ZNF346 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-65	BGRSLV07-66
idx	0	0
TRCN#_or_BGC#	TRCN0000219820	TRCN0000219820
shRNA_or_gRNA_sequence	CCGGCTCATTGGTCCGGGCTAATTCCTCGAGGAATTAGCCCGGACCAATGAGTTTTTG	CCGGCTCATTGGTCCGGGCTAATTCCTCGAGGAATTAGCCCGGACCAATGAGTTTTTG
PAM
Name	ZNF346	ZNF346
Sample_ID	BGRSLV07-65	BGRSLV07-66
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	ZNF346	ZNF346
qPCR_result	65.8	59.2
Ave_qPCR	62.5
RT-qPCR_primer-F	CCTGCTGTCACTGACTTTCCAG
RT-qPCR_primer-R	CTGGTTCTTGTGTTTGAAGCCGC
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	8647	8648

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-65	BGRSLV07-66
Sample_ID	BGRSLV07-65	BGRSLV07-66
Sample Name
Sample Name	ZNF346-BGRSLV07-65	ZNF346-BGRSLV07-66
RBP	ZNF346	ZNF346
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	11856	11857

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-65	BGRSLV07-66
Sample #	37	38
Sample Name	ZNF346-BGRSLV07-65	ZNF346-BGRSLV07-66
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	286	290
Peak_Molarity	82.20	82.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E5.png	DNA_Library_set60-62/set4/F5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/E5.png	RNA_Library_set60-62/set2/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-65	BGRSLV07-66
RBP	ZNF346	ZNF346
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3720	3721

Sequencing Information

	BGRSLV07-65	BGRSLV07-66
Sample_ID	BGRSLV07-65	BGRSLV07-66
Sample Name	ZNF346-BGRSLV07-65	ZNF346-BGRSLV07-66
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	27,273,278	25,593,956
total_aligned_reads	23,301,077	21,861,591
unique_aligned_reads	21,816,644	20,514,264
percent_uniqueAligned	0.79993	0.80153
correlation_replicates	0.988585	0.988585
spikein_reads	21,784	16,612
percent_spikeins	0.00080	0.00065
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2591	2592

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
ZNF346-BGRSLV07-65_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2591	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7906
ZNF346-BGRSLV07-65_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2591	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7950
ZNF346-BGRSLV07-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF346-BGRSLV07-65_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10211
ZNF346-BGRSLV07-65_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65/Aligned.sortedByCoord.out.bam		ENCORE2	10255
ZNF346-BGRSLV07-65_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65/Aligned.sortedByCoord.out.bam		ENCORE2	10299
ZNF346-BGRSLV07-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65/Aligned.sortedByCoord.out.bam		ENCORE2	10343
ZNF346-BGRSLV07-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65/Aligned.sortedByCoord.out.bam		ENCORE2	10387
ZNF346-BGRSLV07-65_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2591					GRCh38	V40	ZNF346-BGRSLV07-65_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF346-BGRSLV07-65_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10431
ZNF346-BGRSLV07-66_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2592	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7907
ZNF346-BGRSLV07-66_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2592	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7951
ZNF346-BGRSLV07-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF346-BGRSLV07-66_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10212
ZNF346-BGRSLV07-66_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66/Aligned.sortedByCoord.out.bam		ENCORE2	10256
ZNF346-BGRSLV07-66_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66/Aligned.sortedByCoord.out.bam		ENCORE2	10300
ZNF346-BGRSLV07-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66/Aligned.sortedByCoord.out.bam		ENCORE2	10344
ZNF346-BGRSLV07-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66/Aligned.sortedByCoord.out.bam		ENCORE2	10388
ZNF346-BGRSLV07-66_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2592					GRCh38	V40	ZNF346-BGRSLV07-66_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF346-BGRSLV07-66_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10432