DZIP3 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-59	BG293LV06-60
idx	0	0
TRCN#_or_BGC#	TRCN0000034247	TRCN0000034247
shRNA_or_gRNA_sequence	CCGGCGATTTGTAGTTACCTAGATTCTCGAGAATCTAGGTAACTACAAATCGTTTTTG	CCGGCGATTTGTAGTTACCTAGATTCTCGAGAATCTAGGTAACTACAAATCGTTTTTG
PAM
Name	DZIP3	DZIP3
Sample_ID	BG293LV06-59	BG293LV06-60
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	DZIP3	DZIP3
qPCR_result	58.6	53.0
Ave_qPCR	55.8
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	12194	12195

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-59	BG293LV06-60
Sample_ID	BG293LV06-59	BG293LV06-60
Sample Name
Sample Name	DZIP3-BG293LV06-59	DZIP3-BG293LV06-60
RBP	DZIP3	DZIP3
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13496	13497

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-59	BG293LV06-60
Sample #	61	62
Sample Name	DZIP3-BG293LV06-59	DZIP3-BG293LV06-60
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	282	277
Peak_Molarity	90.20	87.90
libSampleQC_DNA_Well	DNA_Library_set71/set1/E8.png	DNA_Library_set71/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set71/set1/E8.png	RNA_Library_set71/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-59	BG293LV06-60
RBP	DZIP3	DZIP3
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4486	4487

Sequencing Information

	BG293LV06-59	BG293LV06-60
Sample_ID	BG293LV06-59	BG293LV06-60
Sample Name	DZIP3-BG293LV06-59	DZIP3-BG293LV06-60
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	38,073,953	42,200,153
total_aligned_reads	35,255,045	38,958,213
unique_aligned_reads	32,998,487	36,437,358
percent_uniqueAligned	0.86669	0.86344
correlation_replicates	0.992183	0.992183
spikein_reads	55,534	59,190
percent_spikeins	0.00146	0.00140
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3055	3056

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-BG293LV06-59_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3055	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29319
DZIP3-BG293LV06-59_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3055	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29383
DZIP3-BG293LV06-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3055					GRCh38	V40	DZIP3-BG293LV06-59_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV06-59_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29448
DZIP3-BG293LV06-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3055					GRCh38	V40	DZIP3-BG293LV06-59_Aligned.sortedByCoord.out.bam		ENCORE2	29512
DZIP3-BG293LV06-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3055					GRCh38	V40	DZIP3-BG293LV06-59_Aligned.sortedByCoord.out.bam		ENCORE2	29576
DZIP3-BG293LV06-59_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3055					GRCh38	V40	DZIP3-BG293LV06-59_Aligned.sortedByCoord.out.bam		ENCORE2	29640
DZIP3-BG293LV06-59_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3055					GRCh38	V40	DZIP3-BG293LV06-59_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV06-59_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29704
DZIP3-BG293LV06-60_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3056	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29320
DZIP3-BG293LV06-60_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3056	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29384
DZIP3-BG293LV06-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3056					GRCh38	V40	DZIP3-BG293LV06-60_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV06-60_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29449
DZIP3-BG293LV06-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3056					GRCh38	V40	DZIP3-BG293LV06-60_Aligned.sortedByCoord.out.bam		ENCORE2	29513
DZIP3-BG293LV06-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3056					GRCh38	V40	DZIP3-BG293LV06-60_Aligned.sortedByCoord.out.bam		ENCORE2	29577
DZIP3-BG293LV06-60_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3056					GRCh38	V40	DZIP3-BG293LV06-60_Aligned.sortedByCoord.out.bam		ENCORE2	29641
DZIP3-BG293LV06-60_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3056					GRCh38	V40	DZIP3-BG293LV06-60_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV06-60_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29705