title: JGE08 (500 ug/mL dose)_rep3

description:
Library name: T_9-3-4
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;500 ug/mL dose)_rep3


title: JGE08 (100 ug/mL dose)_rep3

status: Public on Oct 24 2025

type: SRA

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description:
Library name: T_9-3-5
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

library_source: transcriptomic

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation mm10 Gene Transfer Format (GTF) file from UCSC browser
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Muscle

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days. We used differentiated C2C12 myotubes.

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

tag: tissue

value: Muscle

tag: cell line

tag: cell type

value: Myotube

tag: treatment

value: extraction -> mix of Ethanol extracts of JGT (JGW08;100 ug/mL dose)_rep3

tag: batch

value: D


title: JGE07 (20 ug/mL dose)_rep3

description:
Library name: T_9-3-3
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;20 ug/mL dose)_rep3


title: JGE07 (100 ug/mL dose)_rep3

description:
Library name: T_9-3-2
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;100 ug/mL dose)_rep3


title: JGE07 (20 ug/mL dose)_rep2

description:
Library name: T_9-2-3
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;20 ug/mL dose)_rep2

value: C


title: JGE07 (100 ug/mL dose)_rep2

description:
Library name: T_9-2-2
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;100 ug/mL dose)_rep2


title: JGE08 (500 ug/mL dose)_rep2

description:
Library name: T_9-2-4
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;500 ug/mL dose)_rep2


title: JGE07 (500 ug/mL dose)_rep2

description:
Library name: T_9-2-1
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;500 ug/mL dose)_rep2


title: JGE08 (100 ug/mL dose)_rep2

description:
Library name: T_9-2-5
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;100 ug/mL dose)_rep2


title: JGE08 (100 ug/mL dose)_rep1

description:
Library name: T_9-1-5
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;100 ug/mL dose)_rep1


title: JGE08 (500 ug/mL dose)_rep1

description:
Library name: T_9-1-4
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;500 ug/mL dose)_rep1


title: JGE08 (20 ug/mL dose)_rep1

description:
Library name: T_9-1-6
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Ethanol extracts of JGT (JGW08;20 ug/mL dose)_rep1


title: JGE07 (100 ug/mL dose)_rep1

description:
Library name: T_9-1-2
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;100 ug/mL dose)_rep1


title: JGE07 (500 ug/mL dose)_rep1

description:
Library name: T_9-1-1
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;500 ug/mL dose)_rep1


title: JGE06 (100 ug/mL dose)_rep3

description:
Library name: T_8-3-5
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: Muscle

value: extraction -> mix of Ethanol extracts of JGT (JGW06;100 ug/mL dose)_rep3


title: JGE06 (500 ug/mL dose)_rep3

description:
Library name: T_8-3-4
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: Myotube

value: extraction -> mix of Ethanol extracts of JGT (JGW06;500 ug/mL dose)_rep3


title: JGE05 (500 ug/mL dose)_rep3

description:
Library name: T_8-3-1
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;500 ug/mL dose)_rep3


title: JGE05 (20 ug/mL dose)_rep3

description:
Library name: T_8-3-3
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;20 ug/mL dose)_rep3


title: JGE05 (100 ug/mL dose)_rep3

description:
Library name: T_8-3-2
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;100 ug/mL dose)_rep3


title: JGE06 (20 ug/mL dose)_rep3

description:
Library name: T_8-3-6
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;20 ug/mL dose)_rep3

value: C


title: JGE07 (20 ug/mL dose)_rep1

description:
Library name: T_9-1-3
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;20 ug/mL dose)_rep1


title: JGE06 (500 ug/mL dose)_rep2

description:
Library name: T_8-2-4
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;500 ug/mL dose)_rep2


title: JGE05 (20 ug/mL dose)_rep2

description:
Library name: T_8-2-3
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;20 ug/mL dose)_rep2


title: JGE05 (100 ug/mL dose)_rep2

description:
Library name: T_8-2-2
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;100 ug/mL dose)_rep2


title: JGE06 (20 ug/mL dose)_rep2

description:
Library name: T_8-2-6
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;20 ug/mL dose)_rep2


title: JGE06 (100 ug/mL dose)_rep2

description:
Library name: T_8-2-5
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;100 ug/mL dose)_rep2


title: JGE07 (500 ug/mL dose)_rep3

description:
Library name: T_9-3-1
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Ethanol extracts of JGT (JGW07;500 ug/mL dose)_rep3

value: D


title: JGE08 (20 ug/mL dose)_rep2

description:
Library name: T_9-2-6
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: Muscle

value: extraction -> mix of Ethanol extracts of JGT (JGW08;20 ug/mL dose)_rep2


title: JGE06 (500 ug/mL dose)_rep1

description:
Library name: T_8-1-4
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: Myotube

value: extraction -> mix of Ethanol extracts of JGT (JGW06;500 ug/mL dose)_rep1


title: JGE06 (100 ug/mL dose)_rep1

description:
Library name: T_8-1-5
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;100 ug/mL dose)_rep1


title: JGE05 (500 ug/mL dose)_rep2

description:
Library name: T_8-2-1
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;500 ug/mL dose)_rep2


title: JGE06 (20 ug/mL dose)_rep1

description:
Library name: T_8-1-6
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Ethanol extracts of JGT (JGW06;20 ug/mL dose)_rep1


title: JGE05 (100 ug/mL dose)_rep1

description:
Library name: T_8-1-2
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;100 ug/mL dose)_rep1


title: JGE05 (20 ug/mL dose)_rep1

description:
Library name: T_8-1-3
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;20 ug/mL dose)_rep1

value: C


title: JGE05 (500 ug/mL dose)_rep1

description:
Library name: T_8-1-1
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Ethanol extracts of JGT (JGW05;500 ug/mL dose)_rep1


title: JGE04 (20 ug/mL dose)_rep3

description:
Library name: T_7-3-6
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;20 ug/mL dose)_rep3


title: JGE04 (20 ug/mL dose)_rep2

description:
Library name: T_7-2-6
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;20 ug/mL dose)_rep2


title: JGE04 (100 ug/mL dose)_rep2

description:
Library name: T_7-2-5
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;100 ug/mL dose)_rep2


title: JGE04 (500 ug/mL dose)_rep2

description:
Library name: T_7-2-4
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;500 ug/mL dose)_rep2


title: JGE04 (20 ug/mL dose)_rep1

description:
Library name: T_7-1-6
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;20 ug/mL dose)_rep1


title: JGE04 (100 ug/mL dose)_rep1

description:
Library name: T_7-1-5
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;100 ug/mL dose)_rep1


title: JGE02 (500 ug/mL dose)_rep3

description:
Library name: T_6-3-4
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: Muscle

value: mix-> extraction of Ethanol extracts of JGT (JGW02;500 ug/mL dose)_rep3

value: B


title: JGE04 (500 ug/mL dose)_rep1

description:
Library name: T_7-1-4
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: Myotube

value: mix-> extraction of Ethanol extracts of JGT (JGW04;500 ug/mL dose)_rep1


title: JGE01 (100 ug/mL dose)_rep3

description:
Library name: T_6-3-2
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;100 ug/mL dose)_rep3


title: JGE02 (20 ug/mL dose)_rep2

description:
Library name: T_6-2-6
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: mix-> extraction of Ethanol extracts of JGT (JGW02;20 ug/mL dose)_rep2


title: JGE02 (100 ug/mL dose)_rep3

description:
Library name: T_6-3-5
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Ethanol extracts of JGT (JGW02;100 ug/mL dose)_rep3


title: JGE01 (20 ug/mL dose)_rep2

description:
Library name: T_6-2-3
Rep2_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;20 ug/mL dose)_rep2


title: JGE01 (500 ug/mL dose)_rep2

description:
Library name: T_6-2-1
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;500 ug/mL dose)_rep2


title: JGE02 (20 ug/mL dose)_rep1

description:
Library name: T_6-1-6
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: mix-> extraction of Ethanol extracts of JGT (JGW02;20 ug/mL dose)_rep1


title: JGE02 (20 ug/mL dose)_rep3

description:
Library name: T_6-3-6
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: mix-> extraction of Ethanol extracts of JGT (JGW02;20 ug/mL dose)_rep3


title: JGE02 (100 ug/mL dose)_rep1

description:
Library name: T_6-1-5
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Ethanol extracts of JGT (JGW02;100 ug/mL dose)_rep1


title: JGE02 (500 ug/mL dose)_rep1

description:
Library name: T_6-1-4
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Ethanol extracts of JGT (JGW02;500 ug/mL dose)_rep1


title: JGE01 (100 ug/mL dose)_rep2

description:
Library name: T_6-2-2
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;100 ug/mL dose)_rep2


title: JGE01 (500 ug/mL dose)_rep3

description:
Library name: T_6-3-1
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;500 ug/mL dose)_rep3


title: JGE04 (100 ug/mL dose)_rep3

description:
Library name: T_7-3-5
Rep3_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;100 ug/mL dose)_rep3

value: C


title: JGW08 (20 ug/mL dose)_rep3

description:
Library name: T_5-3-6
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: Muscle

