HNRNPD RNA-Seq in HepG2

General Information


RBP	HNRNPD
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPD-BGHLV22-HepG2
ENCODE_series_ID	ENCSR857JCZ
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR660MZN
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	HNRNPD-BGHLV22-25_17760
Rep2	HNRNPD-BGHLV22-26_17761
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	80.9
Rep2_qPCR	79.2
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	12382
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB870XOX
Status	Released
Project	ENCODE3
ID	538

Experiment Information (Status: Released)

	BGHLV22-25	BGHLV22-26
idx	453	454
TRCN#_or_BGC#	TRCN0000001293	TRCN0000001293
shRNA_or_gRNA_sequence	AGAGTGGTTATGGGAAGGTAT	AGAGTGGTTATGGGAAGGTAT
PAM
Name	HNRNPD	HNRNPD
Sample_ID	BGHLV22-25	BGHLV22-26
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	HNRNPD	HNRNPD
qPCR_result	80.9	79.2
Ave_qPCR	80.0
RT-qPCR_primer-F	CTCCAGATACACCTGAAGAGAAA
RT-qPCR_primer-R	CGCCTCTTATTGGTCTTGTTG
protein_conc	7165	7125
WB_result	no clear band	no clear band
Ave_WB
WB_DONE_date	7/21/16	wes
MW	37-48kDa	Cell Signaling Techn
IP		fu's
antibody_Cat#	#12382	#12382
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	85.2	0
Rep2_TPM	59.4	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2522	2523

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-25	BGHLV22-26
Sample_ID	BGHLV22-25	BGHLV22-26
Sample Name	HNRNPD-BGHLV22-25_17760	HNRNPD-BGHLV22-26_17761
Sample Name	HNRNPD-BGHLV22-25_17760	HNRNPD-BGHLV22-26_17761
RBP	HNRNPD	HNRNPD
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	790	791

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-25	BGHLV22-26
Sample #
Sample Name	HNRNPD-BGHLV22-25	HNRNPD-BGHLV22-26
Sample_Name_Alias	HNRNPD-BGHLV22-25_17760	HNRNPD-BGHLV22-26_17761
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G7.png	DNA_Library_LV20-22-23/set1/H7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G1.png	RNA_Library_LV22-23-25/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-25	BGHLV22-26
RBP	HNRNPD	HNRNPD
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2476	2477

Sequencing Information

	BGHLV22-25	BGHLV22-26
Sample_ID	BGHLV22-25	BGHLV22-26
Sample Name	HNRNPD-BGHLV22-25_17760	HNRNPD-BGHLV22-26_17761
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	45,070,000	43,600,000
total_aligned_reads	41,981,810	40,603,050
unique_aligned_reads	39,471,946	38,242,602
percent_uniqueAligned	0.87579	0.87712
correlation_replicates	0.992850	0.992850
spikein_reads	244,604	261,840
percent_spikeins	0.00543	0.00601
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1210	1211

Data Submission Information

	BGHLV22-25	BGHLV22-25
ENCODE_alias	brenton-graveley:HNRNPD-BGHLV22	brenton-graveley:HNRNPD-BGHLV22-HepG2
ENCODE_accession	ENCSR660MZN	ENCSR857JCZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-25	BGHLV22-25
Sample Name	HNRNPD-BGHLV22-25_17760	HNRNPD-BGHLV22-25_17760
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2927	6756

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
HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1210	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16286
HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1210	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16326
HNRNPD-BGHLV22-25_17760_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R1_001.fastq.gz,HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	16424
HNRNPD-BGHLV22-25_17760_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760/Aligned.sortedByCoord.out.bam		ENCORE2	16464
HNRNPD-BGHLV22-25_17760_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760/Aligned.sortedByCoord.out.bam		ENCORE2	16504
HNRNPD-BGHLV22-25_17760_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760/Aligned.sortedByCoord.out.bam		ENCORE2	16544
HNRNPD-BGHLV22-25_17760_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760/Aligned.sortedByCoord.out.bam		ENCORE2	16584
HNRNPD-BGHLV22-25_17760_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1210					GRCh38	V40	HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R1_001.fastq.gz,HNRNPD-BGHLV22-25_17760_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	16624
HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1211	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16287
HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1211	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16327
HNRNPD-BGHLV22-26_17761_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R1_001.fastq.gz,HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	16425
HNRNPD-BGHLV22-26_17761_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761/Aligned.sortedByCoord.out.bam		ENCORE2	16465
HNRNPD-BGHLV22-26_17761_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761/Aligned.sortedByCoord.out.bam		ENCORE2	16505
HNRNPD-BGHLV22-26_17761_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761/Aligned.sortedByCoord.out.bam		ENCORE2	16545
HNRNPD-BGHLV22-26_17761_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761/Aligned.sortedByCoord.out.bam		ENCORE2	16585
HNRNPD-BGHLV22-26_17761_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1211					GRCh38	V40	HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R1_001.fastq.gz,HNRNPD-BGHLV22-26_17761_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	16625