HNRNPA1 RNA-Seq in HepG2

General Information


RBP	HNRNPA1
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPA1-BGHLV20-HepG2
ENCODE_series_ID	ENCSR152VVM
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR182DAW
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	HNRNPA1-BGHLV20-31_17720
Rep2	HNRNPA1-BGHLV20-32_17721
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	71.9
Rep2_qPCR	76.5
Rep1_WB	45.3
Rep2_WB	32.8
Antibody Cat#	sc-32301
Antibody Lot#	sc-32301
Antibody DCC ID	ENCAB603WLW
Status	Released
Project	ENCODE3
ID	495

Experiment Information (Status: Released)

	BGHLV20-31	BGHLV20-32
idx	395	396
TRCN#_or_BGC#	TRCN0000006583	TRCN0000006583
shRNA_or_gRNA_sequence	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA
PAM
Name	HNRNPA1	HNRNPA1
Sample_ID	BGHLV20-31	BGHLV20-32
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	HNRNPA1	HNRNPA1
qPCR_result	71.9	76.5
Ave_qPCR	74.2
RT-qPCR_primer-F	CCTTTGACGACCATGACTCC
RT-qPCR_primer-R	TCTTGCTTTGACAGGGCTTT
protein_conc	4079	3677
WB_result	45.3	32.8
Ave_WB	39.0
WB_DONE_date	7/15/2015
MW	39kDa
IP	1	1
antibody_Cat#	sc-32301	sc-32301
Antibody DCC ID	ENCAB603WLW	ENCAB603WLW
submitted_to_DCC_date	8/6/2015
Rep1_TPM	761.5	0
Rep2_TPM	485.2	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2460	2461

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPA1	Product_ID: sc-32301 Lot_ID: I2413 Source: Santa Cruz Biotech Target Name: HNRNPA1-human

Experiment Status

	BGHLV20-31	BGHLV20-32
Sample_ID	BGHLV20-31	BGHLV20-32
Sample Name	HNRNPA1-BGHLV20-31_17720	HNRNPA1-BGHLV20-32_17721
Sample Name	HNRNPA1-BGHLV20-31_17720	HNRNPA1-BGHLV20-32_17721
RBP	HNRNPA1	HNRNPA1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	720	721

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-31	BGHLV20-32
Sample #
Sample Name	HNRNPA1-BGHLV20-31	HNRNPA1-BGHLV20-32
Sample_Name_Alias	HNRNPA1-BGHLV20-31_17720	HNRNPA1-BGHLV20-32_17721
Index Well Position	S15	S16
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/G2.png	DNA_Library_LV20-22-23/set1/H2.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A9.png	RNA_Library_LV20-22-24/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-31	BGHLV20-32
RBP	HNRNPA1	HNRNPA1
Batch_ID	BGHLV20	BGHLV20
WB_result	45.300	32.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2406	2407

Sequencing Information

	BGHLV20-31	BGHLV20-32
Sample_ID	BGHLV20-31	BGHLV20-32
Sample Name	HNRNPA1-BGHLV20-31_17720	HNRNPA1-BGHLV20-32_17721
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	43,820,000	37,020,000
total_aligned_reads	39,573,962	33,335,280
unique_aligned_reads	37,338,530	31,449,114
percent_uniqueAligned	0.85209	0.84952
correlation_replicates	0.991423	0.991423
spikein_reads	199,470	156,404
percent_spikeins	0.00455	0.00422
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1174	1175

Data Submission Information

	BGHLV20-31	BGHLV20-31
ENCODE_alias	brenton-graveley:HNRNPA1-BGHLV20	brenton-graveley:HNRNPA1-BGHLV20-HepG2
ENCODE_accession	ENCSR182DAW	ENCSR152VVM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-31	BGHLV20-31
Sample Name	HNRNPA1-BGHLV20-31_17720	HNRNPA1-BGHLV20-31_17720
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2909	6748

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
HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1174	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	15598
HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1174	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	15640
HNRNPA1-BGHLV20-31_17720_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R1_001.fastq.gz,HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	15682
HNRNPA1-BGHLV20-31_17720_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	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720/Aligned.sortedByCoord.out.bam		ENCORE2	15724
HNRNPA1-BGHLV20-31_17720_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	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720/Aligned.sortedByCoord.out.bam		ENCORE2	15766
HNRNPA1-BGHLV20-31_17720_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	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720/Aligned.sortedByCoord.out.bam		ENCORE2	15808
HNRNPA1-BGHLV20-31_17720_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	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720/Aligned.sortedByCoord.out.bam		ENCORE2	15850
HNRNPA1-BGHLV20-31_17720_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1174					GRCh38	V40	HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R1_001.fastq.gz,HNRNPA1-BGHLV20-31_17720_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	15892
HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1175	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	15599
HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1175	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	15641
HNRNPA1-BGHLV20-32_17721_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R1_001.fastq.gz,HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	15683
HNRNPA1-BGHLV20-32_17721_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	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721/Aligned.sortedByCoord.out.bam		ENCORE2	15725
HNRNPA1-BGHLV20-32_17721_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	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721/Aligned.sortedByCoord.out.bam		ENCORE2	15767
HNRNPA1-BGHLV20-32_17721_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	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721/Aligned.sortedByCoord.out.bam		ENCORE2	15809
HNRNPA1-BGHLV20-32_17721_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	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721/Aligned.sortedByCoord.out.bam		ENCORE2	15851
HNRNPA1-BGHLV20-32_17721_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1175					GRCh38	V40	HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R1_001.fastq.gz,HNRNPA1-BGHLV20-32_17721_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	15893