ZNF16 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-51	BGRSLV06-52
idx	0	0
TRCN#_or_BGC#	TRCN0000014704	TRCN0000014704
shRNA_or_gRNA_sequence	CCGGGCTTCCTTTATGTGTGATGATCTCGAGATCATCACACATAAAGGAAGCTTTTT	CCGGGCTTCCTTTATGTGTGATGATCTCGAGATCATCACACATAAAGGAAGCTTTTT
PAM
Name	ZNF16	ZNF16
Sample_ID	BGRSLV06-51	BGRSLV06-52
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	ZNF16	ZNF16
qPCR_result	67.9	68.8
Ave_qPCR	68.4
RT-qPCR_primer-F	actgagctggaagccatctg
RT-qPCR_primer-R	tgggaaacatcaccagcata
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	8578	8579

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-51	BGRSLV06-52
Sample_ID	BGRSLV06-51	BGRSLV06-52
Sample Name
Sample Name	ZNF16-BGRSLV06-51	ZNF16-BGRSLV06-52
RBP	ZNF16	ZNF16
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	11710	11711

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-51	BGRSLV06-52
Sample #	93	94
Sample Name	ZNF16-BGRSLV06-51	ZNF16-BGRSLV06-52
Sample_Name_Alias
Index Well Position	E12	F12
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	297	302
Peak_Molarity	119.00	141.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E6.png	DNA_Library_set60-62/set1/F6.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set60-62/set1/E12.png	RNA_Library_set60-62/set1/F12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-51	BGRSLV06-52
RBP	ZNF16	ZNF16
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	3680	3681

Sequencing Information

	BGRSLV06-51	BGRSLV06-52
Sample_ID	BGRSLV06-51	BGRSLV06-52
Sample Name	ZNF16-BGRSLV06-51	ZNF16-BGRSLV06-52
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	24,508,273	44,293,949
total_aligned_reads	21,128,049	38,764,613
unique_aligned_reads	19,924,343	36,513,454
percent_uniqueAligned	0.81296	0.82434
correlation_replicates	0.997339	0.997339
spikein_reads	34,604	39,286
percent_spikeins	0.00141	0.00089
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2551	2552

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
ZNF16-BGRSLV06-51_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2551	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	8628
ZNF16-BGRSLV06-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2551					GRCh38	V40	ZNF16-BGRSLV06-51_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF16-BGRSLV06-51_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10493
ZNF16-BGRSLV06-51_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	2551					GRCh38	V40	ZNF16-BGRSLV06-51/Aligned.sortedByCoord.out.bam		ENCORE2	10545
ZNF16-BGRSLV06-51_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	2551					GRCh38	V40	ZNF16-BGRSLV06-51/Aligned.sortedByCoord.out.bam		ENCORE2	10597
ZNF16-BGRSLV06-51_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	2551					GRCh38	V40	ZNF16-BGRSLV06-51/Aligned.sortedByCoord.out.bam		ENCORE2	10649
ZNF16-BGRSLV06-51_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	2551					GRCh38	V40	ZNF16-BGRSLV06-51/Aligned.sortedByCoord.out.bam		ENCORE2	10701
ZNF16-BGRSLV06-51_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2551					GRCh38	V40	ZNF16-BGRSLV06-51_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF16-BGRSLV06-51_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10753
ZNF16-BGRSLV06-51_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2551	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	28895
ZNF16-BGRSLV06-52_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2552	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	8629
ZNF16-BGRSLV06-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2552					GRCh38	V40	ZNF16-BGRSLV06-52_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF16-BGRSLV06-52_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10494
ZNF16-BGRSLV06-52_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	2552					GRCh38	V40	ZNF16-BGRSLV06-52/Aligned.sortedByCoord.out.bam		ENCORE2	10546
ZNF16-BGRSLV06-52_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	2552					GRCh38	V40	ZNF16-BGRSLV06-52/Aligned.sortedByCoord.out.bam		ENCORE2	10598
ZNF16-BGRSLV06-52_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	2552					GRCh38	V40	ZNF16-BGRSLV06-52/Aligned.sortedByCoord.out.bam		ENCORE2	10650
ZNF16-BGRSLV06-52_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	2552					GRCh38	V40	ZNF16-BGRSLV06-52/Aligned.sortedByCoord.out.bam		ENCORE2	10702
ZNF16-BGRSLV06-52_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2552					GRCh38	V40	ZNF16-BGRSLV06-52_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZNF16-BGRSLV06-52_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10754
ZNF16-BGRSLV06-52_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2552	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	28896