Sequencing analysis
Assess ER folding regulation in the MCF7 treatment experiment
Read the task instructions and deliverables
# Assess ER folding regulation in the MCF7 treatment experiment The lab wants to know whether its 24-hour MCF7 E2 comparison supports preferential transcriptional regulation of a specific protein-folding process in the endoplasmic reticulum (ER). Use all four supplied PRO-seq read sets and the authentic experimental, genome and biochemical records. Identify the specific ER folding process containing the strongest relative reduction in a member’s transcription, among the ER folding proteins described in the supplied sources. Decide whether the labelled libraries support a common decrease of that process relative to the other source-described ER folding proteins. Seek evidence that challenges your decision. Include only proteins with their own folding-role descriptions; exclude roles restricted to another tissue. Complete only findings.json. This decision concerns relative nascent transcription in the supplied libraries, not protein activity or population significance.
How was it graded?
Code compares submitted answer fields with reference values. Written reasoning is not graded.
Fraction of criteria passed; every criterion has weight one.
LLM judge: None — deterministic grading
Task files
Choose an evidence file.
Grading criteria
Identify the process containing the strongest relative transcriptional reduction
Earns credit
In findings.json, result_genes must contain exactly CANX, CALR and PDIA3 (ENSG00000127022, ENSG00000179218, ENSG00000167004), the source-described members of the calnexin/calreticulin folding cycle. This identifies the process containing the strongest relative transcriptional reduction; it does not claim that every member decreases together.
Does not earn credit
No credit if a required gene is omitted, an extra gene is included, a gene is repeated (including under an alias), or result_genes is missing or is not a list of strings.
Accepted alternatives
Gene order does not matter. Use the listed Ensembl IDs, their versioned IDs from the supplied annotation, or the symbols CANX, CALR and PDIA3. Equivalent IDs and symbols may be mixed; each gene must appear exactly once.
Weight: 1
Input evidence
Entire supplied 8,000,000-record FASTQ, both source lanes. · Exact nascent-RNA observations for the labelled library; no computed results are supplied.
Reference evidence
computed-reference · computed-reference.gold/local.policies.*.er_log_share_changes and attempt2_final_endpoints; final-selection-independent-check.json documents all supported rankings
Exact supplied-read reference and independent coverage/count arithmetic support the selected cycle and reject coordinated decrease. Diagnostic contrast is private and is not required in the answer.
Recorded result / GPT 6.1 sol
Failed. result_genes: matched 2 of 3 reference members. Missing: PDIA3.
Reject unsupported coordinated functional decrease
Earns credit
In findings.json, decision must be the JSON boolean false. The labelled-library evidence does not support a common decrease of this folding process relative to the other source-described ER folding proteins. The claim concerns relative nascent transcription, not protein activity or population significance.
Does not earn credit
No credit for true, a missing value, null, a number, or a string such as "false". The grader requires the boolean false.
Weight: 1
Input evidence
Entire supplied 8,000,000-record FASTQ, both source lanes. · Exact nascent-RNA observations for the labelled library; no computed results are supplied.
Reference evidence
computed-reference · computed-reference.gold/local.policies.*.er_log_share_changes and attempt2_final_endpoints; final-selection-independent-check.json documents all supported rankings
Exact supplied-read reference and independent coverage/count arithmetic support the selected cycle and reject coordinated decrease. Diagnostic contrast is private and is not required in the answer.
Recorded result / GPT 6.1 sol
Failed. Submitted decision = true; required the JSON boolean false.