PA2G4 RNA-Seq in HepG2

General Information


RBP	PA2G4
Cell_Line	HepG2
Method	shRNA
Exp_Name	PA2G4-BGHLV16-HepG2
ENCODE_series_ID	ENCSR319INT
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR028YAQ
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	PA2G4_BGHLV16_35
Rep2	PA2G4_BGHLV16_36
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	75.9
Rep2_qPCR	75.5
Rep1_WB	70.8
Rep2_WB	69.2
Antibody Cat#	A303-083A
Antibody Lot#	A303-083A
Antibody DCC ID	ENCAB860TYM
Status	Released
Project	ENCODE3
ID	421

Experiment Information (Status: Released)

	BGHLV16-35	BGHLV16-36
idx	203	204
TRCN#_or_BGC#	TRCN0000050413	TRCN0000050413
shRNA_or_gRNA_sequence	CCACCAGCATTTCGGTAAATA	CCACCAGCATTTCGGTAAATA
PAM
Name	PA2G4	PA2G4
Sample_ID	BGHLV16-35	BGHLV16-36
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	PA2G4	PA2G4
qPCR_result	75.9	75.5
Ave_qPCR	75.7
RT-qPCR_primer-F	ggatggcttcatcgctaatg
RT-qPCR_primer-R	cagcttcagcacaaaggtga
protein_conc	3952	3466
WB_result	70.8	69.2
Ave_WB	70.0
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	35.9	0
Rep2_TPM	35.6	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2268	2269

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

	BGHLV16-35	BGHLV16-36
Sample_ID	BGHLV16-35	BGHLV16-36
Sample Name	PA2G4_BGHLV16_35	PA2G4_BGHLV16_36
Sample Name	PA2G4_BGHLV16_35	PA2G4_BGHLV16_36
RBP	PA2G4	PA2G4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	568	569

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-35	BGHLV16-36
Sample #
Sample Name	PA2G4-BGHLV16-35	PA2G4-BGHLV16-36
Sample_Name_Alias	PA2G4_BGHLV16_35	PA2G4_BGHLV16_36
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A8.png	DNA_Library_LV16-17/set1/B8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G1.png	RNA_Library_LV16-17-18/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-35	BGHLV16-36
RBP	PA2G4	PA2G4
Batch_ID	BGHLV16	BGHLV16
WB_result	70.800	69.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2252	2253

Sequencing Information

	BGHLV16-35	BGHLV16-36
Sample_ID	BGHLV16-35	BGHLV16-36
Sample Name	PA2G4_BGHLV16_35	PA2G4_BGHLV16_36
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	35,080,000	25,770,000
total_aligned_reads	31,348,512	23,203,042
unique_aligned_reads	29,579,826	21,876,532
percent_uniqueAligned	0.84321	0.84891
correlation_replicates	0.993086	0.993086
spikein_reads	98,294	44,138
percent_spikeins	0.00280	0.00171
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	894	895

Data Submission Information

	BGHLV16-35	BGHLV16-35
ENCODE_alias	brenton-graveley:PA2G4_BGHLV16	brenton-graveley:PA2G4-BGHLV16-HepG2
ENCODE_accession	ENCSR028YAQ	ENCSR319INT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-35	BGHLV16-35
Sample Name	PA2G4_BGHLV16_35	PA2G4_BGHLV16_35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2852	6839

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_BGHLV16_35_GTCCGC_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	894	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14294
PA2G4_BGHLV16_35_GTCCGC_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	894	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14320
PA2G4_BGHLV16_35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35_GTCCGC_L007_R1_001.fastq.gz,PA2G4_BGHLV16_35_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	14346
PA2G4_BGHLV16_35_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35/Aligned.sortedByCoord.out.bam		ENCORE2	14372
PA2G4_BGHLV16_35_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35/Aligned.sortedByCoord.out.bam		ENCORE2	14398
PA2G4_BGHLV16_35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35/Aligned.sortedByCoord.out.bam		ENCORE2	14424
PA2G4_BGHLV16_35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35/Aligned.sortedByCoord.out.bam		ENCORE2	14450
PA2G4_BGHLV16_35_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	894					GRCh38	V40	PA2G4_BGHLV16_35_GTCCGC_L007_R1_001.fastq.gz,PA2G4_BGHLV16_35_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	14476
PA2G4_BGHLV16_36_GTGAAA_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	895	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14295
PA2G4_BGHLV16_36_GTGAAA_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	895	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14321
PA2G4_BGHLV16_36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36_GTGAAA_L007_R1_001.fastq.gz,PA2G4_BGHLV16_36_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	14347
PA2G4_BGHLV16_36_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36/Aligned.sortedByCoord.out.bam		ENCORE2	14373
PA2G4_BGHLV16_36_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36/Aligned.sortedByCoord.out.bam		ENCORE2	14399
PA2G4_BGHLV16_36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36/Aligned.sortedByCoord.out.bam		ENCORE2	14425
PA2G4_BGHLV16_36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36/Aligned.sortedByCoord.out.bam		ENCORE2	14451
PA2G4_BGHLV16_36_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	895					GRCh38	V40	PA2G4_BGHLV16_36_GTGAAA_L007_R1_001.fastq.gz,PA2G4_BGHLV16_36_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	14477