TRIP4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-47	BGRSLV02-48
idx	0	0
TRCN#_or_BGC#	TRCN0000022135	TRCN0000022135
shRNA_or_gRNA_sequence	CCGGGCAGAGTATCATAGCAGACTACTCGAGTAGTCTGCTATGATACTCTGCTTTTT	CCGGGCAGAGTATCATAGCAGACTACTCGAGTAGTCTGCTATGATACTCTGCTTTTT
PAM
Name	TRIP4	TRIP4
Sample_ID	BGRSLV02-47	BGRSLV02-48
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	TRIP4	TRIP4
qPCR_result	83.8	81.4
Ave_qPCR	82.6
RT-qPCR_primer-F	ctgggctgtgtggacctaat
RT-qPCR_primer-R	cctgaggatttttgcagatga
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	8284	8285

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-47	BGRSLV02-48
Sample_ID	BGRSLV02-47	BGRSLV02-48
Sample Name
Sample Name	TRIP4-BGRSLV02-47	TRIP4-BGRSLV02-48
RBP	TRIP4	TRIP4
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	11332	11333

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-47	BGRSLV02-48
Sample #	35	36
Sample Name	TRIP4-BGRSLV02-47	TRIP4-BGRSLV02-48
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	310	303
Peak_Molarity	56.60	53.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/C11.png	DNA_Library_set57/set1/D11.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set57/set1/C5.png	RNA_Library_set57/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-47	BGRSLV02-48
RBP	TRIP4	TRIP4
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3496	3497

Sequencing Information

	BGRSLV02-47	BGRSLV02-48
Sample_ID	BGRSLV02-47	BGRSLV02-48
Sample Name	TRIP4-BGRSLV02-47	TRIP4-BGRSLV02-48
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	59,344,089	45,551,280
total_aligned_reads	55,078,703	42,136,371
unique_aligned_reads	51,412,312	39,174,624
percent_uniqueAligned	0.86634	0.86001
correlation_replicates	0.996620	0.996620
spikein_reads	34,858	35,564
percent_spikeins	0.00059	0.00078
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2367	2368

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
TRIP4-BGRSLV02-47_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2367	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8232
TRIP4-BGRSLV02-47_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2367	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8278
TRIP4-BGRSLV02-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIP4-BGRSLV02-47_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11521
TRIP4-BGRSLV02-47_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47/Aligned.sortedByCoord.out.bam		ENCORE2	11567
TRIP4-BGRSLV02-47_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47/Aligned.sortedByCoord.out.bam		ENCORE2	11613
TRIP4-BGRSLV02-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47/Aligned.sortedByCoord.out.bam		ENCORE2	11659
TRIP4-BGRSLV02-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47/Aligned.sortedByCoord.out.bam		ENCORE2	11705
TRIP4-BGRSLV02-47_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2367					GRCh38	V40	TRIP4-BGRSLV02-47_S123_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIP4-BGRSLV02-47_S123_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11751
TRIP4-BGRSLV02-48_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2368	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8233
TRIP4-BGRSLV02-48_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2368	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8279
TRIP4-BGRSLV02-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIP4-BGRSLV02-48_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11522
TRIP4-BGRSLV02-48_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48/Aligned.sortedByCoord.out.bam		ENCORE2	11568
TRIP4-BGRSLV02-48_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48/Aligned.sortedByCoord.out.bam		ENCORE2	11614
TRIP4-BGRSLV02-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48/Aligned.sortedByCoord.out.bam		ENCORE2	11660
TRIP4-BGRSLV02-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48/Aligned.sortedByCoord.out.bam		ENCORE2	11706
TRIP4-BGRSLV02-48_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2368					GRCh38	V40	TRIP4-BGRSLV02-48_S124_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIP4-BGRSLV02-48_S124_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11752