RNF31 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-21	BGRSLV07-22
idx	0	0
TRCN#_or_BGC#	TRCN0000168448	TRCN0000168448
shRNA_or_gRNA_sequence	CCGGGCGTGGTGTCAAGTTTAATAACTCGAGTTATTAAACTTGACACCACGCTTTTTTG	CCGGGCGTGGTGTCAAGTTTAATAACTCGAGTTATTAAACTTGACACCACGCTTTTTTG
PAM
Name	RNF31	RNF31
Sample_ID	BGRSLV07-21	BGRSLV07-22
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	RNF31	RNF31
qPCR_result	74.3	77.3
Ave_qPCR	75.8
RT-qPCR_primer-F	gtcggagctgtgaggacttc
RT-qPCR_primer-R	ggcgtacgagaacttgcatt
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	8603	8604

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-21	BGRSLV07-22
Sample_ID	BGRSLV07-21	BGRSLV07-22
Sample Name
Sample Name	RNF31-BGRSLV07-21	RNF31-BGRSLV07-22
RBP	RNF31	RNF31
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	11848	11849

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-21	BGRSLV07-22
Sample #	29	30
Sample Name	RNF31-BGRSLV07-21	RNF31-BGRSLV07-22
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	294	298
Peak_Molarity	80.50	101.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E4.png	DNA_Library_set60-62/set4/F4.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set60-62/set2/E4.png	RNA_Library_set60-62/set2/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-21	BGRSLV07-22
RBP	RNF31	RNF31
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3712	3713

Sequencing Information

	BGRSLV07-21	BGRSLV07-22
Sample_ID	BGRSLV07-21	BGRSLV07-22
Sample Name	RNF31-BGRSLV07-21	RNF31-BGRSLV07-22
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	21,995,763	20,820,568
total_aligned_reads	18,157,132	18,231,022
unique_aligned_reads	17,019,779	17,110,384
percent_uniqueAligned	0.77378	0.82180
correlation_replicates	0.990201	0.990201
spikein_reads	19,328	18,120
percent_spikeins	0.00088	0.00087
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2583	2584

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
RNF31-BGRSLV07-21_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2583	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7888
RNF31-BGRSLV07-21_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2583	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7932
RNF31-BGRSLV07-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF31-BGRSLV07-21_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10193
RNF31-BGRSLV07-21_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21/Aligned.sortedByCoord.out.bam		ENCORE2	10237
RNF31-BGRSLV07-21_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21/Aligned.sortedByCoord.out.bam		ENCORE2	10281
RNF31-BGRSLV07-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21/Aligned.sortedByCoord.out.bam		ENCORE2	10325
RNF31-BGRSLV07-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21/Aligned.sortedByCoord.out.bam		ENCORE2	10369
RNF31-BGRSLV07-21_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2583					GRCh38	V40	RNF31-BGRSLV07-21_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF31-BGRSLV07-21_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10413
RNF31-BGRSLV07-22_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2584	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7889
RNF31-BGRSLV07-22_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2584	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7933
RNF31-BGRSLV07-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF31-BGRSLV07-22_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10194
RNF31-BGRSLV07-22_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22/Aligned.sortedByCoord.out.bam		ENCORE2	10238
RNF31-BGRSLV07-22_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22/Aligned.sortedByCoord.out.bam		ENCORE2	10282
RNF31-BGRSLV07-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22/Aligned.sortedByCoord.out.bam		ENCORE2	10326
RNF31-BGRSLV07-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22/Aligned.sortedByCoord.out.bam		ENCORE2	10370
RNF31-BGRSLV07-22_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2584					GRCh38	V40	RNF31-BGRSLV07-22_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF31-BGRSLV07-22_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10414