value: extraction -> mix of Water extracts of JGT (JGW08;20 ug/mL dose)_rep3


title: JGE01 (20 ug/mL dose)_rep1

description:
Library name: T_6-1-3
Rep1_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: Myotube

value: mix-> extraction of Ethanol extracts of JGT (JGW01;20 ug/mL dose)_rep1

value: B


title: JGE04 (500 ug/mL dose)_rep3

description:
Library name: T_7-3-4
Rep3_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Ethanol extracts of JGT (JGW04;500 ug/mL dose)_rep3


title: JGW08 (100 ug/mL dose)_rep3

description:
Library name: T_5-3-5
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;100 ug/mL dose)_rep3


title: JGW08 (500 ug/mL dose)_rep3

description:
Library name: T_5-3-4
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;500 ug/mL dose)_rep3


title: JGW07 (20 ug/mL dose)_rep3

description:
Library name: T_5-3-3
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;20 ug/mL dose)_rep3


title: JGW07 (100 ug/mL dose)_rep3

description:
Library name: T_5-3-2
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;100 ug/mL dose)_rep3


title: JGW07 (500 ug/mL dose)_rep3

description:
Library name: T_5-3-1
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;500 ug/mL dose)_rep3


title: JGW08 (100 ug/mL dose)_rep2

description:
Library name: T_5-2-5
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;100 ug/mL dose)_rep2


title: JGE01 (20 ug/mL dose)_rep3

description:
Library name: T_6-3-3
Rep3_Ethanol extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;20 ug/mL dose)_rep3


title: JGE02 (100 ug/mL dose)_rep2

description:
Library name: T_6-2-5
Rep2_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Ethanol extracts of JGT (JGW02;100 ug/mL dose)_rep2


title: JGW08 (20 ug/mL dose)_rep2

description:
Library name: T_5-2-6
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;20 ug/mL dose)_rep2


title: JGW07 (500 ug/mL dose)_rep2

description:
Library name: T_5-2-1
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;500 ug/mL dose)_rep2


title: JGW07 (100 ug/mL dose)_rep2

description:
Library name: T_5-2-2
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;100 ug/mL dose)_rep2


title: JGE01 (500 ug/mL dose)_rep1

description:
Library name: T_6-1-1
Rep1_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: Muscle

value: mix-> extraction of Ethanol extracts of JGT (JGW01;500 ug/mL dose)_rep1


title: JGW08 (20 ug/mL dose)_rep1

description:
Library name: T_5-1-6
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: Myotube

value: extraction -> mix of Water extracts of JGT (JGW08;20 ug/mL dose)_rep1


title: JGE01 (100 ug/mL dose)_rep1

description:
Library name: T_6-1-2
Rep1_Ethanol extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Ethanol extracts of JGT (JGW01;100 ug/mL dose)_rep1

value: B


title: JGE02 (500 ug/mL dose)_rep2

description:
Library name: T_6-2-4
Rep2_Ethanol extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Ethanol extracts of JGT (JGW02;500 ug/mL dose)_rep2


title: JGW07 (20 ug/mL dose)_rep1

description:
Library name: T_5-1-3
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;20 ug/mL dose)_rep1


title: JGW08 (500 ug/mL dose)_rep1

description:
Library name: T_5-1-4
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;500 ug/mL dose)_rep1


title: JGW07 (100 ug/mL dose)_rep1

description:
Library name: T_5-1-2
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;100 ug/mL dose)_rep1


title: JGW06 (20 ug/mL dose)_rep3

description:
Library name: T_4-3-6
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;20 ug/mL dose)_rep3


title: JGW08 (100 ug/mL dose)_rep1

description:
Library name: T_5-1-5
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;100 ug/mL dose)_rep1


title: JGW06 (100 ug/mL dose)_rep3

description:
Library name: T_4-3-5
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;100 ug/mL dose)_rep3


title: JGW05 (20 ug/mL dose)_rep3

description:
Library name: T_4-3-3
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;20 ug/mL dose)_rep3


title: JGW06 (500 ug/mL dose)_rep3

description:
Library name: T_4-3-4
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;500 ug/mL dose)_rep3


title: JGW05 (500 ug/mL dose)_rep3

description:
Library name: T_4-3-1
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;500 ug/mL dose)_rep3


title: JGW06 (100 ug/mL dose)_rep2

description:
Library name: T_4-2-5
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;100 ug/mL dose)_rep2


title: JGW05 (100 ug/mL dose)_rep3

description:
Library name: T_4-3-2
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: Muscle

value: mix-> extraction of Water extracts of JGT (JGW05;100 ug/mL dose)_rep3


title: JGW06 (500 ug/mL dose)_rep2

description:
Library name: T_4-2-4
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: Myotube

value: extraction -> mix of Water extracts of JGT (JGW06;500 ug/mL dose)_rep2


title: JGW05 (100 ug/mL dose)_rep2

description:
Library name: T_4-2-2
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;100 ug/mL dose)_rep2


title: JGW06 (20 ug/mL dose)_rep1

description:
Library name: T_4-1-6
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;20 ug/mL dose)_rep1

value: A


title: JGW05 (500 ug/mL dose)_rep2

description:
Library name: T_4-2-1
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;500 ug/mL dose)_rep2

value: B


title: JGW06 (100 ug/mL dose)_rep1

description:
Library name: T_4-1-5
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;100 ug/mL dose)_rep1


title: JGW06 (500 ug/mL dose)_rep1

description:
Library name: T_4-1-4
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;500 ug/mL dose)_rep1


title: JGW07 (20 ug/mL dose)_rep2

description:
Library name: T_5-2-3
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;20 ug/mL dose)_rep2


title: JGW05 (100 ug/mL dose)_rep1

description:
Library name: T_4-1-2
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;100 ug/mL dose)_rep1


title: JGW05 (20 ug/mL dose)_rep1

description:
Library name: T_4-1-3
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;20 ug/mL dose)_rep1


title: JGW04 (20 ug/mL dose)_rep3

description:
Library name: T_3-3-6
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;20 ug/mL dose)_rep3


title: JGW05 (500 ug/mL dose)_rep1

description:
Library name: T_4-1-1
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;500 ug/mL dose)_rep1


title: JGW07 (500 ug/mL dose)_rep1

description:
Library name: T_5-1-1
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 1.5:1.5

value: extraction -> mix of Water extracts of JGT (JGW07;500 ug/mL dose)_rep1


title: JGW04 (20 ug/mL dose)_rep2

description:
Library name: T_3-2-6
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: Muscle

value: mix-> extraction of Water extracts of JGT (JGW04;20 ug/mL dose)_rep2


title: JGW04 (100 ug/mL dose)_rep3

description:
Library name: T_3-3-5
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: Myotube

value: mix-> extraction of Water extracts of JGT (JGW04;100 ug/mL dose)_rep3


title: JGW04 (500 ug/mL dose)_rep3

description:
Library name: T_3-3-4
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;500 ug/mL dose)_rep3


title: JGW04 (100 ug/mL dose)_rep2

description:
Library name: T_3-2-5
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;100 ug/mL dose)_rep2


title: JGW04 (500 ug/mL dose)_rep2

description:
Library name: T_3-2-4
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;500 ug/mL dose)_rep2

value: A


title: JGW02 (20 ug/mL dose)_rep3

description:
Library name: T_2-3-6
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: mix-> extraction of Water extracts of JGT (JGW02;20 ug/mL dose)_rep3


title: JGW04 (100 ug/mL dose)_rep1

description:
Library name: T_3-1-5
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;100 ug/mL dose)_rep1


title: JGW04 (500 ug/mL dose)_rep1

description:
Library name: T_3-1-4
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;500 ug/mL dose)_rep1


title: JGW06 (20 ug/mL dose)_rep2

description:
Library name: T_4-2-6
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:1

value: extraction -> mix of Water extracts of JGT (JGW06;20 ug/mL dose)_rep2

value: B


title: JGW02 (500 ug/mL dose)_rep3

description:
Library name: T_2-3-4
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Water extracts of JGT (JGW02;500 ug/mL dose)_rep3


title: JGW02 (100 ug/mL dose)_rep3

description:
Library name: T_2-3-5
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Water extracts of JGT (JGW02;100 ug/mL dose)_rep3


title: JGW01 (20 ug/mL dose)_rep3

description:
Library name: T_2-3-3
Rep3_Water extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;20 ug/mL dose)_rep3


title: JGW05 (20 ug/mL dose)_rep2

description:
Library name: T_4-2-3
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 0:3

value: mix-> extraction of Water extracts of JGT (JGW05;20 ug/mL dose)_rep2


title: JGW02 (20 ug/mL dose)_rep2

description:
Library name: T_2-2-6
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: Muscle

value: mix-> extraction of Water extracts of JGT (JGW02;20 ug/mL dose)_rep2


title: JGW01 (100 ug/mL dose)_rep3

description:
Library name: T_2-3-2
Rep3_Water extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: Myotube

value: mix-> extraction of Water extracts of JGT (JGW01;100 ug/mL dose)_rep3


title: JGW01 (500 ug/mL dose)_rep3

description:
Library name: T_2-3-1
Rep3_Water extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;500 ug/mL dose)_rep3


title: JGW02 (100 ug/mL dose)_rep2

description:
Library name: T_2-2-5
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Water extracts of JGT (JGW02;100 ug/mL dose)_rep2


title: JGW08 (500 ug/mL dose)_rep2

description:
Library name: T_5-2-4
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 1:2

value: extraction -> mix of Water extracts of JGT (JGW08;500 ug/mL dose)_rep2


title: JGW01 (20 ug/mL dose)_rep2

description:
Library name: T_2-2-3
Rep2_Water extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;20 ug/mL dose)_rep2

value: A


title: JGW02 (20 ug/mL dose)_rep1

description:
Library name: T_2-1-6
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 2:!

