HNRNPUL1 RNA-Seq in HepG2

General Information


RBP	HNRNPUL1
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPUL1-BGHLV26-HepG2
ENCODE_series_ID	ENCSR925FQW
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR689ZJC
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	HNRNPUL1_BGHLV26-19
Rep2	HNRNPUL1_BGHLV26-20
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	85.5
Rep2_qPCR	88.5
Rep1_WB	78.4
Rep2_WB	83.3
Antibody Cat#	A300-862A
Antibody Lot#	A300-862A
Antibody DCC ID	ENCAB484JUT
Status	Released
Project	ENCODE3
ID	629

Experiment Information (Status: Released)

	BGHLV26-19	BGHLV26-19	BGHLV26-20	BGHLV26-20
idx	573	575	574	576
TRCN#_or_BGC#	TRCN0000074730	TRCN0000074730	TRCN0000074730	TRCN0000074730
shRNA_or_gRNA_sequence	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA
PAM
Name	HNRNPUL1	HNRNPUL1	HNRNPUL1	HNRNPUL1
Sample_ID	BGHLV26-19	BGHLV26-19	BGHLV26-20	BGHLV26-20
transduction_Date	5/25/2015	5/25/2015	5/25/2015	5/25/2015
days
RBP_name	HNRNPUL1	HNRNPUL1	HNRNPUL1	HNRNPUL1
qPCR_result	85.5	85.5	88.5	88.5
Ave_qPCR	87.0	87.0
RT-qPCR_primer-F	ggcaactaccgaggaggttt	ggcaactaccgaggaggttt
RT-qPCR_primer-R	tgttgttatcccggttgttg	tgttgttatcccggttgttg
protein_conc	4354	4354	4405	4405
WB_result	78.4	88.9	83.3	88.8
Ave_WB	80.8	88.9
WB_DONE_date	6/26/2015	12/3/2015
MW	96kDa	96kDa
IP	1IP	FU'S	1IP	Abcam
antibody_Cat#	A300-862A	ab68480	A300-862A	ab68480
Antibody DCC ID	ENCAB484JUT	ENCAB083GDM	ENCAB484JUT	ENCAB083GDM
submitted_to_DCC_date	8/6/2015	12/7/2015
Rep1_TPM	25.1	0	0	0
Rep2_TPM	22	0	0	0
Action
Library_start_date	9/8/2015		9/8/2015
repeat_library
Note	x		x
ID	2654	2656	2655	2657

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPUL1	Product_ID: A300-862A Lot_ID: 1 Source: Bethyl Labs Target Name: HNRNPUL1-human
HNRNPUL1	Product_ID: ab68480 Lot_ID: GR24627-4 Source: Abcam Target Name: HNRNPUL1-human

Experiment Status

	BGHLV26-19	BGHLV26-20
Sample_ID	BGHLV26-19	BGHLV26-20
Sample Name	HNRNPUL1_BGHLV26-19	HNRNPUL1_BGHLV26-20
Sample Name	HNRNPUL1_BGHLV26-19	HNRNPUL1_BGHLV26-20
RBP	HNRNPUL1	HNRNPUL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	940	941

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-19	BGHLV26-20
Sample #
Sample Name	HNRNPUL1-BGHLV26-19	HNRNPUL1-BGHLV26-20
Sample_Name_Alias	HNRNPUL1_BGHLV26-19	HNRNPUL1_BGHLV26-20
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set2/F2.png	DNA_Library_LV24-25-26/set1/D8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV25-26/set1/E1.png	RNA_Library_LV25-26/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-19	BGHLV26-20
RBP	HNRNPUL1	HNRNPUL1
Batch_ID	BGHLV26	BGHLV26
WB_result	78.400	83.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2628	2629

Sequencing Information

	BGHLV26-19	BGHLV26-20
Sample_ID	BGHLV26-19	BGHLV26-20
Sample Name	HNRNPUL1_BGHLV26-19	HNRNPUL1_BGHLV26-20
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	78,956,450	65,818,852
total_aligned_reads	66,595,692	56,588,458
unique_aligned_reads	62,201,008	52,972,050
percent_uniqueAligned	0.78779	0.80482
correlation_replicates	0.998036	0.998036
spikein_reads	187,326	144,422
percent_spikeins	0.00237	0.00219
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1270	1271

Data Submission Information

	BGHLV26-19	BGHLV26-19
ENCODE_alias	brenton-graveley:HNRNPUL1_BGHLV26	brenton-graveley:HNRNPUL1-BGHLV26-HepG2
ENCODE_accession	ENCSR689ZJC	ENCSR925FQW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-19	BGHLV26-19
Sample Name	HNRNPUL1_BGHLV26-19	HNRNPUL1_BGHLV26-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3017	6771

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
HNRNPUL1_BGHLV26-19_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1270	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19814
HNRNPUL1_BGHLV26-19_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1270	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19836
HNRNPUL1_BGHLV26-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19_1.fastq.gz,HNRNPUL1_BGHLV26-19_2.fastq.gz		ENCORE2	19858
HNRNPUL1_BGHLV26-19_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	19880
HNRNPUL1_BGHLV26-19_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	19902
HNRNPUL1_BGHLV26-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	19924
HNRNPUL1_BGHLV26-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	19946
HNRNPUL1_BGHLV26-19_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1270					GRCh38	V40	HNRNPUL1_BGHLV26-19_1.fastq.gz,HNRNPUL1_BGHLV26-19_2.fastq.gz		ENCORE2	20654
HNRNPUL1_BGHLV26-20_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1271	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19815
HNRNPUL1_BGHLV26-20_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1271	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19837
HNRNPUL1_BGHLV26-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20_1.fastq.gz,HNRNPUL1_BGHLV26-20_2.fastq.gz		ENCORE2	19859
HNRNPUL1_BGHLV26-20_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	19881
HNRNPUL1_BGHLV26-20_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	19903
HNRNPUL1_BGHLV26-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	19925
HNRNPUL1_BGHLV26-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	19947
HNRNPUL1_BGHLV26-20_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1271					GRCh38	V40	HNRNPUL1_BGHLV26-20_1.fastq.gz,HNRNPUL1_BGHLV26-20_2.fastq.gz		ENCORE2	20655