PIAS4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-15	BGRSLV06-16
idx	0	0
TRCN#_or_BGC#	TRCN0000004115	TRCN0000004115
shRNA_or_gRNA_sequence	CCGGCACCGAATTAGTCCCACAGAACTCGAGTTCTGTGGGACTAATTCGGTGTTTTT	CCGGCACCGAATTAGTCCCACAGAACTCGAGTTCTGTGGGACTAATTCGGTGTTTTT
PAM
Name	PIAS4	PIAS4
Sample_ID	BGRSLV06-15	BGRSLV06-16
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	PIAS4	PIAS4
qPCR_result	78.2	79.3
Ave_qPCR	78.8
RT-qPCR_primer-F	gctgaagaccattggggtaa
RT-qPCR_primer-R	gatctcgctgtcaggatcaag
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	8542	8543

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-15	BGRSLV06-16
Sample_ID	BGRSLV06-15	BGRSLV06-16
Sample Name
Sample Name	PIAS4-BGRSLV06-15	PIAS4-BGRSLV06-16
RBP	PIAS4	PIAS4
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	11692	11693

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-15	BGRSLV06-16
Sample #	75	76
Sample Name	PIAS4-BGRSLV06-15	PIAS4-BGRSLV06-16
Sample_Name_Alias
Index Well Position	C10	D10
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	276	277
Peak_Molarity	96.20	86.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G10.png	DNA_Library_set60-62/set1/H10.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_set60-62/set1/C10.png	RNA_Library_set60-62/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-15	BGRSLV06-16
RBP	PIAS4	PIAS4
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3662	3663

Sequencing Information

	BGRSLV06-15	BGRSLV06-16
Sample_ID	BGRSLV06-15	BGRSLV06-16
Sample Name	PIAS4-BGRSLV06-15	PIAS4-BGRSLV06-16
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	47,401,270	32,312,556
total_aligned_reads	37,945,013	27,793,524
unique_aligned_reads	35,758,983	26,186,678
percent_uniqueAligned	0.75439	0.81042
correlation_replicates	0.977920	0.977920
spikein_reads	41,086	32,372
percent_spikeins	0.00087	0.00100
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2533	2534

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
PIAS4-BGRSLV06-15_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2533	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8588
PIAS4-BGRSLV06-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2533					GRCh38	V40	PIAS4-BGRSLV06-15_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,PIAS4-BGRSLV06-15_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10453
PIAS4-BGRSLV06-15_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	2533					GRCh38	V40	PIAS4-BGRSLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	10505
PIAS4-BGRSLV06-15_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	2533					GRCh38	V40	PIAS4-BGRSLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	10557
PIAS4-BGRSLV06-15_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	2533					GRCh38	V40	PIAS4-BGRSLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	10609
PIAS4-BGRSLV06-15_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	2533					GRCh38	V40	PIAS4-BGRSLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	10661
PIAS4-BGRSLV06-15_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2533					GRCh38	V40	PIAS4-BGRSLV06-15_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,PIAS4-BGRSLV06-15_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10713
PIAS4-BGRSLV06-15_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2533	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28855
PIAS4-BGRSLV06-16_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2534	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8589
PIAS4-BGRSLV06-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2534					GRCh38	V40	PIAS4-BGRSLV06-16_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,PIAS4-BGRSLV06-16_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10454
PIAS4-BGRSLV06-16_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	2534					GRCh38	V40	PIAS4-BGRSLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	10506
PIAS4-BGRSLV06-16_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	2534					GRCh38	V40	PIAS4-BGRSLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	10558
PIAS4-BGRSLV06-16_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	2534					GRCh38	V40	PIAS4-BGRSLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	10610
PIAS4-BGRSLV06-16_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	2534					GRCh38	V40	PIAS4-BGRSLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	10662
PIAS4-BGRSLV06-16_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2534					GRCh38	V40	PIAS4-BGRSLV06-16_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,PIAS4-BGRSLV06-16_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10714
PIAS4-BGRSLV06-16_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2534	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28856