PHF11 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-33	BGRSLV02-34
idx	0	0
TRCN#_or_BGC#	TRCN0000020110	TRCN0000020110
shRNA_or_gRNA_sequence	CCGGCCCGAAACAATGAAATGTAATCTCGAGATTACATTTCATTGTTTCGGGTTTTT	CCGGCCCGAAACAATGAAATGTAATCTCGAGATTACATTTCATTGTTTCGGGTTTTT
PAM
Name	PHF11	PHF11
Sample_ID	BGRSLV02-33	BGRSLV02-34
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	PHF11	PHF11
qPCR_result	53.7	44.3
Ave_qPCR	49.0
RT-qPCR_primer-F	agaaacccctctcaggcaat
RT-qPCR_primer-R	ctgtgtgtctgccatgctct
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	8270	8271

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-33	BGRSLV02-34
Sample_ID	BGRSLV02-33	BGRSLV02-34
Sample Name
Sample Name	PHF11-BGRSLV02-33	PHF11-BGRSLV02-34
RBP	PHF11	PHF11
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	11320	11321

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-33	BGRSLV02-34
Sample #	23	24
Sample Name	PHF11-BGRSLV02-33	PHF11-BGRSLV02-34
Sample_Name_Alias
Index Well Position	G03	H03
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	284	294
Peak_Molarity	55.20	61.50
libSampleQC_DNA_Well	DNA_Library_set57/set1/G9.png	DNA_Library_set57/set1/H9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set57/set1/G3.png	RNA_Library_set57/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-33	BGRSLV02-34
RBP	PHF11	PHF11
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	3484	3485

Sequencing Information

	BGRSLV02-33	BGRSLV02-34
Sample_ID	BGRSLV02-33	BGRSLV02-34
Sample Name	PHF11-BGRSLV02-33	PHF11-BGRSLV02-34
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	43,812,186	43,418,994
total_aligned_reads	40,353,411	36,814,844
unique_aligned_reads	37,658,711	34,297,931
percent_uniqueAligned	0.85955	0.78993
correlation_replicates	0.973985	0.973985
spikein_reads	23,062	29,026
percent_spikeins	0.00053	0.00067
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2355	2356

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
PHF11-BGRSLV02-33_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2355	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	8226
PHF11-BGRSLV02-33_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2355	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	8272
PHF11-BGRSLV02-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2355					GRCh38	V40	PHF11-BGRSLV02-33_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz,PHF11-BGRSLV02-33_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11515
PHF11-BGRSLV02-33_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	2355					GRCh38	V40	PHF11-BGRSLV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	11561
PHF11-BGRSLV02-33_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	2355					GRCh38	V40	PHF11-BGRSLV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	11607
PHF11-BGRSLV02-33_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	2355					GRCh38	V40	PHF11-BGRSLV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	11653
PHF11-BGRSLV02-33_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	2355					GRCh38	V40	PHF11-BGRSLV02-33/Aligned.sortedByCoord.out.bam		ENCORE2	11699
PHF11-BGRSLV02-33_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2355					GRCh38	V40	PHF11-BGRSLV02-33_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz,PHF11-BGRSLV02-33_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11745
PHF11-BGRSLV02-34_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2356	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	8227
PHF11-BGRSLV02-34_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2356	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	8273
PHF11-BGRSLV02-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2356					GRCh38	V40	PHF11-BGRSLV02-34_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz,PHF11-BGRSLV02-34_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11516
PHF11-BGRSLV02-34_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	2356					GRCh38	V40	PHF11-BGRSLV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	11562
PHF11-BGRSLV02-34_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	2356					GRCh38	V40	PHF11-BGRSLV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	11608
PHF11-BGRSLV02-34_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	2356					GRCh38	V40	PHF11-BGRSLV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	11654
PHF11-BGRSLV02-34_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	2356					GRCh38	V40	PHF11-BGRSLV02-34/Aligned.sortedByCoord.out.bam		ENCORE2	11700
PHF11-BGRSLV02-34_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2356					GRCh38	V40	PHF11-BGRSLV02-34_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz,PHF11-BGRSLV02-34_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11746