DOI: 10.5061/dryad.tdz08kq58
title: Integrin restriction by miR-34 protects germline progenitors from cell death during aging

description: During aging, regenerative tissues must dynamically balance the two
 opposing processes of proliferation and cell death. While many microRNAs
 are differentially expressed during aging, their roles as dynamic
 regulators of tissue regeneration have yet to be described. We show that
 in the highly regenerative Drosophila testis, miR-34 levels are
 significantly elevated during aging. miR-34 modulates germ cell death and
 protects the progenitor germ cells from accelerated aging. However, miR-34
 is not expressed in the progenitors themselves but rather in neighboring
 cyst cells that kill the progenitors. Transcriptomics followed by
 functional analysis revealed that during aging, miR-34 modifies integrin
 signaling by limiting the levels of the heterodimeric integrin receptor
 αPS2 and βPS subunits. In addition, we found that in cyst cells, this
 heterodimer is essential for inducing phagoptosis and degradation of the
 progenitor germ cells. Together, these data suggest that the miR-34 –
 integrin signaling axis acts as a sensor of progenitor germ cell death to
 extend progenitor functionality during aging.
description: Illumina cDNA libraries were prepared from 1 µg total RNA
 extracted from testes of young and aged control <em>w1118</em>
 and <em>miR-34</em> null mutants. Sequencing libraries were
 prepared using INCPM mRNA Sequence Single-Read. Sixty reads were sequenced
 on two lanes of an Illumina HiSeq apparatus. The output was ~22 million
 reads per sample. Poly-A/T stretches and Illumina adapters were trimmed
 from the reads using cutadapt. Resulting reads shorter than 30 bp were
 discarded. Reads were mapped to the <em>Drosophila</em>
 <em>melanogaster</em> dmel reference genome using STAR,
 supplied with gene annotations downloaded from FlyBase (r6.18) (and with
 the EndToEnd option and outFilterMismatchNoverLmax was set to
 0.04).
description: # Integrin restriction by miR-34 protects germline progenitors from cell
 death during aging The
 dataset contains 16 samples. Each Sample contains 2 fastq.gz files from 2
 lanes. There are 4 experimental groups: * w1118 1 day * w1118 30 day *
 mir34 knockout 1 day * mir34 knockout 30 day Each group contains 4
 biological replicates. ## Description of the data and file structure w1118
 1 day Rep1: w1118_1day_Rep1_L6.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype w1118, Age 1 day, Replicate #1, Lane 6
 w1118_1day_Rep1_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #1, Lane 7 w1118 1 day Rep2:
 w1118_1day_Rep2_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #2, Lane 6
 w1118_1day_Rep2_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #2, Lane 7 w1118 1 day Rep3:
 w1118_1day_Rep3_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #3, Lane 6
 w1118_1day_Rep3_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #3, Lane 7 w1118 1 day Rep4:
 w1118_1day_Rep4_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #4, Lane 6
 w1118_1day_Rep4_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 1 day, Replicate #4, Lane 7 w1118 30 days Rep1:
 w1118_30day_Rep1_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #1, Lane 6
 w1118_30day_Rep1_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #1, Lane 7 w1118 30 days Rep2:
 w1118_30day_Rep2_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #2, Lane 6
 w1118_30day_Rep2_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #2, Lane 7 w1118 30 days Rep3:
 w1118_30day_Rep3_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #3, Lane 6
 w1118_30day_Rep3_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #3, Lane 7 w1118 30 days Rep4:
 w1118_30day_Rep4_L6.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #4, Lane 6
 w1118_30day_Rep4_L7.fastq.gz * RNA-Sequencing data from Drosophila testes,
 Genotype w1118, Age 30 days, Replicate #4, Lane 7 mir34 KO 1 day Rep1:
 mir34_KO_1day_Rep1_L6.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 1 day, Replicate #1, Lane 6
 mir34_KO_1day_Rep1_L7.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 1 day, Replicate #1, Lane 7 mir34 KO
 1 day Rep2: mir34_KO_1day_Rep2_L6.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 1 day, Replicate #2, Lane
 6 mir34_KO_1day_Rep2_L7.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 1 day, Replicate #2, Lane 7 mir34 KO
 1 day Rep3: mir34_KO_1day_Rep3_L6.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 1 day, Replicate #3, Lane
 6 mir34_KO_1day_Rep3_L7.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 1 day, Replicate #3, Lane 7 mir34 KO
 1 day Rep4: mir34_KO_1day_Rep4_L6.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 1 day, Replicate #4, Lane
 6 mir34_KO_1day_Rep4_L7.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 1 day, Replicate #4, Lane 7 mir34 KO
 30 days Rep1: mir34_KO_30day_Rep1_L6.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 30 days, Replicate #1,
 Lane 6 mir34_KO_30day_Rep1_L7.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 30 days, Replicate #1,
 Lane 7 mir34 KO 30 days Rep2: mir34_KO_30day_Rep2_L6.fastq.gz *
 RNA-Sequencing data from Drosophila testes, Genotype mir34 knockout, Age
 30 days, Replicate #2, Lane 6 mir34_KO_30day_Rep2_L7.fastq.gz *
 RNA-Sequencing data from Drosophila testes, Genotype mir34 knockout, Age
 30 days, Replicate #2, Lane 7 mir34 KO 30 days Rep3:
 mir34_KO_30day_Rep3_L6.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 30 days, Replicate #3, Lane 6
 mir34_KO_30day_Rep3_L7.fastq.gz * RNA-Sequencing data from Drosophila
 testes, Genotype mir34 knockout, Age 30 days, Replicate #3, Lane 7 mir34
 KO 30 days Rep4: mir34_KO_30day_Rep4_L6.fastq.gz * RNA-Sequencing data
 from Drosophila testes, Genotype mir34 knockout, Age 30 days, Replicate
 #4, Lane 6 mir34_KO_30day_Rep4_L7.fastq.gz * RNA-Sequencing data from
 Drosophila testes, Genotype mir34 knockout, Age 30 days, Replicate #4,
 Lane 7