TRIM2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-23	BGRSLV07-24
idx	0	0
TRCN#_or_BGC#	TRCN0000291872	TRCN0000291872
shRNA_or_gRNA_sequence	CCGGGTCAAGCAGAAAGCTGTGAAACTCGAGTTTCACAGCTTTCTGCTTGACTTTTTG	CCGGGTCAAGCAGAAAGCTGTGAAACTCGAGTTTCACAGCTTTCTGCTTGACTTTTTG
PAM
Name	TRIM2	TRIM2
Sample_ID	BGRSLV07-23	BGRSLV07-24
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	TRIM2	TRIM2
qPCR_result	58.8	51.4
Ave_qPCR	55.1
RT-qPCR_primer-F	acatcccagtggggacataa
RT-qPCR_primer-R	attgcggtccacagaaactc
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	8605	8606

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-23	BGRSLV07-24
Sample_ID	BGRSLV07-23	BGRSLV07-24
Sample Name
Sample Name	TRIM2-BGRSLV07-23	TRIM2-BGRSLV07-24
RBP	TRIM2	TRIM2
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	11850	11851

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-23	BGRSLV07-24
Sample #	31	32
Sample Name	TRIM2-BGRSLV07-23	TRIM2-BGRSLV07-24
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	284	280
Peak_Molarity	85.20	66.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G4.png	DNA_Library_set60-62/set4/H4.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set60-62/set2/G4.png	RNA_Library_set60-62/set2/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-23	BGRSLV07-24
RBP	TRIM2	TRIM2
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3714	3715

Sequencing Information

	BGRSLV07-23	BGRSLV07-24
Sample_ID	BGRSLV07-23	BGRSLV07-24
Sample Name	TRIM2-BGRSLV07-23	TRIM2-BGRSLV07-24
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	20,241,699	29,801,437
total_aligned_reads	17,013,003	24,821,460
unique_aligned_reads	15,933,123	23,308,536
percent_uniqueAligned	0.78714	0.78213
correlation_replicates	0.995926	0.995926
spikein_reads	16,522	36,690
percent_spikeins	0.00082	0.00123
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2585	2586

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
TRIM2-BGRSLV07-23_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2585	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7890
TRIM2-BGRSLV07-23_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2585	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7934
TRIM2-BGRSLV07-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIM2-BGRSLV07-23_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10195
TRIM2-BGRSLV07-23_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23/Aligned.sortedByCoord.out.bam		ENCORE2	10239
TRIM2-BGRSLV07-23_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23/Aligned.sortedByCoord.out.bam		ENCORE2	10283
TRIM2-BGRSLV07-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23/Aligned.sortedByCoord.out.bam		ENCORE2	10327
TRIM2-BGRSLV07-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23/Aligned.sortedByCoord.out.bam		ENCORE2	10371
TRIM2-BGRSLV07-23_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2585					GRCh38	V40	TRIM2-BGRSLV07-23_S31_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIM2-BGRSLV07-23_S31_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10415
TRIM2-BGRSLV07-24_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2586	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7891
TRIM2-BGRSLV07-24_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2586	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7935
TRIM2-BGRSLV07-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIM2-BGRSLV07-24_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10196
TRIM2-BGRSLV07-24_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24/Aligned.sortedByCoord.out.bam		ENCORE2	10240
TRIM2-BGRSLV07-24_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24/Aligned.sortedByCoord.out.bam		ENCORE2	10284
TRIM2-BGRSLV07-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24/Aligned.sortedByCoord.out.bam		ENCORE2	10328
TRIM2-BGRSLV07-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24/Aligned.sortedByCoord.out.bam		ENCORE2	10372
TRIM2-BGRSLV07-24_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2586					GRCh38	V40	TRIM2-BGRSLV07-24_S32_L003_R1_001.filtered.trimmed.paired.fastq.gz,TRIM2-BGRSLV07-24_S32_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10416