HNRNPH1 RNA-Seq in K562

General Information


RBP	HNRNPH1
Cell_Line	K562
Method	CRISPR
Exp_Name	HNRNPH1-BGKcLV06-K562
ENCODE_series_ID	ENCSR608UNA
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR354RSR
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	HNRNPH1-BGKcLV06-15
Rep2	HNRNPH1-BGKcLV06-16
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	70.2
Rep2_WB	67.3
Antibody Cat#	ARP58479
Antibody Lot#
Antibody DCC ID	ENCAB000AVT
Status	Released
Project	ENCODE3
ID	773

Experiment Information (Status: Released)

	BGKcLV06-15	BGKcLV06-16
idx	191	192
TRCN#_or_BGC#	BGC#0000074	BGC#0000074
shRNA_or_gRNA_sequence	TCAACAAAAGCCTCGCCACT	TCAACAAAAGCCTCGCCACT
PAM
Name	HNRNPH1_86	HNRNPH1_86
Sample_ID	BGKcLV06-15	BGKcLV06-16
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	HNRNPH1	HNRNPH1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gtacacatgcggggattacc
RT-qPCR_primer-R	ctgccatcaggaccaatttc
protein_conc	2302	2462
WB_result	70.2	67.3
Ave_WB	68.7
WB_DONE_date	7/6/17
MW	53kD
IP	FU'S
antibody_Cat#	ARP58479
Antibody DCC ID	ENCAB000AVT	ENCAB000AVT
submitted_to_DCC_date	9/29/17
Rep1_TPM	329.4	0
Rep2_TPM	363.3	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4289	4290

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPH1	Product_ID: ARP58479_P050 Lot_ID: QC25591 Source: Aviva Target Name: HNRNPH1-human

Experiment Status

	BGKcLV06-15	BGKcLV06-16
Sample_ID	BGKcLV06-15	BGKcLV06-16
Sample Name	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-16
Sample Name	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-16
RBP	HNRNPH1	HNRNPH1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1361	1362

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-15	BGKcLV06-16
Sample #
Sample Name	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-16
Sample_Name_Alias	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-16
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/E1.png	DNA_Library_set39/set2/F1.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set39/set3/F1.png	RNA_Library_set39/set3/G1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-15	BGKcLV06-16
RBP	HNRNPH1	HNRNPH1
Batch_ID	BGKcLV06	BGKcLV06
WB_result	70.200	67.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3056	3057

Sequencing Information

	BGKcLV06-15	BGKcLV06-16
Sample_ID	BGKcLV06-15	BGKcLV06-16
Sample Name	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-16
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	52,561,700	69,660,238
total_aligned_reads	46,314,820	62,077,760
unique_aligned_reads	42,123,538	56,482,062
percent_uniqueAligned	0.80141	0.81082
correlation_replicates	0.996387	0.996387
spikein_reads	20,958	34,330
percent_spikeins	0.00040	0.00049
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1707	1708

Data Submission Information

	BGKcLV06-15	BGKcLV06-15
ENCODE_alias	brenton-graveley:HNRNPH1-BGKcLV06	brenton-graveley:HNRNPH1-BGKcLV06-K562
ENCODE_accession	ENCSR354RSR	ENCSR608UNA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-15	BGKcLV06-15
Sample Name	HNRNPH1-BGKcLV06-15	HNRNPH1-BGKcLV06-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3220	6761

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
HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1707	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22466
HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1707	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22502
HNRNPH1-BGKcLV06-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R1.fastq.gz,HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22538
HNRNPH1-BGKcLV06-15_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	22574
HNRNPH1-BGKcLV06-15_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	22610
HNRNPH1-BGKcLV06-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	22646
HNRNPH1-BGKcLV06-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15/Aligned.sortedByCoord.out.bam		ENCORE2	22682
HNRNPH1-BGKcLV06-15_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1707					GRCh38	V40	HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R1.fastq.gz,HNRNPH1-BGKcLV06-15_AGTCAA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22718
HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1708	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22467
HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1708	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22503
HNRNPH1-BGKcLV06-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R1.fastq.gz,HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22539
HNRNPH1-BGKcLV06-16_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	22575
HNRNPH1-BGKcLV06-16_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	22611
HNRNPH1-BGKcLV06-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	22647
HNRNPH1-BGKcLV06-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16/Aligned.sortedByCoord.out.bam		ENCORE2	22683
HNRNPH1-BGKcLV06-16_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1708					GRCh38	V40	HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R1.fastq.gz,HNRNPH1-BGKcLV06-16_AGTTCC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22719