HNRNPUL1 RNA-Seq in K562

General Information


RBP	HNRNPUL1
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPUL1-BGKLV28-K562
ENCODE_series_ID	ENCSR478HBC
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR034VBA
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	HNRNPUL1_BGKLV28-23
Rep2	HNRNPUL1_BGKLV28-24
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	89.8
Rep2_qPCR	88.4
Rep1_WB	83.7
Rep2_WB	85.8
Antibody Cat#	A300-862A
Antibody Lot#	A300-862A
Antibody DCC ID	ENCAB484JUT
Status	Released
Project	ENCODE3
ID	649

Experiment Information (Status: Released)

	BGKLV28-23	BGKLV28-23	BGKLV28-24	BGKLV28-24
idx	490	492	491	493
TRCN#_or_BGC#	TRCN0000074730	TRCN0000074730	TRCN0000074730	TRCN0000074730
shRNA_or_gRNA_sequence	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA	CCGGGATAACAACAACTCCAA
PAM
Name	HNRNPUL1_30	HNRNPUL1_30	HNRNPUL1_30	HNRNPUL1_30
Sample_ID	BGKLV28-23	BGKLV28-23	BGKLV28-24	BGKLV28-24
transduction_Date	6/16/2015	6/16/2015	6/16/2015	6/16/2015
days
RBP_name	HNRNPUL1	HNRNPUL1	HNRNPUL1	HNRNPUL1
qPCR_result	89.8	89.8	88.4	88.4
Ave_qPCR	89.1	89.1
RT-qPCR_primer-F	ggcaactaccgaggaggttt	ggcaactaccgaggaggttt
RT-qPCR_primer-R	tgttgttatcccggttgttg	tgttgttatcccggttgttg
protein_conc	2472	2472	3711	3711
WB_result	83.7	81.8	85.8	79.2
Ave_WB	84.7	80.5
WB_DONE_date	6/30/2015	12/3/2015
MW	96kd	96kDa		Abcam
IP	1IP	FU'S	1IP
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	38.7833751	38.7833751	0	0
Rep2_TPM	37.3408918	37.3408918	0	0
Action
Library_start_date	10/28/2015		10/28/2015
repeat_library
Note	x		x
ID	565	567	566	568

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

	BGKLV28-23	BGKLV28-24
Sample_ID	BGKLV28-23	BGKLV28-24
Sample Name	HNRNPUL1_BGKLV28-23	HNRNPUL1_BGKLV28-24
Sample Name	HNRNPUL1_BGKLV28-23	HNRNPUL1_BGKLV28-24
RBP	HNRNPUL1	HNRNPUL1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	982	983

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-23	BGKLV28-24
Sample #
Sample Name	HNRNPUL1-BGKLV28-23	HNRNPUL1-BGKLV28-24
Sample_Name_Alias	HNRNPUL1_BGKLV28-23	HNRNPUL1_BGKLV28-24
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E1.png	DNA_Library_LV28-29-30/set1/F1.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A7.png	RNA_Library_LV26-27-28-29/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-23	BGKLV28-24
RBP	HNRNPUL1	HNRNPUL1
Batch_ID	BGKLV28	BGKLV28
WB_result	83.700	85.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2674	2675

Sequencing Information

	BGKLV28-23	BGKLV28-24
Sample_ID	BGKLV28-23	BGKLV28-24
Sample Name	HNRNPUL1_BGKLV28-23	HNRNPUL1_BGKLV28-24
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	79,996,282	98,547,910
total_aligned_reads	65,397,126	81,740,732
unique_aligned_reads	59,585,516	74,142,774
percent_uniqueAligned	0.74485	0.75235
correlation_replicates	0.989436	0.989436
spikein_reads	233,762	273,652
percent_spikeins	0.00292	0.00278
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1316	1317

Data Submission Information

	BGKLV28-23	BGKLV28-23
ENCODE_alias	brenton-graveley:HNRNPUL1_BGKLV28	brenton-graveley:HNRNPUL1-BGKLV28-K562
ENCODE_accession	ENCSR034VBA	ENCSR478HBC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-23	BGKLV28-23
Sample Name	HNRNPUL1_BGKLV28-23	HNRNPUL1_BGKLV28-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3040	6772

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_BGKLV28-23_ACAGTG_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1316	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20160
HNRNPUL1_BGKLV28-23_ACAGTG_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1316	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20192
HNRNPUL1_BGKLV28-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23_ACAGTG_L001_001.R1.fastq.gz,HNRNPUL1_BGKLV28-23_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	20224
HNRNPUL1_BGKLV28-23_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	20256
HNRNPUL1_BGKLV28-23_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	20288
HNRNPUL1_BGKLV28-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	20320
HNRNPUL1_BGKLV28-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	20352
HNRNPUL1_BGKLV28-23_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1316					GRCh38	V40	HNRNPUL1_BGKLV28-23_ACAGTG_L001_001.R1.fastq.gz,HNRNPUL1_BGKLV28-23_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	20384
HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1317	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20161
HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1317	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20193
HNRNPUL1_BGKLV28-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R1.fastq.gz,HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	20225
HNRNPUL1_BGKLV28-24_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	20257
HNRNPUL1_BGKLV28-24_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	20289
HNRNPUL1_BGKLV28-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	20321
HNRNPUL1_BGKLV28-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	20353
HNRNPUL1_BGKLV28-24_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1317					GRCh38	V40	HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R1.fastq.gz,HNRNPUL1_BGKLV28-24_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	20385