SUPT6H RNA-Seq in K562

General Information


RBP	SUPT6H
Cell_Line	K562
Method	shRNA
Exp_Name	SUPT6H-BGKLV28-K562
ENCODE_series_ID	ENCSR009CGJ
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR530BOP
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	SUPT6H_BGKLV28-57
Rep2	SUPT6H_BGKLV28-58
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	72.0
Rep2_qPCR	82.7
Rep1_WB	61.0
Rep2_WB	79.5
Antibody Cat#	A300-801A
Antibody Lot#	A300-801A
Antibody DCC ID	ENCAB683FFM
Status	Released
Project	ENCODE3
ID	660

Experiment Information (Status: Released)

	BGKLV28-57	BGKLV28-58
idx	526	527
TRCN#_or_BGC#	TRCN0000019733	TRCN0000019733
shRNA_or_gRNA_sequence	CCAACCGTGAATGGACTGTTT	CCAACCGTGAATGGACTGTTT
PAM
Name	SUPT6H	SUPT6H
Sample_ID	BGKLV28-57	BGKLV28-58
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	SUPT6H	SUPT6H
qPCR_result	72.0	82.7
Ave_qPCR	77.4
RT-qPCR_primer-F	CGGCAAGTTCCTACTGGGAT
RT-qPCR_primer-R	TACCGGAATCCCTCTGGAGT
protein_conc	3305	3130
WB_result	61.0	79.5
Ave_WB	70.2
WB_DONE_date	8/26/2015
MW	199KdA
IP
antibody_Cat#	A300-801A	A300-801A
Antibody DCC ID	ENCAB683FFM	ENCAB683FFM
submitted_to_DCC_date	12/7/2015
Rep1_TPM	72.1329141	0
Rep2_TPM	67.2416711	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	603	604

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUPT6H	Product_ID: A300-801A Lot_ID: 1 Source: Bethyl Labs Target Name: SUPT6H-human

Experiment Status

	BGKLV28-57	BGKLV28-58
Sample_ID	BGKLV28-57	BGKLV28-58
Sample Name	SUPT6H_BGKLV28-57	SUPT6H_BGKLV28-58
Sample Name	SUPT6H_BGKLV28-57	SUPT6H_BGKLV28-58
RBP	SUPT6H	SUPT6H
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1006	1007

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-57	BGKLV28-58
Sample #
Sample Name	SUPT6H-BGKLV28-57	SUPT6H-BGKLV28-58
Sample_Name_Alias	SUPT6H_BGKLV28-57	SUPT6H_BGKLV28-58
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/B5.png	DNA_Library_LV28-29-30/set1/D4.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G9.png	RNA_Library_LV26-27-28-29/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-57	BGKLV28-58
RBP	SUPT6H	SUPT6H
Batch_ID	BGKLV28	BGKLV28
WB_result	61.000	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2698	2699

Sequencing Information

	BGKLV28-57	BGKLV28-58
Sample_ID	BGKLV28-57	BGKLV28-58
Sample Name	SUPT6H_BGKLV28-57	SUPT6H_BGKLV28-58
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	86,163,952	116,254,610
total_aligned_reads	69,632,566	93,470,086
unique_aligned_reads	63,551,892	85,252,896
percent_uniqueAligned	0.73757	0.73333
correlation_replicates	0.994658	0.994658
spikein_reads	278,000	330,938
percent_spikeins	0.00323	0.00285
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1340	1341

Data Submission Information

	BGKLV28-57	BGKLV28-57
ENCODE_alias	brenton-graveley:SUPT6H_BGKLV28	brenton-graveley:SUPT6H-BGKLV28-K562
ENCODE_accession	ENCSR530BOP	ENCSR009CGJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-57	BGKLV28-57
Sample Name	SUPT6H_BGKLV28-57	SUPT6H_BGKLV28-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3052	6995

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
SUPT6H_BGKLV28-57_TTAGGC_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1340	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20184
SUPT6H_BGKLV28-57_TTAGGC_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1340	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20216
SUPT6H_BGKLV28-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57_TTAGGC_L004_001.R1.fastq.gz,SUPT6H_BGKLV28-57_TTAGGC_L004_001.R2.fastq.gz		ENCORE2	20248
SUPT6H_BGKLV28-57_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57/Aligned.sortedByCoord.out.bam		ENCORE2	20280
SUPT6H_BGKLV28-57_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57/Aligned.sortedByCoord.out.bam		ENCORE2	20312
SUPT6H_BGKLV28-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57/Aligned.sortedByCoord.out.bam		ENCORE2	20344
SUPT6H_BGKLV28-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57/Aligned.sortedByCoord.out.bam		ENCORE2	20376
SUPT6H_BGKLV28-57_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1340					GRCh38	V40	SUPT6H_BGKLV28-57_TTAGGC_L004_001.R1.fastq.gz,SUPT6H_BGKLV28-57_TTAGGC_L004_001.R2.fastq.gz		ENCORE2	20408
SUPT6H_BGKLV28-58_TGACCA_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1341	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20185
SUPT6H_BGKLV28-58_TGACCA_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1341	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20217
SUPT6H_BGKLV28-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58_TGACCA_L004_001.R1.fastq.gz,SUPT6H_BGKLV28-58_TGACCA_L004_001.R2.fastq.gz		ENCORE2	20249
SUPT6H_BGKLV28-58_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58/Aligned.sortedByCoord.out.bam		ENCORE2	20281
SUPT6H_BGKLV28-58_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58/Aligned.sortedByCoord.out.bam		ENCORE2	20313
SUPT6H_BGKLV28-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58/Aligned.sortedByCoord.out.bam		ENCORE2	20345
SUPT6H_BGKLV28-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58/Aligned.sortedByCoord.out.bam		ENCORE2	20377
SUPT6H_BGKLV28-58_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1341					GRCh38	V40	SUPT6H_BGKLV28-58_TGACCA_L004_001.R1.fastq.gz,SUPT6H_BGKLV28-58_TGACCA_L004_001.R2.fastq.gz		ENCORE2	20409