RNF41 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-53	BGRSLV04-54
idx	0	0
TRCN#_or_BGC#	TRCN0000034249	TRCN0000034249
shRNA_or_gRNA_sequence	CCGGCCGACGCTACTATGAGAACTACTCGAGTAGTTCTCATAGTAGCGTCGGTTTTTG	CCGGCCGACGCTACTATGAGAACTACTCGAGTAGTTCTCATAGTAGCGTCGGTTTTTG
PAM
Name	RNF41	RNF41
Sample_ID	BGRSLV04-53	BGRSLV04-54
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	RNF41	RNF41
qPCR_result	81.0	83.0
Ave_qPCR	82.0
RT-qPCR_primer-F	atgagctgcccaaccataac
RT-qPCR_primer-R	gcctttagcagctggatgtc
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	8433	8434

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-53	BGRSLV04-54
Sample_ID	BGRSLV04-53	BGRSLV04-54
Sample Name
Sample Name	RNF41-BGRSLV04-53	RNF41-BGRSLV04-54
RBP	RNF41	RNF41
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	11466	11467

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-53	BGRSLV04-54
Sample #	31	32
Sample Name	RNF41-BGRSLV04-53	RNF41-BGRSLV04-54
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	291	293
Peak_Molarity	69.60	46.70
libSampleQC_DNA_Well	DNA_Library_set59/set1/G10.png	DNA_Library_set59/set1/H10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set59/set1/G5.png	RNA_Library_set59/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-53	BGRSLV04-54
RBP	RNF41	RNF41
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3580	3581

Sequencing Information

	BGRSLV04-53	BGRSLV04-54
Sample_ID	BGRSLV04-53	BGRSLV04-54
Sample Name	RNF41-BGRSLV04-53	RNF41-BGRSLV04-54
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	56,710,763	56,256,407
total_aligned_reads	48,514,468	48,577,724
unique_aligned_reads	44,873,194	45,357,220
percent_uniqueAligned	0.79126	0.80626
correlation_replicates	0.939833	0.939833
spikein_reads	179,620	165,002
percent_spikeins	0.00317	0.00293
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2451	2452

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
RNF41-BGRSLV04-53_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2451	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8080
RNF41-BGRSLV04-53_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2451	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8118
RNF41-BGRSLV04-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF41-BGRSLV04-53_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11049
RNF41-BGRSLV04-53_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53/Aligned.sortedByCoord.out.bam		ENCORE2	11087
RNF41-BGRSLV04-53_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53/Aligned.sortedByCoord.out.bam		ENCORE2	11125
RNF41-BGRSLV04-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53/Aligned.sortedByCoord.out.bam		ENCORE2	11163
RNF41-BGRSLV04-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53/Aligned.sortedByCoord.out.bam		ENCORE2	11201
RNF41-BGRSLV04-53_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2451					GRCh38	V40	RNF41-BGRSLV04-53_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF41-BGRSLV04-53_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11239
RNF41-BGRSLV04-54_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2452	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8081
RNF41-BGRSLV04-54_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2452	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8119
RNF41-BGRSLV04-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF41-BGRSLV04-54_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11050
RNF41-BGRSLV04-54_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54/Aligned.sortedByCoord.out.bam		ENCORE2	11088
RNF41-BGRSLV04-54_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54/Aligned.sortedByCoord.out.bam		ENCORE2	11126
RNF41-BGRSLV04-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54/Aligned.sortedByCoord.out.bam		ENCORE2	11164
RNF41-BGRSLV04-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54/Aligned.sortedByCoord.out.bam		ENCORE2	11202
RNF41-BGRSLV04-54_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2452					GRCh38	V40	RNF41-BGRSLV04-54_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNF41-BGRSLV04-54_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11240