DZIP3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-55	BGRSLV02-56
idx	0	0
TRCN#_or_BGC#	TRCN0000034244	TRCN0000034244
shRNA_or_gRNA_sequence	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG
PAM
Name	DZIP3	DZIP3
Sample_ID	BGRSLV02-55	BGRSLV02-56
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	DZIP3	DZIP3
qPCR_result	64.7	53.1
Ave_qPCR	58.9
RT-qPCR_primer-F	ccttgagtaccttgcctcca
RT-qPCR_primer-R	actgcaggcatttgaggaac
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	8292	8293

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-55	BGRSLV02-56
Sample_ID	BGRSLV02-55	BGRSLV02-56
Sample Name
Sample Name	DZIP3-BGRSLV02-55	DZIP3-BGRSLV02-56
RBP	DZIP3	DZIP3
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	11338	11339

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-55	BGRSLV02-56
Sample #	41	42
Sample Name	DZIP3-BGRSLV02-55	DZIP3-BGRSLV02-56
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	290	298
Peak_Molarity	39.50	49.70
libSampleQC_DNA_Well	DNA_Library_set57/set1/A12.png	DNA_Library_set57/set1/B12.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set57/set1/A6.png	RNA_Library_set57/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-55	BGRSLV02-56
RBP	DZIP3	DZIP3
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3502	3503

Sequencing Information

	BGRSLV02-55	BGRSLV02-56
Sample_ID	BGRSLV02-55	BGRSLV02-56
Sample Name	DZIP3-BGRSLV02-55	DZIP3-BGRSLV02-56
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	61,623,437	31,600,776
total_aligned_reads	56,472,493	28,901,038
unique_aligned_reads	52,853,458	27,086,834
percent_uniqueAligned	0.85768	0.85716
correlation_replicates	0.994766	0.994766
spikein_reads	41,152	14,946
percent_spikeins	0.00067	0.00047
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2373	2374

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
DZIP3-BGRSLV02-55_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2373	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8216
DZIP3-BGRSLV02-55_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2373	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8262
DZIP3-BGRSLV02-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSLV02-55_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11505
DZIP3-BGRSLV02-55_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55/Aligned.sortedByCoord.out.bam		ENCORE2	11551
DZIP3-BGRSLV02-55_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55/Aligned.sortedByCoord.out.bam		ENCORE2	11597
DZIP3-BGRSLV02-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55/Aligned.sortedByCoord.out.bam		ENCORE2	11643
DZIP3-BGRSLV02-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55/Aligned.sortedByCoord.out.bam		ENCORE2	11689
DZIP3-BGRSLV02-55_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2373					GRCh38	V40	DZIP3-BGRSLV02-55_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSLV02-55_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11735
DZIP3-BGRSLV02-56_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2374	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8217
DZIP3-BGRSLV02-56_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2374	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8263
DZIP3-BGRSLV02-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSLV02-56_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11506
DZIP3-BGRSLV02-56_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56/Aligned.sortedByCoord.out.bam		ENCORE2	11552
DZIP3-BGRSLV02-56_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56/Aligned.sortedByCoord.out.bam		ENCORE2	11598
DZIP3-BGRSLV02-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56/Aligned.sortedByCoord.out.bam		ENCORE2	11644
DZIP3-BGRSLV02-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56/Aligned.sortedByCoord.out.bam		ENCORE2	11690
DZIP3-BGRSLV02-56_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2374					GRCh38	V40	DZIP3-BGRSLV02-56_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSLV02-56_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11736