https://doi.org/10.6078/D1WT6W

Description of the data and file structure

These 'half-cell' RNA sequencing data accompany our preprint:

Genome-wide analysis of anterior-posterior mRNA regionalization in Stentor coeruleus reveals a role for the microtubule cytoskeleton

Link: https://www.biorxiv.org/content/10.1101/2023.01.09.523364v3

Each file is named for a treatment (con/control, tub/tubulin, G04/dynein construct #1, G05/dynein construct #2) and for which half of the cell (A/anterior, P/posterior) the fragment came from.

The tubulin and dynein experiments were conducted separately, and the controls are different. For example, files beginning with con1A_S15 and con1A_S197 are from different experiments. This README lists all file names grouped by category.

metadata.csv contains the file name, the experiment the file is from (bulk, tubulin, or dynein), the condition (control or knockdown), the region (anterior or posterior), and the biological replicate. 

Tubulin

First run:

This run also contains whole cell samples (file name contains W rather than A or P) that were not analyzed in the accompanying manuscript.

con1A_S15_L002_R1_001.fastq.gz
con1A_S15_L002_R2_001.fastq.gz
con1P_S16_L002_R1_001.fastq.gz
con1P_S16_L002_R2_001.fastq.gz
con2A_S17_L002_R1_001.fastq.gz
con2A_S17_L002_R2_001.fastq.gz
con2P_S18_L002_R1_001.fastq.gz
con2P_S18_L002_R2_001.fastq.gz
con4A_S19_L002_R1_001.fastq.gz
con4A_S19_L002_R2_001.fastq.gz
con4P_S20_L002_R1_001.fastq.gz
con4P_S20_L002_R2_001.fastq.gz
con5A_S21_L002_R1_001.fastq.gz
con5A_S21_L002_R2_001.fastq.gz
con5P_S22_L002_R1_001.fastq.gz
con5P_S22_L002_R2_001.fastq.gz
conW1_S23_L002_R1_001.fastq.gz
conW1_S23_L002_R2_001.fastq.gz
conW2_S24_L002_R1_001.fastq.gz
conW2_S24_L002_R2_001.fastq.gz
conW3_S25_L002_R1_001.fastq.gz
conW3_S25_L002_R2_001.fastq.gz
conW4_S26_L002_R1_001.fastq.gz
conW4_S26_L002_R2_001.fastq.gz
conW5_S27_L002_R1_001.fastq.gz
conW5_S27_L002_R2_001.fastq.gz
tub1A_S1_L001_R1_001.fastq.gz
tub1A_S1_L001_R2_001.fastq.gz
tub1P_S2_L001_R1_001.fastq.gz
tub1P_S2_L001_R2_001.fastq.gz
tub2A_S3_L001_R1_001.fastq.gz
tub2A_S3_L001_R2_001.fastq.gz
tub2P_S4_L001_R1_001.fastq.gz
tub2P_S4_L001_R2_001.fastq.gz
tub3A_S5_L001_R1_001.fastq.gz
tub3A_S5_L001_R2_001.fastq.gz
tub3P_S6_L001_R1_001.fastq.gz
tub3P_S6_L001_R2_001.fastq.gz
tub4A_S7_L001_R1_001.fastq.gz
tub4A_S7_L001_R2_001.fastq.gz
tub4P_S8_L001_R1_001.fastq.gz
tub4P_S8_L001_R2_001.fastq.gz
tub5A_S9_L001_R1_001.fastq.gz
tub5A_S9_L001_R2_001.fastq.gz
tub5P_S10_L001_R1_001.fastq.gz
tub5P_S10_L001_R2_001.fastq.gz
tubW1_S11_L001_R1_001.fastq.gz
tubW1_S11_L001_R2_001.fastq.gz
tubW3_S12_L001_R1_001.fastq.gz
tubW3_S12_L001_R2_001.fastq.gz
tubW4_S13_L001_R1_001.fastq.gz
tubW4_S13_L001_R2_001.fastq.gz
tubW5_S14_L001_R1_001.fastq.gz
tubW5_S14_L001_R2_001.fastq.gz

resequenced:

The following samples from the initial tubulin experiment were resequenced. con1A_S15 and con1A_S157 are from the same experiment, but two separate sequencing runs. The following files were merged with their corresponding file from the first run for the final analysis.

con1A_S157_L007_R1_001.fastq.gz
con1A_S157_L007_R2_001.fastq.gz
con1P_S158_L007_R1_001.fastq.gz
con1P_S158_L007_R2_001.fastq.gz
con2A_S159_L007_R1_001.fastq.gz
con2A_S159_L007_R2_001.fastq.gz
con2P_S160_L007_R1_001.fastq.gz
con2P_S160_L007_R2_001.fastq.gz
con4A_S161_L007_R1_001.fastq.gz
con4A_S161_L007_R2_001.fastq.gz
con4P_S162_L007_R1_001.fastq.gz
con4P_S162_L007_R2_001.fastq.gz
con5A_S163_L007_R1_001.fastq.gz
con5A_S163_L007_R2_001.fastq.gz
con5P_S164_L007_R1_001.fastq.gz
con5P_S164_L007_R2_001.fastq.gz
tub1A_S147_L007_R1_001.fastq.gz
tub1A_S147_L007_R2_001.fastq.gz
tub1P_S148_L007_R1_001.fastq.gz
tub1P_S148_L007_R2_001.fastq.gz
tub2A_S149_L007_R1_001.fastq.gz
tub2A_S149_L007_R2_001.fastq.gz
tub2P_S150_L007_R1_001.fastq.gz
tub2P_S150_L007_R2_001.fastq.gz
tub3A_S151_L007_R1_001.fastq.gz
tub3A_S151_L007_R2_001.fastq.gz
tub3P_S152_L007_R1_001.fastq.gz
tub3P_S152_L007_R2_001.fastq.gz
tub4A_S153_L007_R1_001.fastq.gz
tub4A_S153_L007_R2_001.fastq.gz
tub4P_S154_L007_R1_001.fastq.gz
tub4P_S154_L007_R2_001.fastq.gz
tub5A_S155_L007_R1_001.fastq.gz
tub5A_S155_L007_R2_001.fastq.gz
tub5P_S156_L007_R1_001.fastq.gz
tub5P_S156_L007_R2_001.fastq.gz

