HNRNPLL RNA-Seq in HepG2

General Information


RBP	HNRNPLL
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPLL-BGHLV35-HepG2
ENCODE_series_ID	ENCSR370RIN
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR490DYI
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	HNRNPLL_BGHLV35-25
Rep2	HNRNPLL_BGHLV35-26
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	92.3
Rep2_qPCR	86.9
Rep1_WB	91.2
Rep2_WB	94.7
Antibody Cat#	#4783
Antibody Lot#	#4783
Antibody DCC ID	ENCAB698BTS
Status	Released
Project	ENCODE3
ID	735

Experiment Information (Status: Released)

	BGHLV35-25	BGHLV35-26
idx	881	882
TRCN#_or_BGC#	TRCN0000075101	TRCN0000075101
shRNA_or_gRNA_sequence	CGACAGGCTCTAGTGGAATTT	CGACAGGCTCTAGTGGAATTT
PAM
Name	HNRNPLL	HNRNPLL
Sample_ID	BGHLV35-25	BGHLV35-26
transduction_Date	4/29/16	4/29/16
days
RBP_name	HNRNPLL	HNRNPLL
qPCR_result	92.3	86.9
Ave_qPCR	89.6
RT-qPCR_primer-F	TGTTGGCAAAGTGCAACGTA
RT-qPCR_primer-R	GCTCCATTGAGTGCTGCTTT
protein_conc	3017	1824
WB_result	91.2	94.7
Ave_WB	92.9
WB_DONE_date	7/6/16	WES
MW	61kDa
IP		fu's
antibody_Cat#	#4783	#4783
Antibody DCC ID	ENCAB698BTS	ENCAB698BTS
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2970	2971

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPLL	Product_ID: 4783 Lot_ID: 2 Source: Cell Signaling Technology Target Name: HNRNPLL-human

Experiment Status

	BGHLV35-25	BGHLV35-26
Sample_ID	BGHLV35-25	BGHLV35-26
Sample Name	HNRNPLL_BGHLV35-25	HNRNPLL_BGHLV35-26
Sample Name	HNRNPLL_BGHLV35-25	HNRNPLL_BGHLV35-26
RBP	HNRNPLL	HNRNPLL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1259	1260

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-25	BGHLV35-26
Sample #
Sample Name	HNRNPLL-BGHLV35-25	HNRNPLL-BGHLV35-26
Sample_Name_Alias	HNRNPLL_BGHLV35-25	HNRNPLL_BGHLV35-26
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/E2.png	DNA_Library_LV35/set2/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E2.png	RNA_Library_LV35_LV36/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-25	BGHLV35-26
RBP	HNRNPLL	HNRNPLL
Batch_ID	BGHLV35	BGHLV35
WB_result	91.200	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2944	2945

Sequencing Information

	BGHLV35-25	BGHLV35-26
Sample_ID	BGHLV35-25	BGHLV35-26
Sample Name	HNRNPLL_BGHLV35-25	HNRNPLL_BGHLV35-26
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	81,135,506	78,244,918
total_aligned_reads	61,913,174	59,406,262
unique_aligned_reads	58,515,028	56,268,770
percent_uniqueAligned	0.72120	0.71914
correlation_replicates	0.999534	0.999534
spikein_reads	116,252	127,554
percent_spikeins	0.00143	0.00163
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1593	1594

Data Submission Information

	BGHLV35-25	BGHLV35-25
ENCODE_alias	brenton-graveley:HNRNPLL_BGHLV35	brenton-graveley:HNRNPLL-BGHLV35-HepG2
ENCODE_accession	ENCSR490DYI	ENCSR370RIN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-25	BGHLV35-25
Sample Name	HNRNPLL_BGHLV35-25	HNRNPLL_BGHLV35-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3169	6766

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
HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1593	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21692
HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1593	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21718
HNRNPLL_BGHLV35-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R1.fastq.gz,HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R2.fastq.gz		ENCORE2	21744
HNRNPLL_BGHLV35-25_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25/Aligned.sortedByCoord.out.bam		ENCORE2	21770
HNRNPLL_BGHLV35-25_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25/Aligned.sortedByCoord.out.bam		ENCORE2	21796
HNRNPLL_BGHLV35-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25/Aligned.sortedByCoord.out.bam		ENCORE2	21822
HNRNPLL_BGHLV35-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25/Aligned.sortedByCoord.out.bam		ENCORE2	21848
HNRNPLL_BGHLV35-25_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1593					GRCh38	V40	HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R1.fastq.gz,HNRNPLL_BGHLV35-25_AGTCAA_L006_001.R2.fastq.gz		ENCORE2	21874
HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1594	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21693
HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1594	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21719
HNRNPLL_BGHLV35-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R1.fastq.gz,HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R2.fastq.gz		ENCORE2	21745
HNRNPLL_BGHLV35-26_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26/Aligned.sortedByCoord.out.bam		ENCORE2	21771
HNRNPLL_BGHLV35-26_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26/Aligned.sortedByCoord.out.bam		ENCORE2	21797
HNRNPLL_BGHLV35-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26/Aligned.sortedByCoord.out.bam		ENCORE2	21823
HNRNPLL_BGHLV35-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26/Aligned.sortedByCoord.out.bam		ENCORE2	21849
HNRNPLL_BGHLV35-26_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1594					GRCh38	V40	HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R1.fastq.gz,HNRNPLL_BGHLV35-26_AGTTCC_L006_001.R2.fastq.gz		ENCORE2	21875