YTHDC2 RNA-Seq in K562

General Information


RBP	YTHDC2
Cell_Line	K562
Method	shRNA
Exp_Name	YTHDC2-BGKLV28-K562
ENCODE_series_ID	ENCSR355AGS
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR843LYF
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	YTHDC2_BGKLV28-63
Rep2	YTHDC2_BGKLV28-64
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	58.8
Rep2_qPCR	64.1
Rep1_WB	60.1
Rep2_WB	51.8
Antibody Cat#	A303-025A
Antibody Lot#	A303-025A
Antibody DCC ID	ENCAB501IJS
Status	Released
Project	ENCODE3
ID	662

Experiment Information (Status: Released)

	BGKLV28-63	BGKLV28-64
idx	532	533
TRCN#_or_BGC#	TRCN0000154178	TRCN0000154178
shRNA_or_gRNA_sequence	CCCTCGTCACATCTCTTATAT	CCCTCGTCACATCTCTTATAT
PAM
Name	YTHDC2	YTHDC2
Sample_ID	BGKLV28-63	BGKLV28-64
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	YTHDC2	YTHDC2
qPCR_result	58.8	64.1
Ave_qPCR	61.5
RT-qPCR_primer-F	TCCATGGAATGACAACAAGAA
RT-qPCR_primer-R	TGGAGCAACTGTTCACCAAC
protein_conc	2667	2706
WB_result	60.1	51.8
Ave_WB	55.9
WB_DONE_date	8/19/2015
MW	160kDa
IP	1	1
antibody_Cat#	A303-025A	A303-025A
Antibody DCC ID	ENCAB501IJS	ENCAB501IJS
submitted_to_DCC_date	12/7/2015
Rep1_TPM	5.84109396	0
Rep2_TPM	4.84054979	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	609	610

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YTHDC2	Product_ID: A303-025A Lot_ID: 1 Source: Bethyl Labs Target Name: YTHDC2-human

Experiment Status

	BGKLV28-63	BGKLV28-64
Sample_ID	BGKLV28-63	BGKLV28-64
Sample Name	YTHDC2_BGKLV28-63	YTHDC2_BGKLV28-64
Sample Name	YTHDC2_BGKLV28-63	YTHDC2_BGKLV28-64
RBP	YTHDC2	YTHDC2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1010	1011

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-63	BGKLV28-64
Sample #
Sample Name	YTHDC2-BGKLV28-63	YTHDC2-BGKLV28-64
Sample_Name_Alias	YTHDC2_BGKLV28-63	YTHDC2_BGKLV28-64
Index Well Position	S07	S08
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/G4.png	DNA_Library_LV28-29-30/set1/H4.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C10.png	RNA_Library_LV26-27-28-29/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-63	BGKLV28-64
RBP	YTHDC2	YTHDC2
Batch_ID	BGKLV28	BGKLV28
WB_result	60.100	51.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2702	2703

Sequencing Information

	BGKLV28-63	BGKLV28-64
Sample_ID	BGKLV28-63	BGKLV28-64
Sample Name	YTHDC2_BGKLV28-63	YTHDC2_BGKLV28-64
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	101,406,584	97,455,722
total_aligned_reads	82,910,604	80,687,184
unique_aligned_reads	75,733,530	73,588,538
percent_uniqueAligned	0.74683	0.75510
correlation_replicates	0.998451	0.998451
spikein_reads	285,806	268,264
percent_spikeins	0.00282	0.00275
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1344	1345

Data Submission Information

	BGKLV28-63	BGKLV28-63
ENCODE_alias	brenton-graveley:YTHDC2_BGKLV28	brenton-graveley:YTHDC2-BGKLV28-K562
ENCODE_accession	ENCSR843LYF	ENCSR355AGS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-63	BGKLV28-63
Sample Name	YTHDC2_BGKLV28-63	YTHDC2_BGKLV28-63
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3054	7051

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
YTHDC2_BGKLV28-63_CAGATC_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1344	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	20188
YTHDC2_BGKLV28-63_CAGATC_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1344	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	20220
YTHDC2_BGKLV28-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1344					GRCh38	V40	YTHDC2_BGKLV28-63_CAGATC_L004_001.R1.fastq.gz,YTHDC2_BGKLV28-63_CAGATC_L004_001.R2.fastq.gz		ENCORE2	20252
YTHDC2_BGKLV28-63_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	1344					GRCh38	V40	YTHDC2_BGKLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	20284
YTHDC2_BGKLV28-63_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	1344					GRCh38	V40	YTHDC2_BGKLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	20316
YTHDC2_BGKLV28-63_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	1344					GRCh38	V40	YTHDC2_BGKLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	20348
YTHDC2_BGKLV28-63_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	1344					GRCh38	V40	YTHDC2_BGKLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	20380
YTHDC2_BGKLV28-63_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1344					GRCh38	V40	YTHDC2_BGKLV28-63_CAGATC_L004_001.R1.fastq.gz,YTHDC2_BGKLV28-63_CAGATC_L004_001.R2.fastq.gz		ENCORE2	20412
YTHDC2_BGKLV28-64_ACTTGA_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1345	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	20189
YTHDC2_BGKLV28-64_ACTTGA_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1345	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	20221
YTHDC2_BGKLV28-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1345					GRCh38	V40	YTHDC2_BGKLV28-64_ACTTGA_L004_001.R1.fastq.gz,YTHDC2_BGKLV28-64_ACTTGA_L004_001.R2.fastq.gz		ENCORE2	20253
YTHDC2_BGKLV28-64_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	1345					GRCh38	V40	YTHDC2_BGKLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	20285
YTHDC2_BGKLV28-64_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	1345					GRCh38	V40	YTHDC2_BGKLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	20317
YTHDC2_BGKLV28-64_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	1345					GRCh38	V40	YTHDC2_BGKLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	20349
YTHDC2_BGKLV28-64_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	1345					GRCh38	V40	YTHDC2_BGKLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	20381
YTHDC2_BGKLV28-64_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1345					GRCh38	V40	YTHDC2_BGKLV28-64_ACTTGA_L004_001.R1.fastq.gz,YTHDC2_BGKLV28-64_ACTTGA_L004_001.R2.fastq.gz		ENCORE2	20413