PES1 RNA-Seq in K562

General Information


RBP	PES1
Cell_Line	K562
Method	shRNA
Exp_Name	PES1-BGKLV19-K562
ENCODE_series_ID	ENCSR868XDT
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR891DYO
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	PES1_BGKLV19_39B
Rep2	PES1_BGKLV19_40B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	55.3
Rep2_qPCR	54.2
Rep1_WB	34.0
Rep2_WB	48.6
Antibody Cat#	A300-903A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB170HXF
Status	Archived
Project	ENCODE3
ID	477

Experiment Information (Status: Released)

	BGKLV19-39	BGKLV19-40
idx	246	247
TRCN#_or_BGC#	TRCN0000117724	TRCN0000117724
shRNA_or_gRNA_sequence	CTTATCAAAGACATCAGGTTT	CTTATCAAAGACATCAGGTTT
PAM
Name	PES1	PES1
Sample_ID	BGKLV19-39	BGKLV19-40
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	PES1	PES1
qPCR_result	55.3	54.2
Ave_qPCR	54.8
RT-qPCR_primer-F	ccaactacatcacccggaac
RT-qPCR_primer-R	aaatgcccttcagaatgcac
protein_conc	2631	3060
WB_result	34.0	48.6
Ave_WB	41.3
WB_DONE_date	12/12/2014
MW
IP	1	1
antibody_Cat#	A300-903A	A300-903A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	28.95743	0
Rep2_TPM	17.6189422	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	271	272

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-39	BGKLV19-40
Sample_ID	BGKLV19-39	BGKLV19-40
Sample Name	PES1_BGKLV19_39B	PES1_BGKLV19_40B
Sample Name	PES1_BGKLV19_39B	PES1_BGKLV19_40B
RBP	PES1	PES1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	688	689

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-39	BGKLV19-40
Sample #
Sample Name	PES1-BGKLV19-39B	PES1-BGKLV19-40B
Sample_Name_Alias	PES1_BGKLV19_39B	PES1_BGKLV19_40B
Index Well Position	S01	S02
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/A10.png	DNA_Library_LV18-19/set1/B10.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/C1.png	RNA_Library_LV19-21-24/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-39	BGKLV19-40
RBP	PES1	PES1
Batch_ID	BGKLV19	BGKLV19
WB_result	34.000	48.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2372	2373

Sequencing Information

	BGKLV19-39	BGKLV19-40
Sample_ID	BGKLV19-39	BGKLV19-40
Sample Name	PES1_BGKLV19_39B	PES1_BGKLV19_40B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	39,160,000	43,990,000
total_aligned_reads	36,891,220	41,284,860
unique_aligned_reads	33,920,176	37,947,872
percent_uniqueAligned	0.86619	0.86265
correlation_replicates	0.992696	0.992696
spikein_reads	205,116	190,500
percent_spikeins	0.00524	0.00433
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1014	1015

Data Submission Information

	BGKLV19-39	BGKLV19-39
ENCODE_alias	brenton-graveley:PES1_BGKLV19	brenton-graveley:PES1-BGKLV19-K562
ENCODE_accession	ENCSR891DYO	ENCSR868XDT
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-39	BGKLV19-39
Sample Name	PES1_BGKLV19_39B	PES1_BGKLV19_39B
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2892	6854

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
PES1_BGKLV19_39B_ATCACG_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1014	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15130
PES1_BGKLV19_39B_ATCACG_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1014	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15188
PES1_BGKLV19_39B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1014					GRCh38	V40	PES1_BGKLV19_39B_ATCACG_L005_R1_001.fastq.gz,PES1_BGKLV19_39B_ATCACG_L005_R2_001.fastq.gz		ENCORE2	15246
PES1_BGKLV19_39B_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	1014					GRCh38	V40	PES1_BGKLV19_39B/Aligned.sortedByCoord.out.bam		ENCORE2	15317
PES1_BGKLV19_39B_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	1014					GRCh38	V40	PES1_BGKLV19_39B/Aligned.sortedByCoord.out.bam		ENCORE2	15375
PES1_BGKLV19_39B_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	1014					GRCh38	V40	PES1_BGKLV19_39B/Aligned.sortedByCoord.out.bam		ENCORE2	15433
PES1_BGKLV19_39B_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	1014					GRCh38	V40	PES1_BGKLV19_39B/Aligned.sortedByCoord.out.bam		ENCORE2	15491
PES1_BGKLV19_39B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1014					GRCh38	V40	PES1_BGKLV19_39B_ATCACG_L005_R1_001.fastq.gz,PES1_BGKLV19_39B_ATCACG_L005_R2_001.fastq.gz		ENCORE2	16388
PES1_BGKLV19_40B_CGATGT_L005_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1015	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15131
PES1_BGKLV19_40B_CGATGT_L005_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1015	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15189
PES1_BGKLV19_40B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1015					GRCh38	V40	PES1_BGKLV19_40B_CGATGT_L005_R1_001.fastq.gz,PES1_BGKLV19_40B_CGATGT_L005_R2_001.fastq.gz		ENCORE2	15247
PES1_BGKLV19_40B_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	1015					GRCh38	V40	PES1_BGKLV19_40B/Aligned.sortedByCoord.out.bam		ENCORE2	15318
PES1_BGKLV19_40B_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	1015					GRCh38	V40	PES1_BGKLV19_40B/Aligned.sortedByCoord.out.bam		ENCORE2	15376
PES1_BGKLV19_40B_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	1015					GRCh38	V40	PES1_BGKLV19_40B/Aligned.sortedByCoord.out.bam		ENCORE2	15434
PES1_BGKLV19_40B_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	1015					GRCh38	V40	PES1_BGKLV19_40B/Aligned.sortedByCoord.out.bam		ENCORE2	15492
PES1_BGKLV19_40B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1015					GRCh38	V40	PES1_BGKLV19_40B_CGATGT_L005_R1_001.fastq.gz,PES1_BGKLV19_40B_CGATGT_L005_R2_001.fastq.gz		ENCORE2	16389