RNF14 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-33	BGRSDLV03-34
idx	0	0
TRCN#_or_BGC#	TRCN0000010786	TRCN0000010786
shRNA_or_gRNA_sequence	CCGGCTGTGGATGTTGACGACGATACTCGAGTATCGTCGTCAACATCCACAGTTTTT	CCGGCTGTGGATGTTGACGACGATACTCGAGTATCGTCGTCAACATCCACAGTTTTT
PAM
Name	RNF14	RNF14
Sample_ID	BGRSDLV03-33	BGRSDLV03-34
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	RNF14	RNF14
qPCR_result	88.4	88.4
Ave_qPCR	88.4
RT-qPCR_primer-F	atctgctccagctgcaattt
RT-qPCR_primer-R	ccgcttgcaggtattcattt
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	9347	9348

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-33	BGRSDLV03-34
Sample_ID	BGRSDLV03-33	BGRSDLV03-34
Sample Name
Sample Name	RNF14-BGRSDLV03-33	RNF14-BGRSDLV03-34
RBP	RNF14	RNF14
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12626	12627

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-33	BGRSDLV03-34
Sample #	29	30
Sample Name	RNF14-BGRSDLV03-33	RNF14-BGRSDLV03-34
Sample_Name_Alias
Index Well Position	E08	F08
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	265	267
Peak_Molarity	76.10	99.70
libSampleQC_DNA_Well	DNA_Library_set66/set1/E9.png	DNA_Library_set66/set1/F9.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set66/set1/E4.png	RNA_Library_set66/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-33	BGRSDLV03-34
RBP	RNF14	RNF14
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	4062	4063

Sequencing Information

	BGRSDLV03-33	BGRSDLV03-34
Sample_ID	BGRSDLV03-33	BGRSDLV03-34
Sample Name	RNF14-BGRSDLV03-33	RNF14-BGRSDLV03-34
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,312,032	24,206,945
total_aligned_reads	11,660,887	21,095,632
unique_aligned_reads	10,842,394	19,601,450
percent_uniqueAligned	0.81448	0.80974
correlation_replicates	0.997041	0.997041
spikein_reads	2,580	6,840
percent_spikeins	0.00019	0.00028
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2781	2782

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
RNF14-BGRSDLV03-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2781	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	8934
RNF14-BGRSDLV03-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2781	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	8974
RNF14-BGRSDLV03-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2781					GRCh38	V40	RNF14-BGRSDLV03-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9014
RNF14-BGRSDLV03-33_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	2781					GRCh38	V40	RNF14-BGRSDLV03-33/Aligned.sortedByCoord.out.bam		ENCORE2	9054
RNF14-BGRSDLV03-33_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	2781					GRCh38	V40	RNF14-BGRSDLV03-33/Aligned.sortedByCoord.out.bam		ENCORE2	9094
RNF14-BGRSDLV03-33_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	2781					GRCh38	V40	RNF14-BGRSDLV03-33/Aligned.sortedByCoord.out.bam		ENCORE2	9134
RNF14-BGRSDLV03-33_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	2781					GRCh38	V40	RNF14-BGRSDLV03-33/Aligned.sortedByCoord.out.bam		ENCORE2	9174
RNF14-BGRSDLV03-33_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2781					GRCh38	V40	RNF14-BGRSDLV03-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9214
RNF14-BGRSDLV03-34_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2782	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	8935
RNF14-BGRSDLV03-34_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2782	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	8975
RNF14-BGRSDLV03-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2782					GRCh38	V40	RNF14-BGRSDLV03-34_merged_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-34_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9015
RNF14-BGRSDLV03-34_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	2782					GRCh38	V40	RNF14-BGRSDLV03-34/Aligned.sortedByCoord.out.bam		ENCORE2	9055
RNF14-BGRSDLV03-34_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	2782					GRCh38	V40	RNF14-BGRSDLV03-34/Aligned.sortedByCoord.out.bam		ENCORE2	9095
RNF14-BGRSDLV03-34_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	2782					GRCh38	V40	RNF14-BGRSDLV03-34/Aligned.sortedByCoord.out.bam		ENCORE2	9135
RNF14-BGRSDLV03-34_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	2782					GRCh38	V40	RNF14-BGRSDLV03-34/Aligned.sortedByCoord.out.bam		ENCORE2	9175
RNF14-BGRSDLV03-34_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2782					GRCh38	V40	RNF14-BGRSDLV03-34_merged_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-34_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9215