value: mix-> extraction of Water extracts of JGT (JGW02;20 ug/mL dose)_rep1


title: JGW02 (100 ug/mL dose)_rep1

description:
Library name: T_2-1-5
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Water extracts of JGT (JGW02;100 ug/mL dose)_rep1


title: JGW01 (500 ug/mL dose)_rep2

description:
Library name: T_2-2-1
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;500 ug/mL dose)_rep2


title: JGW01 (20 ug/mL dose)_rep1

description:
Library name: T_2-1-3
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;20 ug/mL dose)_rep1


title: JGW04 (20 ug/mL dose)_rep1

description:
Library name: T_3-1-6
Rep1_Water extracts (20ug/mL dose); combination ratios of two herbs into 1:2

value: mix-> extraction of Water extracts of JGT (JGW04;20 ug/mL dose)_rep1


title: JGW01 (500 ug/mL dose)_rep1

description:
Library name: T_2-1-1
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;500 ug/mL dose)_rep1


title: JGW01 (100 ug/mL dose)_rep1

description:
Library name: T_2-1-2
Rep1_Water extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;100 ug/mL dose)_rep1


title: single cell CRISPR screen CROP-Seq libray, transcriptome sub libraries-1

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

country: USA

institute: University of Georgia

description: Library name: CROP_Seq_Transcriptome_1

data_processing:
For bulk RNASeq, raw sequencing data was processed with initial quality control (QC) using FastQC (version 0.11.9) to assess read quality and MultiQC (version 1.14) was used to aggregate and visualize quality control metrics across all samples. After QC, raw sequencing reads were processed using fastp (version 0.23.2) for adaptor trimming and reads filtering with the following filtering parameters: quality score threshold: 20, maximum proportion of unknown bases (N): 10, maximum percentage of unqualified bases: 30%. A reference human hg38 genome index was constructed using HISAT2 (version 2.2.1) with the provided genome sequence. Cleaned reads were aligned to the reference genome using HISAT2. Alignment outputs were converted to sorted BAM files using SAMtools (version 1.6), and BAM files were indexed for downstream analysis. Gene-level read counts were quantified using featureCounts (Subread version 2.0.3). For single cell CRISPR screen analysis, The raw fastq trimming, alignment and generation of cell-gene matrices was performed using the Parse split-pipeline 1.1.2 following the manufacturer's instructions. The cellgene matrix data was processed using the Scanpy package (version 1.9.6) in Pythonn3.8.18. Briefly, the raw count data was imported from a sparse matrix format (.mtx file) along with corresponding gene annotation and cell metadata files. Prior to analysis, genes with missing annotations were removed from the dataset. Gene names were assigned as unique identifiers, cell barcodes and CRISPR guide RNA information were incorporated as observation names in the AnnData object. Initial quality control filtering was performed to remove cells expressing fewer than 300 genes and genes detected in fewer than 5 cells. To ensure reliable transcript counts, cells were further filtered to retain only those with total transcript counts above 2,000. Additional quality control was performed to filter out the cells with more than 60,000 transcripts and 10,000 detected genes to remove potential doublets. Cells with mitochondrial gene content greater than 40% were excluded to remove low-quality or dying cells. After quality control, we obtained transcriptomes for 295,467 cells with an average of 20,127 reads per cell (5.9 billion total reads). The median number of transcripts and genes detected per cell was 3,755 and 2,046, respectively.
Assembly: Hg38
Supplementary files format and content: 7human_myoblast_tpm.csv: WT human myoblast RNA seq TPM from 7 donors
Supplementary files format and content: METTL3_count.csv: METTL3 KO cells RNASeq raw counts
Supplementary files format and content: count_matrix.mtx: transcript count matrix file from single cell CRISPR screen
Supplementary files format and content: cell_metadata.csv: Cell metadata for single cell CRISPR screen, including cell barcode, guide information .etc

molecule: polyA RNA

organism: Homo sapiens

source_name: Skeletal muscle

growth_protocol: Human myoblasts are maintained in skeletal muscle cell basal medium (PromoCell, C-23260) supplemented with 15% fetal bovine serum (FBS; Sigma-Aldrich, F2442), 5% growth medium supplement mix (PromoCell, C-39365), GlutaMAX, and 1% gentamicin sulfate. For differentiation, myoblasts were cultured in differentiation medium comprising DMEM supplemented with 2% horse serum, 10 μM DAPT (Cayman, 13197), and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from human myoblast cells using TRIzol reagent (Thermo Fisher Scientific, 15-596-018) according to the manufacturer’s protocol.
Bulk RNA library will be prepared using NEBNext UltraII directional kit with PolyA selection under manufacturer's protocol. A CRISPR-Cas9 mini-library targeting 250 candidate genes was cloned into the CROPseq-Guide-Puro which was a gift from Christoph Bock (Addgene plasmid #86708). To increase the representation of positive controls, the gRNAs for MyoD and Myomaker were cloned at a higher abundance. Human myoblasts at passage 4 expressing DTAN–InteinN were infected with the lentiviral library at a low multiplicity of infection (MOI = 0.1), ensuring each cell received a single gRNA. Five days post-infection, these myoblasts were mixed with InteinC-DTAC-expressing human myoblasts at a 1:1 ratio. The mixed cells were cultured in differentiation medium for six days following a 24-hour co-culture period. After the depletion of large myotubes, surviving muscle cells were collected and processed for single-cell RNA sequencing using the Evercode Whole Transcriptome kit (Parse, ECW02130) per the manufacturer’s protocol. Two sequencing libraries were generated: a whole transcriptome library and a CRISPR gRNA library, both sequenced on Illumina platforms. Sequencing data analysis was conducted using the ParseBiosciences-Pipeline-v1.1.2.

treatment_protocol: Human myoblasts are differentiated in DM (2% Horse serum in DMEM).

value: Skeletal muscle

value: Human myoblast

value: immortalized cell line

tag: genotype

value: WT


title: A_Hippo_Que_2_1.fq.gz

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Assembly: GRCm38.84
Supplementary files format and content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according  to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2  mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for  15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper  aqueous phase where RNA remained was transferred into a new tube with equal volume of  supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After  deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix  was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the  pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated  water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using  a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented  into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA  synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products  were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on  the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products  from previous step were heated denatured and circularized by the splint oligo sequence to get the  final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The  final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300  copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases  reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: strain

value: hippocampus

tag: age

value: Quercetin  treatment 24 days


title: A_Hippo_Ctrl_2_1.fq.gz

value: PBS containing 10% DMSO as solvent


title: A_Hippo_Que_3_1.fq.gz


title: A_Hippo_Que_1_1.fq.gz


title: A_Hippo_Ctrl_3_1.fq.gz


title: Y_Hippo_Ctrl_3_1.fq.gz


title: PBS, e.coli infected, rep3

city: Lausanne

first: Kathrin

last: Tomasek

address: Rte Cantonale

country: Switzerland

institute: EPFL

description: Library name: PBS_inf_3

data_processing:
STAR (v.2.7.10b) was used to align FASTQ reads to the mouse mm10 reference genome and count reads in genes from  the annotations in Ensembl release 102.
Genes were considered "expressed" if they had more than 10 fragments in at least 4 of the samples (14,114 genes remaining).
DE analysis was perfomed using DESeq2 (v1.36.0).
Assembly: mouse mm10 reference genome with Ensembl release 102 annotations
Supplementary files format and content: raw gene counts output from the STAR "quantMode" parameter. The first column is the ensembl_gene_id (Ensembl release 102) and the following columns represent each library

source_name: mouse bladder organoid

growth_protocol: Mouse primary bladder epithelial cells were obtained from C57BL/6 mice (Charles River Laboratories) aged 3-4 months or female ROSAMT/MG mice (Jackson Laboratories) at age 4 months. Routinely, cells were grown at 37°C and 5% CO2 without antimicrobial or antimycotic agents. Organoids were cultured in either MBO media or DMEM/F-12 media, whereas for monolayers total of 10% FBS was added to DMEM/F-12 media and plastics were coated with gelatin-based coating solution (ABC Biopply). The day prior to infection, 20 mM of HEPES was added and kept throughout the experiments. The well-characterized UPEC strains CFT073  was used. Bacteria were grown in DMEM/F-12 (Thermo Fisher) supplemented with 20 mM HEPES (Thermo Fisher) at 37°C statically.

