeks post tam

value: CD45 neg GFP pos

value: tam induction


title: KD 10 wk CD45 pos

description: n=4 pooled

treatment_protocol: ScRNA sequencing was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit (v 3.1 10xGenomics, Pleasanton, CA) and the Chromium X. Libraries were sequenced on an Illumina Novaseq 6000. Sequencing guidelines for scRNA-seq include producing at least 50,000 sequencing reads per cell to ensure adequate depth of coverage for comparative analysis as we previously reported(9). Demultiplexing, alignment to the mm10 transcriptome, and UMI-collapsing was performed using the Cellranger toolkit (v5.0, 10X Genomics, Pleasanton, CA). Data were collected on 95,037 cells from 12 samples (WT and Tsc2KD 2 days post tamoxifen induction: CD45neg GFPpos(5885cells WT; 3456cells KD), CD45neg, CD45pos; WT and Tsc2KD 10wk post tamoxifen induction: CD45neg GFPpos(6406cells WT; 6019cells KD), CD45neg, CD45pos.

value: CD45 pos


title: WT 10wk CD45 pos

description: n=4 pooled


title: KD 10 wk CD45neg GFP neg

description: n=4 pooled

value: CD45neg GFP neg


title: WT 10wk CD45 neg GFP pos

description: n=4 pooled


title: WT 10wk CD45neg GFP neg

description: n=4 pooled


title: KD D2 CD45 pos

description: n=4 pooled

value: Day 2 pst Tamoxifen


title: KD D2 CD45 neg GFP pos

description: n=4 pooled


title: WT D2 CD45neg GFP neg

description: n=5 pooled


title: 4C_WT_for_BC_del_E_rep2

library_source: genomic

data_processing:
library strategy: QHR4C-seq
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample

extract_protocol:
1 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: cortex

value: cortex-neuron

value: neuron

value: wildtype


title: WT D2 CD45 neg GFP pos

description: n=5 pooled

value: WT


title: 4C_WT_for_BC_del_BC_rep2


title: WT D2 CD45 pos

description: n=5 pooled


title: KD D2 CD45neg GFP neg

description: n=4 pooled


title: 4C_WT_for_BC_del_GC3_rep1


title: 4C_BC_del_GC3_rep2

value: BC del


title: 4C_WT_for_BC_del_E_rep1


title: 4C_WT_for_BC_del_BC_rep1


title: 4C_BC_del_E_rep2


title: 4C_BC_del_GC3_rep1


title: 4C_WT_for_BC_del_GC3_rep2


title: 4C_WT_for_BC_del_D_rep2


title: 4C_WT_for_BC_del_D_rep1


title: 4C_BC_del_D_rep2