Dynein:

control:

con1A_S197_L006_R1_001.fastq.gz
con1A_S197_L006_R2_001.fastq.gz
con1P_S198_L006_R1_001.fastq.gz
con1P_S198_L006_R2_001.fastq.gz
con2A_S199_L006_R1_001.fastq.gz
con2A_S199_L006_R2_001.fastq.gz
con2P_S200_L006_R1_001.fastq.gz
con2P_S200_L006_R2_001.fastq.gz
con3A_S201_L006_R1_001.fastq.gz
con3A_S201_L006_R2_001.fastq.gz
con3P_S202_L006_R1_001.fastq.gz
con3P_S202_L006_R2_001.fastq.gz
con4A_S203_L006_R1_001.fastq.gz
con4A_S203_L006_R2_001.fastq.gz
con4P_S204_L006_R1_001.fastq.gz
con4P_S204_L006_R2_001.fastq.gz
con5A_S205_L006_R1_001.fastq.gz
con5A_S205_L006_R2_001.fastq.gz
con5P_S206_L006_R1_001.fastq.gz
con5P_S206_L006_R2_001.fastq.gz

G04:

G046A_S207_L007_R1_001.fastq.gz
G046A_S207_L007_R2_001.fastq.gz
G046P_S208_L007_R1_001.fastq.gz
G046P_S208_L007_R2_001.fastq.gz
G047A_S209_L007_R1_001.fastq.gz
G047A_S209_L007_R2_001.fastq.gz
G047P_S210_L007_R1_001.fastq.gz
G047P_S210_L007_R2_001.fastq.gz
G048A_S211_L007_R1_001.fastq.gz
G048A_S211_L007_R2_001.fastq.gz
G048P_S212_L007_R1_001.fastq.gz
G048P_S212_L007_R2_001.fastq.gz
G049A_S213_L007_R1_001.fastq.gz
G049A_S213_L007_R2_001.fastq.gz
G049P_S214_L007_R1_001.fastq.gz
G049P_S214_L007_R2_001.fastq.gz
G0410A_S215_L007_R1_001.fastq.gz
G0410A_S215_L007_R2_001.fastq.gz
G0410P_S216_L007_R1_001.fastq.gz
G0410P_S216_L007_R2_001.fastq.gz

G05:

G0511A_S217_L008_R1_001.fastq.gz
G0511A_S217_L008_R2_001.fastq.gz
G0511P_S218_L008_R1_001.fastq.gz
G0511P_S218_L008_R2_001.fastq.gz
G0512A_S219_L008_R1_001.fastq.gz
G0512A_S219_L008_R2_001.fastq.gz
G0512P_S220_L008_R1_001.fastq.gz
G0512P_S220_L008_R2_001.fastq.gz
G0513A_S221_L008_R1_001.fastq.gz
G0513A_S221_L008_R2_001.fastq.gz
G0513P_S222_L008_R1_001.fastq.gz
G0513P_S222_L008_R2_001.fastq.gz
G0514A_S223_L008_R1_001.fastq.gz
G0514A_S223_L008_R2_001.fastq.gz
G0514P_S224_L008_R1_001.fastq.gz
G0514P_S224_L008_R2_001.fastq.gz
G0515A_S225_L008_R1_001.fastq.gz
G0515A_S225_L008_R2_001.fastq.gz
G0515P_S226_L008_R1_001.fastq.gz
G0515P_S226_L008_R2_001.fastq.gz

Bulk:

A1_S1_L001_R1_001.fastq.gz
A1_S1_L001_R2_001.fastq.gz
A2_S2_L001_R1_001.fastq.gz
A2_S2_L001_R2_001.fastq.gz
A5_S5_L001_R1_001.fastq.gz
A5_S5_L001_R2_001.fastq.gz
A6_S6_L001_R1_001.fastq.gz
A6_S6_L001_R2_001.fastq.gz
P1_S3_L001_R1_001.fastq.gz
P1_S3_L001_R2_001.fastq.gz
P2_S4_L001_R1_001.fastq.gz
P2_S4_L001_R2_001.fastq.gz
P5_S7_L001_R1_001.fastq.gz
P5_S7_L001_R2_001.fastq.gz
P6_S8_L001_R1_001.fastq.gz
P6_S8_L001_R2_001.fastq.gz

Code/software

All scripts and analyses are available here: https://github.com/aralbright/2022_AADAWM