extract_protocol:
Organoids were incubated with the appropriate volume of RNA lysis buffer (RNAeasy Plus Mini Kit, QIAGEN) and RNA was isolated following the manufacturer’s instructions.
Libraries were prepared using the “Illumina stranded mRNA ligation" (ISML) prep, according to Illumina protocol 1000000124518 v01. Libraries were then sequenced on the NovaSeq 6000 (Illumina) yielding approximately 25-35 million, 60-bp, paired end reads for all samples.

treatment_protocol: Organoids and monolayers were treated with OM-89 at 500 µg/ml of protein in either MBO or DMEM/F-12 media. For control groups, equal volumes of phosphate buffered saline (PBS, Thermo Fisher) was used instead of OM-89. OM-89 and PBS were added to the media according to the continuous application regime – 72 hour treatment pre-infection and treatment throughout the experiment. For the continuous application, bacteria were microinjected after adjusting their optical density at 600 nm (OD600) in media with either PBS or OM-89. On the day of the experiments, the media of the organoids was replaced with fresh media. The OD600 of bacterial cultures was adjusted to 2.25 in a 1:1 dilution of media and Phenol Red solution (Sigma-Aldrich) to facilitate the visualization of injected organoids. Microinjections were performed using a Pneumatic PicoPump (WPI) using micropipettes prepared from thin wall glass capillary (TW100F-4 with length 100 mm and diameter 1 mm) using a Flaming/Brown Micropipette Puller (Sutter Instruments model P-87) set at pressure 360, heat 866, Vel 200. The micropipettes were then cut with tweezers under a stereomicroscope (Olympus SZX-16) to generate a tip size ejecting roughly 1 nl volume of the adjusted bacterial culture in mineral oil on a Zeiss coverslide (corresponding to 100 mm), corresponding to roughly 300-1000 colony forming units (CFU) per ml. After total of 4h of bacterial growth, organoids were treated with 10x the strain MIC of ampicillin (64.3µg/ml) for 3h before RNA extraction.

value: mouse bladder organoid

value: PBS, e.coli infected


title: Y_Hippo_Ctrl_2_1.fq.gz


title: PBS, e.coli infected, rep4

description: Library name: PBS_inf_4


title: PBS, e.coli infected, rep2

description: Library name: PBS_inf_2


title: PBS, non-infected, rep4

description: Library name: PBS_4

value: PBS, non-infected


title: PBS, non-infected, rep3

description: Library name: PBS_3


title: PBS, non-infected, rep1

description: Library name: PBS_1


title: Y_Hippo_Ctrl_1_1.fq.gz


title: PBS, non-infected, rep2

description: Library name: PBS_2


title: A_Hippo_Ctrl_1_1.fq.gz


title: JGW02 (500 ug/mL dose)_rep2

description:
Library name: T_2-2-4
Rep2_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: Muscle

value: Myotube

value: mix-> extraction of Water extracts of JGT (JGW02;500 ug/mL dose)_rep2

value: A


title: JGW01 (100 ug/mL dose)_rep2

description:
Library name: T_2-2-2
Rep2_Water extracts (100ug/mL dose); combination ratios of two herbs into 3:0

value: mix-> extraction of Water extracts of JGT (JGW01;100 ug/mL dose)_rep2


title: PBS, e.coli infected, rep1

description: Library name: PBS_inf_1


title: OM-89, e.coli infected, rep4

description: Library name: OM-89_inf_4

value: OM-89, e.coli infected


title: OM-89, e.coli infected, rep3

description: Library name: OM-89_inf_3


title: OM-89, e.coli infected, rep1

description: Library name: OM-89_inf_1


title: JGW02 (500 ug/mL dose)_rep1

description:
Library name: T_2-1-4
Rep1_Water extracts (500ug/mL dose); combination ratios of two herbs into 2:1

value: mix-> extraction of Water extracts of JGT (JGW02;500 ug/mL dose)_rep1


title: OM-89, non-infected, rep4

description: Library name: OM-89_4

value: OM-89, non-infected


title: OM-89, e.coli infected, rep2

description: Library name: OM-89_inf_2


title: 24hRV-cis+ [24hRv-Cis-1]

city: Guangzhou

first: Zhang

last: Jing

address: Southern Medical University

institute: Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

growth_protocol: C57BL/6 mice were purchased from Southern Medical University Laboratory Animal Management Centre. The protocol was reviewed and approved by the Medical Ethics Committee and the Biosafety Management Committee of Southern Medical University. Mouse primary Mφ were achieved from femurs of 4-6-week female C57BL/6 mice and treated with 100 ng/mL of murine GM-CSF (PeproTech, Rocky Hill, NJ, USA) for 7 days, during which half medium was replaced every 2 days, thus obtaining bone marrow-derived macrophages (BMDM).

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with Cisatracurium besylate (CIS), one hour after drug treatment, cells were infected with H37Rv at MOI = 2.

value: bone marrow-derived macrophages

value: Cisatracurium Besylate teatment


title: 24hRv+Cis+ [24hRv-Cis-3]

value: H37Rv infected and Cisatracurium Besylate teatment


title: 24hRv+Cis- [24hRv-Cis-2]

value: H37Rv infected and Cisatracurium Besylate untreatment


title: OM-89, non-infected, rep2

description: Library name: OM-89_2


title: OM-89, non-infected, rep3

description: Library name: OM-89_3


title: 6hRv+Cis+ [6hRv-Cis-3]


title: Th2, Linoleic, Atglistatin, H3K27Ac ChIP, rep2

city: Chiba-shi

first: Hiroyuki

last: Yagyu

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

country: Japan

institute: Chiba University

description: Library name: H3K27Ac_A_LA2

library_source: genomic

data_processing:
ChIP-seq and ATAC-seq data were mapped to GRCm38 (mouse) genome references using Bowtie2. MACS2 was used for peak calling with the q-value cutoff of 0.01. Tag directories were created by HOMER (makeTagDirectory) using the aligned Sequence Alignment/Map (SAM) formats generated by SAMtools. Called peaks were annotated to the closest gene or transcriptional start site with proximity-based annotation using the annotatePeaks.pl function of HOMER. Peaks commonly observed in biological replicates were called and subjected to downstream analyses using the mergePeaks function of HOMER. BigWig files were generated from the aligned SAM or Browser Extensible Data (BED) file formats using SAMtools, BEDtools, and deepTools2. The tag count density was normalized as tags per 10 million reads in the original library.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Th2 cells

extract_protocol:
4×10^6 cultured Th2 cells were fixed with 1% (w/v) PFA at 37 °C for 10 min. Nuclei were extracted using lysis buffer and sonicated to reduce the DNA length to between 200 and 1,000 bp using a Bioruptor Pico Sonicator (Diagenode). The soluble fraction was incubated with antibody-conjugated protein-A coated beads overnight at 4 °C using a 1:1 mixture of anti-PPARγ antibody (E-8, from Santa Cruz Biotechnology, Dallas, TX, USA; and A3409A, from Cosmo Bio, Tokyo, Japan), anti-RXRα antibody (D6H10; Cell Signaling Technology), anti-H3K27Ac antibody (D5E4; Cell Signaling Technology), or negative control rabbit IgG antibody included in the kit. Enriched chromatin fragments were purified and de-crosslinked overnight at 65 °C, and immunoprecipitated DNA was extracted. The total input DNA (cellular DNA without immunoprecipitation) was extracted in parallel.
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. DNA libraries were sequenced using an Illumina NovaSeq 6000 Sequencing System.

value: Th2 cells

value: BALB/c

value: Atglistatin

tag: chip antibody


title: OM-89, non-infected, rep1

description: Library name: OM-89_1

value: mouse bladder organoid


title: Th2, Linoleic, Atglistatin, H3K27Ac ChIP, rep1

description: Library name: H3K27Ac_A_LA1


title: 6hRv+Cis- [6hRv-Cis-2]


title: 6hRv-Cis- [6hRv-Cis-1]

value: Cisatracurium Besylate untreatment


title: Th2, Linoleic, DMSO, H3K27Ac ChIP, rep2

description: Library name: H3K27Ac_LA2

value: DMSO


title: Th2, Control, Atglistatin, H3K27Ac ChIP, rep1

description: Library name: H3K27Ac_A_C1


title: mig-32(n4275) ChIP-seq, H3K27me3, replicate 2

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

description:
Library name: alslib97-H3K27me3-mig32
Spike-in scaled

data_processing:
The raw sequencing reads were trimmed for low-quality base calls, with a phred33 < 22, Illumina adapter sequences using a stringency of 12, and poly-G sequences (defined as 13 Gs in a row) using a stringency of 8 with TrimGalore v0.6.5.
Trimmed reads were aligned to a concatenated Caenorhabditis elegans ce11 and Drosophila melanogaster dm6 genome using Bowtie2 v2.3.4.3 with the maximum fragment size parameter set to 2000. Reads mapped to both genomes were discarded and the reads were normalized. Briefly, the ce11 reads were randomly subsampled using factors that reflect the total number of dm6 reads in that sample and were corrected for the ratio of dm6/ce11 reads in the corresponding input samples. Alignments were filtered by removing duplicates and multi-mapping reads with a MAPQ < 42, using Samtools v1.11.
Peaks were called with MACS2 v2.2.7.1 with the --broad option. Peaks that overlap with blacklisted regions, where there is artificially high signal, were removed.
Coverage files were prepared with the BedTools v2.29.0 genomecov function using the -bga and -pc options.
Log2 transformed ChIP/Input ratios were calculated per base with deepTools v3.5.0 bigwigCompare with a pseudocount of 1.
Assembly: ce11
Supplementary files format and content: Processed data files include genome coverage levels in bigWig format, as well as peak locations in BED format (except for input samples and replicate 2 of mig-32(n4275) H2AK119ub ChIP-seq)

