ZDHHC5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-59	BGRSLV05-60
idx	0	0
TRCN#_or_BGC#	TRCN0000160468	TRCN0000160468
shRNA_or_gRNA_sequence	CCGGCCTCAGATGATTCAAAGAGATCTCGAGATCTCTTTGAATCATCTGAGGTTTTTTG	CCGGCCTCAGATGATTCAAAGAGATCTCGAGATCTCTTTGAATCATCTGAGGTTTTTTG
PAM
Name	ZDHHC5	ZDHHC5
Sample_ID	BGRSLV05-59	BGRSLV05-60
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	ZDHHC5	ZDHHC5
qPCR_result	71.6	61.7
Ave_qPCR	66.6
RT-qPCR_primer-F	gataatggcatccagggaga
RT-qPCR_primer-R	tcaggtctggcttaggagga
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	8512	8513

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-59	BGRSLV05-60
Sample_ID	BGRSLV05-59	BGRSLV05-60
Sample Name
Sample Name	ZDHHC5-BGRSLV05-59	ZDHHC5-BGRSLV05-60
RBP	ZDHHC5	ZDHHC5
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	11630	11631

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-59	BGRSLV05-60
Sample #	63	64
Sample Name	ZDHHC5-BGRSLV05-59	ZDHHC5-BGRSLV05-60
Sample_Name_Alias
Index Well Position	G08	H08
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	292	291
Peak_Molarity	121.00	116.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/C9.png	DNA_Library_set60-62/set1/D9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/G8.png	RNA_Library_set60-62/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-59	BGRSLV05-60
RBP	ZDHHC5	ZDHHC5
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	3650	3651

Sequencing Information

	BGRSLV05-59	BGRSLV05-60
Sample_ID	BGRSLV05-59	BGRSLV05-60
Sample Name	ZDHHC5-BGRSLV05-59	ZDHHC5-BGRSLV05-60
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	52,338,913	42,554,219
total_aligned_reads	44,971,110	30,464,861
unique_aligned_reads	41,937,276	28,460,226
percent_uniqueAligned	0.80126	0.66880
correlation_replicates	0.991600	0.991600
spikein_reads	149,050	106,350
percent_spikeins	0.00285	0.00250
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2521	2522

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
ZDHHC5-BGRSLV05-59_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2521	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	8622
ZDHHC5-BGRSLV05-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZDHHC5-BGRSLV05-59_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10487
ZDHHC5-BGRSLV05-59_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	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59/Aligned.sortedByCoord.out.bam		ENCORE2	10539
ZDHHC5-BGRSLV05-59_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	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59/Aligned.sortedByCoord.out.bam		ENCORE2	10591
ZDHHC5-BGRSLV05-59_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	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59/Aligned.sortedByCoord.out.bam		ENCORE2	10643
ZDHHC5-BGRSLV05-59_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	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59/Aligned.sortedByCoord.out.bam		ENCORE2	10695
ZDHHC5-BGRSLV05-59_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2521					GRCh38	V40	ZDHHC5-BGRSLV05-59_S63_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZDHHC5-BGRSLV05-59_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10747
ZDHHC5-BGRSLV05-59_S63_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2521	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	28889
ZDHHC5-BGRSLV05-60_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2522	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	8623
ZDHHC5-BGRSLV05-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZDHHC5-BGRSLV05-60_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10488
ZDHHC5-BGRSLV05-60_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	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60/Aligned.sortedByCoord.out.bam		ENCORE2	10540
ZDHHC5-BGRSLV05-60_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	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60/Aligned.sortedByCoord.out.bam		ENCORE2	10592
ZDHHC5-BGRSLV05-60_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	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60/Aligned.sortedByCoord.out.bam		ENCORE2	10644
ZDHHC5-BGRSLV05-60_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	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60/Aligned.sortedByCoord.out.bam		ENCORE2	10696
ZDHHC5-BGRSLV05-60_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2522					GRCh38	V40	ZDHHC5-BGRSLV05-60_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZDHHC5-BGRSLV05-60_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10748
ZDHHC5-BGRSLV05-60_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2522	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	28890