APEH RNA-Seq in K562

General Information


RBP	APEH
Cell_Line	K562
Method	CRISPR
Exp_Name	APEH-BGKcLV26-K562
ENCODE_series_ID	ENCSR419WNW
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR785JUR
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	APEH-BGKcLV26-25
Rep2	APEH-BGKcLV26-26
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	82.4
Rep2_WB	88.3686745
Antibody Cat#	A304-808A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB652JMJ
Status	Released
Project	ENCODE4
ID	791

Experiment Information (Status: Released)

	BGKcLV26-25	BGKcLV26-26
idx	882	883
TRCN#_or_BGC#	BGC#0000631	BGC#0000631
shRNA_or_gRNA_sequence	GTACGGCGGCCAATACCGGA	GTACGGCGGCCAATACCGGA
PAM	CGG	CGG
Name	APEH_99	APEH_99
Sample_ID	BGKcLV26-25	BGKcLV26-26
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	APEH	APEH
qPCR_result	27.0	15.0
Ave_qPCR	21.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4831	5187
WB_result	82.4	88.3686745
Ave_WB	85.4
WB_DONE_date	4/22/21	jess
MW	81kDa
IP	Rabbit / I
antibody_Cat#	A304-808A	LOT# 1
Antibody DCC ID	ENCAB652JMJ	1/19/22
submitted_to_DCC_date
Rep1_TPM	87.6	0
Rep2_TPM	88.6	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5014	5015

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

	BGKcLV26-25	BGKcLV26-26
Sample_ID	BGKcLV26-25	BGKcLV26-26
Sample Name
Sample Name	APEH-BGKcLV26-25	APEH-BGKcLV26-26
RBP	APEH	APEH
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9763	9764

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-25	BGKcLV26-26
Sample #	21	22
Sample Name	APEH-BGKcLV26-25	APEH-BGKcLV26-26
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	293	290
Peak_Molarity	88.20	94.60
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E3.png	DNA_Library_set48-49/set1/F3.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/E3.png	RNA_Library_set48-49/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-25	BGKcLV26-26
RBP	APEH	APEH
Batch_ID	BGKcLV26	BGKcLV26
WB_result	82.400	88.369
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1580	1581

Sequencing Information

	BGKcLV26-25	BGKcLV26-26
Sample_ID	BGKcLV26-25	BGKcLV26-26
Sample Name	APEH-BGKcLV26-25	APEH-BGKcLV26-26
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	86,102,298	65,565,734
total_aligned_reads	67,684,836	53,621,350
unique_aligned_reads	62,028,404	49,121,072
percent_uniqueAligned	0.72040	0.74919
correlation_replicates	0.997255	0.997255
spikein_reads	29,100	19,660
percent_spikeins	0.00034	0.00030
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1757	1758

Data Submission Information

	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-26	BGKcLV26-26	BGKcLV26-26	BGKcLV26-26
ENCODE_alias	brenton-graveley:APEH-BGKcLV26	brenton-graveley:APEH-BGKcLV26-25	brenton-graveley:L-APEH-BGKcLV26-25	brenton-graveley:APEH-BGKcLV26-25_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGKcLV26-25_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGKcLV26-K562	brenton-graveley:APEH-BGKcLV26-26	brenton-graveley:L-APEH-BGKcLV26-26	brenton-graveley:APEH-BGKcLV26-26_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APEH-BGKcLV26-26_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR785JUR	ENCBS022KRD	ENCLB268TQL	ENCFF680CPH	ENCFF517ULE	ENCSR419WNW	ENCBS652DFI	ENCLB751ZRF	ENCFF629ZPM	ENCFF394TWM
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	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-25	BGKcLV26-26	BGKcLV26-26	BGKcLV26-26	BGKcLV26-26
Sample Name	APEH-BGKcLV26-25	APEH-BGKcLV26-25	APEH-BGKcLV26-25	APEH-BGKcLV26-25	APEH-BGKcLV26-25	APEH-BGKcLV26-25	APEH-BGKcLV26-26	APEH-BGKcLV26-26	APEH-BGKcLV26-26	APEH-BGKcLV26-26
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-19	2022-02-04	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2022-02-04	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		APEH-BGKcLV26-25.pdf	L-APEH-BGKcLV26-25.pdf				APEH-BGKcLV26-26.pdf	L-APEH-BGKcLV26-26.pdf
ID	3456	3546	3680	3814	3948	7085	3547	3681	3815	3949

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-BGKcLV26-25_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1757	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3850
APEH-BGKcLV26-25_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1757	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3900
APEH-BGKcLV26-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGKcLV26-25_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25537
APEH-BGKcLV26-25_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGKcLV26-25_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25587
APEH-BGKcLV26-25_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25/Aligned.sortedByCoord.out.bam		ENCORE2	26553
APEH-BGKcLV26-25_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25/Aligned.sortedByCoord.out.bam		ENCORE2	26603
APEH-BGKcLV26-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25/Aligned.sortedByCoord.out.bam		ENCORE2	26653
APEH-BGKcLV26-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1757					GRCh38	V40	APEH-BGKcLV26-25/Aligned.sortedByCoord.out.bam		ENCORE2	26703
APEH-BGKcLV26-26_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1758	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3851
APEH-BGKcLV26-26_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1758	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3901
APEH-BGKcLV26-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGKcLV26-26_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25538
APEH-BGKcLV26-26_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz,APEH-BGKcLV26-26_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25588
APEH-BGKcLV26-26_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26/Aligned.sortedByCoord.out.bam		ENCORE2	26554
APEH-BGKcLV26-26_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26/Aligned.sortedByCoord.out.bam		ENCORE2	26604
APEH-BGKcLV26-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26/Aligned.sortedByCoord.out.bam		ENCORE2	26654
APEH-BGKcLV26-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1758					GRCh38	V40	APEH-BGKcLV26-26/Aligned.sortedByCoord.out.bam		ENCORE2	26704