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Strains were maintained on nematode growth medium (NGM) agar with E. coli OP50-1 as a food source at 21°C unless specified otherwise. The N2 (Bristol) strain was used as wild-type. Embryos were isolated from gravid adults using standard alkaline hypochlorite treatment (“bleaching”). After three washes in M9 buffer supplemented with 0.01% (v/v) Triton X-100 (M9/Tx), embryos were allowed to develop to L1 diapause in M9/Tx buffer overnight with aeration. The arrested L1s were plated on NGM agar or added to liquid culture with OP50-1 to start synchronous growth. Arrested L1s were counted and seeded into 40 mL of S-Complete medium with OP50-1 as a food source, at a final density of ~0.5-1.5 animals per uL. Animals were grown with aeration for 72 hours to gravid adulthood, and embryos were isolated again by bleaching. After washes with M9/Tx, embryos were processed for ChIP as described below either immediately or after a further 3 hours of growth with aeration.

extract_protocol:
Embryos were collected by centrifugation (1000g, 3 min.) and washed twice in phosphate-buffered saline (PBS) containing 0.01% (v/v) Triton X-100 (PBS/Tx). To crosslink, PBS/Tx was added to at least 80 times the pellet volume, and 37% formaldehyde (Sigma F8775) was added to a final concentration of 1.8%. Samples were incubated at room temperature with rotation for 25 minutes. Glycine was added to a final concentration of 125 mM followed by incubation for an additional 5 minutes. All subsequent steps were performed on ice using pre-chilled buffers and tubes. Embryos were washed twice with PBS/Tx as above and an equal volume of resuspension buffer (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.01% Triton X-100, protease inhibitors (1 tablet per 5 mL, Roche 4693159001) was added to the embryo pellet. The resuspended embryos were aliquoted, snap-frozen in liquid nitrogen and stored at -80°C. Aliquots of cross-linked embryos were thawed in an ice-water bath, the volume was adjusted to 3-4 pellet volumes (PV) using resuspension buffer, and 100 uL was aliquoted to each polystyrene sonication tube (Evergreen 214-3721-010). An equal volume of resuspension buffer containing 2X detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.2% sodium deoxycholate, 0.7% sodium sarkosyl). Samples were sonicated in a Q800R3 water bath sonicator (QSonica Q800R3-110; 50% power, 20s on/20s off) for 4 minutes. Samples were gently mixed by pipetting and sonicated an additional 4 minutes. The lysate was transferred to an Eppendorf tube and an equal volume of resuspension buffer without detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA). The lysate was centrifuged (13,000g, 15 min. 4°C) and the supernatant was transferred to a new tube. Protein concentration was determined using the Bradford assay (Sigma B6916). As a spike-in control for calibration, sonicated Drosophila chromatin (Active Motif, 53083) was added at a ratio of 1:20. The supernatant was aliquoted to tubes for immunoprecipitation (IP), saving 20% of the volume of one IP tube as the ‘input’ control, which was stored at -20°C. Triton X-100 (10%, v/v) was added to a final concentration of 1% (v/v). This step was omitted for anti-H3K27me3 (CST 9733, C36B11), for which this detergent led to increased background. After antibody addition, samples were incubated overnight at 4°C with rotation. Protein G dynabeads (Invitrogen 10003D; 7.5 uL per IP) were pre-washed twice with resuspension buffer and added to IPs, which were then incubated as above for 2 hours. Beads were collected on a magnetic stand (Permagen MSR812) and washed as follows, with each wash incubated for 5 minutes at 4°C with rotation: 2X with FA-150 (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate), 1X with FA-1M (FA-150 with 1 M NaCl), 1X with FA-0.5M (FA-150 with 0.5 M NaCl), 1X with TE-LiCl in a new tube (10 mM Tris-Cl pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), 2X with TE+ (10 mM Tris-Cl pH 8, 1 mM EDTA, 50 mM NaCl, 0.005% IGEPAL CA-630). Elution was performed in a new tube at 65°C for 15 minutes using 50 uL of ChIP elution buffer (10 mM Tris-Cl pH 8, 1 mM EDTA, 200 mM NaCl, 1% SDS). Elution was repeated and the supernatants were pooled. The ‘Input’ aliquot was thawed and brought to 100 uL with ChIP elution buffer. Input and IP samples were treated with RNase A (16.5 ug, Sigma R4642) for 1 hour at 37°C and proteinase K (40 ug, Bioline BIO-37084) for 2 hours at 55°C. Crosslinks were reversed by incubation overnight at 65°C. DNA was isolated using a QIAquick PCR purification kit (Qiagen 28104).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) according to the manufacturer’s instructions, using 25-50 ng of input DNA or half of ChIP DNA. Library concentration was quantified using NEBNext Library Quant Kit for Illumina (NEB E7630). Pooled libraries were sequenced using NextSeq500 in 75 bp paired-end mode.

value: whole animal

tag: developmental stage

value: mixed embryo

tag: chip target

value: anti-H3K27me3 rabbit monoclonal C36B11, 9733; Cell Signaling Technology + Spike-in Ab (anti-Drosophila H2Av Ab #61686, 0.25 ug; Active Motif)

tag: corresponding input

value: mig-32(n4275) ChIP-seq, input, replicate 2


title: N2 ChIP-seq, input, replicate 2

description:
Library name: alslib102-Input-N2
Spike-in scaled

value: Wild-type

value: Input


title: Th2, Control, DMSO, H3K27Ac ChIP, rep1

description: Library name: H3K27Ac_C1


title: N2 ChIP-seq, H3K27me3, replicate 2

description:
Library name: alslib95-H3K27me3-N2
Spike-in scaled

value: N2 ChIP-seq, input, replicate 2


title: mig-32(n4275) ChIP-seq, H2AK119ub, replicate 2

description:
Library name: alslib96-H2AK119ub-mig32
Spike-in scaled

value: anti-H2AK119ub rabbit monoclonal D27C4, 8240; Cell Signaling Technology + Spike-in Ab (anti-Drosophila H2Av Ab #61686, 0.25 ug; Active Motif)


title: mig-32(n4275) ChIP-seq, input, replicate 2

description:
Library name: alslib103-Input-mig32
Spike-in scaled


title: Th2, Linoleic, DMSO, H3K27Ac ChIP, rep1

description: Library name: H3K27Ac_LA1


title: Th2, Control, DMSO, H3K27Ac ChIP, rep2

description: Library name: H3K27Ac_C2


title: N2 ChIP-seq, H2KA119ub, replicate 2

description:
Library name: alslib94-H2AK119ub-N2
Spike-in scaled


title: mig-32(n4275);spat-3(mgw26) RNA-seq, replicate 2

description: mig-32(n4275);spat-3(mgw26)_RNA-seq_replicate_2

data_processing:
The raw sequencing reads were trimmed for low-quality base calls, with a phred33 < 22, Illumina adapter sequences using a stringency of 12, and poly-G sequences (defined as 13 Gs in a row) using a stringency of 8 with TrimGalore v0.6.5.
The trimmed reads were then aligned to the Caenorhabditis elegans ce11 genome using STAR v2.7.9a with default parameters and filtered for those with MAPQ 255 with Samtools v1.12.
Mapped reads were quantified with featureCounts in Subread v2.0.1.
Assembly: ce11
Supplementary files format and content: Processed data file includes the raw number of read pairs aligning to each gene for each sample

growth_protocol: Strains were maintained on nematode growth medium (NGM) agar with E. coli OP50-1 as a food source at 21°C unless specified otherwise. The N2 (Bristol) strain was used as wild-type. Embryos were isolated from gravid adults using standard alkaline hypochlorite treatment (“bleaching”). After three washes in M9 buffer supplemented with 0.01% (v/v) Triton X-100 (M9/Tx), embryos were allowed to develop to L1 diapause in M9/Tx buffer overnight with aeration. The arrested L1s were plated on NGM agar or added to liquid culture with OP50-1 to start synchronous growth. Worms were synchronized by bleaching and grown to gravid adulthood on NGM agar plates with OP50-1. To collect late embryos for RNA-seq, the synchronized gravid adults were bleached 60 hours (N2) or 66 hours (mig-32 and spat-3 mutants) after release from L1 diapause. Embryos of all genotypes were washed three times in M9/Tx buffer and allowed to develop for 4.5 hours post bleaching in M9/Tx buffer with aeration. The developmental stages of a subset of each sample were scored with DIC microscopy before collection.

