YBX3 RNA-Seq in HepG2

General Information


RBP	YBX3
Cell_Line	HepG2
Method	shRNA
Exp_Name	YBX3-BGHLV20-HepG2
ENCODE_series_ID	ENCSR996HAN
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR494VSD
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	CSDA-30-BGHLV20-9_17710
Rep2	CSDA-30-BGHLV20-10_17711
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	67.1
Rep2_qPCR	63.6
Rep1_WB	57.6
Rep2_WB	79.6
Antibody Cat#	A303-070A
Antibody Lot#	A303-070A
Antibody DCC ID	ENCAB021IRD
Status	Released
Project	ENCODE3
ID	490

Experiment Information (Status: Released)

	BGHLV20-9	BGHLV20-10
idx	373	374
TRCN#_or_BGC#	TRCN0000013230	TRCN0000013230
shRNA_or_gRNA_sequence	CGGAAATATCTGCGCAGTGTA	CGGAAATATCTGCGCAGTGTA
PAM
Name	CSDA_30/YBX3	CSDA_30/YBX3
Sample_ID	BGHLV20-9	BGHLV20-10
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	YBX3	YBX3
qPCR_result	67.1	63.6
Ave_qPCR	65.3
RT-qPCR_primer-F	cggttcatcgaaatccaact
RT-qPCR_primer-R	actggtggcttgctgatttt
protein_conc	6282	5791
WB_result	57.6	79.6
Ave_WB	68.6
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	11.4	0
Rep2_TPM	17.9	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2438	2439

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

	BGHLV20-9	BGHLV20-10
Sample_ID	BGHLV20-9	BGHLV20-10
Sample Name	CSDA-30-BGHLV20-9_17710	CSDA-30-BGHLV20-10_17711
Sample Name	CSDA-30-BGHLV20-9_17710	CSDA-30-BGHLV20-10_17711
RBP	YBX3	YBX3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	711	710

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-9	BGHLV20-10
Sample #
Sample Name	YBX3-BGHLV20-9	YBX3-BGHLV20-10
Sample_Name_Alias	CSDA-30-BGHLV20-9_17710	CSDA-30-BGHLV20-10_17711
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E1.png	DNA_Library_LV20-22-23/set1/F1.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G7.png	RNA_Library_LV20-22-24/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-9	BGHLV20-10
RBP	YBX3	YBX3
Batch_ID	BGHLV20	BGHLV20
WB_result	57.600	79.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2397	2396

Sequencing Information

	BGHLV20-9	BGHLV20-10
Sample_ID	BGHLV20-9	BGHLV20-10
Sample Name	CSDA-30-BGHLV20-9_17710	CSDA-30-BGHLV20-10_17711
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	40,610,000	47,820,000
total_aligned_reads	36,671,318	42,445,200
unique_aligned_reads	34,647,054	40,048,218
percent_uniqueAligned	0.85317	0.83748
correlation_replicates	0.996640	0.996640
spikein_reads	197,396	213,004
percent_spikeins	0.00486	0.00445
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1165	1164

Data Submission Information

	BGHLV20-9	BGHLV20-9
ENCODE_alias	brenton-graveley:CSDA-30-BGHLV20	brenton-graveley:YBX3-BGHLV20-HepG2
ENCODE_accession	ENCSR494VSD	ENCSR996HAN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-9	BGHLV20-9
Sample Name	CSDA-30-BGHLV20-9_17710	CSDA-30-BGHLV20-9_17710
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2904	7049

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-30-BGHLV20-9_17710_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1165	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15589
CSDA-30-BGHLV20-9_17710_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1165	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15631
CSDA-30-BGHLV20-9_17710_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710_ACAGTG_L001_R1_001.fastq.gz,CSDA-30-BGHLV20-9_17710_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	15673
CSDA-30-BGHLV20-9_17710_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710/Aligned.sortedByCoord.out.bam		ENCORE2	15715
CSDA-30-BGHLV20-9_17710_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710/Aligned.sortedByCoord.out.bam		ENCORE2	15757
CSDA-30-BGHLV20-9_17710_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710/Aligned.sortedByCoord.out.bam		ENCORE2	15799
CSDA-30-BGHLV20-9_17710_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710/Aligned.sortedByCoord.out.bam		ENCORE2	15841
CSDA-30-BGHLV20-9_17710_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1165					GRCh38	V40	CSDA-30-BGHLV20-9_17710_ACAGTG_L001_R1_001.fastq.gz,CSDA-30-BGHLV20-9_17710_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	15883
CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1164	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15588
CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1164	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15630
CSDA-30-BGHLV20-10_17711_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R1_001.fastq.gz,CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	15672
CSDA-30-BGHLV20-10_17711_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711/Aligned.sortedByCoord.out.bam		ENCORE2	15714
CSDA-30-BGHLV20-10_17711_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711/Aligned.sortedByCoord.out.bam		ENCORE2	15756
CSDA-30-BGHLV20-10_17711_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711/Aligned.sortedByCoord.out.bam		ENCORE2	15798
CSDA-30-BGHLV20-10_17711_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711/Aligned.sortedByCoord.out.bam		ENCORE2	15840
CSDA-30-BGHLV20-10_17711_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1164					GRCh38	V40	CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R1_001.fastq.gz,CSDA-30-BGHLV20-10_17711_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	15882