ZNF473 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDTLV02-89tot	BGRSDTLV02-90tot
idx	0	0
TRCN#_or_BGC#	TRCN0000234628	TRCN0000234628
shRNA_or_gRNA_sequence	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG	CCGGCAAGGAGACTTTCAGCGATAACTCGAGTTATCGCTGAAAGTCTCCTTGTTTTTG
PAM
Name	ZNF473	ZNF473
Sample_ID	BGRSDTLV02-89tot	BGRSDTLV02-90tot
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	sample experiment in BGRSDLV02, Total-RNA	sample experiment in BGRSDLV02, Total-RNA
ID	9310	9311

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDTLV02-89tot	BGRSDTLV02-90tot
Sample_ID	BGRSDTLV02-89tot	BGRSDTLV02-90tot
Sample Name
Sample Name	ZNF473-BGRSDTLV02-89tot	ZNF473-BGRSDTLV02-90tot
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	12416	12417

Library-Prep
Sequencing

Library-Prep Information

	BGRSDTLV02-89tot	BGRSDTLV02-90tot
Sample #	81	82
Sample Name	ZNF473-BGRSDTLV02-89tot	ZNF473-BGRSDTLV02-90tot
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-27	2023-09-27
Lib_ID	Lib-230927	Lib-230927
Tecan_Location
Tecan
Tecan_date
Size_bp	276	277
Peak_Molarity	4.97	1.83
libSampleQC_DNA_Well	DNA_Library_set65_tot/set1/E11.png	DNA_Library_set65_tot/set1/F11.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	2023-10-03	2023-10-03
Sample_ID	BGRSDTLV02-89tot	BGRSDTLV02-90tot
RBP	ZNF473	ZNF473
Batch_ID	BGRSDTLV02	BGRSDTLV02
WB_result	0.000	0.000
Library Description	TruSeq Total RNA	TruSeq Total RNA
Repeat_Library_Suffix	t	t
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4002	4003

Sequencing Information

	BGRSDTLV02-89tot	BGRSDTLV02-90tot
Sample_ID	BGRSDTLV02-89tot	BGRSDTLV02-90tot
Sample Name	ZNF473-BGRSDTLV02-89tot	ZNF473-BGRSDTLV02-90tot
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65_tot	set65_tot
total_reads	45,866,229	42,216,076
total_aligned_reads	33,123,064	31,385,532
unique_aligned_reads	30,357,992	29,357,714
percent_uniqueAligned	0.66188	0.69542
correlation_replicates	0.956574	0.956574
spikein_reads	102,970	52,256
percent_spikeins	0.00225	0.00124
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2749	2750

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-BGRSDTLV02-89tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2749	NovaSeq6000	100	paired-ended	1				NT-BGRSDTLV02-1tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8894
ZNF473-BGRSDTLV02-89tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2749	NovaSeq6000	100	paired-ended	2				NT-BGRSDTLV02-1tot_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8902
ZNF473-BGRSDTLV02-89tot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDTLV02-89tot_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9259
ZNF473-BGRSDTLV02-89tot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot/Aligned.sortedByCoord.out.bam		ENCORE2	9267
ZNF473-BGRSDTLV02-89tot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot/Aligned.sortedByCoord.out.bam		ENCORE2	9275
ZNF473-BGRSDTLV02-89tot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot/Aligned.sortedByCoord.out.bam		ENCORE2	9283
ZNF473-BGRSDTLV02-89tot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot/Aligned.sortedByCoord.out.bam		ENCORE2	9291
ZNF473-BGRSDTLV02-89tot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2749					GRCh38	V40	ZNF473-BGRSDTLV02-89tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDTLV02-89tot_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9299
ZNF473-BGRSDTLV02-90tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2750	NovaSeq6000	100	paired-ended	1				NT-BGRSDTLV02-1tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8895
ZNF473-BGRSDTLV02-90tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2750	NovaSeq6000	100	paired-ended	2				NT-BGRSDTLV02-1tot_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-2tot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8903
ZNF473-BGRSDTLV02-90tot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDTLV02-90tot_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9260
ZNF473-BGRSDTLV02-90tot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot/Aligned.sortedByCoord.out.bam		ENCORE2	9268
ZNF473-BGRSDTLV02-90tot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot/Aligned.sortedByCoord.out.bam		ENCORE2	9276
ZNF473-BGRSDTLV02-90tot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot/Aligned.sortedByCoord.out.bam		ENCORE2	9284
ZNF473-BGRSDTLV02-90tot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot/Aligned.sortedByCoord.out.bam		ENCORE2	9292
ZNF473-BGRSDTLV02-90tot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2750					GRCh38	V40	ZNF473-BGRSDTLV02-90tot_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZNF473-BGRSDTLV02-90tot_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9300