HNRNPH1 RNA-Seq in HepG2

General Information


RBP	HNRNPH1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	HNRNPH1-BGHcLV07-HepG2
ENCODE_series_ID	ENCSR873XLT
Batch_ID	BGHcLV07
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR094HEU
ENCODE_CN_Exp_ID	ENCSR194SPW
Rep1	HNRNPH1-BGHcLV07-15B
Rep2	HNRNPH1-BGHcLV07-16B
CN1	NT-BGHcLV07-1B
CN2	NT-BGHcLV07-2B
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	90.2
Rep2_WB	91.3
Antibody Cat#	ARP58479
Antibody Lot#	lot# QC25591
Antibody DCC ID	ENCAB000AVT
Status	Released
Project	ENCODE4
ID	260

Experiment Information (Status: Released)

	BGHcLV07-15	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16
idx	127	0	128	0
TRCN#_or_BGC#	BGC#0000075	BGC#0000075	BGC#0000075	BGC#0000075
shRNA_or_gRNA_sequence	GCTCGGCCGATGAAGTGCAG	GCTCGGCCGATGAAGTGCAG	GCTCGGCCGATGAAGTGCAG	GCTCGGCCGATGAAGTGCAG
PAM
Name	HNRNPH1_83F_2	HNRNPH1_83F_2	HNRNPH1_83F_2	HNRNPH1_83F_2
Sample_ID	BGHcLV07-15	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16
transduction_Date	6/13/17	6/13/17	6/13/17	6/13/17
days	D6	D6	D6	D6
RBP_name	HNRNPH1	HNRNPH1	HNRNPH1	HNRNPH1
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0	0
RT-qPCR_primer-F	gtacacatgcggggattacc	gtacacatgcggggattacc
RT-qPCR_primer-R	ctgccatcaggaccaatttc	ctgccatcaggaccaatttc
protein_conc	3776	3776	3920	3920
WB_result	90.2	84.9	91.3	82.2
Ave_WB	90.8	83.5
WB_DONE_date	3/22/2019	2/28/19
MW	53kD	53kD
IP	FU'S
antibody_Cat#	ARP58479	PA5-70400	lot# QC25591	LOT UNKNOW
Antibody DCC ID	ENCAB000AVT	no ID
submitted_to_DCC_date	3/11/19	3/11/19
Rep1_TPM	490	490	0	0
Rep2_TPM	604	604	0	0
Action	Ready		Ready
Library_start_date	12/18/17		12/18/17
repeat_library
Note
ID	6268	6270	6269	6271

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
HNRNPH1	Product_ID: PA5-70400 Lot_ID: unknown Source: Thermo Fisher Target Name: HNRNPH1-human

Experiment Status

	BGHcLV07-15	BGHcLV07-16
Sample_ID	BGHcLV07-15	BGHcLV07-16
Sample Name
Sample Name	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-16B
RBP	HNRNPH1	HNRNPH1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6425	6426

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-15	BGHcLV07-16
Sample #	9	10
Sample Name	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-16B
Sample_Name_Alias
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	288	297
Peak_Molarity	7.60	28.10
libSampleQC_DNA_Well	DNA_Library_set40/set1/C8.png	DNA_Library_set40/set1/D8.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set40/set1/E3.png	RNA_Library_set40/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHcLV07-15	BGHcLV07-16
RBP	HNRNPH1	HNRNPH1
Batch_ID	BGHcLV07	BGHcLV07
WB_result	90.200	91.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	932	933

Sequencing Information

	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16
Sample_ID	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16
Sample Name	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B
Pool ID	Pool-180109	Pool-180109	Pool-180316
LocalServer_folder	set40_H	set40_H	set40_H
total_reads	55,150,774	21,230,044	16,378,106
total_aligned_reads	44,875,764	17,230,612	13,066,084
unique_aligned_reads	42,280,710	16,252,344	12,330,706
percent_uniqueAligned	0.76664	0.76554	0.75288
correlation_replicates	0.996500	0.996500
spikein_reads	5,414	3,496	2,542
percent_spikeins	0.00010	0.00016	0.00016
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	335	336	396

