ZNF317 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-61	BGRSLV03-62
idx	0	0
TRCN#_or_BGC#	TRCN0000108167	TRCN0000108167
shRNA_or_gRNA_sequence	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG	CCGGGCTCACTTGTTCGAAGTCTTTCTCGAGAAAGACTTCGAACAAGTGAGCTTTTTG
PAM
Name	ZNF317	ZNF317
Sample_ID	BGRSLV03-61	BGRSLV03-62
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZNF317	ZNF317
qPCR_result	71.5	60.6
Ave_qPCR	66.0
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	8371	8372

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-61	BGRSLV03-62
Sample_ID	BGRSLV03-61	BGRSLV03-62
Sample Name
Sample Name	ZNF317-BGRSLV03-61	ZNF317-BGRSLV03-62
RBP	ZNF317	ZNF317
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11408	11409

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-61	BGRSLV03-62
Sample #	39	40
Sample Name	ZNF317-BGRSLV03-61	ZNF317-BGRSLV03-62
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	295	296
Peak_Molarity	80.10	67.30
libSampleQC_DNA_Well	DNA_Library_set58/set1/G11.png	DNA_Library_set58/set1/H11.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set58/set1/G5.png	RNA_Library_set58/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-61	BGRSLV03-62
RBP	ZNF317	ZNF317
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3546	3547

Sequencing Information

	BGRSLV03-61	BGRSLV03-62
Sample_ID	BGRSLV03-61	BGRSLV03-62
Sample Name	ZNF317-BGRSLV03-61	ZNF317-BGRSLV03-62
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	48,189,493	46,792,538
total_aligned_reads	43,032,878	41,627,096
unique_aligned_reads	40,037,829	38,928,203
percent_uniqueAligned	0.83084	0.83193
correlation_replicates	0.987838	0.987838
spikein_reads	267,222	258,670
percent_spikeins	0.00555	0.00553
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2417	2418

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-BGRSLV03-61_S173_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2417	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8164
ZNF317-BGRSLV03-61_S173_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2417	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8206
ZNF317-BGRSLV03-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61_S173_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSLV03-61_S173_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11285
ZNF317-BGRSLV03-61_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61/Aligned.sortedByCoord.out.bam		ENCORE2	11327
ZNF317-BGRSLV03-61_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61/Aligned.sortedByCoord.out.bam		ENCORE2	11369
ZNF317-BGRSLV03-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61/Aligned.sortedByCoord.out.bam		ENCORE2	11411
ZNF317-BGRSLV03-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61/Aligned.sortedByCoord.out.bam		ENCORE2	11453
ZNF317-BGRSLV03-61_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2417					GRCh38	V40	ZNF317-BGRSLV03-61_S173_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSLV03-61_S173_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11495
ZNF317-BGRSLV03-62_S174_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2418	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8165
ZNF317-BGRSLV03-62_S174_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2418	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8207
ZNF317-BGRSLV03-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62_S174_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSLV03-62_S174_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11286
ZNF317-BGRSLV03-62_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62/Aligned.sortedByCoord.out.bam		ENCORE2	11328
ZNF317-BGRSLV03-62_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62/Aligned.sortedByCoord.out.bam		ENCORE2	11370
ZNF317-BGRSLV03-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62/Aligned.sortedByCoord.out.bam		ENCORE2	11412
ZNF317-BGRSLV03-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62/Aligned.sortedByCoord.out.bam		ENCORE2	11454
ZNF317-BGRSLV03-62_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2418					GRCh38	V40	ZNF317-BGRSLV03-62_S174_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF317-BGRSLV03-62_S174_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11496