HNRNPF RNA-Seq in K562

General Information


RBP	HNRNPF
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPF-BGKLV21-K562
ENCODE_series_ID	ENCSR839OIY
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR392HSJ
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	HNRNPF_BGKLV21_21_17569
Rep2	HNRNPF_BGKLV21_22_17570
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	82.2
Rep2_qPCR	68.9
Rep1_WB	77.4
Rep2_WB	79.4
Antibody Cat#	GTX114476
Antibody Lot#	GTX114476
Antibody DCC ID	ENCAB386GVG
Status	Released
Project	ENCODE3
ID	511

Experiment Information (Status: Released)

	BGKLV21-21	BGKLV21-22
idx	292	293
TRCN#_or_BGC#	TRCN0000001234	TRCN0000001234
shRNA_or_gRNA_sequence	CGAGAACGACATTTACAACTT	CGAGAACGACATTTACAACTT
PAM
Name	HNRNPF	HNRNPF
Sample_ID	BGKLV21-21	BGKLV21-22
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	HNRNPF	HNRNPF
qPCR_result	82.2	68.9
Ave_qPCR	75.5
RT-qPCR_primer-F	GAGGTGAAGGCTTTGTGGTC
RT-qPCR_primer-R	CCCATGCTTTCCCTGTCTT
protein_conc	2725	3359
WB_result	77.4	79.4
Ave_WB	78.4
WB_DONE_date	3/7/2015
MW
IP	1	1
antibody_Cat#	GTX114476	GTX114476
Antibody DCC ID	ENCAB386GVG	ENCAB386GVG
submitted_to_DCC_date	5/4/2015
Rep1_TPM	248.854255	0
Rep2_TPM	263.501593	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	323	324

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

	BGKLV21-21	BGKLV21-22
Sample_ID	BGKLV21-21	BGKLV21-22
Sample Name	HNRNPF_BGKLV21_21_17569	HNRNPF_BGKLV21_22_17570
Sample Name	HNRNPF_BGKLV21_21_17569	HNRNPF_BGKLV21_22_17570
RBP	HNRNPF	HNRNPF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	754	755

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-21	BGKLV21-22
Sample #
Sample Name	HNRNPF-BGKLV21-21	HNRNPF-BGKLV21-22
Sample_Name_Alias	HNRNPF_BGKLV21_21_17569	HNRNPF_BGKLV21_22_17570
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/E6.png	DNA_Library_LV21-24/set1/F6.png
RIN	7.8	8.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A9.png	RNA_Library_LV19-21-24/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-21	BGKLV21-22
RBP	HNRNPF	HNRNPF
Batch_ID	BGKLV21	BGKLV21
WB_result	77.400	79.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2440	2441

Sequencing Information

	BGKLV21-21	BGKLV21-22
Sample_ID	BGKLV21-21	BGKLV21-22
Sample Name	HNRNPF_BGKLV21_21_17569	HNRNPF_BGKLV21_22_17570
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	36,890,000	42,600,000
total_aligned_reads	33,620,246	39,459,386
unique_aligned_reads	30,900,992	36,289,408
percent_uniqueAligned	0.83765	0.85186
correlation_replicates	0.999497	0.999497
spikein_reads	200,344	212,612
percent_spikeins	0.00543	0.00499
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1046	1047

Data Submission Information

	BGKLV21-21	BGKLV21-21
ENCODE_alias	brenton-graveley:HNRNPF_BGKLV21	brenton-graveley:HNRNPF-BGKLV21-K562
ENCODE_accession	ENCSR392HSJ	ENCSR839OIY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-21	BGKLV21-21
Sample Name	HNRNPF_BGKLV21_21_17569	HNRNPF_BGKLV21_21_17569
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2963	6760

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_BGKLV21_21_17569_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1046	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15932
HNRNPF_BGKLV21_21_17569_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1046	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15976
HNRNPF_BGKLV21_21_17569_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569_AGTCAA_L002_R1_001.fastq.gz,HNRNPF_BGKLV21_21_17569_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	16020
HNRNPF_BGKLV21_21_17569_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569/Aligned.sortedByCoord.out.bam		ENCORE2	16064
HNRNPF_BGKLV21_21_17569_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569/Aligned.sortedByCoord.out.bam		ENCORE2	16108
HNRNPF_BGKLV21_21_17569_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569/Aligned.sortedByCoord.out.bam		ENCORE2	16152
HNRNPF_BGKLV21_21_17569_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569/Aligned.sortedByCoord.out.bam		ENCORE2	16196
HNRNPF_BGKLV21_21_17569_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1046					GRCh38	V40	HNRNPF_BGKLV21_21_17569_AGTCAA_L002_R1_001.fastq.gz,HNRNPF_BGKLV21_21_17569_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	16240
HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1047	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15933
HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1047	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15977
HNRNPF_BGKLV21_22_17570_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R1_001.fastq.gz,HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	16021
HNRNPF_BGKLV21_22_17570_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570/Aligned.sortedByCoord.out.bam		ENCORE2	16065
HNRNPF_BGKLV21_22_17570_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570/Aligned.sortedByCoord.out.bam		ENCORE2	16109
HNRNPF_BGKLV21_22_17570_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570/Aligned.sortedByCoord.out.bam		ENCORE2	16153
HNRNPF_BGKLV21_22_17570_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570/Aligned.sortedByCoord.out.bam		ENCORE2	16197
HNRNPF_BGKLV21_22_17570_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1047					GRCh38	V40	HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R1_001.fastq.gz,HNRNPF_BGKLV21_22_17570_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	16241