PHF14 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV06-13	BGRSLV06-14
idx	0	0
TRCN#_or_BGC#	TRCN0000019310	TRCN0000019310
shRNA_or_gRNA_sequence	CCGGCCTGTAGTGATTCTGAAGAAACTCGAGTTTCTTCAGAATCACTACAGGTTTTT	CCGGCCTGTAGTGATTCTGAAGAAACTCGAGTTTCTTCAGAATCACTACAGGTTTTT
PAM
Name	PHF14	PHF14
Sample_ID	BGRSLV06-13	BGRSLV06-14
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	PHF14	PHF14
qPCR_result	64.3	70.1
Ave_qPCR	67.2
RT-qPCR_primer-F	gaaggaggcacacaaaagaca
RT-qPCR_primer-R	gaggaggatccagacatcca
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	10588	10589

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-13	BGRSLV06-14
Sample_ID	BGRSLV06-13	BGRSLV06-14
Sample Name
Sample Name	PHF14-BGRSLV06-13	PHF14-BGRSLV06-14
RBP	PHF14	PHF14
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	11690	11691

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-13	BGRSLV06-14
Sample #	73	74
Sample Name	PHF14-BGRSLV06-13	PHF14-BGRSLV06-14
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	277	284
Peak_Molarity	96.80	89.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E10.png	DNA_Library_set60-62/set1/F10.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set60-62/set1/A10.png	RNA_Library_set60-62/set1/B10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-13	BGRSLV06-14
RBP	PHF14	PHF14
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3660	3661

Sequencing Information

	BGRSLV06-13	BGRSLV06-14
Sample_ID	BGRSLV06-13	BGRSLV06-14
Sample Name	PHF14-BGRSLV06-13	PHF14-BGRSLV06-14
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	25,808,080	26,935,369
total_aligned_reads	17,855,104	21,448,660
unique_aligned_reads	16,778,699	20,198,870
percent_uniqueAligned	0.65013	0.74990
correlation_replicates	0.983193	0.983193
spikein_reads	18,472	1,810
percent_spikeins	0.00072	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2531	2532

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
PHF14-BGRSLV06-13_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2531	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8586
PHF14-BGRSLV06-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,PHF14-BGRSLV06-13_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10451
PHF14-BGRSLV06-13_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	10503
PHF14-BGRSLV06-13_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	10555
PHF14-BGRSLV06-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	10607
PHF14-BGRSLV06-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	10659
PHF14-BGRSLV06-13_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2531					GRCh38	V40	PHF14-BGRSLV06-13_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,PHF14-BGRSLV06-13_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10711
PHF14-BGRSLV06-13_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2531	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28853
PHF14-BGRSLV06-14_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2532	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8587
PHF14-BGRSLV06-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,PHF14-BGRSLV06-14_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10452
PHF14-BGRSLV06-14_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	10504
PHF14-BGRSLV06-14_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	10556
PHF14-BGRSLV06-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	10608
PHF14-BGRSLV06-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	10660
PHF14-BGRSLV06-14_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2532					GRCh38	V40	PHF14-BGRSLV06-14_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,PHF14-BGRSLV06-14_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10712
PHF14-BGRSLV06-14_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2532	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28854