extract_protocol:
TRI Reagent (Sigma Aldrich) was added to the embryo pellet followed by 1-3 cycles of snap-freezing, thawing, and vortexing (1 minute). Following chloroform extraction, the aqueous phase was transferred to an RNA Clean and Concentrator-5 column and purified according to the manufacturer’s instructions including on-column DNaseI digestion (Zymo Research).
PolyA+ RNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) according to the manufacturer’s instructions. Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB E7765S) according to the manufacturer’s directions with NEBNext Multiplex Oligos for Illumina (NEB E6440). Library concentration was quantified using NEBNext Library Quant Kit for Illumina (NEB E7630). Pooled libraries were sequenced using NextSeq500 in 75 bp paired-end mode.

value: late embryo


title: mig-32(n4275);spat-3(mgw26) RNA-seq, replicate 1

description: mig-32(n4275);spat-3(mgw26)_RNA-seq_replicate_1


title: Multiome, TSC, ATAC

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

description:
Library name: TSC_ATAC
ATAC library

library_source: genomic single cell

data_processing:
We obtained the transcript count and peak accessibility matrices using Cell Ranger Arc (v.1.0.0). Preprocessing was performed with Seurat (v.4.0.3) and Signac (v.1.2.1) R packages (GitHub). As a quality control, we filtered out the cells that fulfilled any of the following conditions: <800 RNA reads; >40000 RNA reads; >10% mitochondrial RNA reads; <120 detected genes; >5500 detected genes; > 100000 ATAC reads; <500 ATAC reads; TSS enrichment score < 2; nucleosomal signal score >2.5. To remove unwanted variability, we filtered out a set of housekeeping, cell cycle, and ribosomal genes from the RNA count matrix. Transcript and peak counts were normalized using log and tf-idf normalization, respectively.
The pre-processing of the samples consisted of the following steps: we identified the highly variable genes (HVG) using the FindVariableFeatures, followed by data scaling, and Principal Component Analysis (PCA) using the default parameters of ScaleData and RunPCA functions of Seurat. The ESC and TSC samples were integrated using the Harmony software (v.0.1.0) using the first 30 principal components of the RNA processed data. We then produced a shared 2D UMAP embedding with the main 8 harmony dimensions.
Assembly: mm10
Supplementary files format and content: Barcodes, Features, Count matrices

source_name: Trophoblast stem cells

growth_protocol: ESCs and the CEBPa-ER cell lines were cultured on gelatinized plates in KnockOut DMEM (10829018, Gibco) containing 15% ESC FBS (16141079, Gibco), 1x Penicillin-Streptomycin (15140122, Gibco), 1x L-Glutamine (25030081, Gibco), 1x Non-Essential Amino Acids (11140068, Gibco), 1nM sodium pyruvate (11360070, Gibco), 0.1 mM 2-Mercaptoethanol (31350010, Gibco), and 1000 U/ml fresh leukemia inhibitory factor (LIF) (ESG1106, Sigma-Aldrich).

extract_protocol:
1,000,000 cells from CEBPa-ER ESCs induced for 0h, 3h, 12h, 48h, and 72h, as well as TSCs, were trypsinized and resuspended in PBS containing 0.05% BSA.
Libraries were prepared using the Chromium Single Cell Multiome ATAC + Gene Expression kit (1000283, 10x genomics). Between 6,400 and 14,800 cells per sample were sequenced using an Illumina NovaSeq6000 sequencer.

treatment_protocol: For CEBPa induction, cells were treated with 1 µM Tamoxifen (H7904, Sigma-Aldrich) which shuttles the factor into the cell nucleus.

value: Trophoblast stem cells


title: spat-3(mgw26) RNA-seq, replicate 2


title: Multiome, induced ESC, 72h, GEX

description:
Library name: ESC_72h_GEX
GEX (3’ mRNA) library

library_source: transcriptomic single cell

source_name: ESCs expressing CEBPa-ERT2

value: ESCs expressing CEBPa-ERT2

value: tamoxifen


title: Multiome, induced ESC, 72h, ATAC

description:
Library name: ESC_72h_ATAC
ATAC library


title: mig-32(n4275) RNA-seq, replicate 2


title: spat-3(mgw26) RNA-seq, replicate 1


title: Multiome, induced ESC, 48h, GEX

description:
Library name: ESC_48h_GEX
GEX (3’ mRNA) library


title: mig-32(n4275) RNA-seq, replicate 1


title: Th2, Control, Atglistatin, H3K27Ac ChIP, rep2

description: Library name: H3K27Ac_A_C2

value: Th2 cells

value: BALB/c


title: N2 RNA-seq, replicate 2


title: Multiome, TSC, GEX

description:
Library name: TSC_GEX
GEX (3’ mRNA) library


title: N2 RNA-seq, replicate 1


title: Multiome, induced ESC, 12h, GEX

description:
Library name: ESC_12h_GEX
GEX (3’ mRNA) library


title: Sample_24 neutrophils, mice, sham, Day 1, skull

city: Houston

first: John

middle: P.

last: Hagan

state: Texas

address: 6431 Fannin St.

department: Neurosurgery

institute: UTHealth

data_processing:
Raw reads were checked with FASTQC for quality and trimmed with Trimmomatic
Reads were mapped using RNA STAR (Galaxy Version 2.7.8a)
Mapping quality was verified by SAMtools idxstats, Picard tools MarkDuplicates, and MultiQC
Gene counts were produced with featureCounts assuming reverse strandness
Normalization was conducted using limma-voom
Assembly: mm10
Supplementary files format and content: Raw_counts.xlsx excel file contains a matrix table with raw counts generated from featureCounts of mapped reads. The first column contains official gene symbol and all remaining columns contain counts grouped first by cell line, then force, then replicate.
Supplementary files format and content: Norm_counts.xlsx excel file contains a matrix table with normalized abundance measurements generated from limma-voom. The first column contains EntrezID, the second column contains official gene symbol, and all remaining columns contain counts grouped first by cell line, then force, then replicate.

source_name: Skull

extract_protocol:
The isolated living cells were sorted to RLT buffer with RNase inhibitor and DTT and frozen on dry ice as soon as the sorting is done and sent to The University of Texas Health Science Center at Houston (CPRIT RP180734). The total RNA was isolated following the protocol of RNeasy Mini Kit (#74104, Qiagen) and RNase-free DNase (#79254, Qiagen). These isolated RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).
RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) , and the library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

treatment_protocol:
SAH - SAH was induced via endovascular perforation using a 5-0 suture after advancing the suture through an external carotid artery stump and then in to the skull vasculature via the internal carotid artery. This method causes vessel perforation of the circle of Willis
sham - all surgical manipulations were performed (same as SAH) except the vessel was not punctured

value: Skull

value: Neutrophils from Skull

value: WT

value: sham

tag: time

value: Day 1


title: Sample_22 neutrophils, mice, sham, Day 1, skull


title: Multiome, induced ESC, 3h, ATAC

description:
Library name: ESC_3h_ATAC
ATAC library


title: Sample_23 neutrophils, mice, sham, Day 1, skull


title: mig-32(n4275) ChIP-seq, input, replicate 1

description: Not spike-in scaled

data_processing:
The raw sequencing reads were trimmed for low-quality base calls, with a phred33 < 22, Illumina adapter sequences using a stringency of 12, and poly-G sequences (defined as 13 Gs in a row) using a stringency of 8 with TrimGalore v0.6.5.
The trimmed reads were then aligned to the Caenorhabditis elegans ce11 genome using Bowtie2 v2.3.4.3 with the maximum fragment size parameter set to 2000. Alignments were filtered by removing duplicates and multi-mapping reads with a MAPQ<42, using Samtools v1.11.
Peaks were called with MACS2 v2.2.7.1 with the --broad option. Coverage files were prepared with the BedTools v2.29.0 genomecov function using the -bga and -pc options.
Log2 transformed ChIP/Input ratios were calculated per base with deepTools v3.5.0 bigwigCompare with a pseudocount of 1.
Assembly: ce11
Supplementary files format and content: Processed data files include genome coverage levels in bigWig format, as well as peak locations in both broadPeak and xls format (except for input samples)

