Stability of placental mRNA expression

Enter a fold-change threshold that indicates a meaningful change in expression (range: 1 to 16)

Fold-change threshold:

Select a length of time to view a list of stable or unstable transcripts

Length of time (hours):

Show stable or unstable transcripts:

Download List

Select the minimum number of transcripts necessary to plot a pattern:

Note: the dashed gray line corresponds to the specified fold-change threshold and 'n' indicates the number of transcripts per pattern. Patterns with fewer than the specified number of transcripts per pattern are grouped as variable. For more information on how patterns are determined, see 'Study Information.'

Plot of individual transcript

Select a transcript to plot:

Log₂ fold change (LFC) values for 364 transcripts

Note: pattern and stability determined based on fold-change threshold input

Download LFC Table Download Raw Data

Raw data note: The raw data file includes counts for each transcript across the 8 placentas and 6 collection times. Alphanumeric column names identify the placenta and collection time. Each placenta is identified by a letter (A-H). The number following the letter corresponds to the hour of specimen collection (0, 1, 2, 4, 6, 24). For example, column A0 lists the counts for placenta A at hour 0 (delivery) and column A24 lists the counts for placenta A at 24 hours.

Stability of placental mRNA expression as time from delivery to sample collection increases

Purpose

This app can be used to investigate changes in placental mRNA expression over time and identify common expression patterns.

Study design

Eight placentas from healthy, term, scheduled cesarean sections were collected an average of 27 minutes following delivery (range: 15 to 36 minutes). Placental villous tissue was sampled at delivery and again 1, 2, 4, 6, and 24 hours later. Transcript expression was quantified with the nanoString nCounter system (nanoString) using a custom panel of 382 mRNA probes. To optimize detection of potentially unstable mRNAs of interest, mRNA targets were selected based on two criteria: (1) reported associations with birth outcomes in the literature and/or (2) sufficient variation across samples in a prior pilot study (range of individual transcript expression encompassing >10% of the global range). 18 probes fell below background levels too frequently and were excluded from the analysis. Additional information on study design and expression analysis can be found at (…).

Analysis

Change in expression for each transcript at each timepoint is classified as increased (+), decreased (-), or stable (0) relative to the collection at delivery, based on the fold-change threshold input by the user. Determinations for the five post-delivery collections are then summarized into a string. For example, ‘+++++’ indicates a transcript was increased at 1, 2, 4, 6, and 24-hours relative to delivery and ‘000--’ indicates that a transcript was stable for the first three collections after delivery and decreased for the last two collections. Overall stability is determined by leading 0’s. For example, patterns beginning with ‘0’ are considered stable for the one-hour collection, patterns beginning with ‘00’ are considered stable for the first two collections, and patterns beginning with ‘+’ or ‘-’ are considered unstable.

Funding

This work was supported by NIH grants F32HD100076 and R01MD011749.