ZC3H8 RNA-Seq in K562

General Information


RBP	ZC3H8
Cell_Line	K562
Method	shRNA
Exp_Name	ZC3H8-BGKLV38-K562
ENCODE_series_ID	ENCSR637AJF
Batch_ID	BGKLV38
Pool ID	Pool-161129
Local_Set_Name	set38
ENCODE_KD_Exp_ID	ENCSR448JAM
ENCODE_CN_Exp_ID	ENCSR718EWL
Rep1	ZC3H8_BGKLV38-145
Rep2	ZC3H8_BGKLV38-146
CN1	NT_BGKLV38-1
CN2	NT_BGKLV38-2
Rep1_qPCR	55.6
Rep2_qPCR	62.2
Rep1_WB	49.9
Rep2_WB	53.3
Antibody Cat#	A303-089A
Antibody Lot#	A303-089A
Antibody DCC ID	ENCAB192ZJZ
Status	Released
Project	ENCODE3
ID	758

Experiment Information (Status: Released)

	BGKLV38-145	BGKLV38-146
idx	916	917
TRCN#_or_BGC#	TRCN0000163399	TRCN0000163399
shRNA_or_gRNA_sequence	GCTGGTCACAAGAATGGCAAA	GCTGGTCACAAGAATGGCAAA
PAM
Name	ZC3H8	ZC3H8
Sample_ID	BGKLV38-145	BGKLV38-146
transduction_Date	9/15/16	9/15/16
days
RBP_name	ZC3H8	ZC3H8
qPCR_result	55.6	62.2
Ave_qPCR	58.9
RT-qPCR_primer-F	ccctggaaacaaaggatcaa
RT-qPCR_primer-R	tgaatgcctgactcaaatgc
protein_conc	3917	3904
WB_result	49.9	53.3
Ave_WB	51.6
WB_DONE_date	10/19/16
MW	34kd
IP	1	1
antibody_Cat#	A303-089A	A303-089A
Antibody DCC ID	ENCAB192ZJZ	ENCAB192ZJZ
submitted_to_DCC_date	10/26/17
Rep1_TPM	16	0
Rep2_TPM	18.3	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	1015	1016

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZC3H8	Product_ID: A303-089A Lot_ID: 1 Source: Bethyl Labs Target Name: ZC3H8-human

Experiment Status

	BGKLV38-145	BGKLV38-146
Sample_ID	BGKLV38-145	BGKLV38-146
Sample Name	ZC3H8_BGKLV38-145	ZC3H8_BGKLV38-146
Sample Name	ZC3H8_BGKLV38-145	ZC3H8_BGKLV38-146
RBP	ZC3H8	ZC3H8
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1313	1314

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-145	BGKLV38-146
Sample #
Sample Name	ZC3H8-BGKLV38-145	ZC3H8-BGKLV38-146
Sample_Name_Alias	ZC3H8_BGKLV38-145	ZC3H8_BGKLV38-146
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/D6.png	DNA_Library_LV37-38/set2/B1.png
RIN	9.1	9.1
libSample_RNA_Well	RNA_Library_LV37_38/set2/C1.png	RNA_Library_LV37_38/set2/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV38-145	BGKLV38-146
RBP	ZC3H8	ZC3H8
Batch_ID	BGKLV38	BGKLV38
WB_result	49.900	53.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3004	3005

Sequencing Information

	BGKLV38-145	BGKLV38-146
Sample_ID	BGKLV38-145	BGKLV38-146
Sample Name	ZC3H8_BGKLV38-145	ZC3H8_BGKLV38-146
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set38	set38
total_reads	90,249,100	88,748,968
total_aligned_reads	82,937,284	80,391,394
unique_aligned_reads	75,556,190	72,860,056
percent_uniqueAligned	0.83720	0.82097
correlation_replicates	0.998627	0.998627
spikein_reads	132,306	147,702
percent_spikeins	0.00147	0.00166
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1653	1654

Data Submission Information

	BGKLV38-145	BGKLV38-145
ENCODE_alias	brenton-graveley:ZC3H8_BGKLV38	brenton-graveley:ZC3H8-BGKLV38-K562
ENCODE_accession	ENCSR448JAM	ENCSR637AJF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-145	BGKLV38-145
Sample Name	ZC3H8_BGKLV38-145	ZC3H8_BGKLV38-145
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3196	7053

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
ZC3H8_BGKLV38-145_GTGGCC_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1653	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22184
ZC3H8_BGKLV38-145_GTGGCC_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1653	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22196
ZC3H8_BGKLV38-145_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145_GTGGCC_L008_001.R1.fastq.gz,ZC3H8_BGKLV38-145_GTGGCC_L008_001.R2.fastq.gz		ENCORE2	22208
ZC3H8_BGKLV38-145_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145/Aligned.sortedByCoord.out.bam		ENCORE2	22220
ZC3H8_BGKLV38-145_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145/Aligned.sortedByCoord.out.bam		ENCORE2	22232
ZC3H8_BGKLV38-145_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145/Aligned.sortedByCoord.out.bam		ENCORE2	22244
ZC3H8_BGKLV38-145_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145/Aligned.sortedByCoord.out.bam		ENCORE2	22256
ZC3H8_BGKLV38-145_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1653					GRCh38	V40	ZC3H8_BGKLV38-145_GTGGCC_L008_001.R1.fastq.gz,ZC3H8_BGKLV38-145_GTGGCC_L008_001.R2.fastq.gz		ENCORE2	22268
ZC3H8_BGKLV38-146_GTTTCG_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1654	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22185
ZC3H8_BGKLV38-146_GTTTCG_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1654	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22197
ZC3H8_BGKLV38-146_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146_GTTTCG_L008_001.R1.fastq.gz,ZC3H8_BGKLV38-146_GTTTCG_L008_001.R2.fastq.gz		ENCORE2	22209
ZC3H8_BGKLV38-146_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146/Aligned.sortedByCoord.out.bam		ENCORE2	22221
ZC3H8_BGKLV38-146_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146/Aligned.sortedByCoord.out.bam		ENCORE2	22233
ZC3H8_BGKLV38-146_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146/Aligned.sortedByCoord.out.bam		ENCORE2	22245
ZC3H8_BGKLV38-146_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146/Aligned.sortedByCoord.out.bam		ENCORE2	22257
ZC3H8_BGKLV38-146_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1654					GRCh38	V40	ZC3H8_BGKLV38-146_GTTTCG_L008_001.R1.fastq.gz,ZC3H8_BGKLV38-146_GTTTCG_L008_001.R2.fastq.gz		ENCORE2	22269