HNRNPC RNA-Seq in HepG2

General Information


RBP	HNRNPC
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPC-BGHLV20-HepG2
ENCODE_series_ID	ENCSR308YXN
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR052IYH
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	HNRNPC-BGHLV20-33_17722
Rep2	HNRNPC-BGHLV20-34_17723
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	94.5
Rep2_qPCR	92.0
Rep1_WB	78.3
Rep2_WB	74.9
Antibody Cat#	RN052PW
Antibody Lot#	RN052PW
Antibody DCC ID	ENCAB275OHR
Status	Released
Project	ENCODE3
ID	496

Experiment Information (Status: Released)

	BGHLV20-33	BGHLV20-34
idx	397	398
TRCN#_or_BGC#	TRCN0000006644	TRCN0000006644
shRNA_or_gRNA_sequence	GCGCTTGTCTAAGATCAAATT	GCGCTTGTCTAAGATCAAATT
PAM
Name	HNRNPC	HNRNPC
Sample_ID	BGHLV20-33	BGHLV20-34
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	HNRNPC	HNRNPC
qPCR_result	94.5	92.0
Ave_qPCR	93.2
RT-qPCR_primer-F	GGGACCTACTGGATGATGATG
RT-qPCR_primer-R	TGTCATCCTCTCCTTCCTCAG
protein_conc	4705	5565
WB_result	78.3	74.9
Ave_WB	76.6
WB_DONE_date	2/27/2015
MW	34kDa
IP	1	1
antibody_Cat#	RN052PW	RN052PW
Antibody DCC ID	ENCAB275OHR	ENCAB275OHR
submitted_to_DCC_date	4/2/2015
Rep1_TPM	312.6	0
Rep2_TPM	262.1	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2462	2463

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPC	Product_ID: RN052PW Lot_ID: 1 Source: MBLI Target Name: HNRNPC-human

Experiment Status

	BGHLV20-33	BGHLV20-34
Sample_ID	BGHLV20-33	BGHLV20-34
Sample Name	HNRNPC-BGHLV20-33_17722	HNRNPC-BGHLV20-34_17723
Sample Name	HNRNPC-BGHLV20-33_17722	HNRNPC-BGHLV20-34_17723
RBP	HNRNPC	HNRNPC
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	722	723

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-33	BGHLV20-34
Sample #
Sample Name	HNRNPC-BGHLV20-33	HNRNPC-BGHLV20-34
Sample_Name_Alias	HNRNPC-BGHLV20-33_17722	HNRNPC-BGHLV20-34_17723
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A3.png	DNA_Library_LV20-22-23/set1/B3.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C9.png	RNA_Library_LV20-22-24/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-33	BGHLV20-34
RBP	HNRNPC	HNRNPC
Batch_ID	BGHLV20	BGHLV20
WB_result	78.300	74.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2408	2409

Sequencing Information

	BGHLV20-33	BGHLV20-34
Sample_ID	BGHLV20-33	BGHLV20-34
Sample Name	HNRNPC-BGHLV20-33_17722	HNRNPC-BGHLV20-34_17723
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	47,200,000	48,070,000
total_aligned_reads	42,749,982	43,851,194
unique_aligned_reads	40,455,870	41,517,392
percent_uniqueAligned	0.85712	0.86369
correlation_replicates	0.997365	0.997365
spikein_reads	220,996	208,932
percent_spikeins	0.00468	0.00435
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1176	1177

Data Submission Information

	BGHLV20-33	BGHLV20-33
ENCODE_alias	brenton-graveley:HNRNPC-BGHLV20	brenton-graveley:HNRNPC-BGHLV20-HepG2
ENCODE_accession	ENCSR052IYH	ENCSR308YXN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-33	BGHLV20-33
Sample Name	HNRNPC-BGHLV20-33_17722	HNRNPC-BGHLV20-33_17722
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2910	6754

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-BGHLV20-33_17722_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1176	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15600
HNRNPC-BGHLV20-33_17722_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1176	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15642
HNRNPC-BGHLV20-33_17722_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722_GTCCGC_L003_R1_001.fastq.gz,HNRNPC-BGHLV20-33_17722_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	15684
HNRNPC-BGHLV20-33_17722_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722/Aligned.sortedByCoord.out.bam		ENCORE2	15726
HNRNPC-BGHLV20-33_17722_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722/Aligned.sortedByCoord.out.bam		ENCORE2	15768
HNRNPC-BGHLV20-33_17722_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722/Aligned.sortedByCoord.out.bam		ENCORE2	15810
HNRNPC-BGHLV20-33_17722_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722/Aligned.sortedByCoord.out.bam		ENCORE2	15852
HNRNPC-BGHLV20-33_17722_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1176					GRCh38	V40	HNRNPC-BGHLV20-33_17722_GTCCGC_L003_R1_001.fastq.gz,HNRNPC-BGHLV20-33_17722_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	15894
HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1177	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15601
HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1177	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15643
HNRNPC-BGHLV20-34_17723_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R1_001.fastq.gz,HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	15685
HNRNPC-BGHLV20-34_17723_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723/Aligned.sortedByCoord.out.bam		ENCORE2	15727
HNRNPC-BGHLV20-34_17723_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723/Aligned.sortedByCoord.out.bam		ENCORE2	15769
HNRNPC-BGHLV20-34_17723_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723/Aligned.sortedByCoord.out.bam		ENCORE2	15811
HNRNPC-BGHLV20-34_17723_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723/Aligned.sortedByCoord.out.bam		ENCORE2	15853
HNRNPC-BGHLV20-34_17723_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1177					GRCh38	V40	HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R1_001.fastq.gz,HNRNPC-BGHLV20-34_17723_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	15895