HNRNPF RNA-Seq in HepG2

General Information


RBP	HNRNPF
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPF-BGHLV20-HepG2
ENCODE_series_ID	ENCSR327JVU
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR693MZJ
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	HNRNPF-BGHLV20-35_17724
Rep2	HNRNPF-BGHLV20-36_17725
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	57.9
Rep2_qPCR	62.2
Rep1_WB	78.9
Rep2_WB	58.1
Antibody Cat#	GTX114476
Antibody Lot#	GTX114476
Antibody DCC ID	ENCAB386GVG
Status	Archived
Project	ENCODE3
ID	497

Experiment Information (Status: Released)

	BGHLV20-35	BGHLV20-36
idx	399	400
TRCN#_or_BGC#	TRCN0000001234	TRCN0000001234
shRNA_or_gRNA_sequence	CGAGAACGACATTTACAACTT	CGAGAACGACATTTACAACTT
PAM
Name	HNRNPF	HNRNPF
Sample_ID	BGHLV20-35	BGHLV20-36
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	HNRNPF	HNRNPF
qPCR_result	57.9	62.2
Ave_qPCR	60.0
RT-qPCR_primer-F	GAGGTGAAGGCTTTGTGGTC
RT-qPCR_primer-R	CCCATGCTTTCCCTGTCTT
protein_conc	6008	5671
WB_result	78.9	58.1
Ave_WB	68.5
WB_DONE_date	3/7/2015
MW	46kDa
IP	1	1
antibody_Cat#	GTX114476	GTX114476
Antibody DCC ID	ENCAB386GVG	ENCAB386GVG
submitted_to_DCC_date	5/4/2015
Rep1_TPM	156.5	0
Rep2_TPM	175.7	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2464	2465

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

	BGHLV20-35	BGHLV20-36
Sample_ID	BGHLV20-35	BGHLV20-36
Sample Name	HNRNPF-BGHLV20-35_17724	HNRNPF-BGHLV20-36_17725
Sample Name	HNRNPF-BGHLV20-35_17724	HNRNPF-BGHLV20-36_17725
RBP	HNRNPF	HNRNPF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	724	725

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-35	BGHLV20-36
Sample #
Sample Name	HNRNPF-BGHLV20-35	HNRNPF-BGHLV20-36
Sample_Name_Alias	HNRNPF-BGHLV20-35_17724	HNRNPF-BGHLV20-36_17725
Index Well Position	S20	S21
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/C3.png	DNA_Library_LV20-22-23/set1/D3.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E9.png	RNA_Library_LV20-22-24/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-35	BGHLV20-36
RBP	HNRNPF	HNRNPF
Batch_ID	BGHLV20	BGHLV20
WB_result	78.900	58.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2410	2411

Sequencing Information

	BGHLV20-35	BGHLV20-36
Sample_ID	BGHLV20-35	BGHLV20-36
Sample Name	HNRNPF-BGHLV20-35_17724	HNRNPF-BGHLV20-36_17725
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	51,210,000	45,250,000
total_aligned_reads	46,923,380	41,414,456
unique_aligned_reads	44,354,834	39,083,370
percent_uniqueAligned	0.86614	0.86372
correlation_replicates	0.996606	0.996606
spikein_reads	261,220	216,070
percent_spikeins	0.00510	0.00478
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1178	1179

Data Submission Information

	BGHLV20-35	BGHLV20-35
ENCODE_alias	brenton-graveley:HNRNPF-BGHLV20	brenton-graveley:HNRNPF-BGHLV20-HepG2
ENCODE_accession	ENCSR693MZJ	ENCSR327JVU
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-35	BGHLV20-35
Sample Name	HNRNPF-BGHLV20-35_17724	HNRNPF-BGHLV20-35_17724
Selected	Yes	No
Status	Released	Archived
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2911	6758

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-BGHLV20-35_17724_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1178	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	15602
HNRNPF-BGHLV20-35_17724_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1178	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	15644
HNRNPF-BGHLV20-35_17724_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724_GTGGCC_L003_R1_001.fastq.gz,HNRNPF-BGHLV20-35_17724_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	15686
HNRNPF-BGHLV20-35_17724_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	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724/Aligned.sortedByCoord.out.bam		ENCORE2	15728
HNRNPF-BGHLV20-35_17724_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	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724/Aligned.sortedByCoord.out.bam		ENCORE2	15770
HNRNPF-BGHLV20-35_17724_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	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724/Aligned.sortedByCoord.out.bam		ENCORE2	15812
HNRNPF-BGHLV20-35_17724_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	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724/Aligned.sortedByCoord.out.bam		ENCORE2	15854
HNRNPF-BGHLV20-35_17724_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1178					GRCh38	V40	HNRNPF-BGHLV20-35_17724_GTGGCC_L003_R1_001.fastq.gz,HNRNPF-BGHLV20-35_17724_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	15896
HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1179	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	15603
HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1179	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	15645
HNRNPF-BGHLV20-36_17725_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R1_001.fastq.gz,HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	15687
HNRNPF-BGHLV20-36_17725_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	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725/Aligned.sortedByCoord.out.bam		ENCORE2	15729
HNRNPF-BGHLV20-36_17725_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	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725/Aligned.sortedByCoord.out.bam		ENCORE2	15771
HNRNPF-BGHLV20-36_17725_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	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725/Aligned.sortedByCoord.out.bam		ENCORE2	15813
HNRNPF-BGHLV20-36_17725_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	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725/Aligned.sortedByCoord.out.bam		ENCORE2	15855
HNRNPF-BGHLV20-36_17725_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1179					GRCh38	V40	HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R1_001.fastq.gz,HNRNPF-BGHLV20-36_17725_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	15897