Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

This dataverse is containing supplementary data for the pubblication titled "Lost in HELLS: disentangling the mystery of SALNR existence in senescence cellular models" by Arianna Consiglio, Marco Venturin, Sabrina Briguglio, Clara Rossi, Giorgio Grillo, Stefano Bellosta, Maria Grazia Cattaneo, Flavio Licciulli, Cristina Battaglia (2023), PLoS ONE 18(5), doi: https://doi.org/10.1371/journal.pone.0286104

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1 to 10 of 37 Results

S1_Table._Long-read_RNA-seq_dataset.ods Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models OpenOffice Spreadsheet - 20.3 KB - MD5: a0042bc9412d1cf69def42c6f8c57adb . List of all long-read datasets that were mapped to the human genome to search for reads mapping to HELLS genomic location to identify the isoform that originates them.
S2_Table.txt Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Plain Text - 6.5 KB - MD5: f101d0b269dbbb492f4b6fd9916075f7 List of primers used for quantitative RT-PCR experiments
S3_Fig.png Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models PNG Image - 101.2 KB - MD5: c349d2c45479002db417fe3717f38c7a Visualization of sequence reads (from short-read RNA-seq) aligned to the genomic portion including HELLS and SALNR, using UCSC genome browser. It is not possible to isolate SALNR expression from this type of reads, but the heavy presence of reads covering the 3’ end of the HELLS...
S4_Fig.tif Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models TIFF Image - 171.8 KB - MD5: defa3404f4f2a06762601147dfb2f205 Genomic location of the two amplicons used to amplify the XR_007061960 isoform of HELLS and corresponding primer sequences.
S5_File.fasta Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Unknown - 7.2 KB - MD5: 713e9e3c990f183697b7f625e1868952 Results of Sanger sequencing carried out on RT-PCR products (HELLS_XR_007061960 and HELLS_XR_007061960_3’ amplicons) obtained from HSMC and SH-SY5Y cells exported as sequences in FASTA format.
S6_Table._RSEM_and_MultiDEA_read_count_estimations.tab Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Tabular Data - 70.8 KB - 6 Variables, 1058 Observations - UNF:6:OOjBZQxC55cCbmoRhY/U9A== Read count estimation computed by RSEM and MultiDEA for each isoform in HELLS genomic location, for each sample and for each dataset. Despite the diffuse overlapping among the isoforms, the Bayesian model included in RSEM tends to prefer only a small subset of isoforms, changing...
S7_Table._DESeq2_on_RSEM_and_MultiDEA_expression.tab Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Tabular Data - 24.6 KB - 8 Variables, 368 Observations - UNF:6:7OryrHthHhNRaBm1zPh0Xg== Results of DESeq2 differential expression analysis performed on RSEM and MultiDEA isoform expression estimation. The isoforms are sorted by start position on chr10, and even if RSEM and MultiDEA show some different results, it is possible to deduce that the senescence expression...
FastQC.zip Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models ZIP Archive - 39.6 MB - MD5: c47d90077641d44fff93719a361662c1 Quality reports of the RNA-seq datasets analyzed/
HELLS_XR_007061960_3’_amplicon_HSMC_FW.ab1 Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Unknown - 240.4 KB - MD5: d61cca56df30eb2757070836fe4c53a7
HELLS_XR_007061960_3’_amplicon_HSMC_FW.fasta Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models Unknown - 1004 B - MD5: a03146c13bce284f51bb1760096a0f6c

S1_Table._Long-read_RNA-seq_dataset.ods

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

OpenOffice Spreadsheet - 20.3 KB -

. List of all long-read datasets that were mapped to the human genome to search for reads mapping to HELLS genomic location to identify the isoform that originates them.

S2_Table.txt

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Plain Text - 6.5 KB -

List of primers used for quantitative RT-PCR experiments

S3_Fig.png

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

PNG Image - 101.2 KB -

Visualization of sequence reads (from short-read RNA-seq) aligned to the genomic portion including HELLS and SALNR, using UCSC genome browser. It is not possible to isolate SALNR expression from this type of reads, but the heavy presence of reads covering the 3’ end of the HELLS...

S4_Fig.tif

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

TIFF Image - 171.8 KB -

Genomic location of the two amplicons used to amplify the XR_007061960 isoform of HELLS and corresponding primer sequences.

S5_File.fasta

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Unknown - 7.2 KB -

Results of Sanger sequencing carried out on RT-PCR products (HELLS_XR_007061960 and HELLS_XR_007061960_3’ amplicons) obtained from HSMC and SH-SY5Y cells exported as sequences in FASTA format.

S6_Table._RSEM_and_MultiDEA_read_count_estimations.tab

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Tabular Data - 70.8 KB - 6 Variables, 1058 Observations -

Read count estimation computed by RSEM and MultiDEA for each isoform in HELLS genomic location, for each sample and for each dataset. Despite the diffuse overlapping among the isoforms, the Bayesian model included in RSEM tends to prefer only a small subset of isoforms, changing...

S7_Table._DESeq2_on_RSEM_and_MultiDEA_expression.tab

Apr 5, 2023 - Replication Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Tabular Data - 24.6 KB - 8 Variables, 368 Observations -

Results of DESeq2 differential expression analysis performed on RSEM and MultiDEA isoform expression estimation. The isoforms are sorted by start position on chr10, and even if RSEM and MultiDEA show some different results, it is possible to deduce that the senescence expression...

FastQC.zip

Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

ZIP Archive - 39.6 MB -

Quality reports of the RNA-seq datasets analyzed/

HELLS_XR_007061960_3’_amplicon_HSMC_FW.ab1

Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Unknown - 240.4 KB -

HELLS_XR_007061960_3’_amplicon_HSMC_FW.fasta

Apr 5, 2023 - Raw Data for Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models

Unknown - 1004 B -

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