SF1 RNA-Seq in K562

General Information


RBP	SF1
Cell_Line	K562
Method	shRNA
Exp_Name	SF1-BGKLV28-K562
ENCODE_series_ID	ENCSR675KZH
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR562CCA
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	SF1_BGKLV28-49
Rep2	SF1_BGKLV28-50
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	56.8
Rep2_qPCR	49.7
Rep1_WB	62.6
Rep2_WB	64.2
Antibody Cat#	GTX104540
Antibody Lot#	GTX104540
Antibody DCC ID	ENCAB000AUN
Status	Released
Project	ENCODE3
ID	656

Experiment Information (Status: Released)

	BGKLV28-49	BGKLV28-50
idx	518	519
TRCN#_or_BGC#	TRCN0000001069	TRCN0000001069
shRNA_or_gRNA_sequence	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT
PAM
Name	SF1	SF1
Sample_ID	BGKLV28-49	BGKLV28-50
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	SF1	SF1
qPCR_result	56.8	49.7
Ave_qPCR	53.2
RT-qPCR_primer-F	TGTGTACCAAGTGTGGAGGG
RT-qPCR_primer-R	ATCCGTGCTTTATCCTGAGC
protein_conc	2841	2821
WB_result	62.6	64.2
Ave_WB	63.4	very light band
WB_DONE_date	7/6/2015
MW	68kd
IP	1IP
antibody_Cat#	GTX104540	GTX104540
Antibody DCC ID	ENCAB000AUN	ENCAB000AUN
submitted_to_DCC_date	12/7/2015
Rep1_TPM	99.3475344	0
Rep2_TPM	81.7043814	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	593	594

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF1	Product_ID: GTX104540 Lot_ID: 40002 Source: GeneTex Target Name: SF1-human

Experiment Status

	BGKLV28-49	BGKLV28-50
Sample_ID	BGKLV28-49	BGKLV28-50
Sample Name	SF1_BGKLV28-49	SF1_BGKLV28-50
Sample Name	SF1_BGKLV28-49	SF1_BGKLV28-50
RBP	SF1	SF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	998	999

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-49	BGKLV28-50
Sample #
Sample Name	SF1-BGKLV28-49	SF1-BGKLV28-50
Sample_Name_Alias	SF1_BGKLV28-49	SF1_BGKLV28-50
Index Well Position	S20	S21
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_LV28-29-30/set1/C3.png	DNA_Library_LV28-29-30/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G8.png	RNA_Library_LV26-27-28-29/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-49	BGKLV28-50
RBP	SF1	SF1
Batch_ID	BGKLV28	BGKLV28
WB_result	62.600	64.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2690	2691

Sequencing Information

	BGKLV28-49	BGKLV28-50
Sample_ID	BGKLV28-49	BGKLV28-50
Sample Name	SF1_BGKLV28-49	SF1_BGKLV28-50
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	42,585,514	69,110,900
total_aligned_reads	34,836,974	62,065,720
unique_aligned_reads	32,022,246	56,537,110
percent_uniqueAligned	0.75195	0.81806
correlation_replicates	0.995264	0.995264
spikein_reads	163,954	257,076
percent_spikeins	0.00385	0.00372
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1332	1333

Data Submission Information

	BGKLV28-49	BGKLV28-49
ENCODE_alias	brenton-graveley:SF1_BGKLV28	brenton-graveley:SF1-BGKLV28-K562
ENCODE_accession	ENCSR562CCA	ENCSR675KZH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-49	BGKLV28-49
Sample Name	SF1_BGKLV28-49	SF1_BGKLV28-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3048	6939

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
SF1_BGKLV28-49_GTGGCC_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1332	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	20176
SF1_BGKLV28-49_GTGGCC_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1332	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	20208
SF1_BGKLV28-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1332					GRCh38	V40	SF1_BGKLV28-49_GTGGCC_L001_001.R1.fastq.gz,SF1_BGKLV28-49_GTGGCC_L001_001.R2.fastq.gz		ENCORE2	20240
SF1_BGKLV28-49_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	1332					GRCh38	V40	SF1_BGKLV28-49/Aligned.sortedByCoord.out.bam		ENCORE2	20272
SF1_BGKLV28-49_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	1332					GRCh38	V40	SF1_BGKLV28-49/Aligned.sortedByCoord.out.bam		ENCORE2	20304
SF1_BGKLV28-49_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	1332					GRCh38	V40	SF1_BGKLV28-49/Aligned.sortedByCoord.out.bam		ENCORE2	20336
SF1_BGKLV28-49_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	1332					GRCh38	V40	SF1_BGKLV28-49/Aligned.sortedByCoord.out.bam		ENCORE2	20368
SF1_BGKLV28-49_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1332					GRCh38	V40	SF1_BGKLV28-49_GTGGCC_L001_001.R1.fastq.gz,SF1_BGKLV28-49_GTGGCC_L001_001.R2.fastq.gz		ENCORE2	20400
SF1_BGKLV28-50_GTTTCG_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1333	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	20177
SF1_BGKLV28-50_GTTTCG_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1333	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	20209
SF1_BGKLV28-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1333					GRCh38	V40	SF1_BGKLV28-50_GTTTCG_L001_001.R1.fastq.gz,SF1_BGKLV28-50_GTTTCG_L001_001.R2.fastq.gz		ENCORE2	20241
SF1_BGKLV28-50_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	1333					GRCh38	V40	SF1_BGKLV28-50/Aligned.sortedByCoord.out.bam		ENCORE2	20273
SF1_BGKLV28-50_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	1333					GRCh38	V40	SF1_BGKLV28-50/Aligned.sortedByCoord.out.bam		ENCORE2	20305
SF1_BGKLV28-50_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	1333					GRCh38	V40	SF1_BGKLV28-50/Aligned.sortedByCoord.out.bam		ENCORE2	20337
SF1_BGKLV28-50_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	1333					GRCh38	V40	SF1_BGKLV28-50/Aligned.sortedByCoord.out.bam		ENCORE2	20369
SF1_BGKLV28-50_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1333					GRCh38	V40	SF1_BGKLV28-50_GTTTCG_L001_001.R1.fastq.gz,SF1_BGKLV28-50_GTTTCG_L001_001.R2.fastq.gz		ENCORE2	20401