RECQL RNA-Seq in HepG2

General Information


RBP	RECQL
Cell_Line	HepG2
Method	shRNA
Exp_Name	RECQL-BGHLV12-HepG2
ENCODE_series_ID	ENCSR025SHW
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR572AMC
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	RECQL-BGHLV12-71
Rep2	RECQL-BGHLV12-72
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	73.6
Rep2_qPCR	59.2
Rep1_WB	89.4
Rep2_WB	98.3
Antibody Cat#	A300-450A
Antibody Lot#	A300-450A
Antibody DCC ID	ENCAB680IWE
Status	Released
Project	ENCODE3
ID	352

Experiment Information (Status: Released)

	BGHLV12-71	BGHLV12-71	BGHLV12-72	BGHLV12-72
idx	71	0	72	0
TRCN#_or_BGC#	TRCN0000052001	TRCN0000052001	TRCN0000052001	TRCN0000052001
shRNA_or_gRNA_sequence	GCACATGCTATTACTATGCAA	GCACATGCTATTACTATGCAA	GCACATGCTATTACTATGCAA	GCACATGCTATTACTATGCAA
PAM
Name	RECQL	RECQL	RECQL	RECQL
Sample_ID	BGHLV12-71	BGHLV12-71	BGHLV12-72	BGHLV12-72
transduction_Date	5/15/2014	5/15/2014	5/15/2014	5/15/2014
days
RBP_name	RECQL	RECQL	RECQL	RECQL
qPCR_result	73.6	73.6	59.2	59.2
Ave_qPCR	66.4	66.4
RT-qPCR_primer-F	ttcaatggtggtgatggaaa	ttcaatggtggtgatggaaa
RT-qPCR_primer-R	ccatcaacacacgacgacat	ccatcaacacacgacgacat
protein_conc	2524	2524	2862	2862
WB_result	89.4	90.7	98.3	96.5
Ave_WB	93.9	93.6	94.5
WB_DONE_date		7/9/2019
MW	73kDa	73kDa
IP	1		1
antibody_Cat#	A300-450A	A300-450A	A300-450A
Antibody DCC ID	ENCAB680IWE	ENCAB507GCU	lot #1	lot #2
submitted_to_DCC_date	5/6/2015
Rep1_TPM	15.5	0	0	0
Rep2_TPM	12.8	0	0	0
Action
Library_start_date	6/12/2014		6/12/2014
repeat_library
Note	need change image/(qPCR redone)
ID	2124	2126	2125	2127

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RECQL	Product_ID: A300-450A Lot_ID: 2 Source: Bethyl Labs Target Name: RECQL-human

Experiment Status

	BGHLV12-71	BGHLV12-72
Sample_ID	BGHLV12-71	BGHLV12-72
Sample Name	RECQL-BGHLV12-71	RECQL-BGHLV12-72
Sample Name	RECQL-BGHLV12-71	RECQL-BGHLV12-72
RBP	RECQL	RECQL
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	424	425

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-71	BGHLV12-72
Sample #
Sample Name	RECQL-BGHLV12-71	RECQL-BGHLV12-72
Sample_Name_Alias	RECQL-BGHLV12-71	RECQL-BGHLV12-72
Index Well Position	S05	S06
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/E3.png	DNA_Library_LV12/set3/F3.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/E7.png	RNA_Library_LV12/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-71	BGHLV12-72
RBP	RECQL	RECQL
Batch_ID	BGHLV12	BGHLV12
WB_result	89.400	98.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2048	2049

Sequencing Information

	BGHLV12-71	BGHLV12-72
Sample_ID	BGHLV12-71	BGHLV12-72
Sample Name	RECQL-BGHLV12-71	RECQL-BGHLV12-72
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	64,230,000	64,250,000
total_aligned_reads	58,518,504	57,846,980
unique_aligned_reads	55,171,984	54,498,678
percent_uniqueAligned	0.85898	0.84823
correlation_replicates	0.998878	0.998878
spikein_reads	311,560	246,012
percent_spikeins	0.00485	0.00383
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	746	747

Data Submission Information

	BGHLV12-71	BGHLV12-71
ENCODE_alias	brenton-graveley:RECQL-BGHLV12	brenton-graveley:RECQL-BGHLV12-HepG2
ENCODE_accession	ENCSR572AMC	ENCSR025SHW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-71	BGHLV12-71
Sample Name	RECQL-BGHLV12-71	RECQL-BGHLV12-71
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2761	6909

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
RECQL-BGHLV12-71_ACAGTG_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	746	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12807
RECQL-BGHLV12-71_ACAGTG_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	746	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12876
RECQL-BGHLV12-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	746					GRCh38	V40	RECQL-BGHLV12-71_ACAGTG_L008_R1_001.fastq.gz,RECQL-BGHLV12-71_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	12946
RECQL-BGHLV12-71_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	746					GRCh38	V40	RECQL-BGHLV12-71/Aligned.sortedByCoord.out.bam		ENCORE2	13016
RECQL-BGHLV12-71_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	746					GRCh38	V40	RECQL-BGHLV12-71/Aligned.sortedByCoord.out.bam		ENCORE2	13086
RECQL-BGHLV12-71_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	746					GRCh38	V40	RECQL-BGHLV12-71/Aligned.sortedByCoord.out.bam		ENCORE2	13156
RECQL-BGHLV12-71_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	746					GRCh38	V40	RECQL-BGHLV12-71/Aligned.sortedByCoord.out.bam		ENCORE2	13226
RECQL-BGHLV12-71_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	746					GRCh38	V40	RECQL-BGHLV12-71_ACAGTG_L008_R1_001.fastq.gz,RECQL-BGHLV12-71_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	13296
RECQL-BGHLV12-72_GCCAAT_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	747	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12808
RECQL-BGHLV12-72_GCCAAT_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	747	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12877
RECQL-BGHLV12-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	747					GRCh38	V40	RECQL-BGHLV12-72_GCCAAT_L008_R1_001.fastq.gz,RECQL-BGHLV12-72_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	12947
RECQL-BGHLV12-72_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	747					GRCh38	V40	RECQL-BGHLV12-72/Aligned.sortedByCoord.out.bam		ENCORE2	13017
RECQL-BGHLV12-72_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	747					GRCh38	V40	RECQL-BGHLV12-72/Aligned.sortedByCoord.out.bam		ENCORE2	13087
RECQL-BGHLV12-72_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	747					GRCh38	V40	RECQL-BGHLV12-72/Aligned.sortedByCoord.out.bam		ENCORE2	13157
RECQL-BGHLV12-72_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	747					GRCh38	V40	RECQL-BGHLV12-72/Aligned.sortedByCoord.out.bam		ENCORE2	13227
RECQL-BGHLV12-72_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	747					GRCh38	V40	RECQL-BGHLV12-72_GCCAAT_L008_R1_001.fastq.gz,RECQL-BGHLV12-72_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	13297