PUM1 RNA-Seq in K562

General Information


RBP	PUM1
Cell_Line	K562
Method	shRNA
Exp_Name	PUM1-BGKLV25-K562
ENCODE_series_ID	ENCSR449VKZ
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR745WVZ
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	PUM1-BGKLV25-45
Rep2	PUM1-BGKLV25-46
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	55.0
Rep2_qPCR	60.6
Rep1_WB	97.1
Rep2_WB	97.3
Antibody Cat#	A302-576A
Antibody Lot#	A302-576A
Antibody DCC ID	ENCAB744LEE
Status	Released
Project	ENCODE3
ID	623

Experiment Information (Status: Released)

	BGKLV25-45	BGKLV25-46
idx	448	449
TRCN#_or_BGC#	TRCN0000275489	TRCN0000275489
shRNA_or_gRNA_sequence	GCGTTTAAGGGACAGGTATTT	GCGTTTAAGGGACAGGTATTT
PAM
Name	PUM1_89	PUM1_89
Sample_ID	BGKLV25-45	BGKLV25-46
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	PUM1	PUM1
qPCR_result	55.0	60.6
Ave_qPCR	57.8
RT-qPCR_primer-F	GCCCCAGTCTTTGCAATTTA
RT-qPCR_primer-R	AATCACTCGGCAGCCATAAG
protein_conc	3129	3382
WB_result	97.1	97.3
Ave_WB	97.2
WB_DONE_date	5/11/2015
MW	126kDa
IP	1	1
antibody_Cat#	A302-576A	A302-576A
Antibody DCC ID	ENCAB744LEE	ENCAB744LEE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	17.7485463	0
Rep2_TPM	18.5950205	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	519	520

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUM1	Product_ID: A302-576A Lot_ID: 1 Source: Bethyl Labs Target Name: PUM1-human

Experiment Status

	BGKLV25-45	BGKLV25-46
Sample_ID	BGKLV25-45	BGKLV25-46
Sample Name	PUM1-BGKLV25-45	PUM1-BGKLV25-46
Sample Name	PUM1-BGKLV25-45	PUM1-BGKLV25-46
RBP	PUM1	PUM1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	926	927

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-45	BGKLV25-46
Sample #
Sample Name	PUM1-BGKLV25-45	PUM1-BGKLV25-46
Sample_Name_Alias	PUM1-BGKLV25-45	PUM1-BGKLV25-46
Index Well Position	S07	S08
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/G3.png	DNA_Library_LV24-25-26/set1/H3.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A12.png	RNA_Library_LV22-23-25/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-45	BGKLV25-46
RBP	PUM1	PUM1
Batch_ID	BGKLV25	BGKLV25
WB_result	97.100	97.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2618	2619

Sequencing Information

	BGKLV25-45	BGKLV25-46
Sample_ID	BGKLV25-45	BGKLV25-46
Sample Name	PUM1-BGKLV25-45	PUM1-BGKLV25-46
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	97,136,820	129,518,846
total_aligned_reads	99,062,598	134,166,432
unique_aligned_reads	90,719,356	122,440,156
percent_uniqueAligned	0.93393	0.94535
correlation_replicates	0.999176	0.999176
spikein_reads	545,486	792,280
percent_spikeins	0.00562	0.00612
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1260	1261

Data Submission Information

	BGKLV25-45	BGKLV25-45
ENCODE_alias	brenton-graveley:PUM1-BGKLV25	brenton-graveley:PUM1-BGKLV25-K562
ENCODE_accession	ENCSR745WVZ	ENCSR449VKZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-45	BGKLV25-45
Sample Name	PUM1-BGKLV25-45	PUM1-BGKLV25-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3012	6880

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
PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1260	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19588
PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1260	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19624
PUM1-BGKLV25-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1260					GRCh38	V40	PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz,PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz		ENCORE2	19660
PUM1-BGKLV25-45_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	1260					GRCh38	V40	PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam		ENCORE2	19696
PUM1-BGKLV25-45_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	1260					GRCh38	V40	PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam		ENCORE2	19732
PUM1-BGKLV25-45_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	1260					GRCh38	V40	PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam		ENCORE2	19768
PUM1-BGKLV25-45_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	1260					GRCh38	V40	PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam		ENCORE2	19804
PUM1-BGKLV25-45_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1260					GRCh38	V40	PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz,PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz		ENCORE2	19994
PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1261	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19589
PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1261	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19625
PUM1-BGKLV25-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1261					GRCh38	V40	PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz,PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	19661
PUM1-BGKLV25-46_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	1261					GRCh38	V40	PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam		ENCORE2	19697
PUM1-BGKLV25-46_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	1261					GRCh38	V40	PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam		ENCORE2	19733
PUM1-BGKLV25-46_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	1261					GRCh38	V40	PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam		ENCORE2	19769
PUM1-BGKLV25-46_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	1261					GRCh38	V40	PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam		ENCORE2	19805
PUM1-BGKLV25-46_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1261					GRCh38	V40	PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz,PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	19995