APEH RNA-Seq in HepG2

General Information


RBP	APEH
Cell_Line	HepG2
Method	CRISPR
Exp_Name	APEH-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR933UFA
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR828XJV
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	APEH-BGHcLV27-9
Rep2	APEH-BGHcLV27-10
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	71.8
Rep2_qPCR	65.5
Rep1_WB	85.9
Rep2_WB	87.2
Antibody Cat#	A304-808A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB652JMJ
Status	Released
Project	ENCODE4
ID	808

Experiment Information (Status: Released)

	BGHcLV27-9	BGHcLV27-10
idx	775	776
TRCN#_or_BGC#	BGC#0000631	BGC#0000631
shRNA_or_gRNA_sequence	GTACGGCGGCCAATACCGGA	GTACGGCGGCCAATACCGGA
PAM	CGG	CGG
Name	APEH_99	APEH_99
Sample_ID	BGHcLV27-9	BGHcLV27-10
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	APEH	APEH
qPCR_result	71.8	65.5
Ave_qPCR	68.7
RT-qPCR_primer-F	gctgaagaagccagaccaag
RT-qPCR_primer-R	cccctcaagcacagagatgt
protein_conc	2213	2428
WB_result	85.9	87.2
Ave_WB	86.6
WB_DONE_date	5/25/21	JESS
MW	81kDa
IP	Rabbit / I
antibody_Cat#	A304-808A	LOT# 1
Antibody DCC ID	ENCAB652JMJ	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	6936	6937

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
APEH	Product_ID: A304-808A Lot_ID: 1 Source: Bethyl Labs Target Name: APEH-human

Experiment Status

	BGHcLV27-9	BGHcLV27-10
Sample_ID	BGHcLV27-9	BGHcLV27-10
Sample Name
Sample Name	APEH-BGHcLV27-9	APEH-BGHcLV27-10
RBP	APEH	APEH
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9679	9680

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-9	BGHcLV27-10
Sample #	83	84
Sample Name	APEH-BGHcLV27-9	APEH-BGHcLV27-10
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	290	292
Peak_Molarity	183.00	148.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/G7.png	DNA_Library_set48-49/set2/H7.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/A8.png	RNA_Library_set48-49/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-9	BGHcLV27-10
RBP	APEH	APEH
Batch_ID	BGHcLV27	BGHcLV27
WB_result	85.900	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1642	1643

Sequencing Information

	BGHcLV27-9	BGHcLV27-10
Sample_ID	BGHcLV27-9	BGHcLV27-10
Sample Name	APEH-BGHcLV27-9	APEH-BGHcLV27-10
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	78,011,744	55,325,162
total_aligned_reads	67,449,578	48,396,326
unique_aligned_reads	63,486,652	45,589,104
percent_uniqueAligned	0.81381	0.82402
correlation_replicates	0.997690	0.997690
spikein_reads	24,564	10,656
percent_spikeins	0.00031	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1793	1794

Data Submission Information

	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-10	BGHcLV27-10	BGHcLV27-10	BGHcLV27-10
ENCODE_alias	brenton-graveley:APEH-BGHcLV27	brenton-graveley:APEH-BGHcLV27-9	brenton-graveley:L-APEH-BGHcLV27-9	brenton-graveley:APEH-BGHcLV27-9_S63_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGHcLV27-9_S63_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGHcLV27-HepG2	brenton-graveley:APEH-BGHcLV27-10	brenton-graveley:L-APEH-BGHcLV27-10	brenton-graveley:APEH-BGHcLV27-10_S64_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGHcLV27-10_S64_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR828XJV	ENCBS904ZTD	ENCLB965WKM	ENCFF510SDI	ENCFF003CLT	ENCSR933UFA	ENCBS486BLT	ENCLB282FCX	ENCFF518TOU	ENCFF985BBM
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	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-9	BGHcLV27-10	BGHcLV27-10	BGHcLV27-10	BGHcLV27-10
Sample Name	APEH-BGHcLV27-9	APEH-BGHcLV27-9	APEH-BGHcLV27-9	APEH-BGHcLV27-9	APEH-BGHcLV27-9	APEH-BGHcLV27-9	APEH-BGHcLV27-10	APEH-BGHcLV27-10	APEH-BGHcLV27-10	APEH-BGHcLV27-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		APEH-BGHcLV27-10.pdf	L-APEH-BGHcLV27-9.pdf				APEH-BGHcLV27-9.pdf	L-APEH-BGHcLV27-10.pdf
ID	3436	3506	3640	3774	3908	7084	3507	3641	3775	3909

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
APEH-BGHcLV27-9_S63_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1793	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3785
APEH-BGHcLV27-9_S63_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1793	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3811
APEH-BGHcLV27-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9_S63_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGHcLV27-9_S63_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25472
APEH-BGHcLV27-9_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9_S63_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGHcLV27-9_S63_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25498
APEH-BGHcLV27-9_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9/Aligned.sortedByCoord.out.bam		ENCORE2	26436
APEH-BGHcLV27-9_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9/Aligned.sortedByCoord.out.bam		ENCORE2	26462
APEH-BGHcLV27-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9/Aligned.sortedByCoord.out.bam		ENCORE2	26488
APEH-BGHcLV27-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1793					GRCh38	V40	APEH-BGHcLV27-9/Aligned.sortedByCoord.out.bam		ENCORE2	26514
APEH-BGHcLV27-10_S64_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1794	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3784
APEH-BGHcLV27-10_S64_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1794	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3810
APEH-BGHcLV27-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10_S64_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGHcLV27-10_S64_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25471
APEH-BGHcLV27-10_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10_S64_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGHcLV27-10_S64_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25497
APEH-BGHcLV27-10_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10/Aligned.sortedByCoord.out.bam		ENCORE2	26435
APEH-BGHcLV27-10_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10/Aligned.sortedByCoord.out.bam		ENCORE2	26461
APEH-BGHcLV27-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10/Aligned.sortedByCoord.out.bam		ENCORE2	26487
APEH-BGHcLV27-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1794					GRCh38	V40	APEH-BGHcLV27-10/Aligned.sortedByCoord.out.bam		ENCORE2	26513