U2AF1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-5	BGRSDLV04-6
idx	0	0
TRCN#_or_BGC#	TRCN0000001155	TRCN0000001155
shRNA_or_gRNA_sequence	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC	GAAAGTGTTGTAGTTGATTGACTCGAGTCAATCAACTACAACACTTTC
PAM
Name	U2AF1	U2AF1
Sample_ID	BGRSDLV04-5	BGRSDLV04-6
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	U2AF1	U2AF1
qPCR_result	87.51834	91.34996
Ave_qPCR	89.43415
RT-qPCR_primer-F	GTGACAACCTGGGAGACCAC
RT-qPCR_primer-R	GGTTATTCAAGTCAATCACAGCC
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	9369	9370

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-5	BGRSDLV04-6
Sample_ID	BGRSDLV04-5	BGRSDLV04-6
Sample Name
Sample Name	U2AF1-BGRSDLV04-5	U2AF1-BGRSDLV04-6
RBP	U2AF1	U2AF1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12650	12651

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-5	BGRSDLV04-6
Sample #	5	6
Sample Name	U2AF1-BGRSDLV04-5	U2AF1-BGRSDLV04-6
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	286	292
Peak_Molarity	41.10	55.60
libSampleQC_DNA_Well	DNA_Library_set68/set1/E1.png	DNA_Library_set68/set1/F1.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set68/set1/E1.png	RNA_Library_set68/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-5	BGRSDLV04-6
RBP	U2AF1	U2AF1
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4078	4079

Sequencing Information

	BGRSDLV04-5	BGRSDLV04-6
Sample_ID	BGRSDLV04-5	BGRSDLV04-6
Sample Name	U2AF1-BGRSDLV04-5	U2AF1-BGRSDLV04-6
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	43,768,094	29,995,432
total_aligned_reads	31,816,363	24,599,107
unique_aligned_reads	29,783,502	23,069,335
percent_uniqueAligned	0.68048	0.76909
correlation_replicates	0.996255	0.996255
spikein_reads	6,886	7,966
percent_spikeins	0.00016	0.00027
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2841	2842

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
U2AF1-BGRSDLV04-5_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2841	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27669
U2AF1-BGRSDLV04-5_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2841	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27733
U2AF1-BGRSDLV04-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-5_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27797
U2AF1-BGRSDLV04-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5/Aligned.sortedByCoord.out.bam		ENCORE2	27861
U2AF1-BGRSDLV04-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5/Aligned.sortedByCoord.out.bam		ENCORE2	27925
U2AF1-BGRSDLV04-5_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5/Aligned.sortedByCoord.out.bam		ENCORE2	27989
U2AF1-BGRSDLV04-5_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5/Aligned.sortedByCoord.out.bam		ENCORE2	28053
U2AF1-BGRSDLV04-5_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2841					GRCh38	V40	U2AF1-BGRSDLV04-5_S5_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-5_S5_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28117
U2AF1-BGRSDLV04-6_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2842	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27670
U2AF1-BGRSDLV04-6_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2842	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27734
U2AF1-BGRSDLV04-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-6_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27798
U2AF1-BGRSDLV04-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6/Aligned.sortedByCoord.out.bam		ENCORE2	27862
U2AF1-BGRSDLV04-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6/Aligned.sortedByCoord.out.bam		ENCORE2	27926
U2AF1-BGRSDLV04-6_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6/Aligned.sortedByCoord.out.bam		ENCORE2	27990
U2AF1-BGRSDLV04-6_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6/Aligned.sortedByCoord.out.bam		ENCORE2	28054
U2AF1-BGRSDLV04-6_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2842					GRCh38	V40	U2AF1-BGRSDLV04-6_S6_L004_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1-BGRSDLV04-6_S6_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28118