ZNF473 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-89	BGRSDLV02-90
idx	0	0
TRCN#_or_BGC#	TRCN0000234628	TRCN0000234628
shRNA_or_gRNA_sequence	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG
PAM
Name	ZNF473	ZNF473
Sample_ID	BGRSDLV02-89	BGRSDLV02-90
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZNF473	ZNF473
qPCR_result	75.0	64.6
Ave_qPCR	69.8
RT-qPCR_primer-F	aattgccaggacctcttcct
RT-qPCR_primer-R	aggctccagatcttcactgc
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	9300	9301

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-89	BGRSDLV02-90
Sample_ID	BGRSDLV02-89	BGRSDLV02-90
Sample Name
Sample Name	ZNF473-BGRSDLV02-89	ZNF473-BGRSDLV02-90
RBP	ZNF473	ZNF473
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12392	12393

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-89	BGRSDLV02-90
Sample #	73	74
Sample Name	ZNF473-BGRSDLV02-89	ZNF473-BGRSDLV02-90
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	326	308
Peak_Molarity	58.10	59.40
libSampleQC_DNA_Well	DNA_Library_set65/set1/A10.png	DNA_Library_set65/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/A10.png	RNA_Library_set65/set1/B10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-89	BGRSDLV02-90
RBP	ZNF473	ZNF473
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3994	3995

Sequencing Information

	BGRSDLV02-89	BGRSDLV02-90
Sample_ID	BGRSDLV02-89	BGRSDLV02-90
Sample Name	ZNF473-BGRSDLV02-89	ZNF473-BGRSDLV02-90
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	39,804,657	52,878,896
total_aligned_reads	37,304,432	50,188,622
unique_aligned_reads	34,932,241	47,275,547
percent_uniqueAligned	0.87759	0.89403
correlation_replicates	0.990685	0.990685
spikein_reads	27,688	7,736
percent_spikeins	0.00070	0.00015
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2741	2742

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
ZNF473-BGRSDLV02-89_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2741	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8810
ZNF473-BGRSDLV02-89_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2741	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8886
ZNF473-BGRSDLV02-89_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-89_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9375
ZNF473-BGRSDLV02-89_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89/Aligned.sortedByCoord.out.bam		ENCORE2	9451
ZNF473-BGRSDLV02-89_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89/Aligned.sortedByCoord.out.bam		ENCORE2	9527
ZNF473-BGRSDLV02-89_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89/Aligned.sortedByCoord.out.bam		ENCORE2	9603
ZNF473-BGRSDLV02-89_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89/Aligned.sortedByCoord.out.bam		ENCORE2	9679
ZNF473-BGRSDLV02-89_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2741					GRCh38	V40	ZNF473-BGRSDLV02-89_S73_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-89_S73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9755
ZNF473-BGRSDLV02-90_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2742	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8811
ZNF473-BGRSDLV02-90_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2742	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8887
ZNF473-BGRSDLV02-90_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-90_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9376
ZNF473-BGRSDLV02-90_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90/Aligned.sortedByCoord.out.bam		ENCORE2	9452
ZNF473-BGRSDLV02-90_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90/Aligned.sortedByCoord.out.bam		ENCORE2	9528
ZNF473-BGRSDLV02-90_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90/Aligned.sortedByCoord.out.bam		ENCORE2	9604
ZNF473-BGRSDLV02-90_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90/Aligned.sortedByCoord.out.bam		ENCORE2	9680
ZNF473-BGRSDLV02-90_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2742					GRCh38	V40	ZNF473-BGRSDLV02-90_S74_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-90_S74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9756