TRIM28 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-43	BGRSLV06-44
idx	0	0
TRCN#_or_BGC#	TRCN0000199141	TRCN0000199141
shRNA_or_gRNA_sequence	CCGGCTCTGTTCTCTGTCCTGTCACCTCGAGGTGACAGGACAGAGAACAGAGTTTTTTG	CCGGCTCTGTTCTCTGTCCTGTCACCTCGAGGTGACAGGACAGAGAACAGAGTTTTTTG
PAM
Name	TRIM28	TRIM28
Sample_ID	BGRSLV06-43	BGRSLV06-44
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	TRIM28	TRIM28
qPCR_result	67.1	59.5
Ave_qPCR	63.3
RT-qPCR_primer-F	tgtttccacctggactgtca
RT-qPCR_primer-R	catcctcctccttcaggtca
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	8570	8571

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-43	BGRSLV06-44
Sample_ID	BGRSLV06-43	BGRSLV06-44
Sample Name
Sample Name	TRIM28-BGRSLV06-43	TRIM28-BGRSLV06-44
RBP	TRIM28	TRIM28
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	11706	11707

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-43	BGRSLV06-44
Sample #	89	90
Sample Name	TRIM28-BGRSLV06-43	TRIM28-BGRSLV06-44
Sample_Name_Alias
Index Well Position	A12	B12
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	300	295
Peak_Molarity	71.90	76.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E12.png	DNA_Library_set60-62/set1/F12.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_set60-62/set1/A12.png	RNA_Library_set60-62/set1/B12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-43	BGRSLV06-44
RBP	TRIM28	TRIM28
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3676	3677

Sequencing Information

	BGRSLV06-43	BGRSLV06-44
Sample_ID	BGRSLV06-43	BGRSLV06-44
Sample Name	TRIM28-BGRSLV06-43	TRIM28-BGRSLV06-44
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	22,455,790	51,705,089
total_aligned_reads	16,306,806	40,855,490
unique_aligned_reads	15,358,861	38,540,718
percent_uniqueAligned	0.68396	0.74540
correlation_replicates	0.978697	0.978697
spikein_reads	15,512	13,404
percent_spikeins	0.00069	0.00026
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2547	2548

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
TRIM28-BGRSLV06-43_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2547	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8604
TRIM28-BGRSLV06-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2547					GRCh38	V40	TRIM28-BGRSLV06-43_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM28-BGRSLV06-43_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10469
TRIM28-BGRSLV06-43_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	2547					GRCh38	V40	TRIM28-BGRSLV06-43/Aligned.sortedByCoord.out.bam		ENCORE2	10521
TRIM28-BGRSLV06-43_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	2547					GRCh38	V40	TRIM28-BGRSLV06-43/Aligned.sortedByCoord.out.bam		ENCORE2	10573
TRIM28-BGRSLV06-43_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	2547					GRCh38	V40	TRIM28-BGRSLV06-43/Aligned.sortedByCoord.out.bam		ENCORE2	10625
TRIM28-BGRSLV06-43_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	2547					GRCh38	V40	TRIM28-BGRSLV06-43/Aligned.sortedByCoord.out.bam		ENCORE2	10677
TRIM28-BGRSLV06-43_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2547					GRCh38	V40	TRIM28-BGRSLV06-43_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM28-BGRSLV06-43_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10729
TRIM28-BGRSLV06-43_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2547	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28871
TRIM28-BGRSLV06-44_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2548	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8605
TRIM28-BGRSLV06-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2548					GRCh38	V40	TRIM28-BGRSLV06-44_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM28-BGRSLV06-44_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10470
TRIM28-BGRSLV06-44_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	2548					GRCh38	V40	TRIM28-BGRSLV06-44/Aligned.sortedByCoord.out.bam		ENCORE2	10522
TRIM28-BGRSLV06-44_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	2548					GRCh38	V40	TRIM28-BGRSLV06-44/Aligned.sortedByCoord.out.bam		ENCORE2	10574
TRIM28-BGRSLV06-44_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	2548					GRCh38	V40	TRIM28-BGRSLV06-44/Aligned.sortedByCoord.out.bam		ENCORE2	10626
TRIM28-BGRSLV06-44_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	2548					GRCh38	V40	TRIM28-BGRSLV06-44/Aligned.sortedByCoord.out.bam		ENCORE2	10678
TRIM28-BGRSLV06-44_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2548					GRCh38	V40	TRIM28-BGRSLV06-44_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,TRIM28-BGRSLV06-44_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10730
TRIM28-BGRSLV06-44_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2548	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28872