RNF14 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-35dox	BGRSDLV03-36dox
idx	0	0
TRCN#_or_BGC#	TRCN0000010786	TRCN0000010786
shRNA_or_gRNA_sequence	CCGGCTGTGGATGTTGACGACGATACTCGAGTATCGTCGTCAACATCCACAGTTTTT	CCGGCTGTGGATGTTGACGACGATACTCGAGTATCGTCGTCAACATCCACAGTTTTT
PAM
Name	RNF14	RNF14
Sample_ID	BGRSDLV03-35dox	BGRSDLV03-36dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	RNF14	RNF14
qPCR_result	91.7	91.1
Ave_qPCR	91.4
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	9349	9350

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-35dox	BGRSDLV03-36dox
Sample_ID	BGRSDLV03-35dox	BGRSDLV03-36dox
Sample Name
Sample Name	RNF14-BGRSDLV03-35dox	RNF14-BGRSDLV03-36dox
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	12628	12629

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-35dox	BGRSDLV03-36dox
Sample #	31	32
Sample Name	RNF14-BGRSDLV03-35dox	RNF14-BGRSDLV03-36dox
Sample_Name_Alias
Index Well Position	G08	H08
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	269
Peak_Molarity	63.90	51.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/G9.png	DNA_Library_set66/set1/H9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set66/set1/G4.png	RNA_Library_set66/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-35dox	BGRSDLV03-36dox
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	4064	4065

Sequencing Information

	BGRSDLV03-35dox	BGRSDLV03-36dox
Sample_ID	BGRSDLV03-35dox	BGRSDLV03-36dox
Sample Name	RNF14-BGRSDLV03-35dox	RNF14-BGRSDLV03-36dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	14,525,139	22,482,156
total_aligned_reads	12,817,784	19,553,252
unique_aligned_reads	11,961,657	18,225,025
percent_uniqueAligned	0.82351	0.81064
correlation_replicates	0.995871	0.995871
spikein_reads	4,506	6,430
percent_spikeins	0.00031	0.00029
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2783	2784

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-BGRSDLV03-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2783	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	8936
RNF14-BGRSDLV03-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2783	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	8976
RNF14-BGRSDLV03-35dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9016
RNF14-BGRSDLV03-35dox_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	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9056
RNF14-BGRSDLV03-35dox_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	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9096
RNF14-BGRSDLV03-35dox_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	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9136
RNF14-BGRSDLV03-35dox_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	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9176
RNF14-BGRSDLV03-35dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2783					GRCh38	V40	RNF14-BGRSDLV03-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9216
RNF14-BGRSDLV03-36dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2784	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	8937
RNF14-BGRSDLV03-36dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2784	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	8977
RNF14-BGRSDLV03-36dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-36dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9017
RNF14-BGRSDLV03-36dox_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	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9057
RNF14-BGRSDLV03-36dox_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	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9097
RNF14-BGRSDLV03-36dox_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	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9137
RNF14-BGRSDLV03-36dox_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	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9177
RNF14-BGRSDLV03-36dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2784					GRCh38	V40	RNF14-BGRSDLV03-36dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,RNF14-BGRSDLV03-36dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9217