RNF113A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-29	BGRSDLV03-30
idx	0	0
TRCN#_or_BGC#	TRCN0000218781	TRCN0000218781
shRNA_or_gRNA_sequence	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG
PAM
Name	RNF113A	RNF113A
Sample_ID	BGRSDLV03-29	BGRSDLV03-30
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	RNF113A	RNF113A
qPCR_result	63.9	68.5
Ave_qPCR	66.2
RT-qPCR_primer-F	aggaaaatgagcccgagagt
RT-qPCR_primer-R	atcgcgctctttctctgtgt
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9343	9344

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-29	BGRSDLV03-30
Sample_ID	BGRSDLV03-29	BGRSDLV03-30
Sample Name
Sample Name	RNF113A-BGRSDLV03-29	RNF113A-BGRSDLV03-30
RBP	RNF113A	RNF113A
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12622	12623

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-29	BGRSDLV03-30
Sample #	25	26
Sample Name	RNF113A-BGRSDLV03-29	RNF113A-BGRSDLV03-30
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	260	265
Peak_Molarity	49.70	97.90
libSampleQC_DNA_Well	DNA_Library_set66/set1/A9.png	DNA_Library_set66/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set66/set1/A4.png	RNA_Library_set66/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-29	BGRSDLV03-30
RBP	RNF113A	RNF113A
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4058	4059

Sequencing Information

	BGRSDLV03-29	BGRSDLV03-30
Sample_ID	BGRSDLV03-29	BGRSDLV03-30
Sample Name	RNF113A-BGRSDLV03-29	RNF113A-BGRSDLV03-30
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	16,609,510	13,427,569
total_aligned_reads	14,633,819	11,946,746
unique_aligned_reads	13,542,454	11,101,462
percent_uniqueAligned	0.81534	0.82677
correlation_replicates	0.999118	0.999118
spikein_reads	8,584	840
percent_spikeins	0.00052	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2777	2778

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RNF113A-BGRSDLV03-29_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2777	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8930
RNF113A-BGRSDLV03-29_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2777	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8970
RNF113A-BGRSDLV03-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-29_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9010
RNF113A-BGRSDLV03-29_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	9050
RNF113A-BGRSDLV03-29_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	9090
RNF113A-BGRSDLV03-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	9130
RNF113A-BGRSDLV03-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	9170
RNF113A-BGRSDLV03-29_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2777					GRCh38	V40	RNF113A-BGRSDLV03-29_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-29_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9210
RNF113A-BGRSDLV03-30_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2778	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8931
RNF113A-BGRSDLV03-30_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2778	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8971
RNF113A-BGRSDLV03-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-30_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9011
RNF113A-BGRSDLV03-30_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	9051
RNF113A-BGRSDLV03-30_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	9091
RNF113A-BGRSDLV03-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	9131
RNF113A-BGRSDLV03-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	9171
RNF113A-BGRSDLV03-30_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2778					GRCh38	V40	RNF113A-BGRSDLV03-30_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-30_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9211