TRIM55 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-99dox	BGRSDLV04-100dox
idx	0	0
TRCN#_or_BGC#	TRCN0000034009	TRCN0000034009
shRNA_or_gRNA_sequence	CCGGGCTACTTCTCAGGAGTTAGTACTCGAGTACTAACTCCTGAGAAGTAGCTTTTTG	CCGGGCTACTTCTCAGGAGTTAGTACTCGAGTACTAACTCCTGAGAAGTAGCTTTTTG
PAM
Name	TRIM55	TRIM55
Sample_ID	BGRSDLV04-99dox	BGRSDLV04-100dox
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	9463	9464

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-99dox	BGRSDLV04-100dox
Sample_ID	BGRSDLV04-99dox	BGRSDLV04-100dox
Sample Name
Sample Name	TRIM55-BGRSDLV04-99dox	TRIM55-BGRSDLV04-100dox
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	12700	12701

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-99dox	BGRSDLV04-100dox
Sample #	55	56
Sample Name	TRIM55-BGRSDLV04-99dox	TRIM55-BGRSDLV04-100dox
Sample_Name_Alias
Index Well Position	G07	H07
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	293	295
Peak_Molarity	65.90	62.30
libSampleQC_DNA_Well	DNA_Library_set68/set1/G7.png	DNA_Library_set68/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G7.png	RNA_Library_set68/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-99dox	BGRSDLV04-100dox
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	4128	4129

Sequencing Information

	BGRSDLV04-99dox	BGRSDLV04-100dox
Sample_ID	BGRSDLV04-99dox	BGRSDLV04-100dox
Sample Name	TRIM55-BGRSDLV04-99dox	TRIM55-BGRSDLV04-100dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	37,663,552	48,639,333
total_aligned_reads	34,118,914	44,529,716
unique_aligned_reads	32,151,270	41,974,162
percent_uniqueAligned	0.85364	0.86297
correlation_replicates	0.999191	0.999191
spikein_reads	2,280	10,988
percent_spikeins	0.00006	0.00023
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2891	2892

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-BGRSDLV04-99dox_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2891	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27668
TRIM55-BGRSDLV04-99dox_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2891	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27732
TRIM55-BGRSDLV04-99dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-99dox_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27796
TRIM55-BGRSDLV04-99dox_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	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox/Aligned.sortedByCoord.out.bam		ENCORE2	27860
TRIM55-BGRSDLV04-99dox_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	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox/Aligned.sortedByCoord.out.bam		ENCORE2	27924
TRIM55-BGRSDLV04-99dox_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	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox/Aligned.sortedByCoord.out.bam		ENCORE2	27988
TRIM55-BGRSDLV04-99dox_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	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox/Aligned.sortedByCoord.out.bam		ENCORE2	28052
TRIM55-BGRSDLV04-99dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2891					GRCh38	V40	TRIM55-BGRSDLV04-99dox_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-99dox_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28116
TRIM55-BGRSDLV04-100dox_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2892	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27661
TRIM55-BGRSDLV04-100dox_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2892	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27725
TRIM55-BGRSDLV04-100dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-100dox_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27789
TRIM55-BGRSDLV04-100dox_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	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox/Aligned.sortedByCoord.out.bam		ENCORE2	27853
TRIM55-BGRSDLV04-100dox_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	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox/Aligned.sortedByCoord.out.bam		ENCORE2	27917
TRIM55-BGRSDLV04-100dox_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	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox/Aligned.sortedByCoord.out.bam		ENCORE2	27981
TRIM55-BGRSDLV04-100dox_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	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox/Aligned.sortedByCoord.out.bam		ENCORE2	28045
TRIM55-BGRSDLV04-100dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2892					GRCh38	V40	TRIM55-BGRSDLV04-100dox_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz,TRIM55-BGRSDLV04-100dox_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28109