HNRNPL RNA-Seq in K562

General Information


RBP	HNRNPL
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPL-BGKLV25-K562
ENCODE_series_ID	ENCSR369EIU
Batch_ID	BGKLV25
Pool ID	Pool-160425
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR563YIS
ENCODE_CN_Exp_ID	ENCSR031RRO
Rep1	HNRNPL_BGKLV25-25B
Rep2	HNRNPL_BGKLV25-26B
CN1	NT_BGKLV25-1B
CN2	NT_BGKLV25-2B
Rep1_qPCR	79.7
Rep2_qPCR	79.8
Rep1_WB	65.4
Rep2_WB	58.2
Antibody Cat#	AB6106
Antibody Lot#	AB6106
Antibody DCC ID	ENCAB678XLS
Status	Released
Project	ENCODE3
ID	617

Experiment Information (Status: NotSatisfied)

	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
idx	426	426	427	427
TRCN#_or_BGC#	TRCN0000017245	TRCN0000017245	TRCN0000017245	TRCN0000017245
shRNA_or_gRNA_sequence	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT
PAM
Name	HNRNPL	HNRNPL	HNRNPL	HNRNPL
Sample_ID	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
transduction_Date	3/17/2015	3/17/2015	3/17/2015	3/17/2015
days
RBP_name	HNRNPL	HNRNPL	HNRNPL	HNRNPL
qPCR_result	79.7	79.7	79.8	79.8
Ave_qPCR	79.8	79.8
RT-qPCR_primer-F	CTGGGCTTCCTGAACCATTA	CTGGGCTTCCTGAACCATTA
RT-qPCR_primer-R	TGCTGAGCAGTGGAGAAACA	TGCTGAGCAGTGGAGAAACA
protein_conc	4040	4040	4190	4190
WB_result	65.4	91.2	58.2	94.7
Ave_WB	61.8	92.9
WB_DONE_date	7/7/2017	5/10/2016
MW	64kDa	64kDa		WES
IP		Aviva		Rabbit ant
antibody_Cat#	AB6106	ARP40368	AB6106	fu's
Antibody DCC ID	ENCAB678XLS	ENCAB000AVZ	ENCAB678XLS	ENCAB000AVZ
submitted_to_DCC_date	9/29/2017	10/26/2016
Rep1_TPM	110.102129	110.102129	0	0
Rep2_TPM	70.1313628	70.1313628	0	0
Action
Library_start_date	6/23/2015	6/23/2015	6/23/2015	6/23/2015
repeat_library
Note
ID	489	491	490	492

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPL	Product_ID: ab6106 Lot_ID: GR30383-23 Source: Abcam Target Name: HNRNPL-human
HNRNPL	Product_ID: ARP40368_P050 Lot_ID: QC9464 Source: Aviva Target Name: HNRNPL-human

Experiment Status

	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
Sample_ID	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
Sample Name	HNRNPL_BGKLV25-25	HNRNPL_BGKLV25-25B	HNRNPL_BGKLV25-26	HNRNPL_BGKLV25-26B
Sample Name	HNRNPL_BGKLV25-25	HNRNPL_BGKLV25-25B	HNRNPL_BGKLV25-26	HNRNPL_BGKLV25-26B
RBP	HNRNPL	HNRNPL	HNRNPL	HNRNPL
Cell_Line	K562	K562	K562	K562
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2015-12-08	2016-09-24	2015-12-08	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note	Bad Correlation between replicates		Bad Correlation between replicates
ID	26	1199	27	1200

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
Sample #
Sample Name	HNRNPL-BGKLV25-25	HNRNPL-BGKLV25-25B	HNRNPL-BGKLV25-26	HNRNPL-BGKLV25-26B
Sample_Name_Alias	HNRNPL_BGKLV25-25	HNRNPL_BGKLV25-25B	HNRNPL_BGKLV25-26	HNRNPL_BGKLV25-26B
Index Well Position	S20	S07	S21	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2016-03-04	2015-06-23	2016-03-04
Lib_ID	Lib-150623	Lib-160304	Lib-150623	Lib-160304
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C2.png	DNA_Library_LV33-34-25B-32/set2/G1.png	DNA_Library_LV24-25-26/set1/D2.png	DNA_Library_LV33-34-25B-32/set1/H5.png
RIN	10.0	10.0	9.8	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E10.png	RNA_Library_LV22-23-25/set1/E10.png	RNA_Library_LV22-23-25/set1/F10.png	RNA_Library_LV22-23-25/set1/F10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
RBP	HNRNPL	HNRNPL	HNRNPL	HNRNPL
Batch_ID	BGKLV25	BGKLV25	BGKLV25	BGKLV25
WB_result	65.400	65.400	58.200	58.200
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2604	2898	2605	2899

