APTX RNA-Seq in HepG2

General Information


RBP	APTX
Cell_Line	HepG2
Method	CRISPR
Exp_Name	APTX-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR731TJP
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR489DNH
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	APTX-BGHcLV24-11
Rep2	APTX-BGHcLV24-12
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	76.0
Rep2_WB	77.0
Antibody Cat#	PA5-92422
Antibody Lot#	LOT# UK2881303A
Antibody DCC ID	ENCAB069JSS
Status	Released
Project	ENCODE4
ID	3

Experiment Information (Status: Released)

	BGHcLV24-11	BGHcLV24-12
idx	669	670
TRCN#_or_BGC#	BGC#0000564	BGC#0000564
shRNA_or_gRNA_sequence	CGTGGTAGCCCAATCGGAAG	CGTGGTAGCCCAATCGGAAG
PAM	CGG	CGG
Name	APTX_97	APTX_97
Sample_ID	BGHcLV24-11	BGHcLV24-12
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	APTX	APTX
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gccattccgagtatgagcca
RT-qPCR_primer-R	ccagcctcttgtaccatctcg
protein_conc	4625	4133
WB_result	76.0	77.0
Ave_WB	76.5
WB_DONE_date	11/9/20
MW	40.7KD
IP	Rabbit / I
antibody_Cat#	PA5-92422	LOT# UK2881303A
Antibody DCC ID	ENCAB069JSS
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6824	6825

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
APTX	Product_ID: PA5-92422 Lot_ID: UK2881303A Source: Thermo Fisher Target Name: APTX-human

Experiment Status

	BGHcLV24-11	BGHcLV24-12
Sample_ID	BGHcLV24-11	BGHcLV24-12
Sample Name
Sample Name	APTX-BGHcLV24-11	APTX-BGHcLV24-12
RBP	APTX	APTX
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7785	7786

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-11	BGHcLV24-12
Sample #	7	8
Sample Name	APTX-BGHcLV24-11	APTX-BGHcLV24-12
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	292	293
Peak_Molarity	74.10	93.40
libSampleQC_DNA_Well	DNA_Library_set47/set1/G4.png	DNA_Library_set47/set1/H4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set1/G1.png	RNA_Library_set47/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-11	BGHcLV24-12
RBP	APTX	APTX
Batch_ID	BGHcLV24	BGHcLV24
WB_result	76.000	77.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1470	1471

Sequencing Information

	BGHcLV24-11	BGHcLV24-12
Sample_ID	BGHcLV24-11	BGHcLV24-12
Sample Name	APTX-BGHcLV24-11	APTX-BGHcLV24-12
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	101,257,230	84,386,364
total_aligned_reads	87,967,122	73,809,210
unique_aligned_reads	82,910,954	69,522,780
percent_uniqueAligned	0.81882	0.82386
correlation_replicates	0.988645	0.988645
spikein_reads	48,444	30,438
percent_spikeins	0.00048	0.00036
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	552	553

Data Submission Information

	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-12	BGHcLV24-12	BGHcLV24-12	BGHcLV24-12
ENCODE_alias	brenton-graveley:APTX-BGHcLV24	brenton-graveley:APTX-BGHcLV24-11	brenton-graveley:L-APTX-BGHcLV24-11	brenton-graveley:APTX-BGHcLV24-11_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGHcLV24-11_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGHcLV24-HepG2	brenton-graveley:APTX-BGHcLV24-12	brenton-graveley:L-APTX-BGHcLV24-12	brenton-graveley:APTX-BGHcLV24-12_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGHcLV24-12_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR489DNH	ENCBS689EVR	ENCLB377UHH	ENCFF514QPW	ENCFF029EZV	ENCSR731TJP	ENCBS398SGO	ENCLB557WOW	ENCFF270SKB	ENCFF315NYI
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	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-11	BGHcLV24-12	BGHcLV24-12	BGHcLV24-12	BGHcLV24-12
Sample Name	APTX-BGHcLV24-11	APTX-BGHcLV24-11	APTX-BGHcLV24-11	APTX-BGHcLV24-11	APTX-BGHcLV24-11	APTX-BGHcLV24-11	APTX-BGHcLV24-12	APTX-BGHcLV24-12	APTX-BGHcLV24-12	APTX-BGHcLV24-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		APTX-BGHcLV24-11.pdf	L-APTX-BGHcLV24-11.pdf				APTX-BGHcLV24-12.pdf	L-APTX-BGHcLV24-12.pdf
ID	3238	3263	3307	3351	3395	7090	3264	3308	3352	3396

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
APTX-BGHcLV24-11_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	552	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3708
APTX-BGHcLV24-11_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	552	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3754
APTX-BGHcLV24-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGHcLV24-11_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25397
APTX-BGHcLV24-11_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGHcLV24-11_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25441
APTX-BGHcLV24-11_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11/Aligned.sortedByCoord.out.bam		ENCORE2	26273
APTX-BGHcLV24-11_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11/Aligned.sortedByCoord.out.bam		ENCORE2	26317
APTX-BGHcLV24-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11/Aligned.sortedByCoord.out.bam		ENCORE2	26361
APTX-BGHcLV24-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	552					GRCh38	V40	APTX-BGHcLV24-11/Aligned.sortedByCoord.out.bam		ENCORE2	26405
APTX-BGHcLV24-12_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	553	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3709
APTX-BGHcLV24-12_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	553	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3755
APTX-BGHcLV24-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGHcLV24-12_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25398
APTX-BGHcLV24-12_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGHcLV24-12_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25442
APTX-BGHcLV24-12_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12/Aligned.sortedByCoord.out.bam		ENCORE2	26274
APTX-BGHcLV24-12_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12/Aligned.sortedByCoord.out.bam		ENCORE2	26318
APTX-BGHcLV24-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12/Aligned.sortedByCoord.out.bam		ENCORE2	26362
APTX-BGHcLV24-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	553					GRCh38	V40	APTX-BGHcLV24-12/Aligned.sortedByCoord.out.bam		ENCORE2	26406