U2AF1L4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-31	BGRSLV05-32
idx	0	0
TRCN#_or_BGC#	TRCN0000074648	TRCN0000074648
shRNA_or_gRNA_sequence	CCGGGCTTCACAACAAGCCGACATTCTCGAGAATGTCGGCTTGTTGTGAAGCTTTTTG	CCGGGCTTCACAACAAGCCGACATTCTCGAGAATGTCGGCTTGTTGTGAAGCTTTTTG
PAM
Name	U2AF1L4	U2AF1L4
Sample_ID	BGRSLV05-31	BGRSLV05-32
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	U2AF1L4	U2AF1L4
qPCR_result	54.8	50.5
Ave_qPCR	52.6
RT-qPCR_primer-F	gcttcgatattcgggactga
RT-qPCR_primer-R	gaatgtcggcttgttgtgaa
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	8484	8485

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-31	BGRSLV05-32
Sample_ID	BGRSLV05-31	BGRSLV05-32
Sample Name
Sample Name	U2AF1L4-BGRSLV05-31	U2AF1L4-BGRSLV05-32
RBP	U2AF1L4	U2AF1L4
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	11620	11621

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-31	BGRSLV05-32
Sample #	53	54
Sample Name	U2AF1L4-BGRSLV05-31	U2AF1L4-BGRSLV05-32
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	294	292
Peak_Molarity	69.60	94.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A8.png	DNA_Library_set60-62/set1/B8.png
RIN	9.6	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/E7.png	RNA_Library_set60-62/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-31	BGRSLV05-32
RBP	U2AF1L4	U2AF1L4
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3640	3641

Sequencing Information

	BGRSLV05-31	BGRSLV05-32
Sample_ID	BGRSLV05-31	BGRSLV05-32
Sample Name	U2AF1L4-BGRSLV05-31	U2AF1L4-BGRSLV05-32
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	35,974,774	27,557,668
total_aligned_reads	31,835,075	24,620,050
unique_aligned_reads	29,864,020	23,025,907
percent_uniqueAligned	0.83014	0.83555
correlation_replicates	0.998080	0.998080
spikein_reads	129,528	81,138
percent_spikeins	0.00360	0.00294
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2511	2512

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
U2AF1L4-BGRSLV05-31_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2511	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8612
U2AF1L4-BGRSLV05-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1L4-BGRSLV05-31_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10477
U2AF1L4-BGRSLV05-31_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	10529
U2AF1L4-BGRSLV05-31_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	10581
U2AF1L4-BGRSLV05-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	10633
U2AF1L4-BGRSLV05-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31/Aligned.sortedByCoord.out.bam		ENCORE2	10685
U2AF1L4-BGRSLV05-31_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2511					GRCh38	V40	U2AF1L4-BGRSLV05-31_S53_L002_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1L4-BGRSLV05-31_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10737
U2AF1L4-BGRSLV05-31_S53_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2511	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28879
U2AF1L4-BGRSLV05-32_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2512	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8613
U2AF1L4-BGRSLV05-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1L4-BGRSLV05-32_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10478
U2AF1L4-BGRSLV05-32_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	10530
U2AF1L4-BGRSLV05-32_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	10582
U2AF1L4-BGRSLV05-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	10634
U2AF1L4-BGRSLV05-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32/Aligned.sortedByCoord.out.bam		ENCORE2	10686
U2AF1L4-BGRSLV05-32_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2512					GRCh38	V40	U2AF1L4-BGRSLV05-32_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,U2AF1L4-BGRSLV05-32_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10738
U2AF1L4-BGRSLV05-32_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2512	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28880