ZCWPW1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-57	BGRSLV05-58
idx	0	0
TRCN#_or_BGC#	TRCN0000139148	TRCN0000139148
shRNA_or_gRNA_sequence	CCGGCCCATTCGTAAGCGAGTCAAACTCGAGTTTGACTCGCTTACGAATGGGTTTTTTG	CCGGCCCATTCGTAAGCGAGTCAAACTCGAGTTTGACTCGCTTACGAATGGGTTTTTTG
PAM
Name	ZCWPW1	ZCWPW1
Sample_ID	BGRSLV05-57	BGRSLV05-58
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	ZCWPW1	ZCWPW1
qPCR_result	93.4	89.4
Ave_qPCR	91.4
RT-qPCR_primer-F	ccaattttgcccattcgtaa
RT-qPCR_primer-R	agctgtggatttcctgccta
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	8510	8511

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-57	BGRSLV05-58
Sample_ID	BGRSLV05-57	BGRSLV05-58
Sample Name
Sample Name	ZCWPW1-BGRSLV05-57	ZCWPW1-BGRSLV05-58
RBP	ZCWPW1	ZCWPW1
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	11628	11629

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-57	BGRSLV05-58
Sample #	61	62
Sample Name	ZCWPW1-BGRSLV05-57	ZCWPW1-BGRSLV05-58
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	290	293
Peak_Molarity	66.10	95.60
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A9.png	DNA_Library_set60-62/set1/B9.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set60-62/set1/E8.png	RNA_Library_set60-62/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-57	BGRSLV05-58
RBP	ZCWPW1	ZCWPW1
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3648	3649

Sequencing Information

	BGRSLV05-57	BGRSLV05-58
Sample_ID	BGRSLV05-57	BGRSLV05-58
Sample Name	ZCWPW1-BGRSLV05-57	ZCWPW1-BGRSLV05-58
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	37,998,911	30,408,480
total_aligned_reads	32,903,656	25,249,838
unique_aligned_reads	30,679,464	23,601,178
percent_uniqueAligned	0.80738	0.77614
correlation_replicates	0.993251	0.993251
spikein_reads	10,582	80,948
percent_spikeins	0.00028	0.00266
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2519	2520

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
ZCWPW1-BGRSLV05-57_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2519	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8620
ZCWPW1-BGRSLV05-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCWPW1-BGRSLV05-57_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10485
ZCWPW1-BGRSLV05-57_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	10537
ZCWPW1-BGRSLV05-57_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	10589
ZCWPW1-BGRSLV05-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	10641
ZCWPW1-BGRSLV05-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	10693
ZCWPW1-BGRSLV05-57_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2519					GRCh38	V40	ZCWPW1-BGRSLV05-57_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCWPW1-BGRSLV05-57_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10745
ZCWPW1-BGRSLV05-57_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2519	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28887
ZCWPW1-BGRSLV05-58_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2520	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8621
ZCWPW1-BGRSLV05-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCWPW1-BGRSLV05-58_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10486
ZCWPW1-BGRSLV05-58_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	10538
ZCWPW1-BGRSLV05-58_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	10590
ZCWPW1-BGRSLV05-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	10642
ZCWPW1-BGRSLV05-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	10694
ZCWPW1-BGRSLV05-58_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2520					GRCh38	V40	ZCWPW1-BGRSLV05-58_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCWPW1-BGRSLV05-58_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10746
ZCWPW1-BGRSLV05-58_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2520	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28888