EDF1 RNA-Seq in HepG2

General Information


RBP	EDF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EDF1-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EDF1-BGHcLV39-39
Rep2	EDF1-BGHcLV39-40
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	80.0
Rep2_qPCR	72.5
Rep1_WB	89.8
Rep2_WB	82.3
Antibody Cat#	A304-039A
Antibody Lot#
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1248

Experiment Information (Status: Submitting)

	BGHcLV39-39	BGHcLV39-40
idx	1241	1242
TRCN#_or_BGC#	BGC#0000945	BGC#0000945
shRNA_or_gRNA_sequence	GTGACGGTGCTGCGCAAGAA	GTGACGGTGCTGCGCAAGAA
PAM	ggg	ggg
Name	EDF1_92	EDF1_92
Sample_ID	BGHcLV39-39	BGHcLV39-40
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EDF1	EDF1
qPCR_result	80.0	72.5
Ave_qPCR	76.2
RT-qPCR_primer-F	atcttagcggcacagagacg
RT-qPCR_primer-R	ttggccgtgttcttggtaat
protein_conc	1553	1707
WB_result	89.8	82.3
Ave_WB	86.1
WB_DONE_date	7/5/23
MW	16KD
IP
antibody_Cat#	A304-039A
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7432	7433

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EDF1	Product_ID: A304-039A Lot_ID: 1 Source: Bethyl Labs Target Name: EDF1-human

Experiment Status

	BGHcLV39-39	BGHcLV39-40
Sample_ID	BGHcLV39-39	BGHcLV39-40
Sample Name
Sample Name	EDF1-BGHcLV39-39	EDF1-BGHcLV39-40
RBP	EDF1	EDF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11988	11989

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-39	BGHcLV39-40
Sample #	15	16
Sample Name	EDF1-BGHcLV39-39	EDF1-BGHcLV39-40
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	275	272
Peak_Molarity	35.40	41.80
libSampleQC_DNA_Well	DNA_Library_set63/set1/G10.png	DNA_Library_set63/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/G10.png	RNA_Library_set63/set1/H10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-39	BGHcLV39-40
RBP	EDF1	EDF1
Batch_ID	BGHcLV39	BGHcLV39
WB_result	89.800	82.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3758	3759

Sequencing Information

	BGHcLV39-39	BGHcLV39-40
Sample_ID	BGHcLV39-39	BGHcLV39-40
Sample Name	EDF1-BGHcLV39-39	EDF1-BGHcLV39-40
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	64,371,025	15,202,306
total_aligned_reads	50,723,210	12,272,876
unique_aligned_reads	47,893,705	11,584,394
percent_uniqueAligned	0.74403	0.76202
correlation_replicates	0.999570	0.999570
spikein_reads	19,584	2,828
percent_spikeins	0.00030	0.00019
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2657	2658

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
EDF1-BGHcLV39-39_S10_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2657	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8642
EDF1-BGHcLV39-39_S10_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2657	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8668
EDF1-BGHcLV39-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39_S10_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGHcLV39-39_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9939
EDF1-BGHcLV39-39_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39/Aligned.sortedByCoord.out.bam		ENCORE2	9965
EDF1-BGHcLV39-39_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39/Aligned.sortedByCoord.out.bam		ENCORE2	9991
EDF1-BGHcLV39-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39/Aligned.sortedByCoord.out.bam		ENCORE2	10017
EDF1-BGHcLV39-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39/Aligned.sortedByCoord.out.bam		ENCORE2	10043
EDF1-BGHcLV39-39_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2657					GRCh38	V40	EDF1-BGHcLV39-39_S10_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGHcLV39-39_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10069
EDF1-BGHcLV39-40_S491_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2658	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8643
EDF1-BGHcLV39-40_S491_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2658	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8669
EDF1-BGHcLV39-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40_S491_L004_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGHcLV39-40_S491_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9940
EDF1-BGHcLV39-40_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40/Aligned.sortedByCoord.out.bam		ENCORE2	9966
EDF1-BGHcLV39-40_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40/Aligned.sortedByCoord.out.bam		ENCORE2	9992
EDF1-BGHcLV39-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40/Aligned.sortedByCoord.out.bam		ENCORE2	10018
EDF1-BGHcLV39-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40/Aligned.sortedByCoord.out.bam		ENCORE2	10044
EDF1-BGHcLV39-40_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2658					GRCh38	V40	EDF1-BGHcLV39-40_S491_L004_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGHcLV39-40_S491_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10070