ZNF169 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-53	BGRSLV06-54
idx	0	0
TRCN#_or_BGC#	TRCN0000016258	TRCN0000016258
shRNA_or_gRNA_sequence	CCGGGCCAGAAGTCTCACTTGCATACTCGAGTATGCAAGTGAGACTTCTGGCTTTTT	CCGGGCCAGAAGTCTCACTTGCATACTCGAGTATGCAAGTGAGACTTCTGGCTTTTT
PAM
Name	ZNF169	ZNF169
Sample_ID	BGRSLV06-53	BGRSLV06-54
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	ZNF169	ZNF169
qPCR_result	75.1	77.1
Ave_qPCR	76.1
RT-qPCR_primer-F	ccttggagagaggagaacga
RT-qPCR_primer-R	ggccacttagcgcatattgt
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	8580	8581

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-53	BGRSLV06-54
Sample_ID	BGRSLV06-53	BGRSLV06-54
Sample Name
Sample Name	ZNF169-BGRSLV06-53	ZNF169-BGRSLV06-54
RBP	ZNF169	ZNF169
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	11712	11713

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-53	BGRSLV06-54
Sample #	95	96
Sample Name	ZNF169-BGRSLV06-53	ZNF169-BGRSLV06-54
Sample_Name_Alias
Index Well Position	G12	H12
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	291	303
Peak_Molarity	109.00	60.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G6.png	DNA_Library_set60-62/set1/H6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set60-62/set1/G12.png	RNA_Library_set60-62/set1/H12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-53	BGRSLV06-54
RBP	ZNF169	ZNF169
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	3682	3683

Sequencing Information

	BGRSLV06-53	BGRSLV06-54
Sample_ID	BGRSLV06-53	BGRSLV06-54
Sample Name	ZNF169-BGRSLV06-53	ZNF169-BGRSLV06-54
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	28,261,732	34,723,200
total_aligned_reads	24,136,914	29,064,238
unique_aligned_reads	22,731,611	27,392,643
percent_uniqueAligned	0.80432	0.78889
correlation_replicates	0.998407	0.998407
spikein_reads	15,842	10,772
percent_spikeins	0.00056	0.00031
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2553	2554

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
ZNF169-BGRSLV06-53_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2553	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	8626
ZNF169-BGRSLV06-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2553					GRCh38	V40	ZNF169-BGRSLV06-53_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF169-BGRSLV06-53_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10491
ZNF169-BGRSLV06-53_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	2553					GRCh38	V40	ZNF169-BGRSLV06-53/Aligned.sortedByCoord.out.bam		ENCORE2	10543
ZNF169-BGRSLV06-53_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	2553					GRCh38	V40	ZNF169-BGRSLV06-53/Aligned.sortedByCoord.out.bam		ENCORE2	10595
ZNF169-BGRSLV06-53_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	2553					GRCh38	V40	ZNF169-BGRSLV06-53/Aligned.sortedByCoord.out.bam		ENCORE2	10647
ZNF169-BGRSLV06-53_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	2553					GRCh38	V40	ZNF169-BGRSLV06-53/Aligned.sortedByCoord.out.bam		ENCORE2	10699
ZNF169-BGRSLV06-53_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2553					GRCh38	V40	ZNF169-BGRSLV06-53_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF169-BGRSLV06-53_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10751
ZNF169-BGRSLV06-53_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2553	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	28893
ZNF169-BGRSLV06-54_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2554	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	8627
ZNF169-BGRSLV06-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2554					GRCh38	V40	ZNF169-BGRSLV06-54_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF169-BGRSLV06-54_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10492
ZNF169-BGRSLV06-54_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	2554					GRCh38	V40	ZNF169-BGRSLV06-54/Aligned.sortedByCoord.out.bam		ENCORE2	10544
ZNF169-BGRSLV06-54_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	2554					GRCh38	V40	ZNF169-BGRSLV06-54/Aligned.sortedByCoord.out.bam		ENCORE2	10596
ZNF169-BGRSLV06-54_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	2554					GRCh38	V40	ZNF169-BGRSLV06-54/Aligned.sortedByCoord.out.bam		ENCORE2	10648
ZNF169-BGRSLV06-54_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	2554					GRCh38	V40	ZNF169-BGRSLV06-54/Aligned.sortedByCoord.out.bam		ENCORE2	10700
ZNF169-BGRSLV06-54_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2554					GRCh38	V40	ZNF169-BGRSLV06-54_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF169-BGRSLV06-54_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10752
ZNF169-BGRSLV06-54_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2554	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	28894