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omicseye
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statLens-evaluation-data-example

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domizzz2025

Upload statLens evaluation inputs (57 tasks)

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We grew Chlamydia trachomatis L2 in HEp-2 cells and sequenced the bacterial transcriptome under three conditions. Our groups are the levels of the `stage` column, taken from the sample names: RB is an untreated infection harvested at 24 hours post infection (mostly reticulate bodies), EB is an untreated infection harvested at 72 hours post infection (mostly elementary bodies), and AB is an infection given the iron chelator 2,2'-bipyridyl (BPDL, 100 µM) at 8 hours and harvested at 24 hours post infection (mostly aberrant bodies). The `group` column, identical to `treatment`, records only the treatment (BPDL or none), so it puts RB and EB together. Harvest time is part of what defines each condition; there is no separate time column. There are three flasks per condition, nine samples in all.

Each sample is the bacterial population of one infected T25 flask, made into its own library and sequenced once, so there are no technical replicates. The digits 1 to 3 in the sample names only count the flasks within each condition; nothing records that flasks with the same number were infected or processed together. All samples carry the same batch label (`src_batch` is batch1 for every sample), so we have no batch differences, and we know of no other variable that matters. The GEO titles in `original_sample_id` read "BPDL 24hpi" for every sample, including the untreated RB and EB flasks; the treatments and harvest times are those given above.

The data are bulk RNA-seq of the bacteria, from total RNA of the infected cultures, given as gene-level raw read counts from HTSeq for 889 C. trachomatis genes (CTL locus tags); host reads are not included.

Our question is which C. trachomatis genes are differentially expressed in BPDL-treated cultures (AB) compared with untreated cultures (RB); both were harvested at 24 hours post infection, so they differ only in the treatment. All nine samples are part of this question: the EB flasks come from the same experiment, even though EB is not among the groups being compared.

	We grew Chlamydia trachomatis L2 in HEp-2 cells and sequenced the bacterial transcriptome under three conditions. Our groups are the levels of the `stage` column, taken from the sample names: RB is an untreated infection harvested at 24 hours post infection (mostly reticulate bodies), EB is an untreated infection harvested at 72 hours post infection (mostly elementary bodies), and AB is an infection given the iron chelator 2,2'-bipyridyl (BPDL, 100 µM) at 8 hours and harvested at 24 hours post infection (mostly aberrant bodies). The `group` column, identical to `treatment`, records only the treatment (BPDL or none), so it puts RB and EB together. Harvest time is part of what defines each condition; there is no separate time column. There are three flasks per condition, nine samples in all.

	Each sample is the bacterial population of one infected T25 flask, made into its own library and sequenced once, so there are no technical replicates. The digits 1 to 3 in the sample names only count the flasks within each condition; nothing records that flasks with the same number were infected or processed together. All samples carry the same batch label (`src_batch` is batch1 for every sample), so we have no batch differences, and we know of no other variable that matters. The GEO titles in `original_sample_id` read "BPDL 24hpi" for every sample, including the untreated RB and EB flasks; the treatments and harvest times are those given above.

	The data are bulk RNA-seq of the bacteria, from total RNA of the infected cultures, given as gene-level raw read counts from HTSeq for 889 C. trachomatis genes (CTL locus tags); host reads are not included.

	Our question is which C. trachomatis genes are differentially expressed in BPDL-treated cultures (AB) compared with untreated cultures (RB); both were harvested at 24 hours post infection, so they differ only in the treatment. All nine samples are part of this question: the EB flasks come from the same experiment, even though EB is not among the groups being compared.