DZIP3 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-17	BG293LV05-18
idx	0	0
TRCN#_or_BGC#	TRCN0000034247	TRCN0000034247
shRNA_or_gRNA_sequence	CCGGCGATTTGTAGTTACCTAGATTCTCGAGAATCTAGGTAACTACAAATCGTTTTTG	CCGGCGATTTGTAGTTACCTAGATTCTCGAGAATCTAGGTAACTACAAATCGTTTTTG
PAM
Name	DZIP3	DZIP3
Sample_ID	BG293LV05-17	BG293LV05-18
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	DZIP3	DZIP3
qPCR_result	57	61.2
Ave_qPCR	59.1
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	9989	9990

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-17	BG293LV05-18
Sample_ID	BG293LV05-17	BG293LV05-18
Sample Name
Sample Name	DZIP3-BG293LV05-17	DZIP3-BG293LV05-18
RBP	DZIP3	DZIP3
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12842	12843

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-17	BG293LV05-18
Sample #	9	10
Sample Name	DZIP3-BG293LV05-17	DZIP3-BG293LV05-18
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	282	283
Peak_Molarity	67.80	97.20
libSampleQC_DNA_Well	DNA_Library_set69/set1/A2.png	DNA_Library_set69/set1/B2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set69/set1/A7.png	RNA_Library_set69/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-17	BG293LV05-18
RBP	DZIP3	DZIP3
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4190	4191

Sequencing Information

	BG293LV05-17	BG293LV05-18
Sample_ID	BG293LV05-17	BG293LV05-18
Sample Name	DZIP3-BG293LV05-17	DZIP3-BG293LV05-18
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	22,484,508	16,960,563
total_aligned_reads	18,698,593	13,548,707
unique_aligned_reads	17,405,712	12,597,314
percent_uniqueAligned	0.77412	0.74274
correlation_replicates	0.991752	0.991752
spikein_reads	5,696	1,814
percent_spikeins	0.00025	0.00011
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2909	2910

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-BG293LV05-17_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2909	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28497
DZIP3-BG293LV05-17_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2909	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28541
DZIP3-BG293LV05-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV05-17_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28585
DZIP3-BG293LV05-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	28629
DZIP3-BG293LV05-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	28673
DZIP3-BG293LV05-17_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	28717
DZIP3-BG293LV05-17_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17/Aligned.sortedByCoord.out.bam		ENCORE2	28761
DZIP3-BG293LV05-17_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2909					GRCh38	V40	DZIP3-BG293LV05-17_S141_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV05-17_S141_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28805
DZIP3-BG293LV05-18_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2910	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28498
DZIP3-BG293LV05-18_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2910	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28542
DZIP3-BG293LV05-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV05-18_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28586
DZIP3-BG293LV05-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	28630
DZIP3-BG293LV05-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	28674
DZIP3-BG293LV05-18_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	28718
DZIP3-BG293LV05-18_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18/Aligned.sortedByCoord.out.bam		ENCORE2	28762
DZIP3-BG293LV05-18_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2910					GRCh38	V40	DZIP3-BG293LV05-18_S142_L002_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BG293LV05-18_S142_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28806