extract_protocol:
Embryos were collected by centrifugation (1000g, 3 min.) and washed twice in phosphate-buffered saline (PBS) containing 0.01% (v/v) Triton X-100 (PBS/Tx). To crosslink, PBS/Tx was added to at least 80 times the pellet volume, and 37% formaldehyde (Sigma F8775) was added to a final concentration of 1.8%. Samples were incubated at room temperature with rotation for 25 minutes. Glycine was added to a final concentration of 125 mM followed by incubation for an additional 5 minutes. All subsequent steps were performed on ice using pre-chilled buffers and tubes. Embryos were washed twice with PBS/Tx as above and an equal volume of resuspension buffer (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.01% Triton X-100, protease inhibitors (1 tablet per 5 mL, Roche 4693159001) was added to the embryo pellet. The resuspended embryos were aliquoted, snap-frozen in liquid nitrogen and stored at -80°C. Aliquots of cross-linked embryos were thawed in an ice-water bath, the volume was adjusted to 3-4 pellet volumes (PV) using resuspension buffer, and 100 uL was aliquoted to each polystyrene sonication tube (Evergreen 214-3721-010). An equal volume of resuspension buffer containing 2X detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.2% sodium deoxycholate, 0.7% sodium sarkosyl). Samples were sonicated in a Q800R3 water bath sonicator (QSonica Q800R3-110; 50% power, 20s on/20s off) for 4 minutes. Samples were gently mixed by pipetting and sonicated an additional 4 minutes. The lysate was transferred to an Eppendorf tube and an equal volume of resuspension buffer without detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA). The lysate was centrifuged (13,000g, 15 min. 4°C) and the supernatant was transferred to a new tube. Protein concentration was determined using the Bradford assay (Sigma B6916). The supernatant was aliquoted to tubes for immunoprecipitation (IP), saving 20% of the volume of one IP tube as the ‘input’ control, which was stored at -20°C. Triton X-100 (10%, v/v) was added to a final concentration of 1% (v/v). This step was omitted for anti-H3K27me3 (CST 9733, C36B11), for which this detergent led to increased background. After antibody addition, samples were incubated overnight at 4°C with rotation. Protein G dynabeads (Invitrogen 10003D; 7.5 uL per IP) were pre-washed twice with resuspension buffer and added to IPs, which were then incubated as above for 2 hours. Beads were collected on a magnetic stand (Permagen MSR812) and washed as follows, with each wash incubated for 5 minutes at 4°C with rotation: 2X with FA-150 (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate), 1X with FA-1M (FA-150 with 1 M NaCl), 1X with FA-0.5M (FA-150 with 0.5 M NaCl), 1X with TE-LiCl in a new tube (10 mM Tris-Cl pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), 2X with TE+ (10 mM Tris-Cl pH 8, 1 mM EDTA, 50 mM NaCl, 0.005% IGEPAL CA-630). Elution was performed in a new tube at 65°C for 15 minutes using 50 uL of ChIP elution buffer (10 mM Tris-Cl pH 8, 1 mM EDTA, 200 mM NaCl, 1% SDS). Elution was repeated and the supernatants were pooled. The ‘Input’ aliquot was thawed and brought to 100 uL with ChIP elution buffer. Input and IP samples were treated with RNase A (16.5 ug, Sigma R4642) for 1 hour at 37°C and proteinase K (40 ug, Bioline BIO-37084) for 2 hours at 55°C. Crosslinks were reversed by incubation overnight at 65°C. DNA was isolated using a QIAquick PCR purification kit (Qiagen 28104).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) according to the manufacturer’s instructions, using 25-50 ng of input DNA or half of ChIP DNA. Library concentration was quantified using NEBNext Library Quant Kit for Illumina (NEB E7630). Pooled libraries were sequenced using NextSeq500 in 75 bp paired-end mode.

value: whole animal

value: mixed embryo


title: N2 ChIP-seq, input, replicate 1

description: Not spike-in scaled

value: Wild-type


title: Multiome, induced ESC, 3h, GEX

description:
Library name: ESC_3h_GEX
GEX (3’ mRNA) library


title: Sample_21 neutrophils, mice, sham, Day 1, skull


title: Sample_19 neutrophils, mice, SAH, Day 1, skull

value: SAH


title: Sample_20 neutrophils, mice, SAH, Day 1, skull


title: Sample_18 neutrophils, mice, SAH, Day 1, skull


title: Multiome, induced ESC, 0h, GEX

description:
Library name: ESC_0h_GEX
GEX (3’ mRNA) library


title: mig-32(n4275) ChIP-seq, H3K27me3, replicate 1

description: Not spike-in scaled

value: anti-H3K27me3 rabbit monoclonal C36B11, 9733; Cell Signaling Technology

value: mig-32(n4275) ChIP-seq, input, replicate 1


title: Sample_16 neutrophils, mice, SAH, Day 3, skull

value: Day 3


title: Sample_17 neutrophils, mice, SAH, Day 1, skull


title: WT D14 3

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Raw sequencing data was processed with Cellranger Multi (v7.2.0, 10X Genomics) using the mm10-2020A reference transcriptome and Chromium Mouse Transcriptome Probe Set v1.0.1 which generated raw and filtered feature count matrices per sample as well as a BAM file for each sample based on barcode.
Assembly: mm10-2020A
Supplementary files format and content: Feature barcode matrices provided in HDF5 format (.H5) as generated by cellranger. Both raw and filtered matrices (filtered on nuclei as called by cellranger) are provided.

molecule: nuclear RNA

source_name: Lumbar Spine

growth_protocol: C57BL6/J mice were obtained initially from Jackson Laboratory then bred in house. MIF-E22Q transgenic mice were generated at Johns Hopkins as described in Park et al 2022 (PMID 35545089). Animals were housed in temperature and humidity-controlled rooms, maintained on fixed light/dark cycle, and were age and sex matched. (All mice were female).

extract_protocol:
14 days after immunization, mice were euthanized via isoflurane overdose then perfused with chilled phosphate buffered saline. Lumbar spinal cords were manually dissected out and flash frozen immediately in liquid nitrogen then kept in liquid nitrogen. Lumbar tissue was later removed from liquid nitrogen and lysed in Nuclei Extraction Buffer (Miltenyi Biotec) with RNAse inhibitor (40U/mL RNasin Plus) in a gentleMACS tissue dissociator (Miltenyi) using octo coolers to keep nuclei chilled during digestion. Nuclei then were filtered over 100μM SmartStrainer into pre-chilled 5mL conicl tube. Nuclei were incubated with magnetic anti-nucleus microbeads (Miltenyi 130-132-997) for 15 minutes at 4c then were washed and passed onto LS magnetic column in cold room. Column was washed twice then nuclei were eluted and counted. RNase inhibitor was maintained in all buffers until nuclei were fixed. Nuclei were pelleted and resuspended in Fix/Perm Buffer (4% formaldehyde, 10X Genomics PN-2000517) and incubated overnight at 4c. The following morning fixation was quenched and then undewrent 10X Genomics Flex (Fixed RNA Profiling) protocol according to manufacturer recommendations including probe hybridization, washing (as individual samples), and then pooled and loaded onto a single lane of a Chip Q (10X Genomics PN-2000518) targeting 8000 nuclei per sample. Nuclei were partitioned into Gel Bead in Emulsion (GEMs) using a Chromium iX device (10X genomics).
Libraries were prepared according to manufacturer's recommendation (10X Genomics "Chromium Fixed RNA Profiling Reagent Kits User Guide CG000527 Rev E") in which GEMs are incubated to allow for probe ligation and GEM barcoding, then libraries were amplified in bulk followed by size selection, sample index addition (using 9 amplification cycles), followed by a final size selection step. 1 NGS library was sequenced on a NovaSeq 6000 S4 flow cell in 1 lane (150bp paired end) with 10% PhiX spike-in at Novogene
OTHER: single nucleus RNA templated ligation

treatment_protocol: EAE was induced by subcutaneous immunization with 150μL of emulsion that was a 1:1 mix of 2mg/mL MOG35-55 peptide and 8mg/mL Complete Freund's Adjuvant (Mtb in IFA). In total each mouse got 150μg MOG35-55 peptide and 600μg Mtb. In addition, mice received 500ng pertussis toxin on day of immunization via intraperitoneal injection and second IP injection of pertussis toxin two days after immunization. Mice were followed for 2 weeks, developing disease at approximately day 12, and then euthanized on day 14. CFA control mice received the same volume and amount of emulsion but without any MOG35-55 peptide. They also received the same treatment with pertussis toxin.

