HNRNPK RNA-Seq in HepG2

General Information


RBP	HNRNPK
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPK-BGHLV12-HepG2
ENCODE_series_ID	ENCSR608NVZ
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR853ZJS
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	HNRNPK-BGHLV12-37
Rep2	HNRNPK-BGHLV12-38
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	53.3
Rep2_qPCR	42.4
Rep1_WB	64.2
Rep2_WB	81.3
Antibody Cat#	RN019P
Antibody Lot#	RN019P
Antibody DCC ID	ENCAB000BFN
Status	Released
Project	ENCODE3
ID	340

Experiment Information (Status: Released)

	BGHLV12-37	BGHLV12-38
idx	37	38
TRCN#_or_BGC#	TRCN0000062455	TRCN0000062455
shRNA_or_gRNA_sequence	GCCAGTGTTTCAGTCCCAGAC	GCCAGTGTTTCAGTCCCAGAC
PAM
Name	HNRNPK	HNRNPK
Sample_ID	BGHLV12-37	BGHLV12-38
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	HNRNPK	HNRNPK
qPCR_result	53.3	42.4
Ave_qPCR	47.9
RT-qPCR_primer-F	CCATTACAGGAACACAGGACC
RT-qPCR_primer-R	TCTTGCATTAGAATCCTTCAACA
protein_conc	3046	3189
WB_result	64.2	81.3
Ave_WB	72.8
WB_DONE_date	6/27/2014
MW	51kDa
IP	1	1
antibody_Cat#	RN019P	RN019P
Antibody DCC ID	ENCAB000BFN	ENCAB000BFN
submitted_to_DCC_date	5/4/2015
Rep1_TPM	189.8	0
Rep2_TPM	169.5	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2084	2085

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPK	Product_ID: RN019P Lot_ID: 1 Source: MBLI Target Name: HNRNPK-human

Experiment Status

	BGHLV12-37	BGHLV12-38
Sample_ID	BGHLV12-37	BGHLV12-38
Sample Name	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-38
Sample Name	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-38
RBP	HNRNPK	HNRNPK
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	394	395

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-37	BGHLV12-38
Sample #
Sample Name	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-38
Sample_Name_Alias	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-38
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set2/D2.png	DNA_Library_LV12/set2/E2.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/C4.png	RNA_Library_LV12/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-37	BGHLV12-38
RBP	HNRNPK	HNRNPK
Batch_ID	BGHLV12	BGHLV12
WB_result	64.200	81.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2018	2019

Sequencing Information

	BGHLV12-37	BGHLV12-38
Sample_ID	BGHLV12-37	BGHLV12-38
Sample Name	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-38
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	75,070,000	72,900,000
total_aligned_reads	69,744,916	68,235,370
unique_aligned_reads	65,579,332	64,241,016
percent_uniqueAligned	0.87358	0.88122
correlation_replicates	0.999250	0.999250
spikein_reads	455,006	414,766
percent_spikeins	0.00606	0.00569
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	718	719

Data Submission Information

	BGHLV12-37	BGHLV12-37
ENCODE_alias	brenton-graveley:HNRNPK-BGHLV12	brenton-graveley:HNRNPK-BGHLV12-HepG2
ENCODE_accession	ENCSR853ZJS	ENCSR608NVZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-37	BGHLV12-37
Sample Name	HNRNPK-BGHLV12-37	HNRNPK-BGHLV12-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2746	6762

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
HNRNPK-BGHLV12-37_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	718	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12775
HNRNPK-BGHLV12-37_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	718	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12844
HNRNPK-BGHLV12-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37_TTAGGC_L004_R1_001.fastq.gz,HNRNPK-BGHLV12-37_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	12914
HNRNPK-BGHLV12-37_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37/Aligned.sortedByCoord.out.bam		ENCORE2	12984
HNRNPK-BGHLV12-37_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37/Aligned.sortedByCoord.out.bam		ENCORE2	13054
HNRNPK-BGHLV12-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37/Aligned.sortedByCoord.out.bam		ENCORE2	13124
HNRNPK-BGHLV12-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37/Aligned.sortedByCoord.out.bam		ENCORE2	13194
HNRNPK-BGHLV12-37_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	718					GRCh38	V40	HNRNPK-BGHLV12-37_TTAGGC_L004_R1_001.fastq.gz,HNRNPK-BGHLV12-37_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	13264
HNRNPK-BGHLV12-38_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	719	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12776
HNRNPK-BGHLV12-38_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	719	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12845
HNRNPK-BGHLV12-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38_TGACCA_L004_R1_001.fastq.gz,HNRNPK-BGHLV12-38_TGACCA_L004_R2_001.fastq.gz		ENCORE2	12915
HNRNPK-BGHLV12-38_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38/Aligned.sortedByCoord.out.bam		ENCORE2	12985
HNRNPK-BGHLV12-38_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38/Aligned.sortedByCoord.out.bam		ENCORE2	13055
HNRNPK-BGHLV12-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38/Aligned.sortedByCoord.out.bam		ENCORE2	13125
HNRNPK-BGHLV12-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38/Aligned.sortedByCoord.out.bam		ENCORE2	13195
HNRNPK-BGHLV12-38_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	719					GRCh38	V40	HNRNPK-BGHLV12-38_TGACCA_L004_R1_001.fastq.gz,HNRNPK-BGHLV12-38_TGACCA_L004_R2_001.fastq.gz		ENCORE2	13265