ZNF317 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-79dox	BGRSDLV02-80dox
idx	0	0
TRCN#_or_BGC#	TRCN0000108167	TRCN0000108167
shRNA_or_gRNA_sequence	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG
PAM
Name	ZNF317	ZNF317
Sample_ID	BGRSDLV02-79dox	BGRSDLV02-80dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZNF317	ZNF317
qPCR_result	79.7	80.6
Ave_qPCR	80.1
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	9290	9291

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-79dox	BGRSDLV02-80dox
Sample_ID	BGRSDLV02-79dox	BGRSDLV02-80dox
Sample Name
Sample Name	ZNF317-BGRSDLV02-79dox	ZNF317-BGRSDLV02-80dox
RBP	ZNF317	ZNF317
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12386	12387

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-79dox	BGRSDLV02-80dox
Sample #	67	68
Sample Name	ZNF317-BGRSDLV02-79dox	ZNF317-BGRSDLV02-80dox
Sample_Name_Alias
Index Well Position	C09	D09
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	290	291
Peak_Molarity	77.10	73.50
libSampleQC_DNA_Well	DNA_Library_set65/set1/C9.png	DNA_Library_set65/set1/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C9.png	RNA_Library_set65/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-79dox	BGRSDLV02-80dox
RBP	ZNF317	ZNF317
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	3988	3989

Sequencing Information

	BGRSDLV02-79dox	BGRSDLV02-80dox
Sample_ID	BGRSDLV02-79dox	BGRSDLV02-80dox
Sample Name	ZNF317-BGRSDLV02-79dox	ZNF317-BGRSDLV02-80dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	44,568,904	23,262,012
total_aligned_reads	41,853,513	21,618,327
unique_aligned_reads	39,048,485	20,236,173
percent_uniqueAligned	0.87614	0.86992
correlation_replicates	0.997281	0.997281
spikein_reads	6,690	2,728
percent_spikeins	0.00015	0.00012
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2735	2736

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
ZNF317-BGRSDLV02-79dox_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2735	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	8808
ZNF317-BGRSDLV02-79dox_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2735	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	8884
ZNF317-BGRSDLV02-79dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-79dox_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9373
ZNF317-BGRSDLV02-79dox_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	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	9449
ZNF317-BGRSDLV02-79dox_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	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	9525
ZNF317-BGRSDLV02-79dox_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	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	9601
ZNF317-BGRSDLV02-79dox_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	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	9677
ZNF317-BGRSDLV02-79dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2735					GRCh38	V40	ZNF317-BGRSDLV02-79dox_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-79dox_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9753
ZNF317-BGRSDLV02-80dox_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2736	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	8809
ZNF317-BGRSDLV02-80dox_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2736	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	8885
ZNF317-BGRSDLV02-80dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-80dox_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9374
ZNF317-BGRSDLV02-80dox_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	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	9450
ZNF317-BGRSDLV02-80dox_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	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	9526
ZNF317-BGRSDLV02-80dox_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	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	9602
ZNF317-BGRSDLV02-80dox_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	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	9678
ZNF317-BGRSDLV02-80dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2736					GRCh38	V40	ZNF317-BGRSDLV02-80dox_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-80dox_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9754