PPIL4 RNA-Seq in K562

General Information


RBP	PPIL4
Cell_Line	K562
Method	shRNA
Exp_Name	PPIL4-BGKLV24-K562
ENCODE_series_ID	ENCSR431ZHM
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR556FNN
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	PPIL4_BGKLV24_45B
Rep2	PPIL4_BGKLV24_46B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	48.8
Rep2_qPCR	58.2
Rep1_WB	87.2
Rep2_WB	88.6
Antibody Cat#	GTX117014
Antibody Lot#	GTX117014
Antibody DCC ID	ENCAB535ZKU
Status	Released
Project	ENCODE3
ID	607

Experiment Information (Status: Released)

	BGKLV24-45	BGKLV24-46
idx	382	383
TRCN#_or_BGC#	TRCN0000049413	TRCN0000049413
shRNA_or_gRNA_sequence	redo qPCR, need resubmitte image to DCC	CCACCTAATTTGGTTCTGAAA
PAM
Name	PPIL4	PPIL4
Sample_ID	BGKLV24-45	BGKLV24-46
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	PPIL4	PPIL4
qPCR_result	48.8	58.2
Ave_qPCR	53.5
RT-qPCR_primer-F	GAAGATGAGGACTACATGCCAA
RT-qPCR_primer-R	TCTCCCAACAGCTTTCTTCTTC
protein_conc	3989	4348
WB_result	87.2	88.6
Ave_WB	87.9
WB_DONE_date	5/1/2015
MW
IP	1	1
antibody_Cat#	GTX117014	GTX117014
Antibody DCC ID	ENCAB535ZKU	ENCAB535ZKU
submitted_to_DCC_date	5/4/2015
Rep1_TPM	41.0393415	0
Rep2_TPM	26.1924908	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	439	440

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

	BGKLV24-45	BGKLV24-46
Sample_ID	BGKLV24-45	BGKLV24-46
Sample Name	PPIL4_BGKLV24_45B	PPIL4_BGKLV24_46B
Sample Name	PPIL4_BGKLV24_45B	PPIL4_BGKLV24_46B
RBP	PPIL4	PPIL4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	896	897

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-45	BGKLV24-46
Sample #
Sample Name	PPIL4-BGKLV24-45B	PPIL4-BGKLV24-46B
Sample_Name_Alias	PPIL4_BGKLV24_45B	PPIL4_BGKLV24_46B
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E6.png	DNA_Library_LV24-25-26/set1/F6.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C5.png	RNA_Library_LV20-22-24/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-45	BGKLV24-46
RBP	PPIL4	PPIL4
Batch_ID	BGKLV24	BGKLV24
WB_result	87.200	88.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2584	2585

Sequencing Information

	BGKLV24-45	BGKLV24-46
Sample_ID	BGKLV24-45	BGKLV24-46
Sample Name	PPIL4_BGKLV24_45B	PPIL4_BGKLV24_46B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	80,460,912	81,298,200
total_aligned_reads	77,606,426	78,040,490
unique_aligned_reads	70,306,404	70,177,902
percent_uniqueAligned	0.87380	0.86322
correlation_replicates	0.999353	0.999353
spikein_reads	242,878	212,940
percent_spikeins	0.00302	0.00262
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1226	1227

Data Submission Information

	BGKLV24-45	BGKLV24-45
ENCODE_alias	brenton-graveley:PPIL4_BGKLV24_B	brenton-graveley:PPIL4-BGKLV24-K562
ENCODE_accession	ENCSR556FNN	ENCSR431ZHM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-45	BGKLV24-45
Sample Name	PPIL4_BGKLV24_45B	PPIL4_BGKLV24_45B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2997	6865

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_BGKLV24_45B_AGTCAA_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1226	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17482
PPIL4_BGKLV24_45B_AGTCAA_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1226	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17506
PPIL4_BGKLV24_45B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B_AGTCAA_L002_001.R1.fastq.gz,PPIL4_BGKLV24_45B_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	17530
PPIL4_BGKLV24_45B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B/Aligned.sortedByCoord.out.bam		ENCORE2	17554
PPIL4_BGKLV24_45B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B/Aligned.sortedByCoord.out.bam		ENCORE2	17578
PPIL4_BGKLV24_45B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B/Aligned.sortedByCoord.out.bam		ENCORE2	17602
PPIL4_BGKLV24_45B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B/Aligned.sortedByCoord.out.bam		ENCORE2	17626
PPIL4_BGKLV24_45B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1226					GRCh38	V40	PPIL4_BGKLV24_45B_AGTCAA_L002_001.R1.fastq.gz,PPIL4_BGKLV24_45B_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	17650
PPIL4_BGKLV24_46B_AGTTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1227	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17483
PPIL4_BGKLV24_46B_AGTTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1227	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17507
PPIL4_BGKLV24_46B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B_AGTTCC_L002_001.R1.fastq.gz,PPIL4_BGKLV24_46B_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	17531
PPIL4_BGKLV24_46B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B/Aligned.sortedByCoord.out.bam		ENCORE2	17555
PPIL4_BGKLV24_46B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B/Aligned.sortedByCoord.out.bam		ENCORE2	17579
PPIL4_BGKLV24_46B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B/Aligned.sortedByCoord.out.bam		ENCORE2	17603
PPIL4_BGKLV24_46B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B/Aligned.sortedByCoord.out.bam		ENCORE2	17627
PPIL4_BGKLV24_46B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1227					GRCh38	V40	PPIL4_BGKLV24_46B_AGTTCC_L002_001.R1.fastq.gz,PPIL4_BGKLV24_46B_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	17651