DTX3L RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV03-21	BGRSLV03-22
idx	0	0
TRCN#_or_BGC#	TRCN0000073210	TRCN0000073210
shRNA_or_gRNA_sequence	CCGGCCGATGGACATTGATAGCGATCTCGAGATCGCTATCAATGTCCATCGGTTTTTG	CCGGCCGATGGACATTGATAGCGATCTCGAGATCGCTATCAATGTCCATCGGTTTTTG
PAM
Name	DTX3L	DTX3L
Sample_ID	BGRSLV03-21	BGRSLV03-22
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	DTX3L	DTX3L
qPCR_result	88.8	59.8
Ave_qPCR	74.3
RT-qPCR_primer-F	gtggggtactctcgcgtatt
RT-qPCR_primer-R	ggctttcagctcctctttga
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	10379	10380

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-21	BGRSLV03-22
Sample_ID	BGRSLV03-21	BGRSLV03-22
Sample Name
Sample Name	DTX3L-BGRSLV03-21	DTX3L-BGRSLV03-22
RBP	DTX3L	DTX3L
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	11386	11387

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-21	BGRSLV03-22
Sample #	17	18
Sample Name	DTX3L-BGRSLV03-21	DTX3L-BGRSLV03-22
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	300	284
Peak_Molarity	47.10	59.70
libSampleQC_DNA_Well	DNA_Library_set58/set1/A9.png	DNA_Library_set58/set1/B9.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set58/set1/A3.png	RNA_Library_set58/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-21	BGRSLV03-22
RBP	DTX3L	DTX3L
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3524	3525

Sequencing Information

	BGRSLV03-21	BGRSLV03-22
Sample_ID	BGRSLV03-21	BGRSLV03-22
Sample Name	DTX3L-BGRSLV03-21	DTX3L-BGRSLV03-22
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	53,536,983	32,101,440
total_aligned_reads	39,350,444	20,448,168
unique_aligned_reads	36,586,566	18,972,446
percent_uniqueAligned	0.68339	0.59102
correlation_replicates	0.972379	0.972379
spikein_reads	351,768	183,716
percent_spikeins	0.00657	0.00572
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2395	2396

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
DTX3L-BGRSLV03-21_S151_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2395	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8140
DTX3L-BGRSLV03-21_S151_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2395	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8182
DTX3L-BGRSLV03-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21_S151_L004_R1_001.filtered.trimmed.paired.fastq.gz,DTX3L-BGRSLV03-21_S151_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11261
DTX3L-BGRSLV03-21_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21/Aligned.sortedByCoord.out.bam		ENCORE2	11303
DTX3L-BGRSLV03-21_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21/Aligned.sortedByCoord.out.bam		ENCORE2	11345
DTX3L-BGRSLV03-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21/Aligned.sortedByCoord.out.bam		ENCORE2	11387
DTX3L-BGRSLV03-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21/Aligned.sortedByCoord.out.bam		ENCORE2	11429
DTX3L-BGRSLV03-21_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2395					GRCh38	V40	DTX3L-BGRSLV03-21_S151_L004_R1_001.filtered.trimmed.paired.fastq.gz,DTX3L-BGRSLV03-21_S151_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11471
DTX3L-BGRSLV03-22_S152_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2396	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8141
DTX3L-BGRSLV03-22_S152_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2396	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8183
DTX3L-BGRSLV03-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22_S152_L004_R1_001.filtered.trimmed.paired.fastq.gz,DTX3L-BGRSLV03-22_S152_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11262
DTX3L-BGRSLV03-22_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22/Aligned.sortedByCoord.out.bam		ENCORE2	11304
DTX3L-BGRSLV03-22_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22/Aligned.sortedByCoord.out.bam		ENCORE2	11346
DTX3L-BGRSLV03-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22/Aligned.sortedByCoord.out.bam		ENCORE2	11388
DTX3L-BGRSLV03-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22/Aligned.sortedByCoord.out.bam		ENCORE2	11430
DTX3L-BGRSLV03-22_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2396					GRCh38	V40	DTX3L-BGRSLV03-22_S152_L004_R1_001.filtered.trimmed.paired.fastq.gz,DTX3L-BGRSLV03-22_S152_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11472