GFPT1 RNA-Seq in K562

General Information


RBP	GFPT1
Cell_Line	K562
Method	CRISPR
Exp_Name	GFPT1-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	GFPT1-BGKcLV42-37
Rep2	GFPT1-BGKcLV42-38
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	68.8
Rep2_qPCR	60.8
Rep1_WB	84.6
Rep2_WB	85.7
Antibody Cat#	5322S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1541

Experiment Information (Status: Submitting)

	BGKcLV42-37	BGKcLV42-38
idx	0	0
TRCN#_or_BGC#	BGC#0001139	BGC#0001139
shRNA_or_gRNA_sequence	ATCCTGGAGACCCTAATCAA	ATCCTGGAGACCCTAATCAA
PAM	AGG	AGG
Name	GFPT1_81	GFPT1_81
Sample_ID	BGKcLV42-37	BGKcLV42-38
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	GFPT1	GFPT1
qPCR_result	68.8	60.8
Ave_qPCR	64.8
RT-qPCR_primer-F	gcctgcaaaatccagcttat
RT-qPCR_primer-R	cccaacgggtatgagctatt
protein_conc	2734	2764
WB_result	84.6	85.7
Ave_WB	85.2
WB_DONE_date	5/6/24
MW	80kd
IP
antibody_Cat#	5322S	lot # 1
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	5799	5800

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GFPT1	Product_ID: 5322S Lot_ID: 1 Source: Cell Signaling Technology Target Name: GFPT1-human

Experiment Status

	BGKcLV42-37	BGKcLV42-38
Sample_ID	BGKcLV42-37	BGKcLV42-38
Sample Name
Sample Name	GFPT1-BGKcLV42-37	GFPT1-BGKcLV42-38
RBP	GFPT1	GFPT1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13076	13077

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-37	BGKcLV42-38
Sample #	33	34
Sample Name	GFPT1-BGKcLV42-37	GFPT1-BGKcLV42-38
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	316	297
Peak_Molarity	113.00	127.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/A5.png	DNA_Library_set73/set1/B5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A5.png	RNA_Library_set73/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-37	BGKcLV42-38
RBP	GFPT1	GFPT1
Batch_ID	BGKcLV42	BGKcLV42
WB_result	84.600	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4302	4303

Sequencing Information

	BGKcLV42-37	BGKcLV42-38
Sample_ID	BGKcLV42-37	BGKcLV42-38
Sample Name	GFPT1-BGKcLV42-37	GFPT1-BGKcLV42-38
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	108,607,614	31,554,848
total_aligned_reads	97,189,816	28,961,347
unique_aligned_reads	90,085,687	26,748,454
percent_uniqueAligned	0.82946	0.84768
correlation_replicates	0.996137	0.996137
spikein_reads	9,516	938
percent_spikeins	0.00009	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3169	3170

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
GFPT1-BGKcLV42-37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3169	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30370
GFPT1-BGKcLV42-37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3169	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30460
GFPT1-BGKcLV42-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGKcLV42-37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31302
GFPT1-BGKcLV42-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_Aligned.sortedByCoord.out.bam		ENCORE2	31392
GFPT1-BGKcLV42-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_Aligned.sortedByCoord.out.bam		ENCORE2	31482
GFPT1-BGKcLV42-37_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_Aligned.sortedByCoord.out.bam		ENCORE2	31572
GFPT1-BGKcLV42-37_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_Aligned.sortedByCoord.out.bam		ENCORE2	31662
GFPT1-BGKcLV42-37_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3169					GRCh38	V40	GFPT1-BGKcLV42-37_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGKcLV42-37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31752
GFPT1-BGKcLV42-38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3170	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30371
GFPT1-BGKcLV42-38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3170	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30461
GFPT1-BGKcLV42-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGKcLV42-38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31303
GFPT1-BGKcLV42-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_Aligned.sortedByCoord.out.bam		ENCORE2	31393
GFPT1-BGKcLV42-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_Aligned.sortedByCoord.out.bam		ENCORE2	31483
GFPT1-BGKcLV42-38_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_Aligned.sortedByCoord.out.bam		ENCORE2	31573
GFPT1-BGKcLV42-38_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_Aligned.sortedByCoord.out.bam		ENCORE2	31663
GFPT1-BGKcLV42-38_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3170					GRCh38	V40	GFPT1-BGKcLV42-38_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGKcLV42-38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31753