TRIM55 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-101	BGRSDLV04-102
idx	0	0
TRCN#_or_BGC#	TRCN0000034010	TRCN0000034010
shRNA_or_gRNA_sequence	CCGGGCTTTGTGAGAAGTTTGATTACTCGAGTAATCAAACTTCTCACAAAGCTTTTTG	CCGGGCTTTGTGAGAAGTTTGATTACTCGAGTAATCAAACTTCTCACAAAGCTTTTTG
PAM
Name	TRIM55	TRIM55
Sample_ID	BGRSDLV04-101	BGRSDLV04-102
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	TRIM55	TRIM55
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9465	9466

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-101	BGRSDLV04-102
Sample_ID	BGRSDLV04-101	BGRSDLV04-102
Sample Name
Sample Name	TRIM55-BGRSDLV04-101	TRIM55-BGRSDLV04-102
RBP	TRIM55	TRIM55
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12702	12703

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-101	BGRSDLV04-102
Sample #	57	58
Sample Name	TRIM55-BGRSDLV04-101	TRIM55-BGRSDLV04-102
Sample_Name_Alias
Index Well Position	A08	B08
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	289	287
Peak_Molarity	76.80	52.20
libSampleQC_DNA_Well	DNA_Library_set68/set1/A8.png	DNA_Library_set68/set1/B8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/A8.png	RNA_Library_set68/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-101	BGRSDLV04-102
RBP	TRIM55	TRIM55
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	4130	4131

Sequencing Information

	BGRSDLV04-101	BGRSDLV04-102
Sample_ID	BGRSDLV04-101	BGRSDLV04-102
Sample Name	TRIM55-BGRSDLV04-101	TRIM55-BGRSDLV04-102
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	58,284,220	40,710,649
total_aligned_reads	53,110,373	36,368,016
unique_aligned_reads	50,041,516	34,091,245
percent_uniqueAligned	0.85858	0.83740
correlation_replicates	0.966576	0.966576
spikein_reads	15,906	6,842
percent_spikeins	0.00027	0.00017
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2893	2894

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
TRIM55-BGRSDLV04-101_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2893	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	27662
TRIM55-BGRSDLV04-101_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2893	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	27726
TRIM55-BGRSDLV04-101_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2893					GRCh38	V40	TRIM55-BGRSDLV04-101_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-101_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27790
TRIM55-BGRSDLV04-101_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	2893					GRCh38	V40	TRIM55-BGRSDLV04-101/Aligned.sortedByCoord.out.bam		ENCORE2	27854
TRIM55-BGRSDLV04-101_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	2893					GRCh38	V40	TRIM55-BGRSDLV04-101/Aligned.sortedByCoord.out.bam		ENCORE2	27918
TRIM55-BGRSDLV04-101_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	2893					GRCh38	V40	TRIM55-BGRSDLV04-101/Aligned.sortedByCoord.out.bam		ENCORE2	27982
TRIM55-BGRSDLV04-101_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	2893					GRCh38	V40	TRIM55-BGRSDLV04-101/Aligned.sortedByCoord.out.bam		ENCORE2	28046
TRIM55-BGRSDLV04-101_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2893					GRCh38	V40	TRIM55-BGRSDLV04-101_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-101_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28110
TRIM55-BGRSDLV04-102_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2894	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	27663
TRIM55-BGRSDLV04-102_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2894	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	27727
TRIM55-BGRSDLV04-102_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2894					GRCh38	V40	TRIM55-BGRSDLV04-102_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-102_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27791
TRIM55-BGRSDLV04-102_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	2894					GRCh38	V40	TRIM55-BGRSDLV04-102/Aligned.sortedByCoord.out.bam		ENCORE2	27855
TRIM55-BGRSDLV04-102_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	2894					GRCh38	V40	TRIM55-BGRSDLV04-102/Aligned.sortedByCoord.out.bam		ENCORE2	27919
TRIM55-BGRSDLV04-102_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	2894					GRCh38	V40	TRIM55-BGRSDLV04-102/Aligned.sortedByCoord.out.bam		ENCORE2	27983
TRIM55-BGRSDLV04-102_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	2894					GRCh38	V40	TRIM55-BGRSDLV04-102/Aligned.sortedByCoord.out.bam		ENCORE2	28047
TRIM55-BGRSDLV04-102_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2894					GRCh38	V40	TRIM55-BGRSDLV04-102_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-102_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28111