SYNCRIP RNA-Seq in K562

General Information


RBP	SYNCRIP
Cell_Line	K562
Method	CRISPR
Exp_Name	SYNCRIP-BGKcLV06-K562
ENCODE_series_ID	ENCSR112CSN
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR680OJB
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	SYNCRIP-BGKcLV06-37
Rep2	SYNCRIP-BGKcLV06-38
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	8.4
Rep2_qPCR	30.5
Rep1_WB	49.3
Rep2_WB	64.3
Antibody Cat#	RN046PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB548DAU
Status	Released
Project	ENCODE3
ID	779

Experiment Information (Status: Released)

	BGKcLV06-37	BGKcLV06-38
idx	213	214
TRCN#_or_BGC#	BGC#0000103	BGC#0000103
shRNA_or_gRNA_sequence	TAGATGAAATTTACGTTGCA	TAGATGAAATTTACGTTGCA
PAM
Name	SYNCRIP-78	SYNCRIP-78
Sample_ID	BGKcLV06-37	BGKcLV06-38
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	SYNCRIP	SYNCRIP
qPCR_result	8.4	30.5
Ave_qPCR	19.5
RT-qPCR_primer-F	GAAAAGCTCAGAGGCAAGCA
RT-qPCR_primer-R	GGGCATATGAGGTGGACCAT
protein_conc	915	826
WB_result	49.3	64.3
Ave_WB	56.8
WB_DONE_date	7/6/17
MW	70kD
IP
antibody_Cat#	RN046PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	196.1	0
Rep2_TPM	196.4	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4311	4312

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SYNCRIP	Product_ID: RN046PW Lot_ID: 1 Source: MBLI Target Name: SYNCRIP-human

Experiment Status

	BGKcLV06-37	BGKcLV06-38
Sample_ID	BGKcLV06-37	BGKcLV06-38
Sample Name	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-38
Sample Name	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-38
RBP	SYNCRIP	SYNCRIP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1375	1376

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-37	BGKcLV06-38
Sample #
Sample Name	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-38
Sample_Name_Alias	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-38
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/A3.png	DNA_Library_set39/set2/B3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set39/set1/A3.png	RNA_Library_set39/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-37	BGKcLV06-38
RBP	SYNCRIP	SYNCRIP
Batch_ID	BGKcLV06	BGKcLV06
WB_result	49.300	64.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3070	3071

Sequencing Information

	BGKcLV06-37	BGKcLV06-38
Sample_ID	BGKcLV06-37	BGKcLV06-38
Sample Name	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-38
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	57,729,188	50,320,112
total_aligned_reads	51,348,092	44,785,054
unique_aligned_reads	46,999,446	40,914,824
percent_uniqueAligned	0.81414	0.81309
correlation_replicates	0.982744	0.982744
spikein_reads	59,394	24,906
percent_spikeins	0.00103	0.00049
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1721	1722

Data Submission Information

	BGKcLV06-37	BGKcLV06-37
ENCODE_alias	brenton-graveley:SYNCRIP-BGKcLV06	brenton-graveley:SYNCRIP-BGKcLV06-K562
ENCODE_accession	ENCSR680OJB	ENCSR112CSN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-37	BGKcLV06-37
Sample Name	SYNCRIP-BGKcLV06-37	SYNCRIP-BGKcLV06-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3227	6998

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
SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1721	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22490
SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1721	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22526
SYNCRIP-BGKcLV06-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R1.fastq.gz,SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22562
SYNCRIP-BGKcLV06-37_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	22598
SYNCRIP-BGKcLV06-37_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	22634
SYNCRIP-BGKcLV06-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	22670
SYNCRIP-BGKcLV06-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	22706
SYNCRIP-BGKcLV06-37_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1721					GRCh38	V40	SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R1.fastq.gz,SYNCRIP-BGKcLV06-37_ATCACG_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22742
SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1722	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22491
SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1722	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22527
SYNCRIP-BGKcLV06-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R1.fastq.gz,SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22563
SYNCRIP-BGKcLV06-38_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	22599
SYNCRIP-BGKcLV06-38_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	22635
SYNCRIP-BGKcLV06-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	22671
SYNCRIP-BGKcLV06-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	22707
SYNCRIP-BGKcLV06-38_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1722					GRCh38	V40	SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R1.fastq.gz,SYNCRIP-BGKcLV06-38_CGATGT_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22743