ZNF593 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-67dox	BGRSDLV04-68dox
idx	0	0
TRCN#_or_BGC#	TRCN0000240807	TRCN0000240807
shRNA_or_gRNA_sequence	CCGGTCGATTCCACCAACCTGAAGACTCGAGTCTTCAGGTTGGTGGAATCGATTTTTG	CCGGTCGATTCCACCAACCTGAAGACTCGAGTCTTCAGGTTGGTGGAATCGATTTTTG
PAM
Name	ZNF593	ZNF593
Sample_ID	BGRSDLV04-67dox	BGRSDLV04-68dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	ZNF593	ZNF593
qPCR_result	65.25811	69.99346
Ave_qPCR	67.625785
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	9431	9432

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-67dox	BGRSDLV04-68dox
Sample_ID	BGRSDLV04-67dox	BGRSDLV04-68dox
Sample Name
Sample Name	ZNF593-BGRSDLV04-67dox	ZNF593-BGRSDLV04-68dox
RBP	ZNF593	ZNF593
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12680	12681

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-67dox	BGRSDLV04-68dox
Sample #	35	36
Sample Name	ZNF593-BGRSDLV04-67dox	ZNF593-BGRSDLV04-68dox
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	290	293
Peak_Molarity	68.80	54.90
libSampleQC_DNA_Well	DNA_Library_set68/set1/C5.png	DNA_Library_set68/set1/D5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/C5.png	RNA_Library_set68/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-67dox	BGRSDLV04-68dox
RBP	ZNF593	ZNF593
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4108	4109

Sequencing Information

	BGRSDLV04-67dox	BGRSDLV04-68dox
Sample_ID	BGRSDLV04-67dox	BGRSDLV04-68dox
Sample Name	ZNF593-BGRSDLV04-67dox	ZNF593-BGRSDLV04-68dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	63,443,603	81,495,656
total_aligned_reads	56,793,679	73,065,915
unique_aligned_reads	53,221,651	68,589,836
percent_uniqueAligned	0.83888	0.84164
correlation_replicates	0.998733	0.998733
spikein_reads	13,728	19,160
percent_spikeins	0.00022	0.00024
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2871	2872

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-BGRSDLV04-67dox_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2871	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27683
ZNF593-BGRSDLV04-67dox_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2871	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27747
ZNF593-BGRSDLV04-67dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSDLV04-67dox_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27811
ZNF593-BGRSDLV04-67dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	27875
ZNF593-BGRSDLV04-67dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	27939
ZNF593-BGRSDLV04-67dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	28003
ZNF593-BGRSDLV04-67dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	28067
ZNF593-BGRSDLV04-67dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2871					GRCh38	V40	ZNF593-BGRSDLV04-67dox_S35_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSDLV04-67dox_S35_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28131
ZNF593-BGRSDLV04-68dox_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2872	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27684
ZNF593-BGRSDLV04-68dox_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2872	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27748
ZNF593-BGRSDLV04-68dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSDLV04-68dox_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27812
ZNF593-BGRSDLV04-68dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	27876
ZNF593-BGRSDLV04-68dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	27940
ZNF593-BGRSDLV04-68dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	28004
ZNF593-BGRSDLV04-68dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	28068
ZNF593-BGRSDLV04-68dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2872					GRCh38	V40	ZNF593-BGRSDLV04-68dox_S36_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF593-BGRSDLV04-68dox_S36_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28132