PABPC4 RNA-Seq in HepG2

General Information


RBP	PABPC4
Cell_Line	HepG2
Method	shRNA
Exp_Name	PABPC4-BGHLV12-HepG2
ENCODE_series_ID	ENCSR475UTA
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR455VZH
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	PABPC4-BGHLV12-53
Rep2	PABPC4-BGHLV12-54
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	80.1
Rep2_qPCR	75.1
Rep1_WB	91.1
Rep2_WB	92.1
Antibody Cat#	A301-466A
Antibody Lot#	A301-466A
Antibody DCC ID	ENCAB596MHX
Status	Released
Project	ENCODE3
ID	347

Experiment Information (Status: Released)

	BGHLV12-53	BGHLV12-54
idx	53	54
TRCN#_or_BGC#	TRCN0000074658	TRCN0000074658
shRNA_or_gRNA_sequence	CCTCAACACCAAGGATTACAA	CCTCAACACCAAGGATTACAA
PAM
Name	PABPC4	PABPC4
Sample_ID	BGHLV12-53	BGHLV12-54
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	PABPC4	PABPC4
qPCR_result	80.1	75.1
Ave_qPCR	77.6
RT-qPCR_primer-F	CAAATACGCCTCCAGTGTCC
RT-qPCR_primer-R	GCAGTCAGTGGCTCCTGC
protein_conc	3627	4733
WB_result	91.1	92.1
Ave_WB	91.6
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A301-466A	A301-466A
Antibody DCC ID	ENCAB596MHX	ENCAB596MHX
submitted_to_DCC_date	4/2/2015
Rep1_TPM	91.2	0
Rep2_TPM	64.3	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2100	2101

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PABPC4	Product_ID: A301-466A Lot_ID: 1 Source: Bethyl Labs Target Name: PABPC4-human

Experiment Status

	BGHLV12-53	BGHLV12-54
Sample_ID	BGHLV12-53	BGHLV12-54
Sample Name	PABPC4-BGHLV12-53	PABPC4-BGHLV12-54
Sample Name	PABPC4-BGHLV12-53	PABPC4-BGHLV12-54
RBP	PABPC4	PABPC4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	412	413

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-53	BGHLV12-54
Sample #
Sample Name	PABPC4-BGHLV12-53	PABPC4-BGHLV12-54
Sample_Name_Alias	PABPC4-BGHLV12-53	PABPC4-BGHLV12-54
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/A2.png	DNA_Library_LV12/set3/B2.png
RIN	9.1	9.7
libSample_RNA_Well	RNA_Library_LV12/set1/A6.png	RNA_Library_LV12/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-53	BGHLV12-54
RBP	PABPC4	PABPC4
Batch_ID	BGHLV12	BGHLV12
WB_result	91.100	92.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2036	2037

Sequencing Information

	BGHLV12-53	BGHLV12-54
Sample_ID	BGHLV12-53	BGHLV12-54
Sample Name	PABPC4-BGHLV12-53	PABPC4-BGHLV12-54
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	64,480,000	67,750,000
total_aligned_reads	59,030,208	62,556,204
unique_aligned_reads	55,956,420	59,249,676
percent_uniqueAligned	0.86781	0.87453
correlation_replicates	0.998148	0.998148
spikein_reads	560,382	511,802
percent_spikeins	0.00869	0.00755
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	736	737

Data Submission Information

	BGHLV12-53	BGHLV12-53
ENCODE_alias	brenton-graveley:PABPC4-BGHLV12	brenton-graveley:PABPC4-BGHLV12-HepG2
ENCODE_accession	ENCSR455VZH	ENCSR475UTA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-53	BGHLV12-53
Sample Name	PABPC4-BGHLV12-53	PABPC4-BGHLV12-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2755	6843

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
PABPC4-BGHLV12-53_GTCCGC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	736	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12795
PABPC4-BGHLV12-53_GTCCGC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	736	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12864
PABPC4-BGHLV12-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53_GTCCGC_L006_R1_001.fastq.gz,PABPC4-BGHLV12-53_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	12934
PABPC4-BGHLV12-53_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53/Aligned.sortedByCoord.out.bam		ENCORE2	13004
PABPC4-BGHLV12-53_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53/Aligned.sortedByCoord.out.bam		ENCORE2	13074
PABPC4-BGHLV12-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53/Aligned.sortedByCoord.out.bam		ENCORE2	13144
PABPC4-BGHLV12-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53/Aligned.sortedByCoord.out.bam		ENCORE2	13214
PABPC4-BGHLV12-53_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	736					GRCh38	V40	PABPC4-BGHLV12-53_GTCCGC_L006_R1_001.fastq.gz,PABPC4-BGHLV12-53_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	13284
PABPC4-BGHLV12-54_GTGAAA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	737	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12796
PABPC4-BGHLV12-54_GTGAAA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	737	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12865
PABPC4-BGHLV12-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54_GTGAAA_L006_R1_001.fastq.gz,PABPC4-BGHLV12-54_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	12935
PABPC4-BGHLV12-54_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54/Aligned.sortedByCoord.out.bam		ENCORE2	13005
PABPC4-BGHLV12-54_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54/Aligned.sortedByCoord.out.bam		ENCORE2	13075
PABPC4-BGHLV12-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54/Aligned.sortedByCoord.out.bam		ENCORE2	13145
PABPC4-BGHLV12-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54/Aligned.sortedByCoord.out.bam		ENCORE2	13215
PABPC4-BGHLV12-54_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	737					GRCh38	V40	PABPC4-BGHLV12-54_GTGAAA_L006_R1_001.fastq.gz,PABPC4-BGHLV12-54_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	13285