HNRNPL RNA-Seq in HepG2

General Information


RBP	HNRNPL
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPL-BGHLV23-HepG2
ENCODE_series_ID	ENCSR826GBS
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR155BMF
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	HNRNPL-BGHLV23-21
Rep2	HNRNPL-BGHLV23-22
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	86.4
Rep2_qPCR	87.3
Rep1_WB	72.4
Rep2_WB	71.8
Antibody Cat#	AB6106
Antibody Lot#	AB6106
Antibody DCC ID	ENCAB678XLS
Status	Released
Project	ENCODE3
ID	545

Experiment Information (Status: Released)

	BGHLV23-21	BGHLV23-21	BGHLV23-22	BGHLV23-22
idx	513	513	514	514
TRCN#_or_BGC#	TRCN0000017245	TRCN0000017245	TRCN0000017245	TRCN0000017245
shRNA_or_gRNA_sequence	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT	CCTCAACAACAACTTCATGTT
PAM
Name	HNRNPL	HNRNPL	HNRNPL	HNRNPL
Sample_ID	BGHLV23-21	BGHLV23-21	BGHLV23-22	BGHLV23-22
transduction_Date	10/29/2014	10/29/2014	10/29/2014	10/29/2014
days
RBP_name	HNRNPL	HNRNPL	HNRNPL	HNRNPL
qPCR_result	86.4	86.4	87.3	87.3
Ave_qPCR	86.8	86.8
RT-qPCR_primer-F	CTGGGCTTCCTGAACCATTA	CTGGGCTTCCTGAACCATTA
RT-qPCR_primer-R	TGCTGAGCAGTGGAGAAACA	TGCTGAGCAGTGGAGAAACA
protein_conc	6122	6122	4709	4709
WB_result	72.4	90.0	71.8	77.7
Ave_WB	72.1	83.9
WB_DONE_date	7/7/2017	2/12/2016
MW	64KkDa	64KkDa		wes
IP		fu's
antibody_Cat#	AB6106	ARP40368	AB6106	ARP40368
Antibody DCC ID	ENCAB678XLS	ENCAB000AVZ	ENCAB678XLS	ENCAB000AVZ
submitted_to_DCC_date	9/29/2017	3/8/2016
Rep1_TPM	77	77	0	0
Rep2_TPM	56.4	56.4	0	0
Action
Library_start_date	6/10/2015	6/10/2015	6/10/2015	6/10/2015
repeat_library
Note
ID	2592	2594	2593	2595

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPL	Product_ID: ab6106 Lot_ID: GR30383-23 Source: Abcam Target Name: HNRNPL-human
HNRNPL	Product_ID: ARP40368_P050 Lot_ID: QC9464 Source: Aviva Target Name: HNRNPL-human

Experiment Status

	BGHLV23-21	BGHLV23-22
Sample_ID	BGHLV23-21	BGHLV23-22
Sample Name	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-22
Sample Name	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-22
RBP	HNRNPL	HNRNPL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	826	827

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-21	BGHLV23-22
Sample #
Sample Name	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-22
Sample_Name_Alias	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-22
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/D2.png	DNA_Library_LV20-22-23/set4/B1.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/C6.png	RNA_Library_LV19-21-24/set2/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-21	BGHLV23-22
RBP	HNRNPL	HNRNPL
Batch_ID	BGHLV23	BGHLV23
WB_result	72.400	71.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2514	2515

Sequencing Information

	BGHLV23-21	BGHLV23-22
Sample_ID	BGHLV23-21	BGHLV23-22
Sample Name	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-22
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	54,450,000	58,770,000
total_aligned_reads	44,800,084	50,822,888
unique_aligned_reads	42,016,602	47,693,432
percent_uniqueAligned	0.77165	0.81153
correlation_replicates	0.998653	0.998653
spikein_reads	284,118	330,384
percent_spikeins	0.00522	0.00562
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1136	1137

Data Submission Information

	BGHLV23-21	BGHLV23-21
ENCODE_alias	brenton-graveley:HNRNPL-BGHLV23	brenton-graveley:HNRNPL-BGHLV23-HepG2
ENCODE_accession	ENCSR155BMF	ENCSR826GBS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-21	BGHLV23-21
Sample Name	HNRNPL-BGHLV23-21	HNRNPL-BGHLV23-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2945	6764

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
HNRNPL-BGHLV23-21_GATCAG_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1136	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16664
HNRNPL-BGHLV23-21_GATCAG_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1136	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16702
HNRNPL-BGHLV23-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21_GATCAG_L006_R1_001.fastq.gz,HNRNPL-BGHLV23-21_GATCAG_L006_R2_001.fastq.gz		ENCORE2	16740
HNRNPL-BGHLV23-21_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	16778
HNRNPL-BGHLV23-21_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	16816
HNRNPL-BGHLV23-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	16854
HNRNPL-BGHLV23-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	16892
HNRNPL-BGHLV23-21_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1136					GRCh38	V40	HNRNPL-BGHLV23-21_GATCAG_L006_R1_001.fastq.gz,HNRNPL-BGHLV23-21_GATCAG_L006_R2_001.fastq.gz		ENCORE2	16930
HNRNPL-BGHLV23-22_TAGCTT_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1137	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16665
HNRNPL-BGHLV23-22_TAGCTT_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1137	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16703
HNRNPL-BGHLV23-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22_TAGCTT_L006_R1_001.fastq.gz,HNRNPL-BGHLV23-22_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	16741
HNRNPL-BGHLV23-22_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	16779
HNRNPL-BGHLV23-22_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	16817
HNRNPL-BGHLV23-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	16855
HNRNPL-BGHLV23-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	16893
HNRNPL-BGHLV23-22_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1137					GRCh38	V40	HNRNPL-BGHLV23-22_TAGCTT_L006_R1_001.fastq.gz,HNRNPL-BGHLV23-22_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	16931