RNF113A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-29	BGRSLV06-30
idx	0	0
TRCN#_or_BGC#	TRCN0000218781	TRCN0000218781
shRNA_or_gRNA_sequence	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG	GTACCGGATCCAGCGAAAGAATTGATTGCTCGAGCAATCAATTCTTTCGCTGGATTTTTTTG
PAM
Name	RNF113A	RNF113A
Sample_ID	BGRSLV06-29	BGRSLV06-30
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	RNF113A	RNF113A
qPCR_result	57.7	60.2
Ave_qPCR	58.9
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	8556	8557

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-29	BGRSLV06-30
Sample_ID	BGRSLV06-29	BGRSLV06-30
Sample Name
Sample Name	RNF113A-BGRSLV06-29	RNF113A-BGRSLV06-30
RBP	RNF113A	RNF113A
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11696	11697

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-29	BGRSLV06-30
Sample #	79	80
Sample Name	RNF113A-BGRSLV06-29	RNF113A-BGRSLV06-30
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	292	288
Peak_Molarity	100.00	79.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/C11.png	DNA_Library_set60-62/set1/D11.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set60-62/set1/G10.png	RNA_Library_set60-62/set1/H10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-29	BGRSLV06-30
RBP	RNF113A	RNF113A
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3666	3667

Sequencing Information

	BGRSLV06-29	BGRSLV06-30
Sample_ID	BGRSLV06-29	BGRSLV06-30
Sample Name	RNF113A-BGRSLV06-29	RNF113A-BGRSLV06-30
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	52,885,202	32,665,491
total_aligned_reads	44,422,118	26,786,492
unique_aligned_reads	41,734,379	25,226,187
percent_uniqueAligned	0.78915	0.77226
correlation_replicates	0.998237	0.998237
spikein_reads	47,196	34,288
percent_spikeins	0.00089	0.00105
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2537	2538

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-BGRSLV06-29_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2537	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8592
RNF113A-BGRSLV06-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSLV06-29_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10457
RNF113A-BGRSLV06-29_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	10509
RNF113A-BGRSLV06-29_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	10561
RNF113A-BGRSLV06-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	10613
RNF113A-BGRSLV06-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	10665
RNF113A-BGRSLV06-29_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2537					GRCh38	V40	RNF113A-BGRSLV06-29_S79_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSLV06-29_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10717
RNF113A-BGRSLV06-29_S79_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2537	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28859
RNF113A-BGRSLV06-30_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2538	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8593
RNF113A-BGRSLV06-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSLV06-30_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10458
RNF113A-BGRSLV06-30_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	10510
RNF113A-BGRSLV06-30_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	10562
RNF113A-BGRSLV06-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	10614
RNF113A-BGRSLV06-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	10666
RNF113A-BGRSLV06-30_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2538					GRCh38	V40	RNF113A-BGRSLV06-30_S80_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNF113A-BGRSLV06-30_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10718
RNF113A-BGRSLV06-30_S80_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2538	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28860