---------------------------------------
README – PREDIX LumB Sequencing Dataset
---------------------------------------

--------
Overview
--------

This dataset contains bulk whole-exome sequencing (WES) and RNA sequencing (RNA-seq) data from pre-treatment core biopsies collected in the randomized phase II clinical trial PREDIX LumB (ClinicalTrials.gov identifier: NCT02603679). 
The trial was conducted at three sites in Sweden between March 2016 and July 2021.

The objective of this dataset is to enable identification of molecular predictors of response to neoadjuvant treatment (NAT) with standard chemotherapy (paclitaxel) versus CDK4/6 inhibitor (palbociclib) plus endocrine therapy.

The dataset includes raw paired-end sequencing data in .fastq.gz format (RNA-seq and WES) and associated metadata. 

In total:

166 WES samples (including tumor and matched normal blood)

163 RNA-seq samples (tumor only)

--------------------------------
Sample Collection and Processing
--------------------------------

Biopsies: Pre-treatment ultrasound-guided core biopsies (14-gauge). Three fresh-frozen (FF) tissue samples were stored at –80 °C. Two samples were fixed in 10% neutral-buffered formalin and processed into FFPE blocks.

Blood samples: Whole blood collected before NAT in 4 mL EDTA tubes and stored at –80 °C. Plasma and serum collected at baseline, every six weeks during treatment, and at follow-up.

Nucleic acid isolation: RNA and DNA were co-extracted from fresh-frozen tumor biopsies using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN). DNA was also isolated from whole blood using the FlexiGene DNA Kit (QIAGEN).

Quality control: Concentration and purity were assessed using Qubit™ and NanoDrop ND-1000. Samples with <20 ng/µL RNA or DNA at extraction were excluded.

----------------------------------
Library preparation and Sequencing
----------------------------------

RNA libraries: Illumina Stranded Total RNA with Ribo-Zero Plus.

DNA libraries: Twist Library Preparation EF Kit 2.0 with Twist Comprehensive Exome panel.

Sequencing: Conducted at the National Genomics Infrastructure (NGI), SciLifeLab, Uppsala, Sweden using NovaSeq X Plus (150 bp paired-end, 25B flow cell, XLEAP-SBS chemistry).

----------------
Dataset Contents
----------------

The dataset consists of the following:

1) WES_data/Sample.fastq.gz
Folder containing raw paired-end FASTQ files from WES. 
Each tumor sample was multiplexed across nine sequencing sample/lane index combinations (18 FASTQ files: 9 × R1/R2). 
Each blood sample was multiplexed across five sequencing sample/lane index combinations (10 FASTQ files: 5 × R1/R2). 
File names begin with the sample anonymized ID and include R1 or R2, denoting forward and reverse reads, respectively.

2) RNA-seq_data/Sample.fastq.gz
Folder containing raw paired-end FASTQ files from RNA-seq. 
File names begin with the sample anonymized ID and include R1 or R2, denoting forward and reverse reads, respectively.

3) PREDIX-LumB_WES_RNA-seq_meta.csv
Metadata file containing patient anonymized ID, treatment arm, gender, and the corresponding WES and RNA-seq sample anonymized IDs.

4) PREDIX-LumB_WES_file_sizes.csv
Summary table of WES FASTQ files. Each row lists the FASTQ file name, the corresponding file size (in bytes), and the tissue type of origin (tumor or blood).

5) PREDIX-LumB_RNA-seq_file_sizes.csv
Summary table of RNA-seq FASTQ files. Each row lists the FASTQ file name, the corresponding file size (in bytes).