Data Submission Information

	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16
ENCODE_alias	brenton-graveley:HNRNPH1-BGHcLV07-B	brenton-graveley:HNRNPH1-BGHcLV07-15B	brenton-graveley:L-HNRNPH1-BGHcLV07-15B	brenton-graveley:HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R1.fastq.gz	brenton-graveley:HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R2.fastq.gz	brenton-graveley:HNRNPH1-BGHcLV07-HepG2	brenton-graveley:HNRNPH1-BGHcLV07-16B	brenton-graveley:L-HNRNPH1-BGHcLV07-16B	brenton-graveley:HNRNPH1-BGHcLV07-16B_TGACCA_ACBYWVANXX_L004_001.R1.fastq.gz	brenton-graveley:HNRNPH1-BGHcLV07-16B_TGACCA_AHFKCFBCX2_L002_001.R1.fastq.gz	brenton-graveley:HNRNPH1-BGHcLV07-16B_TGACCA_ACBYWVANXX_L004_001.R2.fastq.gz	brenton-graveley:HNRNPH1-BGHcLV07-16B_TGACCA_AHFKCFBCX2_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR094HEU	ENCBS388SIY	ENCLB909PXV	ENCFF685BIE	ENCFF736ZWG	ENCSR873XLT	ENCBS381JXX	ENCLB135VBI	ENCFF812WHY	ENCFF390CPT	ENCFF525YMY	ENCFF370ZMO
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-15	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16	BGHcLV07-16
Sample Name	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-15B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B	HNRNPH1-BGHcLV07-16B
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		HNRNPH1-BGHcLV07-15B.pdf	L-HNRNPH1-BGHcLV07-15B.pdf				HNRNPH1-BGHcLV07-16B.pdf	L-HNRNPH1-BGHcLV07-16B.pdf
ID	1438	1474	1530	1583	1620	7241	1475	1531	1584	1585	1621	1622

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-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	335	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	650
HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	335	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	692
HNRNPH1-BGHcLV07-15B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R1.fastq.gz,HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R2.fastq.gz		ENCORE2	23256
HNRNPH1-BGHcLV07-15B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B/Aligned.sortedByCoord.out.bam		ENCORE2	23290
HNRNPH1-BGHcLV07-15B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B/Aligned.sortedByCoord.out.bam		ENCORE2	23324
HNRNPH1-BGHcLV07-15B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B/Aligned.sortedByCoord.out.bam		ENCORE2	23358
HNRNPH1-BGHcLV07-15B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B/Aligned.sortedByCoord.out.bam		ENCORE2	23392
HNRNPH1-BGHcLV07-15B_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	335					GRCh38	V40	HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R1.fastq.gz,HNRNPH1-BGHcLV07-15B_TTAGGC_ACBYWVANXX_L004_001.R2.fastq.gz		ENCORE2	23426
HNRNPH1-BGHcLV07-16B_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	336	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	23233
HNRNPH1-BGHcLV07-16B_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	336	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	23241
HNRNPH1-BGHcLV07-16B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B_L001_001.R1.fastq.gz,HNRNPH1-BGHcLV07-16B_L001_001.R2.fastq.gz		ENCORE2	23257
HNRNPH1-BGHcLV07-16B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B/Aligned.sortedByCoord.out.bam		ENCORE2	23291
HNRNPH1-BGHcLV07-16B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B/Aligned.sortedByCoord.out.bam		ENCORE2	23325
HNRNPH1-BGHcLV07-16B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B/Aligned.sortedByCoord.out.bam		ENCORE2	23359
HNRNPH1-BGHcLV07-16B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B/Aligned.sortedByCoord.out.bam		ENCORE2	23393
HNRNPH1-BGHcLV07-16B_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	336					GRCh38	V40	HNRNPH1-BGHcLV07-16B_L001_001.R1.fastq.gz,HNRNPH1-BGHcLV07-16B_L001_001.R2.fastq.gz		ENCORE2	23427