ZNF593 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-35	BGRSLV08-36
idx	0	0
TRCN#_or_BGC#	TRCN0000240807	TRCN0000240809
shRNA_or_gRNA_sequence	CCGGTCGATTCCACCAACCTGAAGACTCGAGTCTTCAGGTTGGTGGAATCGATTTTTG	CCGGGAAGACCCACTTCCGATCCAACTCGAGTTGGATCGGAAGTGGGTCTTCTTTTTG
PAM
Name	ZNF593	ZNF593
Sample_ID	BGRSLV08-35	BGRSLV08-36
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZNF593	ZNF593
qPCR_result	72.5	59.8
Ave_qPCR	66.2
RT-qPCR_primer-F	caccaacctgaagacccact
RT-qPCR_primer-R	ccgcctcttcctgactgtag
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	8684	8685

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-35	BGRSLV08-36
Sample_ID	BGRSLV08-35	BGRSLV08-36
Sample Name
Sample Name	ZNF593-BGRSLV08-35	ZNF593-BGRSLV08-36
RBP	ZNF593	ZNF593
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	11790	11791

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-35	BGRSLV08-36
Sample #	55	56
Sample Name	ZNF593-BGRSLV08-35	ZNF593-BGRSLV08-36
Sample_Name_Alias
Index Well Position	G07	H07
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	300	288
Peak_Molarity	65.20	53.40
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G7.png	DNA_Library_set60-62/set4/H7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/G7.png	RNA_Library_set60-62/set2/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-35	BGRSLV08-36
RBP	ZNF593	ZNF593
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3738	3739

Sequencing Information

	BGRSLV08-35	BGRSLV08-36
Sample_ID	BGRSLV08-35	BGRSLV08-36
Sample Name	ZNF593-BGRSLV08-35	ZNF593-BGRSLV08-36
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	30,787,866	32,811,662
total_aligned_reads	26,806,703	27,567,389
unique_aligned_reads	25,179,099	25,876,379
percent_uniqueAligned	0.81783	0.78863
correlation_replicates	0.998404	0.998404
spikein_reads	22,856	39,594
percent_spikeins	0.00074	0.00121
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2609	2610

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
ZNF593-BGRSLV08-35_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2609	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7912
ZNF593-BGRSLV08-35_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2609	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7956
ZNF593-BGRSLV08-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2609					GRCh38	V40	ZNF593-BGRSLV08-35_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSLV08-35_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10217
ZNF593-BGRSLV08-35_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	2609					GRCh38	V40	ZNF593-BGRSLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	10261
ZNF593-BGRSLV08-35_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	2609					GRCh38	V40	ZNF593-BGRSLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	10305
ZNF593-BGRSLV08-35_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	2609					GRCh38	V40	ZNF593-BGRSLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	10349
ZNF593-BGRSLV08-35_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	2609					GRCh38	V40	ZNF593-BGRSLV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	10393
ZNF593-BGRSLV08-35_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2609					GRCh38	V40	ZNF593-BGRSLV08-35_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSLV08-35_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10437
ZNF593-BGRSLV08-36_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2610	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7913
ZNF593-BGRSLV08-36_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2610	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7957
ZNF593-BGRSLV08-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2610					GRCh38	V40	ZNF593-BGRSLV08-36_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSLV08-36_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10218
ZNF593-BGRSLV08-36_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	2610					GRCh38	V40	ZNF593-BGRSLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	10262
ZNF593-BGRSLV08-36_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	2610					GRCh38	V40	ZNF593-BGRSLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	10306
ZNF593-BGRSLV08-36_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	2610					GRCh38	V40	ZNF593-BGRSLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	10350
ZNF593-BGRSLV08-36_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	2610					GRCh38	V40	ZNF593-BGRSLV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	10394
ZNF593-BGRSLV08-36_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2610					GRCh38	V40	ZNF593-BGRSLV08-36_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSLV08-36_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10438