PHF7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-51dox	BGRSDLV02-52dox
idx	0	0
TRCN#_or_BGC#	TRCN0000016795	TRCN0000016795
shRNA_or_gRNA_sequence	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT
PAM
Name	PHF7	PHF7
Sample_ID	BGRSDLV02-51dox	BGRSDLV02-52dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	PHF7	PHF7
qPCR_result	89.4	88.5
Ave_qPCR	89.0
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	9262	9263

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-51dox	BGRSDLV02-52dox
Sample_ID	BGRSDLV02-51dox	BGRSDLV02-52dox
Sample Name
Sample Name	PHF7-BGRSDLV02-51dox	PHF7-BGRSDLV02-52dox
RBP	PHF7	PHF7
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12366	12367

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-51dox	BGRSDLV02-52dox
Sample #	47	48
Sample Name	PHF7-BGRSDLV02-51dox	PHF7-BGRSDLV02-52dox
Sample_Name_Alias
Index Well Position	G06	H06
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	294	290
Peak_Molarity	75.30	84.70
libSampleQC_DNA_Well	DNA_Library_set65/set1/G6.png	DNA_Library_set65/set1/H6.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set65/set1/G6.png	RNA_Library_set65/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-51dox	BGRSDLV02-52dox
RBP	PHF7	PHF7
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	3968	3969

Sequencing Information

	BGRSDLV02-51dox	BGRSDLV02-52dox
Sample_ID	BGRSDLV02-51dox	BGRSDLV02-52dox
Sample Name	PHF7-BGRSDLV02-51dox	PHF7-BGRSDLV02-52dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	22,611,686	43,871,422
total_aligned_reads	19,125,774	41,093,577
unique_aligned_reads	17,904,260	38,503,350
percent_uniqueAligned	0.79181	0.87764
correlation_replicates	0.976669	0.976669
spikein_reads	8,128	13,910
percent_spikeins	0.00036	0.00032
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2715	2716

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
PHF7-BGRSDLV02-51dox_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2715	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	8788
PHF7-BGRSDLV02-51dox_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2715	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	8864
PHF7-BGRSDLV02-51dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-51dox_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9353
PHF7-BGRSDLV02-51dox_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	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox/Aligned.sortedByCoord.out.bam		ENCORE2	9429
PHF7-BGRSDLV02-51dox_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	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox/Aligned.sortedByCoord.out.bam		ENCORE2	9505
PHF7-BGRSDLV02-51dox_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	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox/Aligned.sortedByCoord.out.bam		ENCORE2	9581
PHF7-BGRSDLV02-51dox_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	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox/Aligned.sortedByCoord.out.bam		ENCORE2	9657
PHF7-BGRSDLV02-51dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2715					GRCh38	V40	PHF7-BGRSDLV02-51dox_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-51dox_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9733
PHF7-BGRSDLV02-52dox_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2716	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	8789
PHF7-BGRSDLV02-52dox_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2716	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	8865
PHF7-BGRSDLV02-52dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-52dox_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9354
PHF7-BGRSDLV02-52dox_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	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox/Aligned.sortedByCoord.out.bam		ENCORE2	9430
PHF7-BGRSDLV02-52dox_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	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox/Aligned.sortedByCoord.out.bam		ENCORE2	9506
PHF7-BGRSDLV02-52dox_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	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox/Aligned.sortedByCoord.out.bam		ENCORE2	9582
PHF7-BGRSDLV02-52dox_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	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox/Aligned.sortedByCoord.out.bam		ENCORE2	9658
PHF7-BGRSDLV02-52dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2716					GRCh38	V40	PHF7-BGRSDLV02-52dox_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-52dox_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9734