PPIL4 RNA-Seq in HepG2

General Information


RBP	PPIL4
Cell_Line	HepG2
Method	shRNA
Exp_Name	PPIL4-BGHLV20-HepG2
ENCODE_series_ID	ENCSR067NIT
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR851KEX
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	PPIL4-BGHLV20-51_17732
Rep2	PPIL4-BGHLV20-52_17733
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	77.5
Rep2_qPCR	70.8
Rep1_WB	79.1
Rep2_WB	79.7
Antibody Cat#	GTX117014
Antibody Lot#	GTX117014
Antibody DCC ID	ENCAB535ZKU
Status	Released
Project	ENCODE3
ID	501

Experiment Information (Status: Released)

	BGHLV20-51	BGHLV20-52
idx	415	416
TRCN#_or_BGC#	TRCN0000049413	TRCN0000049413
shRNA_or_gRNA_sequence	CCACCTAATTTGGTTCTGAAA	CCACCTAATTTGGTTCTGAAA
PAM
Name	PPIL4	PPIL4
Sample_ID	BGHLV20-51	BGHLV20-52
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	PPIL4	PPIL4
qPCR_result	77.5	70.8
Ave_qPCR	74.2
RT-qPCR_primer-F	GAAGATGAGGACTACATGCCAA
RT-qPCR_primer-R	TCTCCCAACAGCTTTCTTCTTC
protein_conc	6927	7155
WB_result	79.1	79.7
Ave_WB	79.4
WB_DONE_date	5/1/2015
MW	57kDa
IP	1	1
antibody_Cat#	GTX117014	GTX117014
Antibody DCC ID	ENCAB535ZKU	ENCAB535ZKU
submitted_to_DCC_date	5/6/2015
Rep1_TPM	72.2	0
Rep2_TPM	60.9	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2480	2481

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PPIL4	Product_ID: GTX117014 Lot_ID: 40555 Source: GeneTex Target Name: PPIL4-human

Experiment Status

	BGHLV20-51	BGHLV20-52
Sample_ID	BGHLV20-51	BGHLV20-52
Sample Name	PPIL4-BGHLV20-51_17732	PPIL4-BGHLV20-52_17733
Sample Name	PPIL4-BGHLV20-51_17732	PPIL4-BGHLV20-52_17733
RBP	PPIL4	PPIL4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	734	735

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-51	BGHLV20-52
Sample #
Sample Name	PPIL4-BGHLV20-51	PPIL4-BGHLV20-52
Sample_Name_Alias	PPIL4-BGHLV20-51_17732	PPIL4-BGHLV20-52_17733
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C4.png	DNA_Library_LV20-22-23/set1/D4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E10.png	RNA_Library_LV20-22-24/set1/F10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-51	BGHLV20-52
RBP	PPIL4	PPIL4
Batch_ID	BGHLV20	BGHLV20
WB_result	79.100	79.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2420	2421

Sequencing Information

	BGHLV20-51	BGHLV20-52
Sample_ID	BGHLV20-51	BGHLV20-52
Sample Name	PPIL4-BGHLV20-51_17732	PPIL4-BGHLV20-52_17733
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	45,230,000	45,300,000
total_aligned_reads	39,696,722	40,265,344
unique_aligned_reads	37,489,674	38,076,096
percent_uniqueAligned	0.82887	0.84053
correlation_replicates	0.998613	0.998613
spikein_reads	192,598	182,478
percent_spikeins	0.00426	0.00403
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1188	1189

Data Submission Information

	BGHLV20-51	BGHLV20-51
ENCODE_alias	brenton-graveley:PPIL4-BGHLV20	brenton-graveley:PPIL4-BGHLV20-HepG2
ENCODE_accession	ENCSR851KEX	ENCSR067NIT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-51	BGHLV20-51
Sample Name	PPIL4-BGHLV20-51_17732	PPIL4-BGHLV20-51_17732
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2916	6864

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
PPIL4-BGHLV20-51_17732_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1188	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15616
PPIL4-BGHLV20-51_17732_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1188	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15658
PPIL4-BGHLV20-51_17732_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732_TTAGGC_L004_R1_001.fastq.gz,PPIL4-BGHLV20-51_17732_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	15700
PPIL4-BGHLV20-51_17732_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732/Aligned.sortedByCoord.out.bam		ENCORE2	15742
PPIL4-BGHLV20-51_17732_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732/Aligned.sortedByCoord.out.bam		ENCORE2	15784
PPIL4-BGHLV20-51_17732_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732/Aligned.sortedByCoord.out.bam		ENCORE2	15826
PPIL4-BGHLV20-51_17732_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732/Aligned.sortedByCoord.out.bam		ENCORE2	15868
PPIL4-BGHLV20-51_17732_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1188					GRCh38	V40	PPIL4-BGHLV20-51_17732_TTAGGC_L004_R1_001.fastq.gz,PPIL4-BGHLV20-51_17732_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	15910
PPIL4-BGHLV20-52_17733_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1189	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15617
PPIL4-BGHLV20-52_17733_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1189	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15659
PPIL4-BGHLV20-52_17733_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733_TGACCA_L004_R1_001.fastq.gz,PPIL4-BGHLV20-52_17733_TGACCA_L004_R2_001.fastq.gz		ENCORE2	15701
PPIL4-BGHLV20-52_17733_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733/Aligned.sortedByCoord.out.bam		ENCORE2	15743
PPIL4-BGHLV20-52_17733_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733/Aligned.sortedByCoord.out.bam		ENCORE2	15785
PPIL4-BGHLV20-52_17733_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733/Aligned.sortedByCoord.out.bam		ENCORE2	15827
PPIL4-BGHLV20-52_17733_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733/Aligned.sortedByCoord.out.bam		ENCORE2	15869
PPIL4-BGHLV20-52_17733_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1189					GRCh38	V40	PPIL4-BGHLV20-52_17733_TGACCA_L004_R1_001.fastq.gz,PPIL4-BGHLV20-52_17733_TGACCA_L004_R2_001.fastq.gz		ENCORE2	15911