HNRNPF RNA-Seq in HepG2

General Information


RBP	HNRNPF
Cell_Line	HepG2
Method	CRISPR
Exp_Name	HNRNPF-BGHcLV03-HepG2
ENCODE_series_ID	ENCSR745IXO
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID	ENCSR599NNK
ENCODE_CN_Exp_ID	ENCSR105NML
Rep1	HNRNPF_BGHcLV03-7
Rep2	HNRNPF_BGHcLV03-8
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	76.8
Rep2_qPCR	63.1
Rep1_WB	82.6
Rep2_WB	82.4
Antibody Cat#	GTX114476
Antibody Lot#	GTX114476
Antibody DCC ID	ENCAB386GVG
Status	Released
Project	ENCODE3
ID	573

Experiment Information (Status: Released)

	BGHcLV03-7	BGHcLV03-8
idx	7	8
TRCN#_or_BGC#	BGC#0000008	BGC#0000008
shRNA_or_gRNA_sequence	GTTCGTGCAGTTTGCCTCGC	GTTCGTGCAGTTTGCCTCGC
PAM
Name	HNRNPF-Z1-B	HNRNPF-Z1-B
Sample_ID	BGHcLV03-7	BGHcLV03-8
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	HNRNPF	HNRNPF
qPCR_result	76.8	63.1
Ave_qPCR	69.9
RT-qPCR_primer-F	GAGGTGAAGGCTTTGTGGTC
RT-qPCR_primer-R	CCCATGCTTTCCCTGTCTT
protein_conc	3154	3050
WB_result	82.6	82.4
Ave_WB	82.5
WB_DONE_date	12/28/2015
MW	46kDa
IP	1
antibody_Cat#	GTX114476	GTX114476
Antibody DCC ID	ENCAB386GVG	ENCAB386GVG
submitted_to_DCC_date	9/28/16
Rep1_TPM	157	0
Rep2_TPM	176	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6148	6149

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPF	Product_ID: GTX114476 Lot_ID: 40135 Source: GeneTex Target Name: HNRNPF-human

Experiment Status

	BGHcLV03-7	BGHcLV03-8
Sample_ID	BGHcLV03-7	BGHcLV03-8
Sample Name	HNRNPF_BGHcLV03-7	HNRNPF_BGHcLV03-8
Sample Name	HNRNPF_BGHcLV03-7	HNRNPF_BGHcLV03-8
RBP	HNRNPF	HNRNPF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1099	1100

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-7	BGHcLV03-8
Sample #
Sample Name	HNRNPF-BGHcLV03-7	HNRNPF-BGHcLV03-8
Sample_Name_Alias	HNRNPF_BGHcLV03-7	HNRNPF_BGHcLV03-8
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/G1.png	DNA_Library_cLV02/set1/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/A3.png	RNA_Library_cLV02/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-7	BGHcLV03-8
RBP	HNRNPF	HNRNPF
Batch_ID	BGHcLV03	BGHcLV03
WB_result	82.600	82.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2794	2795

Sequencing Information

	BGHcLV03-7	BGHcLV03-8
Sample_ID	BGHcLV03-7	BGHcLV03-8
Sample Name	HNRNPF_BGHcLV03-7	HNRNPF_BGHcLV03-8
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	55,712,132	57,414,496
total_aligned_reads	48,510,538	50,721,080
unique_aligned_reads	45,651,000	47,786,732
percent_uniqueAligned	0.81941	0.83231
correlation_replicates	0.996325	0.996325
spikein_reads	93,536	104,118
percent_spikeins	0.00168	0.00181
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1443	1444

Data Submission Information

	BGHcLV03-7	BGHcLV03-7
ENCODE_alias	brenton-graveley:HNRNPF_BGHcLV03	brenton-graveley:HNRNPF-BGHcLV03-HepG2
ENCODE_accession	ENCSR599NNK	ENCSR745IXO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-7	BGHcLV03-7
Sample Name	HNRNPF_BGHcLV03-7	HNRNPF_BGHcLV03-7
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3111	6757

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
HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1443	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22916
HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1443	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22934
HNRNPF_BGHcLV03-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R1.fastq.gz,HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R2.fastq.gz		ENCORE2	22952
HNRNPF_BGHcLV03-7_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7/Aligned.sortedByCoord.out.bam		ENCORE2	22970
HNRNPF_BGHcLV03-7_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7/Aligned.sortedByCoord.out.bam		ENCORE2	22988
HNRNPF_BGHcLV03-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7/Aligned.sortedByCoord.out.bam		ENCORE2	23006
HNRNPF_BGHcLV03-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7/Aligned.sortedByCoord.out.bam		ENCORE2	23024
HNRNPF_BGHcLV03-7_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1443					GRCh38	V40	HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R1.fastq.gz,HNRNPF_BGHcLV03-7_ACTGAT_L005_001.R2.fastq.gz		ENCORE2	23042
HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1444	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22917
HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1444	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22935
HNRNPF_BGHcLV03-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R1.fastq.gz,HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R2.fastq.gz		ENCORE2	22953
HNRNPF_BGHcLV03-8_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8/Aligned.sortedByCoord.out.bam		ENCORE2	22971
HNRNPF_BGHcLV03-8_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8/Aligned.sortedByCoord.out.bam		ENCORE2	22989
HNRNPF_BGHcLV03-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8/Aligned.sortedByCoord.out.bam		ENCORE2	23007
HNRNPF_BGHcLV03-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8/Aligned.sortedByCoord.out.bam		ENCORE2	23025
HNRNPF_BGHcLV03-8_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1444					GRCh38	V40	HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R1.fastq.gz,HNRNPF_BGHcLV03-8_ATTCCT_L005_001.R2.fastq.gz		ENCORE2	23043