ZNF302 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-57	BGRSDLV04-58
idx	0	0
TRCN#_or_BGC#	TRCN0000016379	TRCN0000016379
shRNA_or_gRNA_sequence	CCGGCCCAACCAGTAACAATGGAAACTCGAGTTTCCATTGTTACTGGTTGGGTTTTT	CCGGCCCAACCAGTAACAATGGAAACTCGAGTTTCCATTGTTACTGGTTGGGTTTTT
PAM
Name	ZNF302	ZNF302
Sample_ID	BGRSDLV04-57	BGRSDLV04-58
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	ZNF302	ZNF302
qPCR_result	70.41362	80.89639
Ave_qPCR	75.655005
RT-qPCR_primer-F	ggcatgcctagattctgctc
RT-qPCR_primer-R	catcatccagggctcttttc
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	9421	9422

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-57	BGRSDLV04-58
Sample_ID	BGRSDLV04-57	BGRSDLV04-58
Sample Name
Sample Name	ZNF302-BGRSDLV04-57	ZNF302-BGRSDLV04-58
RBP	ZNF302	ZNF302
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12674	12675

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-57	BGRSDLV04-58
Sample #	29	30
Sample Name	ZNF302-BGRSDLV04-57	ZNF302-BGRSDLV04-58
Sample_Name_Alias
Index Well Position	E04	F04
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	283	288
Peak_Molarity	57.90	59.40
libSampleQC_DNA_Well	DNA_Library_set68/set1/E4.png	DNA_Library_set68/set1/F4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/E4.png	RNA_Library_set68/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-57	BGRSDLV04-58
RBP	ZNF302	ZNF302
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	4102	4103

Sequencing Information

	BGRSDLV04-57	BGRSDLV04-58
Sample_ID	BGRSDLV04-57	BGRSDLV04-58
Sample Name	ZNF302-BGRSDLV04-57	ZNF302-BGRSDLV04-58
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	44,419,157	38,703,852
total_aligned_reads	40,152,414	34,668,879
unique_aligned_reads	37,701,054	32,605,816
percent_uniqueAligned	0.84876	0.84244
correlation_replicates	0.999389	0.999389
spikein_reads	5,242	7,268
percent_spikeins	0.00012	0.00019
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2865	2866

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
ZNF302-BGRSDLV04-57_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2865	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27677
ZNF302-BGRSDLV04-57_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2865	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27741
ZNF302-BGRSDLV04-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2865					GRCh38	V40	ZNF302-BGRSDLV04-57_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-57_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27805
ZNF302-BGRSDLV04-57_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	2865					GRCh38	V40	ZNF302-BGRSDLV04-57/Aligned.sortedByCoord.out.bam		ENCORE2	27869
ZNF302-BGRSDLV04-57_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	2865					GRCh38	V40	ZNF302-BGRSDLV04-57/Aligned.sortedByCoord.out.bam		ENCORE2	27933
ZNF302-BGRSDLV04-57_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	2865					GRCh38	V40	ZNF302-BGRSDLV04-57/Aligned.sortedByCoord.out.bam		ENCORE2	27997
ZNF302-BGRSDLV04-57_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	2865					GRCh38	V40	ZNF302-BGRSDLV04-57/Aligned.sortedByCoord.out.bam		ENCORE2	28061
ZNF302-BGRSDLV04-57_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2865					GRCh38	V40	ZNF302-BGRSDLV04-57_S29_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-57_S29_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28125
ZNF302-BGRSDLV04-58_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2866	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27678
ZNF302-BGRSDLV04-58_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2866	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27742
ZNF302-BGRSDLV04-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2866					GRCh38	V40	ZNF302-BGRSDLV04-58_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-58_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27806
ZNF302-BGRSDLV04-58_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	2866					GRCh38	V40	ZNF302-BGRSDLV04-58/Aligned.sortedByCoord.out.bam		ENCORE2	27870
ZNF302-BGRSDLV04-58_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	2866					GRCh38	V40	ZNF302-BGRSDLV04-58/Aligned.sortedByCoord.out.bam		ENCORE2	27934
ZNF302-BGRSDLV04-58_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	2866					GRCh38	V40	ZNF302-BGRSDLV04-58/Aligned.sortedByCoord.out.bam		ENCORE2	27998
ZNF302-BGRSDLV04-58_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	2866					GRCh38	V40	ZNF302-BGRSDLV04-58/Aligned.sortedByCoord.out.bam		ENCORE2	28062
ZNF302-BGRSDLV04-58_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2866					GRCh38	V40	ZNF302-BGRSDLV04-58_S30_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-58_S30_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28126