CD3EAP RNA-Seq in K562

General Information


RBP	CD3EAP
Cell_Line	K562
Method	CRISPR
Exp_Name	CD3EAP-BGKcLV28-K562
ENCODE_series_ID	ENCSR837ZEJ
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR323SDL
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CD3EAP-BGKcLV28-9
Rep2	CD3EAP-BGKcLV28-10
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	60.2
Rep2_WB	64.5
Antibody Cat#	A301-294A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB469OLR
Status	Released
Project	ENCODE4
ID	821

Experiment Information (Status: Released)

	BGKcLV28-9	BGKcLV28-10
idx	943	944
TRCN#_or_BGC#	BGC#0000684	BGC#0000684
shRNA_or_gRNA_sequence	GCGCCTCCAAGGAGAAACGA	GCGCCTCCAAGGAGAAACGA
PAM	GGG	GGG
Name	POLR1G_85	POLR1G_85
Sample_ID	BGKcLV28-9	BGKcLV28-10
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CD3EAP	CD3EAP
qPCR_result	12.2	28.0
Ave_qPCR	20.1
RT-qPCR_primer-F	ggagctgtggcttattcagg
RT-qPCR_primer-R	caatttgcccttgacgatct
protein_conc	1564	1760
WB_result	60.2	64.5
Ave_WB	62.3
WB_DONE_date	6/22/21	JESS
MW	55kd
IP
antibody_Cat#	A301-294A	LOT# 2
Antibody DCC ID	ENCAB469OLR	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5077	5078

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CD3EAP	Product_ID: A301-294A Lot_ID: 2 Source: Bethyl Labs Target Name: CD3EAP-human

Experiment Status

	BGKcLV28-9	BGKcLV28-10
Sample_ID	BGKcLV28-9	BGKcLV28-10
Sample Name
Sample Name	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-10
RBP	CD3EAP	CD3EAP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9901	9902

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-9	BGKcLV28-10
Sample #	9	10
Sample Name	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-10
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	383	321
Peak_Molarity	74.90	112.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A2.png	DNA_Library_set48-49/set3/B2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/A2.png	RNA_Library_set48-49/set2/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-9	BGKcLV28-10
RBP	CD3EAP	CD3EAP
Batch_ID	BGKcLV28	BGKcLV28
WB_result	60.200	64.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2070	2071

Sequencing Information

	BGKcLV28-9	BGKcLV28-10
Sample_ID	BGKcLV28-9	BGKcLV28-10
Sample Name	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-10
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	151,378,504	77,017,448
total_aligned_reads	143,867,402	69,547,182
unique_aligned_reads	132,397,798	63,870,248
percent_uniqueAligned	0.87461	0.82930
correlation_replicates	0.996846	0.996846
spikein_reads	46,010	29,628
percent_spikeins	0.00030	0.00038
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1821	1822

Data Submission Information

	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-10	BGKcLV28-10	BGKcLV28-10	BGKcLV28-10
ENCODE_alias	brenton-graveley:CD3EAP-BGKcLV28	brenton-graveley:CD3EAP-BGKcLV28-9	brenton-graveley:L-CD3EAP-BGKcLV28-9	brenton-graveley:CD3EAP-BGKcLV28-9_S91_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV28-9_S91_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV28-K562	brenton-graveley:CD3EAP-BGKcLV28-10	brenton-graveley:L-CD3EAP-BGKcLV28-10	brenton-graveley:CD3EAP-BGKcLV28-10_S92_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV28-10_S92_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR323SDL	ENCBS598YTE	ENCLB713HZE	ENCFF552ORH	ENCFF681SAB	ENCSR837ZEJ	ENCBS099LSY	ENCLB290PZH	ENCFF403LTK	ENCFF987XAJ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-9	BGKcLV28-10	BGKcLV28-10	BGKcLV28-10	BGKcLV28-10
Sample Name	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-9	CD3EAP-BGKcLV28-10	CD3EAP-BGKcLV28-10	CD3EAP-BGKcLV28-10	CD3EAP-BGKcLV28-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CD3EAP-BGKcLV28-9.pdf	L-CD3EAP-BGKcLV28-10.pdf				CD3EAP-BGKcLV28-10.pdf	L-CD3EAP-BGKcLV28-9.pdf
ID	3475	3584	3718	3852	3986	7127	3585	3719	3853	3987

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
CD3EAP-BGKcLV28-9_S91_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1821	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3939
CD3EAP-BGKcLV28-9_S91_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1821	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3997
CD3EAP-BGKcLV28-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9_S91_L004_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV28-9_S91_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19221
CD3EAP-BGKcLV28-9_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9/Aligned.sortedByCoord.out.bam		ENCORE2	19279
CD3EAP-BGKcLV28-9_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9/Aligned.sortedByCoord.out.bam		ENCORE2	19337
CD3EAP-BGKcLV28-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9/Aligned.sortedByCoord.out.bam		ENCORE2	19395
CD3EAP-BGKcLV28-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9/Aligned.sortedByCoord.out.bam		ENCORE2	19453
CD3EAP-BGKcLV28-9_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1821					GRCh38	V40	CD3EAP-BGKcLV28-9_S91_L004_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV28-9_S91_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19511
CD3EAP-BGKcLV28-10_S92_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1822	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3938
CD3EAP-BGKcLV28-10_S92_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1822	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3996
CD3EAP-BGKcLV28-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10_S92_L004_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV28-10_S92_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19220
CD3EAP-BGKcLV28-10_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10/Aligned.sortedByCoord.out.bam		ENCORE2	19278
CD3EAP-BGKcLV28-10_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10/Aligned.sortedByCoord.out.bam		ENCORE2	19336
CD3EAP-BGKcLV28-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10/Aligned.sortedByCoord.out.bam		ENCORE2	19394
CD3EAP-BGKcLV28-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10/Aligned.sortedByCoord.out.bam		ENCORE2	19452
CD3EAP-BGKcLV28-10_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1822					GRCh38	V40	CD3EAP-BGKcLV28-10_S92_L004_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV28-10_S92_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19510