HNRNPC RNA-Seq in K562

General Information


RBP	HNRNPC
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPC-BGKLV21-K562
ENCODE_series_ID	ENCSR865TSU
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR634KBO
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	HNRNPC_BGKLV21_19_17567
Rep2	HNRNPC_BGKLV21_20_17568
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	90.1
Rep2_qPCR	88.9
Rep1_WB	94.2
Rep2_WB	93.8
Antibody Cat#	RN052PW
Antibody Lot#	RN052PW
Antibody DCC ID	ENCAB275OHR
Status	Released
Project	ENCODE3
ID	510

Experiment Information (Status: Released)

	BGKLV21-19	BGKLV21-19	BGKLV21-20	BGKLV21-20
idx	290	0	291	0
TRCN#_or_BGC#	TRCN0000006644	TRCN0000006644	TRCN0000006644	TRCN0000006644
shRNA_or_gRNA_sequence	GCGCTTGTCTAAGATCAAATT	GCGCTTGTCTAAGATCAAATT	GCGCTTGTCTAAGATCAAATT	GCGCTTGTCTAAGATCAAATT
PAM
Name	HNRNPC	HNRNPC	HNRNPC	HNRNPC
Sample_ID	BGKLV21-19	BGKLV21-19	BGKLV21-20	BGKLV21-20
transduction_Date	10/9/2014	10/9/2014	10/9/2014	10/9/2014
days
RBP_name	HNRNPC	HNRNPC	HNRNPC	HNRNPC
qPCR_result	90.1	90.1	88.9	88.9
Ave_qPCR	89.5	89.5
RT-qPCR_primer-F	GGGACCTACTGGATGATGATG	GGGACCTACTGGATGATGATG
RT-qPCR_primer-R	TGTCATCCTCTCCTTCCTCAG	TGTCATCCTCTCCTTCCTCAG
protein_conc	2958	2958	2678	2678
WB_result	94.2	41.0	93.8	48.0
Ave_WB	94.0	44.5
WB_DONE_date	2/27/2015	12/11/2015		Santa Cruz Biotechno
MW	34kDa	40kDa		FU'S
IP	1		1
antibody_Cat#	RN052PW	sc-10037	RN052PW	sc-10037
Antibody DCC ID	ENCAB275OHR		ENCAB275OHR
submitted_to_DCC_date	4/2/2015
Rep1_TPM	300.155734	0	0	0
Rep2_TPM	205.986104	0	0	0
Action
Library_start_date	5/19/2015		5/19/2015
repeat_library
Note
ID	319	321	320	322

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPC	Product_ID: sc-10037 Lot_ID: E0912 Source: Santa Cruz Biotech Target Name: HNRNPC-human
HNRNPC	Product_ID: RN052PW Lot_ID: 1 Source: MBLI Target Name: HNRNPC-human

Experiment Status

	BGKLV21-19	BGKLV21-20
Sample_ID	BGKLV21-19	BGKLV21-20
Sample Name	HNRNPC_BGKLV21_19_17567	HNRNPC_BGKLV21_20_17568
Sample Name	HNRNPC_BGKLV21_19_17567	HNRNPC_BGKLV21_20_17568
RBP	HNRNPC	HNRNPC
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	752	753

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-19	BGKLV21-20
Sample #
Sample Name	HNRNPC-BGKLV21-19	HNRNPC-BGKLV21-20
Sample_Name_Alias	HNRNPC_BGKLV21_19_17567	HNRNPC_BGKLV21_20_17568
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/C6.png	DNA_Library_LV21-24/set1/D6.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G8.png	RNA_Library_LV19-21-24/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-19	BGKLV21-20
RBP	HNRNPC	HNRNPC
Batch_ID	BGKLV21	BGKLV21
WB_result	94.200	93.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2438	2439

Sequencing Information

	BGKLV21-19	BGKLV21-20
Sample_ID	BGKLV21-19	BGKLV21-20
Sample Name	HNRNPC_BGKLV21_19_17567	HNRNPC_BGKLV21_20_17568
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	42,360,000	43,810,000
total_aligned_reads	38,644,028	40,061,866
unique_aligned_reads	35,487,112	36,718,824
percent_uniqueAligned	0.83775	0.83814
correlation_replicates	0.998329	0.998329
spikein_reads	213,650	225,344
percent_spikeins	0.00504	0.00514
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1044	1045

Data Submission Information

	BGKLV21-19	BGKLV21-19
ENCODE_alias	brenton-graveley:HNRNPC_BGKLV21	brenton-graveley:HNRNPC-BGKLV21-K562
ENCODE_accession	ENCSR634KBO	ENCSR865TSU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-19	BGKLV21-19
Sample Name	HNRNPC_BGKLV21_19_17567	HNRNPC_BGKLV21_19_17567
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2962	6755

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
HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1044	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15930
HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1044	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15974
HNRNPC_BGKLV21_19_17567_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R1_001.fastq.gz,HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	16018
HNRNPC_BGKLV21_19_17567_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567/Aligned.sortedByCoord.out.bam		ENCORE2	16062
HNRNPC_BGKLV21_19_17567_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567/Aligned.sortedByCoord.out.bam		ENCORE2	16106
HNRNPC_BGKLV21_19_17567_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567/Aligned.sortedByCoord.out.bam		ENCORE2	16150
HNRNPC_BGKLV21_19_17567_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567/Aligned.sortedByCoord.out.bam		ENCORE2	16194
HNRNPC_BGKLV21_19_17567_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1044					GRCh38	V40	HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R1_001.fastq.gz,HNRNPC_BGKLV21_19_17567_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	16238
HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1045	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15931
HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1045	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15975
HNRNPC_BGKLV21_20_17568_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R1_001.fastq.gz,HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	16019
HNRNPC_BGKLV21_20_17568_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568/Aligned.sortedByCoord.out.bam		ENCORE2	16063
HNRNPC_BGKLV21_20_17568_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568/Aligned.sortedByCoord.out.bam		ENCORE2	16107
HNRNPC_BGKLV21_20_17568_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568/Aligned.sortedByCoord.out.bam		ENCORE2	16151
HNRNPC_BGKLV21_20_17568_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568/Aligned.sortedByCoord.out.bam		ENCORE2	16195
HNRNPC_BGKLV21_20_17568_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1045					GRCh38	V40	HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R1_001.fastq.gz,HNRNPC_BGKLV21_20_17568_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	16239