Sequencing Information

	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
Sample_ID	BGKLV25-25	BGKLV25-25	BGKLV25-26	BGKLV25-26
Sample Name	HNRNPL_BGKLV25-25	HNRNPL_BGKLV25-25B	HNRNPL_BGKLV25-26	HNRNPL_BGKLV25-26B
Pool ID	Pool-151101	Pool-160425	Pool-151101	Pool-160425
LocalServer_folder	set25	set25	set25	set25
total_reads	79,439,180	76,735,098	62,789,408	83,837,958
total_aligned_reads	80,569,028	58,653,046	55,776,936	63,210,044
unique_aligned_reads	73,309,814	53,335,788	51,159,692	57,397,602
percent_uniqueAligned	0.92284	0.69506	0.81478	0.68463
correlation_replicates	0.762179	0.997256	0.762179	0.997256
spikein_reads	427,002	242,232	4,494	357,582
percent_spikeins	0.00538	0.00316	0.00007	0.00427
original_ReadLength	100	100	100	100
QC_Status	BadCorrelation	Submitted	BadCorrelation	Submitted
ID	1246	1547	1247	1548

Data Submission Information

	BGKLV25-25	BGKLV25-25
ENCODE_alias	brenton-graveley:HNRNPL_BGKLV25	brenton-graveley:HNRNPL-BGKLV25-K562
ENCODE_accession	ENCSR563YIS	ENCSR369EIU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-25	BGKLV25-25
Sample Name	HNRNPL_BGKLV25-25B	HNRNPL_BGKLV25-25B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3139	6765

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
HNRNPL_BGKLV25-25B_CAGATC_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1547	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19572
HNRNPL_BGKLV25-25B_CAGATC_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1547	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19608
HNRNPL_BGKLV25-25B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1547					GRCh38	V40	HNRNPL_BGKLV25-25B_CAGATC_L008_001.R1.fastq.gz,HNRNPL_BGKLV25-25B_CAGATC_L008_001.R2.fastq.gz		ENCORE2	19644
HNRNPL_BGKLV25-25B_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	1547					GRCh38	V40	HNRNPL_BGKLV25-25B/Aligned.sortedByCoord.out.bam		ENCORE2	19680
HNRNPL_BGKLV25-25B_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	1547					GRCh38	V40	HNRNPL_BGKLV25-25B/Aligned.sortedByCoord.out.bam		ENCORE2	19716
HNRNPL_BGKLV25-25B_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	1547					GRCh38	V40	HNRNPL_BGKLV25-25B/Aligned.sortedByCoord.out.bam		ENCORE2	19752
HNRNPL_BGKLV25-25B_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	1547					GRCh38	V40	HNRNPL_BGKLV25-25B/Aligned.sortedByCoord.out.bam		ENCORE2	19788
HNRNPL_BGKLV25-25B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1547					GRCh38	V40	HNRNPL_BGKLV25-25B_CAGATC_L008_001.R1.fastq.gz,HNRNPL_BGKLV25-25B_CAGATC_L008_001.R2.fastq.gz		ENCORE2	19978
HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1548	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19573
HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1548	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19609
HNRNPL_BGKLV25-26B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1548					GRCh38	V40	HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R1.fastq.gz,HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	19645
HNRNPL_BGKLV25-26B_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	1548					GRCh38	V40	HNRNPL_BGKLV25-26B/Aligned.sortedByCoord.out.bam		ENCORE2	19681
HNRNPL_BGKLV25-26B_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	1548					GRCh38	V40	HNRNPL_BGKLV25-26B/Aligned.sortedByCoord.out.bam		ENCORE2	19717
HNRNPL_BGKLV25-26B_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	1548					GRCh38	V40	HNRNPL_BGKLV25-26B/Aligned.sortedByCoord.out.bam		ENCORE2	19753
HNRNPL_BGKLV25-26B_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	1548					GRCh38	V40	HNRNPL_BGKLV25-26B/Aligned.sortedByCoord.out.bam		ENCORE2	19789
HNRNPL_BGKLV25-26B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1548					GRCh38	V40	HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R1.fastq.gz,HNRNPL_BGKLV25-26B_ACTTGA_L008_001.R2.fastq.gz		ENCORE2	19979