ZNHIT3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-45	BGRSLV02-46
idx	0	0
TRCN#_or_BGC#	TRCN0000022091	TRCN0000022091
shRNA_or_gRNA_sequence	CCGGCTCAATAGTGATGAGGAAGAACTCGAGTTCTTCCTCATCACTATTGAGTTTTT	CCGGCTCAATAGTGATGAGGAAGAACTCGAGTTCTTCCTCATCACTATTGAGTTTTT
PAM
Name	ZNHIT3	ZNHIT3
Sample_ID	BGRSLV02-45	BGRSLV02-46
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZNHIT3	ZNHIT3
qPCR_result	72.3	77.1
Ave_qPCR	74.7
RT-qPCR_primer-F	aaaaccgtaaagcctgtgga
RT-qPCR_primer-R	gcaaagaaactctgtcttcttcc
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	8282	8283

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-45	BGRSLV02-46
Sample_ID	BGRSLV02-45	BGRSLV02-46
Sample Name
Sample Name	ZNHIT3-BGRSLV02-45	ZNHIT3-BGRSLV02-46
RBP	ZNHIT3	ZNHIT3
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	11330	11331

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-45	BGRSLV02-46
Sample #	33	34
Sample Name	ZNHIT3-BGRSLV02-45	ZNHIT3-BGRSLV02-46
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	302	311
Peak_Molarity	46.80	50.80
libSampleQC_DNA_Well	DNA_Library_set57/set1/A11.png	DNA_Library_set57/set1/B11.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set57/set1/A5.png	RNA_Library_set57/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-45	BGRSLV02-46
RBP	ZNHIT3	ZNHIT3
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3494	3495

Sequencing Information

	BGRSLV02-45	BGRSLV02-46
Sample_ID	BGRSLV02-45	BGRSLV02-46
Sample Name	ZNHIT3-BGRSLV02-45	ZNHIT3-BGRSLV02-46
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	58,422,130	47,146,334
total_aligned_reads	52,405,866	41,827,761
unique_aligned_reads	48,967,583	39,081,169
percent_uniqueAligned	0.83817	0.82893
correlation_replicates	0.996618	0.996618
spikein_reads	39,670	28,818
percent_spikeins	0.00068	0.00061
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2365	2366

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
ZNHIT3-BGRSLV02-45_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2365	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8252
ZNHIT3-BGRSLV02-45_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2365	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8298
ZNHIT3-BGRSLV02-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNHIT3-BGRSLV02-45_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11541
ZNHIT3-BGRSLV02-45_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	11587
ZNHIT3-BGRSLV02-45_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	11633
ZNHIT3-BGRSLV02-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	11679
ZNHIT3-BGRSLV02-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	11725
ZNHIT3-BGRSLV02-45_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2365					GRCh38	V40	ZNHIT3-BGRSLV02-45_S121_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNHIT3-BGRSLV02-45_S121_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11771
ZNHIT3-BGRSLV02-46_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2366	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8253
ZNHIT3-BGRSLV02-46_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2366	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8299
ZNHIT3-BGRSLV02-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNHIT3-BGRSLV02-46_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11542
ZNHIT3-BGRSLV02-46_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	11588
ZNHIT3-BGRSLV02-46_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	11634
ZNHIT3-BGRSLV02-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	11680
ZNHIT3-BGRSLV02-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	11726
ZNHIT3-BGRSLV02-46_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2366					GRCh38	V40	ZNHIT3-BGRSLV02-46_S122_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNHIT3-BGRSLV02-46_S122_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11772