ZRANB2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-21	BGRSLV02-22
idx	0	0
TRCN#_or_BGC#	TRCN0000013427	TRCN0000013427
shRNA_or_gRNA_sequence	CCGGCTTCACATTCACGATCTTCATCTCGAGATGAAGATCGTGAATGTGAAGTTTTT	CCGGCTTCACATTCACGATCTTCATCTCGAGATGAAGATCGTGAATGTGAAGTTTTT
PAM
Name	ZRANB2	ZRANB2
Sample_ID	BGRSLV02-21	BGRSLV02-22
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZRANB2	ZRANB2
qPCR_result	51.0	56.7
Ave_qPCR	53.9
RT-qPCR_primer-F	atgtgaattgggccagaaga
RT-qPCR_primer-R	aaaccaccaccatatcctgttc
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	8258	8259

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-21	BGRSLV02-22
Sample_ID	BGRSLV02-21	BGRSLV02-22
Sample Name
Sample Name	ZRANB2-BGRSLV02-21	ZRANB2-BGRSLV02-22
RBP	ZRANB2	ZRANB2
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	11308	11309

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-21	BGRSLV02-22
Sample #	11	12
Sample Name	ZRANB2-BGRSLV02-21	ZRANB2-BGRSLV02-22
Sample_Name_Alias
Index Well Position	C02	D02
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	291	290
Peak_Molarity	47.50	59.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/C8.png	DNA_Library_set57/set1/D8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set57/set1/C2.png	RNA_Library_set57/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-21	BGRSLV02-22
RBP	ZRANB2	ZRANB2
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	3472	3473

Sequencing Information

	BGRSLV02-21	BGRSLV02-22
Sample_ID	BGRSLV02-21	BGRSLV02-22
Sample Name	ZRANB2-BGRSLV02-21	ZRANB2-BGRSLV02-22
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	45,027,925	38,555,278
total_aligned_reads	41,374,446	34,988,161
unique_aligned_reads	38,290,402	31,956,510
percent_uniqueAligned	0.85037	0.82885
correlation_replicates	0.989872	0.989872
spikein_reads	29,224	28,126
percent_spikeins	0.00065	0.00073
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2343	2344

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
ZRANB2-BGRSLV02-21_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2343	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	8254
ZRANB2-BGRSLV02-21_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2343	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	8300
ZRANB2-BGRSLV02-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2343					GRCh38	V40	ZRANB2-BGRSLV02-21_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZRANB2-BGRSLV02-21_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11543
ZRANB2-BGRSLV02-21_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	2343					GRCh38	V40	ZRANB2-BGRSLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	11589
ZRANB2-BGRSLV02-21_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	2343					GRCh38	V40	ZRANB2-BGRSLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	11635
ZRANB2-BGRSLV02-21_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	2343					GRCh38	V40	ZRANB2-BGRSLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	11681
ZRANB2-BGRSLV02-21_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	2343					GRCh38	V40	ZRANB2-BGRSLV02-21/Aligned.sortedByCoord.out.bam		ENCORE2	11727
ZRANB2-BGRSLV02-21_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2343					GRCh38	V40	ZRANB2-BGRSLV02-21_S99_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZRANB2-BGRSLV02-21_S99_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11773
ZRANB2-BGRSLV02-22_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2344	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	8255
ZRANB2-BGRSLV02-22_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2344	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	8301
ZRANB2-BGRSLV02-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2344					GRCh38	V40	ZRANB2-BGRSLV02-22_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZRANB2-BGRSLV02-22_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11544
ZRANB2-BGRSLV02-22_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	2344					GRCh38	V40	ZRANB2-BGRSLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	11590
ZRANB2-BGRSLV02-22_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	2344					GRCh38	V40	ZRANB2-BGRSLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	11636
ZRANB2-BGRSLV02-22_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	2344					GRCh38	V40	ZRANB2-BGRSLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	11682
ZRANB2-BGRSLV02-22_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	2344					GRCh38	V40	ZRANB2-BGRSLV02-22/Aligned.sortedByCoord.out.bam		ENCORE2	11728
ZRANB2-BGRSLV02-22_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2344					GRCh38	V40	ZRANB2-BGRSLV02-22_S100_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZRANB2-BGRSLV02-22_S100_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11774