HNRNPU RNA-Seq in HepG2

General Information


RBP	HNRNPU
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPU-BGHLV20-HepG2
ENCODE_series_ID	ENCSR304WXJ
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR308IKH
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	HNRNPU-BGHLV20-37_17726
Rep2	HNRNPU-BGHLV20-38_17727
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	71.2
Rep2_qPCR	67.1
Rep1_WB	68.0
Rep2_WB	81.7
Antibody Cat#	sc-32315
Antibody Lot#	sc-32315
Antibody DCC ID	ENCAB502MPG
Status	Released
Project	ENCODE3
ID	498

Experiment Information (Status: Released)

	BGHLV20-37	BGHLV20-38
idx	401	402
TRCN#_or_BGC#	TRCN0000001298	TRCN0000001298
shRNA_or_gRNA_sequence	CAGTGCTTCTTCCCTTACAAT	CAGTGCTTCTTCCCTTACAAT
PAM
Name	HNRNPU	HNRNPU
Sample_ID	BGHLV20-37	BGHLV20-38
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	HNRNPU	HNRNPU
qPCR_result	71.2	67.1
Ave_qPCR	69.2
RT-qPCR_primer-F	GGAGGATTCAATATGCGTGG
RT-qPCR_primer-R	GATAATGCTGACTCCATGGCT
protein_conc	5108	5540
WB_result	68.0	81.7
Ave_WB	74.9
WB_DONE_date	6/30/2015
MW	91kDa
IP	1MW	1MW
antibody_Cat#	sc-32315	sc-32315
Antibody DCC ID	ENCAB502MPG	ENCAB502MPG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	129.4	0
Rep2_TPM	94.3	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2466	2467

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPU	Product_ID: sc-32315 Lot_ID: C3012 Source: Santa Cruz Biotech Target Name: HNRNPU-human

Experiment Status

	BGHLV20-37	BGHLV20-38
Sample_ID	BGHLV20-37	BGHLV20-38
Sample Name	HNRNPU-BGHLV20-37_17726	HNRNPU-BGHLV20-38_17727
Sample Name	HNRNPU-BGHLV20-37_17726	HNRNPU-BGHLV20-38_17727
RBP	HNRNPU	HNRNPU
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	726	727

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-37	BGHLV20-38
Sample #
Sample Name	HNRNPU-BGHLV20-37	HNRNPU-BGHLV20-38
Sample_Name_Alias	HNRNPU-BGHLV20-37_17726	HNRNPU-BGHLV20-38_17727
Index Well Position	S22	S23
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/E3.png	DNA_Library_LV20-22-23/set1/F3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G9.png	RNA_Library_LV20-22-24/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-37	BGHLV20-38
RBP	HNRNPU	HNRNPU
Batch_ID	BGHLV20	BGHLV20
WB_result	68.000	81.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2412	2413

Sequencing Information

	BGHLV20-37	BGHLV20-38
Sample_ID	BGHLV20-37	BGHLV20-38
Sample Name	HNRNPU-BGHLV20-37_17726	HNRNPU-BGHLV20-38_17727
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	50,000,000	42,400,000
total_aligned_reads	45,949,352	38,357,256
unique_aligned_reads	43,365,108	36,157,098
percent_uniqueAligned	0.86730	0.85276
correlation_replicates	0.998907	0.998907
spikein_reads	212,154	172,954
percent_spikeins	0.00424	0.00408
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1180	1181

Data Submission Information

	BGHLV20-37	BGHLV20-37
ENCODE_alias	brenton-graveley:HNRNPU-BGHLV20	brenton-graveley:HNRNPU-BGHLV20-HepG2
ENCODE_accession	ENCSR308IKH	ENCSR304WXJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-37	BGHLV20-37
Sample Name	HNRNPU-BGHLV20-37_17726	HNRNPU-BGHLV20-37_17726
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2912	6769

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
HNRNPU-BGHLV20-37_17726_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1180	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	15604
HNRNPU-BGHLV20-37_17726_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1180	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	15646
HNRNPU-BGHLV20-37_17726_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726_CGTACG_L003_R1_001.fastq.gz,HNRNPU-BGHLV20-37_17726_CGTACG_L003_R2_001.fastq.gz		ENCORE2	15688
HNRNPU-BGHLV20-37_17726_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	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726/Aligned.sortedByCoord.out.bam		ENCORE2	15730
HNRNPU-BGHLV20-37_17726_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	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726/Aligned.sortedByCoord.out.bam		ENCORE2	15772
HNRNPU-BGHLV20-37_17726_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	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726/Aligned.sortedByCoord.out.bam		ENCORE2	15814
HNRNPU-BGHLV20-37_17726_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	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726/Aligned.sortedByCoord.out.bam		ENCORE2	15856
HNRNPU-BGHLV20-37_17726_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1180					GRCh38	V40	HNRNPU-BGHLV20-37_17726_CGTACG_L003_R1_001.fastq.gz,HNRNPU-BGHLV20-37_17726_CGTACG_L003_R2_001.fastq.gz		ENCORE2	15898
HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1181	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	15605
HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1181	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	15647
HNRNPU-BGHLV20-38_17727_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R1_001.fastq.gz,HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	15689
HNRNPU-BGHLV20-38_17727_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	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727/Aligned.sortedByCoord.out.bam		ENCORE2	15731
HNRNPU-BGHLV20-38_17727_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	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727/Aligned.sortedByCoord.out.bam		ENCORE2	15773
HNRNPU-BGHLV20-38_17727_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	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727/Aligned.sortedByCoord.out.bam		ENCORE2	15815
HNRNPU-BGHLV20-38_17727_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	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727/Aligned.sortedByCoord.out.bam		ENCORE2	15857
HNRNPU-BGHLV20-38_17727_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1181					GRCh38	V40	HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R1_001.fastq.gz,HNRNPU-BGHLV20-38_17727_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	15899