APEX1 RNA-Seq in HepG2

General Information


RBP	APEX1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	APEX1-BGHcLV14-HepG2
ENCODE_series_ID	ENCSR874EVV
Batch_ID	BGHcLV14
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR367BWL
ENCODE_CN_Exp_ID	ENCSR750CPT
Rep1	APEX1-BGHcLV14-5
Rep2	APEX1-BGHcLV14-6
CN1	NT-BGHcLV14-1
CN2	NT-BGHcLV14-2
Rep1_qPCR	69.6
Rep2_qPCR	67.8
Rep1_WB	65.6
Rep2_WB	60.5
Antibody Cat#	MA1-440
Antibody Lot#	LOT# TB260470
Antibody DCC ID	ENCAB328DHC
Status	Released
Project	ENCODE4
ID	163

Experiment Information (Status: Released)

	BGHcLV14-5	BGHcLV14-6
idx	360	361
TRCN#_or_BGC#	BGC#0000305	BGC#0000305
shRNA_or_gRNA_sequence	CTGGTCAGCTCCTTCGGACA	CTGGTCAGCTCCTTCGGACA
PAM	agg	agg
Name	APEX1_91	APEX1_91
Sample_ID	BGHcLV14-5	BGHcLV14-6
transduction_Date	12/5/18	12/5/18
days	D6	D6
RBP_name	APEX1	APEX1
qPCR_result	69.6	67.8
Ave_qPCR	68.7
RT-qPCR_primer-F	tcggacaaggaagggtacag
RT-qPCR_primer-R	gctgttaccagcacaaacga
protein_conc	3672	2911
WB_result	65.6	60.5
Ave_WB	63.1
WB_DONE_date	2/28/19
MW	35KD
IP	MOUSE
antibody_Cat#	MA1-440	LOT# TB260470
Antibody DCC ID	NO ID
submitted_to_DCC_date	3/11/19
Rep1_TPM	281	0
Rep2_TPM	302	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	6505	6506

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

	BGHcLV14-5	BGHcLV14-6
Sample_ID	BGHcLV14-5	BGHcLV14-6
Sample Name	APEX1-BGHcLV14-5	APEX1-BGHcLV14-6
Sample Name	APEX1-BGHcLV14-5	APEX1-BGHcLV14-6
RBP	APEX1	APEX1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2979	2980

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV14-5	BGHcLV14-6
Sample #	73	74
Sample Name	APEX1-BGHcLV14-5	APEX1-BGHcLV14-6
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-A2	2-B2
Tecan	47.07	75.34
Tecan_date	2019-03-18	2019-03-18
Size_bp	276	291
Peak_Molarity	41.70	49.70
libSampleQC_DNA_Well	DNA_Library_set42/set1/A10.png	DNA_Library_set42/set1/B10.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_set42/set1/A10.png	RNA_Library_set42/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGHcLV14-5	BGHcLV14-6
RBP	APEX1	APEX1
Batch_ID	BGHcLV14	BGHcLV14
WB_result	65.600	60.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	73	74

Sequencing Information

	BGHcLV14-5	BGHcLV14-6
Sample_ID	BGHcLV14-5	BGHcLV14-6
Sample Name	APEX1-BGHcLV14-5	APEX1-BGHcLV14-6
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	60,201,652	51,878,068
total_aligned_reads	56,725,612	48,367,714
unique_aligned_reads	53,386,784	45,558,632
percent_uniqueAligned	0.88680	0.87819
correlation_replicates	0.997434	0.997434
spikein_reads	54,436	26,992
percent_spikeins	0.00090	0.00052
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	5	6

Data Submission Information

	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-6	BGHcLV14-6	BGHcLV14-6	BGHcLV14-6
ENCODE_alias	brenton-graveley:APEX1-BGHcLV14	brenton-graveley:APEX1-BGHcLV14-5	brenton-graveley:L-APEX1-BGHcLV14-5	brenton-graveley:APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGHcLV14-HepG2	brenton-graveley:APEX1-BGHcLV14-6	brenton-graveley:L-APEX1-BGHcLV14-6	brenton-graveley:APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR367BWL	ENCBS708MXU	ENCLB692GYF	ENCFF801NUT	ENCFF078FMT	ENCSR874EVV	ENCBS208YNU	ENCLB024PIE	ENCFF267RCF	ENCFF990GXR
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	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-5	BGHcLV14-6	BGHcLV14-6	BGHcLV14-6	BGHcLV14-6
Sample Name	APEX1-BGHcLV14-5	APEX1-BGHcLV14-5	APEX1-BGHcLV14-5	APEX1-BGHcLV14-5	APEX1-BGHcLV14-5	APEX1-BGHcLV14-5	APEX1-BGHcLV14-6	APEX1-BGHcLV14-6	APEX1-BGHcLV14-6	APEX1-BGHcLV14-6
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-BGHcLV14-5.pdf	L-APEX1-BGHcLV14-5.pdf				APEX1-BGHcLV14-6.pdf	L-APEX1-BGHcLV14-6.pdf
ID	755	805	887	955	1037	7086	806	888	956	1038

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-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	5	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	337
APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	5	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	419
APEX1-BGHcLV14-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	5					GRCh38	V40	APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23676
APEX1-BGHcLV14-5_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	5					GRCh38	V40	APEX1-BGHcLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	23758
APEX1-BGHcLV14-5_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	5					GRCh38	V40	APEX1-BGHcLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	23840
APEX1-BGHcLV14-5_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	5					GRCh38	V40	APEX1-BGHcLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	23922
APEX1-BGHcLV14-5_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	5					GRCh38	V40	APEX1-BGHcLV14-5/Aligned.sortedByCoord.out.bam		ENCORE2	24004
APEX1-BGHcLV14-5_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	5					GRCh38	V40	APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGHcLV14-5_CAATTAAC+CGAGATAT_HK3H2DSXX_S73_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24086
APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	6	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	338
APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	6	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	420
APEX1-BGHcLV14-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	6					GRCh38	V40	APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23677
APEX1-BGHcLV14-6_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	6					GRCh38	V40	APEX1-BGHcLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	23759
APEX1-BGHcLV14-6_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	6					GRCh38	V40	APEX1-BGHcLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	23841
APEX1-BGHcLV14-6_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	6					GRCh38	V40	APEX1-BGHcLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	23923
APEX1-BGHcLV14-6_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	6					GRCh38	V40	APEX1-BGHcLV14-6/Aligned.sortedByCoord.out.bam		ENCORE2	24005
APEX1-BGHcLV14-6_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	6					GRCh38	V40	APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R1_001.filtered.trimmed.paired.fastq.gz,APEX1-BGHcLV14-6_TGGCCGGT+TAGAGCGC_HK3H2DSXX_S74_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24087