ZNF317 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-77	BGRSDLV02-78
idx	0	0
TRCN#_or_BGC#	TRCN0000108167	TRCN0000108167
shRNA_or_gRNA_sequence	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG
PAM
Name	ZNF317	ZNF317
Sample_ID	BGRSDLV02-77	BGRSDLV02-78
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZNF317	ZNF317
qPCR_result	75.7	82.2
Ave_qPCR	78.9
RT-qPCR_primer-F	ctgttcgtgtgcagtggtct
RT-qPCR_primer-R	cacagcgacatcttggaaag
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	9288	9289

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-77	BGRSDLV02-78
Sample_ID	BGRSDLV02-77	BGRSDLV02-78
Sample Name
Sample Name	ZNF317-BGRSDLV02-77	ZNF317-BGRSDLV02-78
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	12384	12385

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-77	BGRSDLV02-78
Sample #	65	66
Sample Name	ZNF317-BGRSDLV02-77	ZNF317-BGRSDLV02-78
Sample_Name_Alias
Index Well Position	A09	B09
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	292	297
Peak_Molarity	80.60	78.80
libSampleQC_DNA_Well	DNA_Library_set65/set1/A9.png	DNA_Library_set65/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/A9.png	RNA_Library_set65/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-77	BGRSDLV02-78
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	3986	3987

Sequencing Information

	BGRSDLV02-77	BGRSDLV02-78
Sample_ID	BGRSDLV02-77	BGRSDLV02-78
Sample Name	ZNF317-BGRSDLV02-77	ZNF317-BGRSDLV02-78
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	51,196,671	37,420,802
total_aligned_reads	47,172,825	34,577,248
unique_aligned_reads	44,161,704	32,440,476
percent_uniqueAligned	0.86259	0.86691
correlation_replicates	0.998150	0.998150
spikein_reads	13,926	4,052
percent_spikeins	0.00027	0.00011
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2733	2734

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-BGRSDLV02-77_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2733	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	8806
ZNF317-BGRSDLV02-77_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2733	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	8882
ZNF317-BGRSDLV02-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2733					GRCh38	V40	ZNF317-BGRSDLV02-77_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-77_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9371
ZNF317-BGRSDLV02-77_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	2733					GRCh38	V40	ZNF317-BGRSDLV02-77/Aligned.sortedByCoord.out.bam		ENCORE2	9447
ZNF317-BGRSDLV02-77_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	2733					GRCh38	V40	ZNF317-BGRSDLV02-77/Aligned.sortedByCoord.out.bam		ENCORE2	9523
ZNF317-BGRSDLV02-77_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	2733					GRCh38	V40	ZNF317-BGRSDLV02-77/Aligned.sortedByCoord.out.bam		ENCORE2	9599
ZNF317-BGRSDLV02-77_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	2733					GRCh38	V40	ZNF317-BGRSDLV02-77/Aligned.sortedByCoord.out.bam		ENCORE2	9675
ZNF317-BGRSDLV02-77_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2733					GRCh38	V40	ZNF317-BGRSDLV02-77_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-77_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9751
ZNF317-BGRSDLV02-78_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2734	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	8807
ZNF317-BGRSDLV02-78_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2734	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	8883
ZNF317-BGRSDLV02-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2734					GRCh38	V40	ZNF317-BGRSDLV02-78_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-78_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9372
ZNF317-BGRSDLV02-78_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	2734					GRCh38	V40	ZNF317-BGRSDLV02-78/Aligned.sortedByCoord.out.bam		ENCORE2	9448
ZNF317-BGRSDLV02-78_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	2734					GRCh38	V40	ZNF317-BGRSDLV02-78/Aligned.sortedByCoord.out.bam		ENCORE2	9524
ZNF317-BGRSDLV02-78_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	2734					GRCh38	V40	ZNF317-BGRSDLV02-78/Aligned.sortedByCoord.out.bam		ENCORE2	9600
ZNF317-BGRSDLV02-78_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	2734					GRCh38	V40	ZNF317-BGRSDLV02-78/Aligned.sortedByCoord.out.bam		ENCORE2	9676
ZNF317-BGRSDLV02-78_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2734					GRCh38	V40	ZNF317-BGRSDLV02-78_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSDLV02-78_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9752