ZNF302 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-59dox	BGRSDLV04-60dox
idx	0	0
TRCN#_or_BGC#	TRCN0000016379	TRCN0000016379
shRNA_or_gRNA_sequence	CCGGCCCAACCAGTAACAATGGAAACTCGAGTTTCCATTGTTACTGGTTGGGTTTTT	CCGGCCCAACCAGTAACAATGGAAACTCGAGTTTCCATTGTTACTGGTTGGGTTTTT
PAM
Name	ZNF302	ZNF302
Sample_ID	BGRSDLV04-59dox	BGRSDLV04-60dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	ZNF302	ZNF302
qPCR_result	90.38188	98.63466
Ave_qPCR	94.50827
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	9423	9424

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-59dox	BGRSDLV04-60dox
Sample_ID	BGRSDLV04-59dox	BGRSDLV04-60dox
Sample Name
Sample Name	ZNF302-BGRSDLV04-59dox	ZNF302-BGRSDLV04-60dox
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	12676	12677

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-59dox	BGRSDLV04-60dox
Sample #	31	32
Sample Name	ZNF302-BGRSDLV04-59dox	ZNF302-BGRSDLV04-60dox
Sample_Name_Alias
Index Well Position	G04	H04
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	291	294
Peak_Molarity	30.90	50.80
libSampleQC_DNA_Well	DNA_Library_set68/set1/G4.png	DNA_Library_set68/set1/H4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G4.png	RNA_Library_set68/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-59dox	BGRSDLV04-60dox
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	4104	4105

Sequencing Information

	BGRSDLV04-59dox	BGRSDLV04-60dox
Sample_ID	BGRSDLV04-59dox	BGRSDLV04-60dox
Sample Name	ZNF302-BGRSDLV04-59dox	ZNF302-BGRSDLV04-60dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	43,691,870	30,556,734
total_aligned_reads	39,840,158	26,857,956
unique_aligned_reads	37,493,442	25,324,630
percent_uniqueAligned	0.85813	0.82877
correlation_replicates	0.998721	0.998721
spikein_reads	3,290	7,490
percent_spikeins	0.00008	0.00025
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2867	2868

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-BGRSDLV04-59dox_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2867	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	27679
ZNF302-BGRSDLV04-59dox_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2867	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	27743
ZNF302-BGRSDLV04-59dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-59dox_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27807
ZNF302-BGRSDLV04-59dox_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	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox/Aligned.sortedByCoord.out.bam		ENCORE2	27871
ZNF302-BGRSDLV04-59dox_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	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox/Aligned.sortedByCoord.out.bam		ENCORE2	27935
ZNF302-BGRSDLV04-59dox_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	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox/Aligned.sortedByCoord.out.bam		ENCORE2	27999
ZNF302-BGRSDLV04-59dox_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	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox/Aligned.sortedByCoord.out.bam		ENCORE2	28063
ZNF302-BGRSDLV04-59dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2867					GRCh38	V40	ZNF302-BGRSDLV04-59dox_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-59dox_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28127
ZNF302-BGRSDLV04-60dox_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2868	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	27680
ZNF302-BGRSDLV04-60dox_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2868	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	27744
ZNF302-BGRSDLV04-60dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-60dox_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27808
ZNF302-BGRSDLV04-60dox_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	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox/Aligned.sortedByCoord.out.bam		ENCORE2	27872
ZNF302-BGRSDLV04-60dox_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	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox/Aligned.sortedByCoord.out.bam		ENCORE2	27936
ZNF302-BGRSDLV04-60dox_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	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox/Aligned.sortedByCoord.out.bam		ENCORE2	28000
ZNF302-BGRSDLV04-60dox_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	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox/Aligned.sortedByCoord.out.bam		ENCORE2	28064
ZNF302-BGRSDLV04-60dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2868					GRCh38	V40	ZNF302-BGRSDLV04-60dox_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF302-BGRSDLV04-60dox_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28128