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statLens-evaluation-data-example

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domizzz2025

Upload statLens evaluation inputs (57 tasks)

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We studied long-term hematopoietic stem cells (LT-HSCs) sorted from the bone marrow of young (10-16 weeks old) and aged (>80 weeks old) C57BL/6 mice and cultured ex vivo for 16 hours; the RhoA inhibitor Rhosin (Ri, 100 µM) was added to aged cells only. The three conditions, three samples each, are in the `condition` column: young_control (young cells without Ri), aged_control (aged cells without Ri) and aged_Ri (aged cells with Ri). The `group` column, copied in `treatment`, records only whether Ri was added, so its control level pools young and aged cells. The `time` column, copied in `age`, holds the donor age, not a sampling time: all samples were collected at the end of the 16-hour culture, so there is no time variable.

Each sample is one cultured population of sorted LT-HSCs and one library; there are no technical replicates. No mouse or sort identifiers are recorded, and no record links an aged control to a particular Ri-treated sample; the numbers 1 to 3 in the sample names only count the samples within each condition. The GEO records also carry a code labelled 'sequencing batch', copied into `batch` and `src_batch` (1, 2, 3, and '1+3' for one young sample), with no explanation beyond that label. We cannot tell what the codes, including '1+3', correspond to in practice, and the expression data show no clear grouping by them, so the batch structure of these samples is unknown to us. No other variable matters to us; the remaining columns are annotations or constant.

These are bulk RNA-seq data from SMART-Seq v4 low-input libraries. The matrix holds gene-level read-pair counts from featureCounts for protein-coding genes; multi-mapping reads were counted fractionally, so the counts have been rounded to whole numbers.

Our question is which genes are differentially expressed in aged LT-HSCs treated with the RhoA inhibitor (aged_Ri) compared with untreated aged LT-HSCs (aged_control). Only the six samples with `condition` aged_control or aged_Ri are part of this question; the young_control samples are not.

	We studied long-term hematopoietic stem cells (LT-HSCs) sorted from the bone marrow of young (10-16 weeks old) and aged (>80 weeks old) C57BL/6 mice and cultured ex vivo for 16 hours; the RhoA inhibitor Rhosin (Ri, 100 µM) was added to aged cells only. The three conditions, three samples each, are in the `condition` column: young_control (young cells without Ri), aged_control (aged cells without Ri) and aged_Ri (aged cells with Ri). The `group` column, copied in `treatment`, records only whether Ri was added, so its control level pools young and aged cells. The `time` column, copied in `age`, holds the donor age, not a sampling time: all samples were collected at the end of the 16-hour culture, so there is no time variable.

	Each sample is one cultured population of sorted LT-HSCs and one library; there are no technical replicates. No mouse or sort identifiers are recorded, and no record links an aged control to a particular Ri-treated sample; the numbers 1 to 3 in the sample names only count the samples within each condition. The GEO records also carry a code labelled 'sequencing batch', copied into `batch` and `src_batch` (1, 2, 3, and '1+3' for one young sample), with no explanation beyond that label. We cannot tell what the codes, including '1+3', correspond to in practice, and the expression data show no clear grouping by them, so the batch structure of these samples is unknown to us. No other variable matters to us; the remaining columns are annotations or constant.

	These are bulk RNA-seq data from SMART-Seq v4 low-input libraries. The matrix holds gene-level read-pair counts from featureCounts for protein-coding genes; multi-mapping reads were counted fractionally, so the counts have been rounded to whole numbers.

	Our question is which genes are differentially expressed in aged LT-HSCs treated with the RhoA inhibitor (aged_Ri) compared with untreated aged LT-HSCs (aged_control). Only the six samples with `condition` aged_control or aged_Ri are part of this question; the young_control samples are not.