DZIP3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-15dox	BGRSDLV04-16dox
idx	0	0
TRCN#_or_BGC#	TRCN0000034244	TRCN0000034244
shRNA_or_gRNA_sequence	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG	CCGGCGGAAATTGAAGGATGCTTATCTCGAGATAAGCATCCTTCAATTTCCGTTTTTG
PAM
Name	DZIP3	DZIP3
Sample_ID	BGRSDLV04-15dox	BGRSDLV04-16dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	DZIP3	DZIP3
qPCR_result	59.10297	59.46737
Ave_qPCR	59.28517
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	9379	9380

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-15dox	BGRSDLV04-16dox
Sample_ID	BGRSDLV04-15dox	BGRSDLV04-16dox
Sample Name
Sample Name	DZIP3-BGRSDLV04-15dox	DZIP3-BGRSDLV04-16dox
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	12660	12661

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-15dox	BGRSDLV04-16dox
Sample #	15	16
Sample Name	DZIP3-BGRSDLV04-15dox	DZIP3-BGRSDLV04-16dox
Sample_Name_Alias
Index Well Position	G02	H02
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	293	287
Peak_Molarity	29.60	30.60
libSampleQC_DNA_Well	DNA_Library_set68/set1/G2.png	DNA_Library_set68/set1/H2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G2.png	RNA_Library_set68/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-15dox	BGRSDLV04-16dox
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	4088	4089

Sequencing Information

	BGRSDLV04-15dox	BGRSDLV04-16dox
Sample_ID	BGRSDLV04-15dox	BGRSDLV04-16dox
Sample Name	DZIP3-BGRSDLV04-15dox	DZIP3-BGRSDLV04-16dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	30,028,954	34,587,401
total_aligned_reads	25,344,840	29,128,270
unique_aligned_reads	23,734,685	27,249,452
percent_uniqueAligned	0.79039	0.78784
correlation_replicates	0.993971	0.993971
spikein_reads	2,208	9,160
percent_spikeins	0.00007	0.00026
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2851	2852

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-BGRSDLV04-15dox_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2851	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27639
DZIP3-BGRSDLV04-15dox_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2851	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27703
DZIP3-BGRSDLV04-15dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-15dox_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27767
DZIP3-BGRSDLV04-15dox_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	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox/Aligned.sortedByCoord.out.bam		ENCORE2	27831
DZIP3-BGRSDLV04-15dox_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	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox/Aligned.sortedByCoord.out.bam		ENCORE2	27895
DZIP3-BGRSDLV04-15dox_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	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox/Aligned.sortedByCoord.out.bam		ENCORE2	27959
DZIP3-BGRSDLV04-15dox_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	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox/Aligned.sortedByCoord.out.bam		ENCORE2	28023
DZIP3-BGRSDLV04-15dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2851					GRCh38	V40	DZIP3-BGRSDLV04-15dox_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-15dox_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28087
DZIP3-BGRSDLV04-16dox_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2852	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27640
DZIP3-BGRSDLV04-16dox_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2852	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27704
DZIP3-BGRSDLV04-16dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-16dox_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27768
DZIP3-BGRSDLV04-16dox_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	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox/Aligned.sortedByCoord.out.bam		ENCORE2	27832
DZIP3-BGRSDLV04-16dox_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	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox/Aligned.sortedByCoord.out.bam		ENCORE2	27896
DZIP3-BGRSDLV04-16dox_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	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox/Aligned.sortedByCoord.out.bam		ENCORE2	27960
DZIP3-BGRSDLV04-16dox_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	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox/Aligned.sortedByCoord.out.bam		ENCORE2	28024
DZIP3-BGRSDLV04-16dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2852					GRCh38	V40	DZIP3-BGRSDLV04-16dox_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz,DZIP3-BGRSDLV04-16dox_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28088