PA2G4 RNA-Seq in K562

General Information


RBP	PA2G4
Cell_Line	K562
Method	shRNA
Exp_Name	PA2G4-BGKLV19-K562
ENCODE_series_ID	ENCSR810YNG
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR309PPC
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	PA2G4_BGKLV19_37B
Rep2	PA2G4_BGKLV19_38B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	92.9
Rep2_qPCR	96.0
Rep1_WB	67.0
Rep2_WB	71.7
Antibody Cat#	A303-083A
Antibody Lot#	A303-083A
Antibody DCC ID	ENCAB860TYM
Status	Released
Project	ENCODE3
ID	476

Experiment Information (Status: Released)

	BGKLV19-37	BGKLV19-38
idx	244	245
TRCN#_or_BGC#	TRCN0000050413	TRCN0000050413
shRNA_or_gRNA_sequence	CCACCAGCATTTCGGTAAATA	CCACCAGCATTTCGGTAAATA
PAM
Name	PA2G4	PA2G4
Sample_ID	BGKLV19-37	BGKLV19-38
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	PA2G4	PA2G4
qPCR_result	92.9	96.0
Ave_qPCR	94.4
RT-qPCR_primer-F	ggatggcttcatcgctaatg
RT-qPCR_primer-R	cagcttcagcacaaaggtga
protein_conc	3018	3346
WB_result	67.0	71.7
Ave_WB	69.3
WB_DONE_date	1/12/2015
MW	44kDa
IP	1	1
antibody_Cat#	A303-083A	A303-083A
Antibody DCC ID	ENCAB860TYM	ENCAB860TYM
submitted_to_DCC_date	4/2/2015
Rep1_TPM	157.389887	0
Rep2_TPM	105.966673	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	269	270

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PA2G4	Product_ID: A303-083A Lot_ID: 1 Source: Bethyl Labs Target Name: PA2G4-human

Experiment Status

	BGKLV19-37	BGKLV19-38
Sample_ID	BGKLV19-37	BGKLV19-38
Sample Name	PA2G4_BGKLV19_37B	PA2G4_BGKLV19_38B
Sample Name	PA2G4_BGKLV19_37B	PA2G4_BGKLV19_38B
RBP	PA2G4	PA2G4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	686	687

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-37	BGKLV19-38
Sample #
Sample Name	PA2G4-BGKLV19-37B	PA2G4-BGKLV19-38B
Sample_Name_Alias	PA2G4_BGKLV19_37B	PA2G4_BGKLV19_38B
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G9.png	DNA_Library_LV18-19/set1/H9.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C4.png	RNA_Library_LV19-21-24/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-37	BGKLV19-38
RBP	PA2G4	PA2G4
Batch_ID	BGKLV19	BGKLV19
WB_result	67.000	71.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2370	2371

Sequencing Information

	BGKLV19-37	BGKLV19-38
Sample_ID	BGKLV19-37	BGKLV19-38
Sample Name	PA2G4_BGKLV19_37B	PA2G4_BGKLV19_38B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	52,840,000	51,190,000
total_aligned_reads	49,137,320	47,697,740
unique_aligned_reads	45,143,450	43,608,512
percent_uniqueAligned	0.85434	0.85190
correlation_replicates	0.987024	0.987024
spikein_reads	286,776	427,460
percent_spikeins	0.00543	0.00835
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1012	1013

Data Submission Information

	BGKLV19-37	BGKLV19-37
ENCODE_alias	brenton-graveley:PA2G4_BGKLV19	brenton-graveley:PA2G4-BGKLV19-K562
ENCODE_accession	ENCSR309PPC	ENCSR810YNG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-37	BGKLV19-37
Sample Name	PA2G4_BGKLV19_37B	PA2G4_BGKLV19_37B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2891	6840

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
PA2G4_BGKLV19_37B_ACTGAT_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1012	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15128
PA2G4_BGKLV19_37B_ACTGAT_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1012	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15186
PA2G4_BGKLV19_37B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B_ACTGAT_L005_R1_001.fastq.gz,PA2G4_BGKLV19_37B_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	15244
PA2G4_BGKLV19_37B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B/Aligned.sortedByCoord.out.bam		ENCORE2	15315
PA2G4_BGKLV19_37B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B/Aligned.sortedByCoord.out.bam		ENCORE2	15373
PA2G4_BGKLV19_37B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B/Aligned.sortedByCoord.out.bam		ENCORE2	15431
PA2G4_BGKLV19_37B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B/Aligned.sortedByCoord.out.bam		ENCORE2	15489
PA2G4_BGKLV19_37B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1012					GRCh38	V40	PA2G4_BGKLV19_37B_ACTGAT_L005_R1_001.fastq.gz,PA2G4_BGKLV19_37B_ACTGAT_L005_R2_001.fastq.gz		ENCORE2	16386
PA2G4_BGKLV19_38B_ATTCCT_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1013	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15129
PA2G4_BGKLV19_38B_ATTCCT_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1013	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15187
PA2G4_BGKLV19_38B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B_ATTCCT_L005_R1_001.fastq.gz,PA2G4_BGKLV19_38B_ATTCCT_L005_R2_001.fastq.gz		ENCORE2	15245
PA2G4_BGKLV19_38B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B/Aligned.sortedByCoord.out.bam		ENCORE2	15316
PA2G4_BGKLV19_38B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B/Aligned.sortedByCoord.out.bam		ENCORE2	15374
PA2G4_BGKLV19_38B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B/Aligned.sortedByCoord.out.bam		ENCORE2	15432
PA2G4_BGKLV19_38B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B/Aligned.sortedByCoord.out.bam		ENCORE2	15490
PA2G4_BGKLV19_38B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1013					GRCh38	V40	PA2G4_BGKLV19_38B_ATTCCT_L005_R1_001.fastq.gz,PA2G4_BGKLV19_38B_ATTCCT_L005_R2_001.fastq.gz		ENCORE2	16387