PUM1 RNA-Seq in HepG2

General Information


RBP	PUM1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PUM1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR674VQM
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR945XKW
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	PUM1-BGHLV23-33
Rep2	PUM1-BGHLV23-34
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	69.6
Rep2_qPCR	76.3
Rep1_WB	87.8
Rep2_WB	78.6
Antibody Cat#	A302-576A
Antibody Lot#	A302-576A
Antibody DCC ID	ENCAB744LEE
Status	Released
Project	ENCODE3
ID	548

Experiment Information (Status: Released)

	BGHLV23-33	BGHLV23-34
idx	525	526
TRCN#_or_BGC#	TRCN0000275489	TRCN0000275489
shRNA_or_gRNA_sequence	GCGTTTAAGGGACAGGTATTT	GCGTTTAAGGGACAGGTATTT
PAM
Name	PUM1_89	PUM1_89
Sample_ID	BGHLV23-33	BGHLV23-34
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	PUM1	PUM1
qPCR_result	69.6	76.3
Ave_qPCR	72.9
RT-qPCR_primer-F	AAACATCGATGGCCTACTGG
RT-qPCR_primer-R	TCTTCCCTCCAGAGCAAGTG
protein_conc	5609	3361
WB_result	87.8	78.6
Ave_WB	83.2
WB_DONE_date	5/11/2015
MW	126kDa
IP	1	1
antibody_Cat#	A302-576A	A302-576A
Antibody DCC ID	ENCAB744LEE	ENCAB744LEE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	18.4	0
Rep2_TPM	18.2	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2606	2607

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUM1	Product_ID: A302-576A Lot_ID: 1 Source: Bethyl Labs Target Name: PUM1-human

Experiment Status

	BGHLV23-33	BGHLV23-34
Sample_ID	BGHLV23-33	BGHLV23-34
Sample Name	PUM1-BGHLV23-33	PUM1-BGHLV23-34
Sample Name	PUM1-BGHLV23-33	PUM1-BGHLV23-34
RBP	PUM1	PUM1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	834	835

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-33	BGHLV23-34
Sample #
Sample Name	PUM1-BGHLV23-33	PUM1-BGHLV23-34
Sample_Name_Alias	PUM1-BGHLV23-33	PUM1-BGHLV23-34
Index Well Position	S15	S16
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/set4/G1.png	DNA_Library_LV20-22-23/set4/H1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C7.png	RNA_Library_LV22-23-25/set1/D7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-33	BGHLV23-34
RBP	PUM1	PUM1
Batch_ID	BGHLV23	BGHLV23
WB_result	87.800	78.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2522	2523

Sequencing Information

	BGHLV23-33	BGHLV23-34
Sample_ID	BGHLV23-33	BGHLV23-34
Sample Name	PUM1-BGHLV23-33	PUM1-BGHLV23-34
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	66,790,000	57,350,000
total_aligned_reads	60,385,020	51,525,780
unique_aligned_reads	56,678,158	48,464,404
percent_uniqueAligned	0.84860	0.84506
correlation_replicates	0.998680	0.998680
spikein_reads	340,084	293,534
percent_spikeins	0.00509	0.00512
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1144	1145

Data Submission Information

	BGHLV23-33	BGHLV23-33
ENCODE_alias	brenton-graveley:PUM1-BGHLV23	brenton-graveley:PUM1-BGHLV23-HepG2
ENCODE_accession	ENCSR945XKW	ENCSR674VQM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-33	BGHLV23-33
Sample Name	PUM1-BGHLV23-33	PUM1-BGHLV23-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2949	6879

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
PUM1-BGHLV23-33_ATGTCA_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1144	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	16674
PUM1-BGHLV23-33_ATGTCA_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1144	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	16712
PUM1-BGHLV23-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1144					GRCh38	V40	PUM1-BGHLV23-33_ATGTCA_L007_R1_001.fastq.gz,PUM1-BGHLV23-33_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	16750
PUM1-BGHLV23-33_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	1144					GRCh38	V40	PUM1-BGHLV23-33/Aligned.sortedByCoord.out.bam		ENCORE2	16788
PUM1-BGHLV23-33_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	1144					GRCh38	V40	PUM1-BGHLV23-33/Aligned.sortedByCoord.out.bam		ENCORE2	16826
PUM1-BGHLV23-33_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	1144					GRCh38	V40	PUM1-BGHLV23-33/Aligned.sortedByCoord.out.bam		ENCORE2	16864
PUM1-BGHLV23-33_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	1144					GRCh38	V40	PUM1-BGHLV23-33/Aligned.sortedByCoord.out.bam		ENCORE2	16902
PUM1-BGHLV23-33_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1144					GRCh38	V40	PUM1-BGHLV23-33_ATGTCA_L007_R1_001.fastq.gz,PUM1-BGHLV23-33_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	16940
PUM1-BGHLV23-34_CCGTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1145	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	16675
PUM1-BGHLV23-34_CCGTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1145	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	16713
PUM1-BGHLV23-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1145					GRCh38	V40	PUM1-BGHLV23-34_CCGTCC_L007_R1_001.fastq.gz,PUM1-BGHLV23-34_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	16751
PUM1-BGHLV23-34_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	1145					GRCh38	V40	PUM1-BGHLV23-34/Aligned.sortedByCoord.out.bam		ENCORE2	16789
PUM1-BGHLV23-34_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	1145					GRCh38	V40	PUM1-BGHLV23-34/Aligned.sortedByCoord.out.bam		ENCORE2	16827
PUM1-BGHLV23-34_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	1145					GRCh38	V40	PUM1-BGHLV23-34/Aligned.sortedByCoord.out.bam		ENCORE2	16865
PUM1-BGHLV23-34_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	1145					GRCh38	V40	PUM1-BGHLV23-34/Aligned.sortedByCoord.out.bam		ENCORE2	16903
PUM1-BGHLV23-34_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1145					GRCh38	V40	PUM1-BGHLV23-34_CCGTCC_L007_R1_001.fastq.gz,PUM1-BGHLV23-34_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	16941