ZNF184 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-19	BGRSLV08-20
idx	0	0
TRCN#_or_BGC#	TRCN0000107996	TRCN0000107996
shRNA_or_gRNA_sequence	CCGGCTTGCTAGAAAGTTGGGAATACTCGAGTATTCCCAACTTTCTAGCAAGTTTTTG	CCGGCTTGCTAGAAAGTTGGGAATACTCGAGTATTCCCAACTTTCTAGCAAGTTTTTG
PAM
Name	ZNF184	ZNF184
Sample_ID	BGRSLV08-19	BGRSLV08-20
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZNF184	ZNF184
qPCR_result	84.5	84.5
Ave_qPCR	84.5
RT-qPCR_primer-F	gagccaagcattccagtagg
RT-qPCR_primer-R	tggggctgacacactattttc
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	8668	8669

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-19	BGRSLV08-20
Sample_ID	BGRSLV08-19	BGRSLV08-20
Sample Name
Sample Name	ZNF184-BGRSLV08-19	ZNF184-BGRSLV08-20
RBP	ZNF184	ZNF184
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	11784	11785

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-19	BGRSLV08-20
Sample #	49	50
Sample Name	ZNF184-BGRSLV08-19	ZNF184-BGRSLV08-20
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	290	297
Peak_Molarity	49.50	55.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A7.png	DNA_Library_set60-62/set4/B7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A7.png	RNA_Library_set60-62/set2/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-19	BGRSLV08-20
RBP	ZNF184	ZNF184
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3732	3733

Sequencing Information

	BGRSLV08-19	BGRSLV08-20
Sample_ID	BGRSLV08-19	BGRSLV08-20
Sample Name	ZNF184-BGRSLV08-19	ZNF184-BGRSLV08-20
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	24,919,897	23,071,233
total_aligned_reads	19,095,184	18,327,920
unique_aligned_reads	17,886,231	17,218,043
percent_uniqueAligned	0.71775	0.74630
correlation_replicates	0.976332	0.976332
spikein_reads	58,114	27,648
percent_spikeins	0.00233	0.00120
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2603	2604

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
ZNF184-BGRSLV08-19_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2603	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7902
ZNF184-BGRSLV08-19_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2603	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7946
ZNF184-BGRSLV08-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF184-BGRSLV08-19_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10207
ZNF184-BGRSLV08-19_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	10251
ZNF184-BGRSLV08-19_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	10295
ZNF184-BGRSLV08-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	10339
ZNF184-BGRSLV08-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	10383
ZNF184-BGRSLV08-19_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2603					GRCh38	V40	ZNF184-BGRSLV08-19_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF184-BGRSLV08-19_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10427
ZNF184-BGRSLV08-20_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2604	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7903
ZNF184-BGRSLV08-20_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2604	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7947
ZNF184-BGRSLV08-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF184-BGRSLV08-20_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10208
ZNF184-BGRSLV08-20_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	10252
ZNF184-BGRSLV08-20_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	10296
ZNF184-BGRSLV08-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	10340
ZNF184-BGRSLV08-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	10384
ZNF184-BGRSLV08-20_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2604					GRCh38	V40	ZNF184-BGRSLV08-20_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF184-BGRSLV08-20_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10428