EDF1 RNA-Seq in K562

General Information


RBP	EDF1
Cell_Line	K562
Method	CRISPR
Exp_Name	EDF1-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EDF1-BGKcLV40-13
Rep2	EDF1-BGKcLV40-14
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	75.3
Rep2_qPCR	67.2
Rep1_WB	82.0
Rep2_WB	85.2
Antibody Cat#	A304-039A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1359

Experiment Information (Status: Submitting)

	BGKcLV40-13	BGKcLV40-14
idx	0	0
TRCN#_or_BGC#	BGC#0000945	BGC#0000945
shRNA_or_gRNA_sequence	GTGACGGTGCTGCGCAAGAA	GTGACGGTGCTGCGCAAGAA
PAM	ggg	ggg
Name	EDF1_92	EDF1_92
Sample_ID	BGKcLV40-13	BGKcLV40-14
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	EDF1	EDF1
qPCR_result	75.3	67.2
Ave_qPCR	71.3
RT-qPCR_primer-F	atcttagcggcacagagacg
RT-qPCR_primer-R	ttggccgtgttcttggtaat
protein_conc	3783	3929
WB_result	82.0	85.2
Ave_WB	83.6
WB_DONE_date	11/8/23
MW	16kd
IP
antibody_Cat#	A304-039A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5682	5683

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

	BGKcLV40-13	BGKcLV40-14
Sample_ID	BGKcLV40-13	BGKcLV40-14
Sample Name
Sample Name	EDF1-BGKcLV40-13	EDF1-BGKcLV40-14
RBP	EDF1	EDF1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12762	12763

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-13	BGKcLV40-14
Sample #	9	10
Sample Name	EDF1-BGKcLV40-13	EDF1-BGKcLV40-14
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	286	284
Peak_Molarity	72.50	101.00
libSampleQC_DNA_Well	DNA_Library_set67/set1/A8.png	DNA_Library_set67/set1/B8.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set67/set1/A2.png	RNA_Library_set67/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-13	BGKcLV40-14
RBP	EDF1	EDF1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	82.000	85.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4146	4147

Sequencing Information

	BGKcLV40-13	BGKcLV40-14
Sample_ID	BGKcLV40-13	BGKcLV40-14
Sample Name	EDF1-BGKcLV40-13	EDF1-BGKcLV40-14
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	20,131,344	38,131,828
total_aligned_reads	17,059,708	31,958,484
unique_aligned_reads	15,679,997	29,377,083
percent_uniqueAligned	0.77888	0.77041
correlation_replicates	0.999309	0.999309
spikein_reads	3,868	2,304
percent_spikeins	0.00019	0.00006
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2801	2802

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-BGKcLV40-13_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2801	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28147
EDF1-BGKcLV40-13_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2801	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28191
EDF1-BGKcLV40-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGKcLV40-13_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28235
EDF1-BGKcLV40-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13/Aligned.sortedByCoord.out.bam		ENCORE2	28279
EDF1-BGKcLV40-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13/Aligned.sortedByCoord.out.bam		ENCORE2	28323
EDF1-BGKcLV40-13_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13/Aligned.sortedByCoord.out.bam		ENCORE2	28367
EDF1-BGKcLV40-13_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13/Aligned.sortedByCoord.out.bam		ENCORE2	28411
EDF1-BGKcLV40-13_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2801					GRCh38	V40	EDF1-BGKcLV40-13_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGKcLV40-13_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28455
EDF1-BGKcLV40-14_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2802	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28148
EDF1-BGKcLV40-14_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2802	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28192
EDF1-BGKcLV40-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGKcLV40-14_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28236
EDF1-BGKcLV40-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14/Aligned.sortedByCoord.out.bam		ENCORE2	28280
EDF1-BGKcLV40-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14/Aligned.sortedByCoord.out.bam		ENCORE2	28324
EDF1-BGKcLV40-14_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14/Aligned.sortedByCoord.out.bam		ENCORE2	28368
EDF1-BGKcLV40-14_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14/Aligned.sortedByCoord.out.bam		ENCORE2	28412
EDF1-BGKcLV40-14_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2802					GRCh38	V40	EDF1-BGKcLV40-14_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDF1-BGKcLV40-14_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28456