ZNF277 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV03-59	BGRSLV03-60
idx	0	0
TRCN#_or_BGC#	TRCN0000019624	TRCN0000019624
shRNA_or_gRNA_sequence	CCGGCGTGGGATCAACTGGAGTATTCTCGAGAATACTCCAGTTGATCCCACGTTTTT	CCGGCGTGGGATCAACTGGAGTATTCTCGAGAATACTCCAGTTGATCCCACGTTTTT
PAM
Name	ZNF277	ZNF277
Sample_ID	BGRSLV03-59	BGRSLV03-60
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZNF277	ZNF277
qPCR_result	82.0	83.3
Ave_qPCR	82.7
RT-qPCR_primer-F	tgcacacgaatttgatcttctc
RT-qPCR_primer-R	ggtgaacttgcctccgaata
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	10417	10418

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-59	BGRSLV03-60
Sample_ID	BGRSLV03-59	BGRSLV03-60
Sample Name
Sample Name	ZNF277-BGRSLV03-59	ZNF277-BGRSLV03-60
RBP	ZNF277	ZNF277
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	11406	11407

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-59	BGRSLV03-60
Sample #	37	38
Sample Name	ZNF277-BGRSLV03-59	ZNF277-BGRSLV03-60
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	295	296
Peak_Molarity	92.00	69.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/E11.png	DNA_Library_set58/set1/F11.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set58/set1/E5.png	RNA_Library_set58/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-59	BGRSLV03-60
RBP	ZNF277	ZNF277
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3544	3545

Sequencing Information

	BGRSLV03-59	BGRSLV03-60
Sample_ID	BGRSLV03-59	BGRSLV03-60
Sample Name	ZNF277-BGRSLV03-59	ZNF277-BGRSLV03-60
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	41,755,591	47,379,128
total_aligned_reads	36,735,384	42,721,042
unique_aligned_reads	34,345,461	40,003,265
percent_uniqueAligned	0.82254	0.84432
correlation_replicates	0.980851	0.980851
spikein_reads	244,766	291,134
percent_spikeins	0.00586	0.00614
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2415	2416

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-BGRSLV03-59_S171_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2415	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8160
ZNF277-BGRSLV03-59_S171_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2415	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8202
ZNF277-BGRSLV03-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59_S171_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSLV03-59_S171_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11281
ZNF277-BGRSLV03-59_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59/Aligned.sortedByCoord.out.bam		ENCORE2	11323
ZNF277-BGRSLV03-59_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59/Aligned.sortedByCoord.out.bam		ENCORE2	11365
ZNF277-BGRSLV03-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59/Aligned.sortedByCoord.out.bam		ENCORE2	11407
ZNF277-BGRSLV03-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59/Aligned.sortedByCoord.out.bam		ENCORE2	11449
ZNF277-BGRSLV03-59_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2415					GRCh38	V40	ZNF277-BGRSLV03-59_S171_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSLV03-59_S171_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11491
ZNF277-BGRSLV03-60_S172_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2416	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8161
ZNF277-BGRSLV03-60_S172_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2416	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8203
ZNF277-BGRSLV03-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60_S172_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSLV03-60_S172_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11282
ZNF277-BGRSLV03-60_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60/Aligned.sortedByCoord.out.bam		ENCORE2	11324
ZNF277-BGRSLV03-60_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60/Aligned.sortedByCoord.out.bam		ENCORE2	11366
ZNF277-BGRSLV03-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60/Aligned.sortedByCoord.out.bam		ENCORE2	11408
ZNF277-BGRSLV03-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60/Aligned.sortedByCoord.out.bam		ENCORE2	11450
ZNF277-BGRSLV03-60_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2416					GRCh38	V40	ZNF277-BGRSLV03-60_S172_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF277-BGRSLV03-60_S172_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11492