DZIP3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-13	BGRSDLV04-14
idx	0	0
TRCN#_or_BGC#	TRCN0000034244	TRCN0000034244
shRNA_or_gRNA_sequence	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG
PAM
Name	DZIP3	DZIP3
Sample_ID	BGRSDLV04-13	BGRSDLV04-14
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	DZIP3	DZIP3
qPCR_result	61.49127	63.61552
Ave_qPCR	62.553395
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	9377	9378

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-13	BGRSDLV04-14
Sample_ID	BGRSDLV04-13	BGRSDLV04-14
Sample Name
Sample Name	DZIP3-BGRSDLV04-13	DZIP3-BGRSDLV04-14
RBP	DZIP3	DZIP3
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12658	12659

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-13	BGRSDLV04-14
Sample #	13	14
Sample Name	DZIP3-BGRSDLV04-13	DZIP3-BGRSDLV04-14
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	288	292
Peak_Molarity	40.20	44.40
libSampleQC_DNA_Well	DNA_Library_set68/set1/E2.png	DNA_Library_set68/set1/F2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set68/set1/E2.png	RNA_Library_set68/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-13	BGRSDLV04-14
RBP	DZIP3	DZIP3
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4086	4087

Sequencing Information

	BGRSDLV04-13	BGRSDLV04-14
Sample_ID	BGRSDLV04-13	BGRSDLV04-14
Sample Name	DZIP3-BGRSDLV04-13	DZIP3-BGRSDLV04-14
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	39,361,369	30,595,330
total_aligned_reads	34,188,074	26,607,682
unique_aligned_reads	31,966,074	24,906,380
percent_uniqueAligned	0.81212	0.81406
correlation_replicates	0.998659	0.998659
spikein_reads	6,844	8,272
percent_spikeins	0.00017	0.00027
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2849	2850

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-BGRSDLV04-13_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2849	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27637
DZIP3-BGRSDLV04-13_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2849	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27701
DZIP3-BGRSDLV04-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-13_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27765
DZIP3-BGRSDLV04-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	27829
DZIP3-BGRSDLV04-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	27893
DZIP3-BGRSDLV04-13_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	27957
DZIP3-BGRSDLV04-13_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	28021
DZIP3-BGRSDLV04-13_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2849					GRCh38	V40	DZIP3-BGRSDLV04-13_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-13_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28085
DZIP3-BGRSDLV04-14_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2850	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27638
DZIP3-BGRSDLV04-14_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2850	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27702
DZIP3-BGRSDLV04-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-14_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27766
DZIP3-BGRSDLV04-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	27830
DZIP3-BGRSDLV04-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	27894
DZIP3-BGRSDLV04-14_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	27958
DZIP3-BGRSDLV04-14_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	28022
DZIP3-BGRSDLV04-14_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2850					GRCh38	V40	DZIP3-BGRSDLV04-14_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-14_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28086