YBX3 RNA-Seq in K562

General Information


RBP	YBX3
Cell_Line	K562
Method	shRNA
Exp_Name	YBX3-BGKLV24-K562
ENCODE_series_ID	ENCSR571TRS
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR306EIU
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	CSDA_BGKLV24_11_17602
Rep2	CSDA_BGKLV24_12_17603
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	53.8
Rep2_qPCR	55.7
Rep1_WB	79.2
Rep2_WB	77.8
Antibody Cat#	A303-070A
Antibody Lot#	A303-070A
Antibody DCC ID	ENCAB021IRD
Status	Released
Project	ENCODE3
ID	558

Experiment Information (Status: Released)

	BGKLV24-11	BGKLV24-12
idx	348	349
TRCN#_or_BGC#	TRCN0000013230	TRCN0000013230
shRNA_or_gRNA_sequence	CGGAAATATCTGCGCAGTGTA	CGGAAATATCTGCGCAGTGTA
PAM
Name	CSDA_30/YBX3	CSDA_30/YBX3
Sample_ID	BGKLV24-11	BGKLV24-12
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	YBX3	YBX3
qPCR_result	53.8	55.7
Ave_qPCR	54.7
RT-qPCR_primer-F	cggttcatcgaaatccaact
RT-qPCR_primer-R	actggtggcttgctgatttt
protein_conc	3800	2934
WB_result	79.2	77.8
Ave_WB	78.5
WB_DONE_date	4/17/2015
MW	40kDa
IP	1	1
antibody_Cat#	A303-070A	A303-070A
Antibody DCC ID	ENCAB021IRD	ENCAB021IRD
submitted_to_DCC_date	8/6/2015
Rep1_TPM	6.67710631	0
Rep2_TPM	6.92829402	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	395	396

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YBX3	Product_ID: A303-070A Lot_ID: 1 Source: Bethyl Labs Target Name: YBX3-human

Experiment Status

	BGKLV24-11	BGKLV24-12
Sample_ID	BGKLV24-11	BGKLV24-12
Sample Name	CSDA_BGKLV24_11_17602	CSDA_BGKLV24_12_17603
Sample Name	CSDA_BGKLV24_11_17602	CSDA_BGKLV24_12_17603
RBP	YBX3	YBX3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	854	855

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-11	BGKLV24-12
Sample #
Sample Name	YBX3-BGKLV24-11	YBX3-BGKLV24-12
Sample_Name_Alias	CSDA_BGKLV24_11_17602	CSDA_BGKLV24_12_17603
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/B2.png	DNA_Library_LV21-24/set1/C2.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G1.png	RNA_Library_LV19-21-24/set2/A3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-11	BGKLV24-12
RBP	YBX3	YBX3
Batch_ID	BGKLV24	BGKLV24
WB_result	79.200	77.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2542	2543

Sequencing Information

	BGKLV24-11	BGKLV24-12
Sample_ID	BGKLV24-11	BGKLV24-12
Sample Name	CSDA_BGKLV24_11_17602	CSDA_BGKLV24_12_17603
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	34,270,000	41,910,000
total_aligned_reads	32,105,544	39,313,128
unique_aligned_reads	29,475,652	36,048,576
percent_uniqueAligned	0.86010	0.86014
correlation_replicates	0.995684	0.995684
spikein_reads	185,840	210,306
percent_spikeins	0.00542	0.00502
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1076	1077

Data Submission Information

	BGKLV24-11	BGKLV24-11
ENCODE_alias	brenton-graveley:CSDA_BGKLV24	brenton-graveley:YBX3-BGKLV24-K562
ENCODE_accession	ENCSR306EIU	ENCSR571TRS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-11	BGKLV24-11
Sample Name	CSDA_BGKLV24_11_17602	CSDA_BGKLV24_11_17602
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2978	7050

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
CSDA_BGKLV24_11_17602_ATCACG_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1076	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17188
CSDA_BGKLV24_11_17602_ATCACG_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1076	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17224
CSDA_BGKLV24_11_17602_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602_ATCACG_L006_R1_001.fastq.gz,CSDA_BGKLV24_11_17602_ATCACG_L006_R2_001.fastq.gz		ENCORE2	17260
CSDA_BGKLV24_11_17602_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602/Aligned.sortedByCoord.out.bam		ENCORE2	17296
CSDA_BGKLV24_11_17602_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602/Aligned.sortedByCoord.out.bam		ENCORE2	17332
CSDA_BGKLV24_11_17602_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602/Aligned.sortedByCoord.out.bam		ENCORE2	17368
CSDA_BGKLV24_11_17602_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602/Aligned.sortedByCoord.out.bam		ENCORE2	17404
CSDA_BGKLV24_11_17602_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1076					GRCh38	V40	CSDA_BGKLV24_11_17602_ATCACG_L006_R1_001.fastq.gz,CSDA_BGKLV24_11_17602_ATCACG_L006_R2_001.fastq.gz		ENCORE2	17440
CSDA_BGKLV24_12_17603_CGATGT_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1077	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17189
CSDA_BGKLV24_12_17603_CGATGT_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1077	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17225
CSDA_BGKLV24_12_17603_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603_CGATGT_L006_R1_001.fastq.gz,CSDA_BGKLV24_12_17603_CGATGT_L006_R2_001.fastq.gz		ENCORE2	17261
CSDA_BGKLV24_12_17603_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603/Aligned.sortedByCoord.out.bam		ENCORE2	17297
CSDA_BGKLV24_12_17603_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603/Aligned.sortedByCoord.out.bam		ENCORE2	17333
CSDA_BGKLV24_12_17603_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603/Aligned.sortedByCoord.out.bam		ENCORE2	17369
CSDA_BGKLV24_12_17603_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603/Aligned.sortedByCoord.out.bam		ENCORE2	17405
CSDA_BGKLV24_12_17603_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1077					GRCh38	V40	CSDA_BGKLV24_12_17603_CGATGT_L006_R1_001.fastq.gz,CSDA_BGKLV24_12_17603_CGATGT_L006_R2_001.fastq.gz		ENCORE2	17441