HNRNPF RNA-Seq in K562

General Information


RBP	HNRNPF
Cell_Line	K562
Method	CRISPR
Exp_Name	HNRNPF-BGKcLV02-K562
ENCODE_series_ID	ENCSR714ASX
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR380RRP
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	HNRNPF_BGKcLV02-9
Rep2	HNRNPF_BGKcLV02-10
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	44.5
Rep2_qPCR	47.3
Rep1_WB	73.3
Rep2_WB	74.4
Antibody Cat#	GTX114476
Antibody Lot#	GTX114476
Antibody DCC ID	ENCAB386GVG
Status	Archived
Project	ENCODE3
ID	585

Experiment Information (Status: Released)

	BGKcLV02-9	BGKcLV02-10
idx	11	12
TRCN#_or_BGC#	BGC#0000007	BGC#0000007
shRNA_or_gRNA_sequence	AGTGCCGACAGCGCCAACGA	AGTGCCGACAGCGCCAACGA
PAM
Name	HNRNPF-C1-A	HNRNPF-C1-A
Sample_ID	BGKcLV02-9	BGKcLV02-10
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	HNRNPF	HNRNPF
qPCR_result	44.5	47.3
Ave_qPCR	45.9
RT-qPCR_primer-F	GAGGTGAAGGCTTTGTGGTC
RT-qPCR_primer-R	CCCATGCTTTCCCTGTCTT
protein_conc	3394	2980
WB_result	73.3	74.4
Ave_WB	73.8
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	248.9	0
Rep2_TPM	263.5	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4105	4106

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

	BGKcLV02-9	BGKcLV02-10
Sample_ID	BGKcLV02-9	BGKcLV02-10
Sample Name	HNRNPF_BGKcLV02-9	HNRNPF_BGKcLV02-10
Sample Name	HNRNPF_BGKcLV02-9	HNRNPF_BGKcLV02-10
RBP	HNRNPF	HNRNPF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1088	1087

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-9	BGKcLV02-10
Sample #
Sample Name	HNRNPF-BGKcLV02-9	HNRNPF-BGKcLV02-10
Sample_Name_Alias	HNRNPF_BGKcLV02-9	HNRNPF_BGKcLV02-10
Index Well Position	S20	S21
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/C4.png	DNA_Library_cLV02/set1/D4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/E5.png	RNA_Library_cLV02/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-9	BGKcLV02-10
RBP	HNRNPF	HNRNPF
Batch_ID	BGKcLV02	BGKcLV02
WB_result	73.300	74.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2777	2776

Sequencing Information

	BGKcLV02-9	BGKcLV02-10
Sample_ID	BGKcLV02-9	BGKcLV02-10
Sample Name	HNRNPF_BGKcLV02-9	HNRNPF_BGKcLV02-10
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	63,342,310	65,433,850
total_aligned_reads	57,999,198	59,710,294
unique_aligned_reads	52,947,730	54,437,786
percent_uniqueAligned	0.83590	0.83195
correlation_replicates	0.999265	0.999265
spikein_reads	134,842	179,052
percent_spikeins	0.00213	0.00274
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1426	1425

Data Submission Information

	BGKcLV02-9	BGKcLV02-9
ENCODE_alias	brenton-graveley:HNRNPF_BGKcLV02	brenton-graveley:HNRNPF-BGKcLV02-K562
ENCODE_accession	ENCSR380RRP	ENCSR714ASX
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-9	BGKcLV02-9
Sample Name	HNRNPF_BGKcLV02-9	HNRNPF_BGKcLV02-9
Selected	Yes	No
Status	Released	Archived
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3105	6759

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_BGKcLV02-9_GTGGCC_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1426	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22759
HNRNPF_BGKcLV02-9_GTGGCC_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1426	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22779
HNRNPF_BGKcLV02-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9_GTGGCC_L007_001.R1.fastq.gz,HNRNPF_BGKcLV02-9_GTGGCC_L007_001.R2.fastq.gz		ENCORE2	22799
HNRNPF_BGKcLV02-9_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	22819
HNRNPF_BGKcLV02-9_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	22839
HNRNPF_BGKcLV02-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	22859
HNRNPF_BGKcLV02-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	22879
HNRNPF_BGKcLV02-9_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1426					GRCh38	V40	HNRNPF_BGKcLV02-9_GTGGCC_L007_001.R1.fastq.gz,HNRNPF_BGKcLV02-9_GTGGCC_L007_001.R2.fastq.gz		ENCORE2	22899
HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1425	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22758
HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1425	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22778
HNRNPF_BGKcLV02-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R1.fastq.gz,HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R2.fastq.gz		ENCORE2	22798
HNRNPF_BGKcLV02-10_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	22818
HNRNPF_BGKcLV02-10_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	22838
HNRNPF_BGKcLV02-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	22858
HNRNPF_BGKcLV02-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	22878
HNRNPF_BGKcLV02-10_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1425					GRCh38	V40	HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R1.fastq.gz,HNRNPF_BGKcLV02-10_GTTTCG_L007_001.R2.fastq.gz		ENCORE2	22898