APEX1 RNA-Seq in K562

General Information


RBP	APEX1
Cell_Line	K562
Method	CRISPR
Exp_Name	APEX1-BGKcLV13-K562
ENCODE_series_ID	ENCSR645SRS
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR989ZNZ
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	APEX1-BGKcLV13-3
Rep2	APEX1-BGKcLV13-4
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	28.3
Rep2_qPCR	39.9
Rep1_WB	70.4
Rep2_WB	71.9
Antibody Cat#	MA1-440
Antibody Lot#	LOT# TB260470
Antibody DCC ID	ENCAB328DHC
Status	Released
Project	ENCODE4
ID	164

Experiment Information (Status: Released)

	BGKcLV13-3	BGKcLV13-4
idx	448	449
TRCN#_or_BGC#	BGC#0000304	BGC#0000304
shRNA_or_gRNA_sequence	GATCAGAAAACCTCACCCAG	GATCAGAAAACCTCACCCAG
PAM	tgg	tgg
Name	APEX1_69	APEX1_69
Sample_ID	BGKcLV13-3	BGKcLV13-4
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	APEX1	APEX1
qPCR_result	28.3	39.9
Ave_qPCR	34.1
RT-qPCR_primer-F	tcggacaaggaagggtacag
RT-qPCR_primer-R	gctgttaccagcacaaacga
protein_conc	3798	3427
WB_result	70.4	71.9
Ave_WB	71.2
WB_DONE_date	1/4/19
MW	35KD
IP	MOUSE
antibody_Cat#	MA1-440	LOT# TB260470
Antibody DCC ID	ENCAB328DHC
submitted_to_DCC_date	3/11/19
Rep1_TPM	154	0
Rep2_TPM	185	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4552	4553

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
APEX1	Product_ID: MA1-440 Lot_ID: TB260470 Source: Thermo Fisher Target Name: APEX1-human

Experiment Status

	BGKcLV13-3	BGKcLV13-4
Sample_ID	BGKcLV13-3	BGKcLV13-4
Sample Name	APEX1-BGKcLV13-3	APEX1-BGKcLV13-4
Sample Name	APEX1-BGKcLV13-3	APEX1-BGKcLV13-4
RBP	APEX1	APEX1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2897	2898

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-3	BGKcLV13-4
Sample #	51	52
Sample Name	APEX1-BGKcLV13-3	APEX1-BGKcLV13-4
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-C1	1-D1
Tecan	52.22	68.26
Tecan_date	2019-03-18	2019-03-18
Size_bp	291	292
Peak_Molarity	38.70	45.40
libSampleQC_DNA_Well	DNA_Library_set42/set1/C7.png	DNA_Library_set42/set1/D7.png
RIN	9.5	9.9
libSample_RNA_Well	RNA_Library_set42/set1/C7.png	RNA_Library_set42/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-3	BGKcLV13-4
RBP	APEX1	APEX1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	70.400	71.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	51	52

Sequencing Information

	BGKcLV13-3	BGKcLV13-4
Sample_ID	BGKcLV13-3	BGKcLV13-4
Sample Name	APEX1-BGKcLV13-3	APEX1-BGKcLV13-4
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	76,553,046	59,813,528
total_aligned_reads	72,947,818	57,019,138
unique_aligned_reads	66,367,492	52,085,392
percent_uniqueAligned	0.86695	0.87080
correlation_replicates	0.996736	0.996736
spikein_reads	69,750	66,622
percent_spikeins	0.00091	0.00111
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	7	8

Data Submission Information

	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-4	BGKcLV13-4	BGKcLV13-4	BGKcLV13-4
ENCODE_alias	brenton-graveley:APEX1-BGKcLV13	brenton-graveley:APEX1-BGKcLV13-3	brenton-graveley:L-APEX1-BGKcLV13-3	brenton-graveley:APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGKcLV13-K562	brenton-graveley:APEX1-BGKcLV13-4	brenton-graveley:L-APEX1-BGKcLV13-4	brenton-graveley:APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR989ZNZ	ENCBS298FYO	ENCLB317NYX	ENCFF193JOW	ENCFF089BME	ENCSR645SRS	ENCBS099GWR	ENCLB185GRI	ENCFF086MEB	ENCFF263QFS
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-3	BGKcLV13-4	BGKcLV13-4	BGKcLV13-4	BGKcLV13-4
Sample Name	APEX1-BGKcLV13-3	APEX1-BGKcLV13-3	APEX1-BGKcLV13-3	APEX1-BGKcLV13-3	APEX1-BGKcLV13-3	APEX1-BGKcLV13-3	APEX1-BGKcLV13-4	APEX1-BGKcLV13-4	APEX1-BGKcLV13-4	APEX1-BGKcLV13-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		APEX1-BGKcLV13-3.pdf	L-APEX1-BGKcLV13-3.pdf				APEX1-BGKcLV13-4.pdf	L-APEX1-BGKcLV13-4.pdf
ID	776	847	929	957	1039	7087	848	930	958	1040

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
APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	7	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	339
APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	7	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	421
APEX1-BGKcLV13-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23678
APEX1-BGKcLV13-3_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3/Aligned.sortedByCoord.out.bam		ENCORE2	23760
APEX1-BGKcLV13-3_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3/Aligned.sortedByCoord.out.bam		ENCORE2	23842
APEX1-BGKcLV13-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3/Aligned.sortedByCoord.out.bam		ENCORE2	23924
APEX1-BGKcLV13-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3/Aligned.sortedByCoord.out.bam		ENCORE2	24006
APEX1-BGKcLV13-3_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	7					GRCh38	V40	APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGKcLV13-3_AACAGGTT+ATACCAAG_HK3H2DSXX_S51_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24088
APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	8	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	340
APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	8	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	422
APEX1-BGKcLV13-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23679
APEX1-BGKcLV13-4_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4/Aligned.sortedByCoord.out.bam		ENCORE2	23761
APEX1-BGKcLV13-4_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4/Aligned.sortedByCoord.out.bam		ENCORE2	23843
APEX1-BGKcLV13-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4/Aligned.sortedByCoord.out.bam		ENCORE2	23925
APEX1-BGKcLV13-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4/Aligned.sortedByCoord.out.bam		ENCORE2	24007
APEX1-BGKcLV13-4_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	8					GRCh38	V40	APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGKcLV13-4_GGTGAACC+GCGTTGGA_HK3H2DSXX_S52_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24089