GFPT1 RNA-Seq in HepG2

General Information


RBP	GFPT1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GFPT1-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	GFPT1-BGHcLV45-39
Rep2	GFPT1-BGHcLV45-40
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	92.1
Rep2_qPCR	89.4
Rep1_WB	74.2
Rep2_WB	78.0
Antibody Cat#	5322S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1624

Experiment Information (Status: Submitting)

	BGHcLV45-39	BGHcLV45-40
idx	1217	1217
TRCN#_or_BGC#	BGC#0001142	BGC#0001142
shRNA_or_gRNA_sequence	TGGAATAGCTCATACCCGTT	TGGAATAGCTCATACCCGTT
PAM	GGG	GGG
Name	GFPT1_95	GFPT1_95
Sample_ID	BGHcLV45-39	BGHcLV45-40
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	GFPT1	GFPT1
qPCR_result	92.1	89.4
Ave_qPCR	90.7
RT-qPCR_primer-F	gcctgcaaaatccagcttat
RT-qPCR_primer-R	cccaacgggtatgagctatt
protein_conc	4653	4700
WB_result	74.2	78.0
Ave_WB
WB_DONE_date	10/10/24
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	9729	9730

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

	BGHcLV45-39	BGHcLV45-40
Sample_ID	BGHcLV45-39	BGHcLV45-40
Sample Name
Sample Name	GFPT1-BGHcLV45-39	GFPT1-BGHcLV45-40
RBP	GFPT1	GFPT1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13706	13707

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-39	BGHcLV45-40
Sample #	21	22
Sample Name	GFPT1-BGHcLV45-39	GFPT1-BGHcLV45-40
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	288	283
Peak_Molarity	78.60	81.00
libSampleQC_DNA_Well	DNA_Library_set76/set1/E9.png	DNA_Library_set76/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/E3.png	RNA_Library_set76/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-39	BGHcLV45-40
RBP	GFPT1	GFPT1
Batch_ID	BGHcLV45	BGHcLV45
WB_result	74.200	78.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4630	4631

Sequencing Information

	BGHcLV45-39	BGHcLV45-40
Sample_ID	BGHcLV45-39	BGHcLV45-40
Sample Name	GFPT1-BGHcLV45-39	GFPT1-BGHcLV45-40
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	31,967,303	35,166,680
total_aligned_reads	28,761,686	30,485,851
unique_aligned_reads	27,096,713	28,693,562
percent_uniqueAligned	0.84764	0.81593
correlation_replicates	0.998685	0.998685
spikein_reads	13,448	16,194
percent_spikeins	0.00042	0.00046
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3341	3342

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-BGHcLV45-39_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3341	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31830
GFPT1-BGHcLV45-39_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3341	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31872
GFPT1-BGHcLV45-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGHcLV45-39_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31914
GFPT1-BGHcLV45-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_Aligned.sortedByCoord.out.bam		ENCORE2	31956
GFPT1-BGHcLV45-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_Aligned.sortedByCoord.out.bam		ENCORE2	31998
GFPT1-BGHcLV45-39_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_Aligned.sortedByCoord.out.bam		ENCORE2	32040
GFPT1-BGHcLV45-39_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_Aligned.sortedByCoord.out.bam		ENCORE2	32082
GFPT1-BGHcLV45-39_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3341					GRCh38	V40	GFPT1-BGHcLV45-39_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGHcLV45-39_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32124
GFPT1-BGHcLV45-40_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3342	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31831
GFPT1-BGHcLV45-40_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3342	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31873
GFPT1-BGHcLV45-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGHcLV45-40_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31915
GFPT1-BGHcLV45-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_Aligned.sortedByCoord.out.bam		ENCORE2	31957
GFPT1-BGHcLV45-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_Aligned.sortedByCoord.out.bam		ENCORE2	31999
GFPT1-BGHcLV45-40_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_Aligned.sortedByCoord.out.bam		ENCORE2	32041
GFPT1-BGHcLV45-40_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_Aligned.sortedByCoord.out.bam		ENCORE2	32083
GFPT1-BGHcLV45-40_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3342					GRCh38	V40	GFPT1-BGHcLV45-40_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,GFPT1-BGHcLV45-40_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32125