ZNF473 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-91dox	BGRSDLV02-92dox
idx	0	0
TRCN#_or_BGC#	TRCN0000234628	TRCN0000234628
shRNA_or_gRNA_sequence	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG
PAM
Name	ZNF473	ZNF473
Sample_ID	BGRSDLV02-91dox	BGRSDLV02-92dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZNF473	ZNF473
qPCR_result	78.4	81.1
Ave_qPCR	79.8
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	9302	9303

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-91dox	BGRSDLV02-92dox
Sample_ID	BGRSDLV02-91dox	BGRSDLV02-92dox
Sample Name
Sample Name	ZNF473-BGRSDLV02-91dox	ZNF473-BGRSDLV02-92dox
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	12394	12395

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-91dox	BGRSDLV02-92dox
Sample #	75	76
Sample Name	ZNF473-BGRSDLV02-91dox	ZNF473-BGRSDLV02-92dox
Sample_Name_Alias
Index Well Position	C10	D10
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	304	292
Peak_Molarity	75.30	74.90
libSampleQC_DNA_Well	DNA_Library_set65/set1/C10.png	DNA_Library_set65/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C10.png	RNA_Library_set65/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-91dox	BGRSDLV02-92dox
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	3996	3997

Sequencing Information

	BGRSDLV02-91dox	BGRSDLV02-92dox
Sample_ID	BGRSDLV02-91dox	BGRSDLV02-92dox
Sample Name	ZNF473-BGRSDLV02-91dox	ZNF473-BGRSDLV02-92dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	58,729,234	26,311,936
total_aligned_reads	55,546,419	23,063,207
unique_aligned_reads	51,976,800	21,637,303
percent_uniqueAligned	0.88502	0.82234
correlation_replicates	0.984394	0.984394
spikein_reads	10,462	3,172
percent_spikeins	0.00018	0.00012
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2743	2744

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-BGRSDLV02-91dox_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2743	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8812
ZNF473-BGRSDLV02-91dox_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2743	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8888
ZNF473-BGRSDLV02-91dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-91dox_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9377
ZNF473-BGRSDLV02-91dox_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	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	9453
ZNF473-BGRSDLV02-91dox_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	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	9529
ZNF473-BGRSDLV02-91dox_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	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	9605
ZNF473-BGRSDLV02-91dox_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	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox/Aligned.sortedByCoord.out.bam		ENCORE2	9681
ZNF473-BGRSDLV02-91dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2743					GRCh38	V40	ZNF473-BGRSDLV02-91dox_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-91dox_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9757
ZNF473-BGRSDLV02-92dox_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2744	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8813
ZNF473-BGRSDLV02-92dox_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2744	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8889
ZNF473-BGRSDLV02-92dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-92dox_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9378
ZNF473-BGRSDLV02-92dox_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	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	9454
ZNF473-BGRSDLV02-92dox_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	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	9530
ZNF473-BGRSDLV02-92dox_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	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	9606
ZNF473-BGRSDLV02-92dox_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	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox/Aligned.sortedByCoord.out.bam		ENCORE2	9682
ZNF473-BGRSDLV02-92dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2744					GRCh38	V40	ZNF473-BGRSDLV02-92dox_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDLV02-92dox_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9758