GSM4728719: vargas3_FIB-1; Entamoeba histolytica HM-1:IMSS; RIP-Seq - SRA

SRX8952028: GSM4728719: vargas3_FIB-1; Entamoeba histolytica HM-1:IMSS; RIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 1.3M spots, 65.7M bases, 42.1Mb downloads

Submitted by: NCBI (GEO)

Study: The orphan actin-related protein EhARPv2 belongs to the nucleolar snoRNPs molecular complexes of Entamoeba histolytica

PRJNA657364 • SRP277602 • All experiments • All runs

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In eukaryotes, ribosomal RNA biogenesis consists of ribosomal DNA transcription to pre-rRNA, which must be modified and processed in the nucleus resulting in the 18S, 5.8S, and 28S ribosomal units. Molecular components involved in this process comprise the catalytic ribonucleoproteins complexes (snoRNPs) formed by non-coding RNAs classified as box C/D and box H/ACA snoRNA that associates to at least four proteins highly conserved through evolution and combined to multiple transient proteins. Taking advantage of computational and multidisciplinary experimental approaches, we determine that the orphan EhARPv2, a member of the Actin-related family from Entamoeba histolytica, interacts with nucleolar proteins. EhARPv2 and its partners here identified colocalize in the nuclear periphery, considered the nucleolus, and interact with both box C/D and H/ACA snoRNAs. Moreover, we find the reassortment of some components of snoRNPs from C/D- or H/ACA complexes mixed in vitro and in entire cells indicating that in E. histolytica snoRNP of C/D or H/ACA machineries alternate using common elements and that EhARPv2 is a part of this peculiar snoRNP. Our findings substantiate a role for EhARPv2 in the biogenesis of ribosomal RNA. Overall design: CLIP-seq assay with a-EhARPv2, a-EhNop58, a-EhABP-12035 and a-EhFibrillarin in Entamoeba histolytica HM1: IMSS.

Sample: vargas3_FIB-1

SAMN15825350 • SRS7207194 • All experiments • All runs

Organism: Entamoeba histolytica HM-1:IMSS

Library:

Instrument: Illumina HiSeq 2500

Strategy: RIP-Seq

Source: TRANSCRIPTOMIC

Selection: other

Layout: SINGLE

Construction protocol: RNA molecules were released by protein digestion adding SDS (0.5% to 1%) and proteinase K (1.2mg/mL) for 1h at 55°C and purified by homogenization in 3 vols of TRIzol and filtering through RNA purification Direct-zol™ RNA Miniprep Kit (Zymo Research) columns Purified RNA was fragmented for 5 min with Ambion reagent at 70°C (Ambion, #AM8740), recovered with the RNeasy MinElute Cleanup Kit (Qiagen #74204), dephosporylated with Antartic phosphatase at 37°C for 30 min (NEB #M0289S) and phosphorylated with T4 Polynucleotide Kinase (NEB #M0201S). Libraries were constructed according to manufacter's recommendations using TruSeq Small RNA Sample Prep Kit (Illumina, #RS-200-0012) and were purified with AMPure XP beads (Agencourt, #A63880). Then, sequencing was performed using HiSeq 2500 platform (Illumina) in a multiplexed 51+7 bases single read using a TruSeq SR Cluster kit v3-cBot-HS (Illumina, #GD-401-3002) and a TruSeq SBS kit v3-HS 50 cycles (Illumina, #FC-401-3002).

Experiment attributes:

GEO Accession: GSM4728719

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 1.3M spots, 65.7M bases, 42.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR12457647	1,314,748	65.7M	42.1Mb	2020-08-17

ID:: 11636667

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