RNF113A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-31dox	BGRSDLV03-32dox
idx	0	0
TRCN#_or_BGC#	TRCN0000218781	TRCN0000218781
shRNA_or_gRNA_sequence	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG
PAM
Name	RNF113A	RNF113A
Sample_ID	BGRSDLV03-31dox	BGRSDLV03-32dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	RNF113A	RNF113A
qPCR_result	67.0	56.6
Ave_qPCR	61.8
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9345	9346

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-31dox	BGRSDLV03-32dox
Sample_ID	BGRSDLV03-31dox	BGRSDLV03-32dox
Sample Name
Sample Name	RNF113A-BGRSDLV03-31dox	RNF113A-BGRSDLV03-32dox
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	12624	12625

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-31dox	BGRSDLV03-32dox
Sample #	27	28
Sample Name	RNF113A-BGRSDLV03-31dox	RNF113A-BGRSDLV03-32dox
Sample_Name_Alias
Index Well Position	C08	D08
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	270	272
Peak_Molarity	51.90	78.80
libSampleQC_DNA_Well	DNA_Library_set66/set1/C9.png	DNA_Library_set66/set1/D9.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set66/set1/C4.png	RNA_Library_set66/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-31dox	BGRSDLV03-32dox
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	4060	4061

Sequencing Information

	BGRSDLV03-31dox	BGRSDLV03-32dox
Sample_ID	BGRSDLV03-31dox	BGRSDLV03-32dox
Sample Name	RNF113A-BGRSDLV03-31dox	RNF113A-BGRSDLV03-32dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	14,692,470	13,699,092
total_aligned_reads	13,054,082	12,392,212
unique_aligned_reads	12,094,688	11,519,656
percent_uniqueAligned	0.82319	0.84091
correlation_replicates	0.997471	0.997471
spikein_reads	3,400	1,780
percent_spikeins	0.00023	0.00013
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2779	2780

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-BGRSDLV03-31dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2779	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8932
RNF113A-BGRSDLV03-31dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2779	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8972
RNF113A-BGRSDLV03-31dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-31dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9012
RNF113A-BGRSDLV03-31dox_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	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox/Aligned.sortedByCoord.out.bam		ENCORE2	9052
RNF113A-BGRSDLV03-31dox_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	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox/Aligned.sortedByCoord.out.bam		ENCORE2	9092
RNF113A-BGRSDLV03-31dox_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	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox/Aligned.sortedByCoord.out.bam		ENCORE2	9132
RNF113A-BGRSDLV03-31dox_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	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox/Aligned.sortedByCoord.out.bam		ENCORE2	9172
RNF113A-BGRSDLV03-31dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2779					GRCh38	V40	RNF113A-BGRSDLV03-31dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-31dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9212
RNF113A-BGRSDLV03-32dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2780	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8933
RNF113A-BGRSDLV03-32dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2780	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8973
RNF113A-BGRSDLV03-32dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-32dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9013
RNF113A-BGRSDLV03-32dox_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	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox/Aligned.sortedByCoord.out.bam		ENCORE2	9053
RNF113A-BGRSDLV03-32dox_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	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox/Aligned.sortedByCoord.out.bam		ENCORE2	9093
RNF113A-BGRSDLV03-32dox_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	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox/Aligned.sortedByCoord.out.bam		ENCORE2	9133
RNF113A-BGRSDLV03-32dox_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	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox/Aligned.sortedByCoord.out.bam		ENCORE2	9173
RNF113A-BGRSDLV03-32dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2780					GRCh38	V40	RNF113A-BGRSDLV03-32dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSDLV03-32dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9213