PUM2 RNA-Seq in K562

General Information


RBP	PUM2
Cell_Line	K562
Method	shRNA
Exp_Name	PUM2-BGKLV25-K562
ENCODE_series_ID	ENCSR064PGJ
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR118XYK
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	PUM2-BGKLV25-47
Rep2	PUM2-BGKLV25-48
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	42.7
Rep2_qPCR	42.1
Rep1_WB	79.5
Rep2_WB	88.6
Antibody Cat#	A300-202A
Antibody Lot#	A300-202A
Antibody DCC ID	ENCAB818JWN
Status	Released
Project	ENCODE3
ID	624

Experiment Information (Status: Released)

	BGKLV25-47	BGKLV25-48
idx	450	451
TRCN#_or_BGC#	TRCN0000296986	TRCN0000296986
shRNA_or_gRNA_sequence	TTGACTTTATTCATCCATTTGCTCGAGCAAATGGATGAATAAAGTCAA	TTGACTTTATTCATCCATTTGCTCGAGCAAATGGATGAATAAAGTCAA
PAM
Name	PUM2_86	PUM2_86
Sample_ID	BGKLV25-47	BGKLV25-48
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	PUM2	PUM2
qPCR_result	42.7	42.1
Ave_qPCR	42.4
RT-qPCR_primer-F	tgccaattacgtggttcaaa
RT-qPCR_primer-R	tgtgaggtcgaatcttgtgc
protein_conc	3426	3523
WB_result	79.5	88.6
Ave_WB	84.0
WB_DONE_date	6/10/2015
MW	114kDa
IP	1	1
antibody_Cat#	A300-202A	A300-202A
Antibody DCC ID	ENCAB818JWN	ENCAB818JWN
submitted_to_DCC_date	8/6/2015
Rep1_TPM	11.5611265	0
Rep2_TPM	10.3453652	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	523	524

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUM2	Product_ID: A300-202A Lot_ID: 2 Source: Bethyl Labs Target Name: PUM2-human

Experiment Status

	BGKLV25-47	BGKLV25-48
Sample_ID	BGKLV25-47	BGKLV25-48
Sample Name	PUM2-BGKLV25-47	PUM2-BGKLV25-48
Sample Name	PUM2-BGKLV25-47	PUM2-BGKLV25-48
RBP	PUM2	PUM2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	928	929

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-47	BGKLV25-48
Sample #
Sample Name	PUM2-BGKLV25-47	PUM2-BGKLV25-48
Sample_Name_Alias	PUM2-BGKLV25-47	PUM2-BGKLV25-48
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A4.png	DNA_Library_LV24-25-26/set1/B4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C12.png	RNA_Library_LV22-23-25/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-47	BGKLV25-48
RBP	PUM2	PUM2
Batch_ID	BGKLV25	BGKLV25
WB_result	79.500	88.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2620	2621

Sequencing Information

	BGKLV25-47	BGKLV25-48
Sample_ID	BGKLV25-47	BGKLV25-48
Sample Name	PUM2-BGKLV25-47	PUM2-BGKLV25-48
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	102,674,704	100,349,280
total_aligned_reads	103,755,760	102,089,182
unique_aligned_reads	94,971,156	93,407,292
percent_uniqueAligned	0.92497	0.93082
correlation_replicates	0.999511	0.999511
spikein_reads	592,472	570,996
percent_spikeins	0.00577	0.00569
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1262	1263

Data Submission Information

	BGKLV25-47	BGKLV25-47
ENCODE_alias	brenton-graveley:PUM2-BGKLV25	brenton-graveley:PUM2-BGKLV25-K562
ENCODE_accession	ENCSR118XYK	ENCSR064PGJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-47	BGKLV25-47
Sample Name	PUM2-BGKLV25-47	PUM2-BGKLV25-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3013	6882

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
PUM2-BGKLV25-47_GATCAG_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1262	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19590
PUM2-BGKLV25-47_GATCAG_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1262	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19626
PUM2-BGKLV25-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47_GATCAG_L008_001.R1.fastq.gz,PUM2-BGKLV25-47_GATCAG_L008_001.R2.fastq.gz		ENCORE2	19662
PUM2-BGKLV25-47_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47/Aligned.sortedByCoord.out.bam		ENCORE2	19698
PUM2-BGKLV25-47_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47/Aligned.sortedByCoord.out.bam		ENCORE2	19734
PUM2-BGKLV25-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47/Aligned.sortedByCoord.out.bam		ENCORE2	19770
PUM2-BGKLV25-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47/Aligned.sortedByCoord.out.bam		ENCORE2	19806
PUM2-BGKLV25-47_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1262					GRCh38	V40	PUM2-BGKLV25-47_GATCAG_L008_001.R1.fastq.gz,PUM2-BGKLV25-47_GATCAG_L008_001.R2.fastq.gz		ENCORE2	19996
PUM2-BGKLV25-48_TAGCTT_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1263	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19591
PUM2-BGKLV25-48_TAGCTT_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1263	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19627
PUM2-BGKLV25-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48_TAGCTT_L008_001.R1.fastq.gz,PUM2-BGKLV25-48_TAGCTT_L008_001.R2.fastq.gz		ENCORE2	19663
PUM2-BGKLV25-48_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48/Aligned.sortedByCoord.out.bam		ENCORE2	19699
PUM2-BGKLV25-48_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48/Aligned.sortedByCoord.out.bam		ENCORE2	19735
PUM2-BGKLV25-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48/Aligned.sortedByCoord.out.bam		ENCORE2	19771
PUM2-BGKLV25-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48/Aligned.sortedByCoord.out.bam		ENCORE2	19807
PUM2-BGKLV25-48_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1263					GRCh38	V40	PUM2-BGKLV25-48_TAGCTT_L008_001.R1.fastq.gz,PUM2-BGKLV25-48_TAGCTT_L008_001.R2.fastq.gz		ENCORE2	19997