ZNF277 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-75dox	BGRSDLV02-76dox
idx	0	0
TRCN#_or_BGC#	TRCN0000019624	TRCN0000019624
shRNA_or_gRNA_sequence	CCGGCGTGGGATCAACTGGAGTATTCTCGAGAATACTCCAGTTGATCCCACGTTTTT	CCGGCGTGGGATCAACTGGAGTATTCTCGAGAATACTCCAGTTGATCCCACGTTTTT
PAM
Name	ZNF277	ZNF277
Sample_ID	BGRSDLV02-75dox	BGRSDLV02-76dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZNF277	ZNF277
qPCR_result	89.0	88.9
Ave_qPCR	88.9
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9286	9287

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-75dox	BGRSDLV02-76dox
Sample_ID	BGRSDLV02-75dox	BGRSDLV02-76dox
Sample Name
Sample Name	ZNF277-BGRSDLV02-75dox	ZNF277-BGRSDLV02-76dox
RBP	ZNF277	ZNF277
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12382	12383

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-75dox	BGRSDLV02-76dox
Sample #	63	64
Sample Name	ZNF277-BGRSDLV02-75dox	ZNF277-BGRSDLV02-76dox
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	287	292
Peak_Molarity	88.00	73.10
libSampleQC_DNA_Well	DNA_Library_set65/set1/G8.png	DNA_Library_set65/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/G8.png	RNA_Library_set65/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-75dox	BGRSDLV02-76dox
RBP	ZNF277	ZNF277
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3984	3985

Sequencing Information

	BGRSDLV02-75dox	BGRSDLV02-76dox
Sample_ID	BGRSDLV02-75dox	BGRSDLV02-76dox
Sample Name	ZNF277-BGRSDLV02-75dox	ZNF277-BGRSDLV02-76dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	22,278,717	20,259,736
total_aligned_reads	20,998,225	19,037,085
unique_aligned_reads	19,677,519	17,854,092
percent_uniqueAligned	0.88324	0.88126
correlation_replicates	0.980838	0.980838
spikein_reads	1,390	3,968
percent_spikeins	0.00006	0.00020
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2731	2732

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
ZNF277-BGRSDLV02-75dox_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2731	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8804
ZNF277-BGRSDLV02-75dox_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2731	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8880
ZNF277-BGRSDLV02-75dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSDLV02-75dox_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9369
ZNF277-BGRSDLV02-75dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox/Aligned.sortedByCoord.out.bam		ENCORE2	9445
ZNF277-BGRSDLV02-75dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox/Aligned.sortedByCoord.out.bam		ENCORE2	9521
ZNF277-BGRSDLV02-75dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox/Aligned.sortedByCoord.out.bam		ENCORE2	9597
ZNF277-BGRSDLV02-75dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox/Aligned.sortedByCoord.out.bam		ENCORE2	9673
ZNF277-BGRSDLV02-75dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2731					GRCh38	V40	ZNF277-BGRSDLV02-75dox_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSDLV02-75dox_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9749
ZNF277-BGRSDLV02-76dox_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2732	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8805
ZNF277-BGRSDLV02-76dox_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2732	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8881
ZNF277-BGRSDLV02-76dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSDLV02-76dox_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9370
ZNF277-BGRSDLV02-76dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox/Aligned.sortedByCoord.out.bam		ENCORE2	9446
ZNF277-BGRSDLV02-76dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox/Aligned.sortedByCoord.out.bam		ENCORE2	9522
ZNF277-BGRSDLV02-76dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox/Aligned.sortedByCoord.out.bam		ENCORE2	9598
ZNF277-BGRSDLV02-76dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox/Aligned.sortedByCoord.out.bam		ENCORE2	9674
ZNF277-BGRSDLV02-76dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2732					GRCh38	V40	ZNF277-BGRSDLV02-76dox_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSDLV02-76dox_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9750