tag: background strain

value: Lumbar Spine

tag: cell compartment

value: Nuclei

tag: score

tag: barcode


title: N2 ChIP-seq, H3K27me3, replicate 1

description: Not spike-in scaled

tag: tissue

value: N2 ChIP-seq, input, replicate 1


title: Multiome, induced ESC, 48h, ATAC

description:
Library name: ESC_48h_ATAC
ATAC library

tag: cell line

value: ESCs expressing CEBPa-ERT2

value: tamoxifen


title: Multiome, induced ESC, 12h, ATAC

description:
Library name: ESC_12h_ATAC
ATAC library


title: Sample_15 neutrophils, mice, SAH, Day 3, skull

value: Skull

tag: cell type


title: WT D14 2

tag: treatment


title: N2 ChIP-seq, H3K27me3, replicate 0

description: Not spike-in scaled

value: late embryo

value: N2 ChIP-seq, input, replicate 0


title: Sample_13 neutrophils, mice, SAH, Day 3, skull

value: Neutrophils from Skull

value: WT


title: Sample_12 neutrophils, mice, sham, Day 1, femur

source_name: Femur

value: Femur

value: Neutrophils from Femur

value: sham

value: Day 1


title: Multiome, induced ESC, 0h, ATAC

description:
Library name: ESC_0h_ATAC
ATAC library


title: WT D14 1


title: mig-32(n4275) ChIP-seq, H2AK119ub, replicate 1

description: Not spike-in scaled

value: whole animal

value: mixed embryo

value: anti-H2AK119ub rabbit monoclonal D27C4, 8240; Cell Signaling Technology


title: N2 ChIP-seq, input, replicate 0

description: Not spike-in scaled

value: Wild-type

value: Input


title: Sample_11 neutrophils, mice, sham, Day 1, femur


title: Sample_10 neutrophils, mice, sham, Day 1, femur


title: Sample_7 neutrophils, mice, SAH, Day 1, femur

value: SAH


title: WT CFA 1

value: Lumbar Spine

value: Nuclei

value: CFA


title: Sample_8 neutrophils, mice, SAH, Day 1, femur


title: WT CFA 2


title: E22Q D14 3


title: N2 ChIP-seq, H2KA119ub, replicate 0

description: Not spike-in scaled

value: late embryo


title: ref6-5, 10DAG, H2Aub

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

country: United Kingdom

institute: University of Warwick

description: Library name: ref6_10DAG_H2Aub

data_processing:
Quality control was performed using the software package FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) Read mapping to the reference genome was performed using bowtie with default parameters (http://bowtie-bio.sourceforge.net/index.shtml) Peak calling was performed using MACS2 with default parameters and -f BAM -g 1.1e8 (https://github.com/taoliu/MACS) Peak annotation was performed using PeakAnalyzer with NDG criterion (http://www.bioinformatics.org/peakanalyzer/wiki/) CPM normalizations and bw generation were performed using the deepTools utility bamCoverage with a bin size of 10  using -bs 10 --normalizeUsing CPM parameters (https://deeptools.readthedocs.io/en/latest/)
Assembly: TAIR10
Supplementary files format and content: Bigwig format (.bw) files were generated with the deepTools utility bamCoverage with 10 bp as bin and normalized by CPM.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Sterilized WT, bmi1abc and bmi1abc/ref6 seeds were cold-stratified in the dark at 4°C for 2–4 days and then grown under long-day conditions (16 h light and 8 h dark) at 21 °C on Murashige and Skoog (MS) agar plates containing 1.5% sucrose and 0.8% agar for 10 DAGs or 48 HAI.

extract_protocol:
ChIP experiments were performed on 1 g of 10-day-old seedling tissue and 5 g of 48-hour imbibed seeds (48 HAI) fixed in 1% formaldehyde. Chromatin was extracted from the fixed tissue and fragmented using a Bioruptor Pico (Diagenode). The sheared chromatin was immunoprecipitated overnight using the following antibodies and dilutions: anti-H3K27me3 (1:300, Millipore 07-449), anti-HsH2Aub (1:100, CST 8240S), anti-H3K27me1 (1:150, Millipore 07–448) or anti-HTA9 (1:300) antibodies. Immunocomplexes were captured using Protein-A Sepharose beads CL-4B (GE Healthcare) and crosslinking was reversed overnight at 65ºC. Final ChIP DNA was purified with MicroChIP DiaPure columns kit (Diagenode C03040001).
Libraries for ChIP-seq samples were prepared with TruSeq ChIP Library Preparation Kit (Illumina) and sequenced using Illumina NextSeq with single-end 75 bp reads

value: seedling

tag: Stage

value: 10 DAG

value: HsH2Aub (CST 8240S)


title: Sample_5 neutrophils, mice, SAH, Day 1, femur

value: Femur

tag: genotype

value: WT


title: Sample_6 neutrophils, mice, SAH, Day 1, femur

value: Neutrophils from Femur


title: Sample_4 neutrophils, mice, SAH, Day 3, Femur

value: Day 3


title: E22Q D14 2


title: bmi1abc,  10DAG, H3K27me1, Rep2

extract_protocol:
ChIP experiments were performed on 1 g of 10-day-old seedling tissue and 5 g of 48-hour imbibed seeds (48 HAI) fixed in 1% formaldehyde. Chromatin was extracted from the fixed tissue and fragmented using a Bioruptor Pico (Diagenode). The sheared chromatin was immunoprecipitated overnight using the following antibodies and dilutions: anti-H3K27me3 (1:300, Millipore 07-449), anti-H3K27me1 (1:150, Millipore 07–448) or anti-HTA9 (1:300) antibodies. Immunocomplexes were captured using Protein-A Sepharose beads CL-4B (GE Healthcare) and crosslinking was reversed overnight at 65ºC. Final ChIP DNA was purified with MicroChIP DiaPure columns kit (Diagenode C03040001).
Libraries for ChIP-seq samples were prepared with TruSeq ChIP Library Preparation Kit (Illumina) and sequenced using Illumina NextSeq with single-end 75 bp reads

value: H3K27me1 (Millipore #07-448)


title: E22Q D14 1


title: Sample_14 neutrophils, mice, SAH, Day 3, skull

value: Skull

value: Neutrophils from Skull


title: Sample_2 neutrophils, mice, SAH, Day 3, Femur


title: bmi1abc,  10DAG, H3K27me1,  Rep1


title: E22Q CFA 2


title: Sample_1 neutrophils, mice, SAH, Day 3, Femur


title: bmi1abc,  10DAG, input


title: RB039_heart

city: Tampa

first: Olha

last: Kravtsova

state: Florida

address: 560 Channelside Dr

institute: University of South Florida

description: Library name: RB039_heart

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: excel file with FPKM

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: heart

tag: Sex

value: Male

value: Maresin 1


title: E22Q CFA 1

value: Lumbar Spine


title: RB037_heart

description: Library name: RB037_heart


title: Sample_9 neutrophils, mice, sham, Day 1, femur

value: sham

value: Day 1


title: RB036_heart

description: Library name: RB036_heart


title: wt,  10DAG, H3K27me1, Rep2

value: wt


title: N2 ChIP-seq, H2KA119ub, replicate 1

description: Not spike-in scaled

value: whole animal

tag: strain

value: Wild-type

value: mixed embryo

value: anti-H2AK119ub rabbit monoclonal D27C4, 8240; Cell Signaling Technology

value: N2 ChIP-seq, input, replicate 1


title: RB035_heart

description: Library name: RB035_heart

value: WT


title: RB033_heart

description: Library name: RB033_heart

value: control


title: wt,  10DAG, input, Rep2

value: seedling

value: 10 DAG

tag: chip antibody


title: HSPCs, mdf3, RNA-seq

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline
RNA-Seq: Clean sequenced reads were alignmented to mm10 by HISAT2 (2.0.5) with default parameters. Alignmented SAM files were handled using samtools (1.7). Aligned reads were extracted by HTSeq (0.9.1) with default parameters. scRNA-seq: STAR v2.6.1a (Ref) to map reads to the reference genome GRCh38 (ensembl version 92 annotation)/ GRCm38 (ensembl version 92 annotation).UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref) software, and used to generate expression matrix files for subsequent analysis
Assembly: mm10 for RNA-seq and scRNA-seq,hg38 for scRNA-seq
Supplementary files format and content: FPKM were calculated by R script, and differential genes were generated by R package Deseq2 (1.22.2).For cell clustering and annotation, the R package Seurat (v.3.2.0) was utilized.

source_name: Bone Marrow

extract_protocol:
scRNA-seq were performed with Lin- c-Kit+ HSPCs from Mx1-Cre+ wild-type (WT), Mx1-Cre+ Srsf2P95H/+, Mx1-Cre+ Setd2fl/fl Srsf2P95H/+ mice bone marrow at 4 weeks post pIpC induction in BMT model.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) according to the manufacturer’s recommendations. RNA-Seq: mRNA libraries were sequenced with Illumina NovaSeq 6000.

value: Bone Marrow

value: HSPCs

value: Setd2 knockout and Srsf2 mutated


title: RB034_heart

description: Library name: RB034_heart

value: heart

value: Male


title: wt,  10DAG, H3K27me1,  Rep1

value: H3K27me1 (Millipore #07-448)


title: Sample_3 neutrophils, mice, SAH, Day 3, Femur

value: Femur

value: Neutrophils from Femur

value: SAH

value: Day 3


title: HSPCs, mdf1, RNA-seq


title: bmi1abc/ref6, 10DAG, H3K27me3, Rep2

value: H3K27me3 (Millipore #07-449)


title: RB030_heart

description: Library name: RB030_heart


title: RB031_heart

description: Library name: RB031_heart


title: HSPCs, mdf2, RNA-seq


title: RB038_kidney

description: Library name: RB038_kidney

source_name: Kidney

value: Kidney

value: Maresin 1


title: RB037_kidney

description: Library name: RB037_kidney

value: WT


title: HSPCs, mf3, RNA-seq

value: Srsf2 mutated


title: RB039_kidney

description: Library name: RB039_kidney


title: HSPCs, mf2, RNA-seq


title: RB038_heart

description: Library name: RB038_heart


title: bmi1abc/ref6, 10DAG, input

value: seedling


title: HSPCs, mf1, RNA-seq


title: bmi1abc/ref6, 10DAG, H3K27me3, Rep1

value: 10 DAG


title: RB033_kidney

description: Library name: RB033_kidney

value: control


title: RB034_kidney

description: Library name: RB034_kidney


title: HSPCs, md2, RNA-seq

value: Bone Marrow

value: HSPCs

value: Setd2 knockout


title: wt, 10DAG, HTA9, Rep2

value: wt

value: HTA9 (this study)


title: RB036_kidney

description: Library name: RB036_kidney

value: Male


title: RB035_kidney

description: Library name: RB035_kidney


title: wt, 10DAG, HTA9, Rep1


title: RB032_heart

description: Library name: RB032_heart

value: heart


title: RB031_kidney

description: Library name: RB031_kidney


title: RB032_kidney

description: Library name: RB032_kidney


title: CD8+ T cells in MC38 tumor, ADT

city: Kyoto

first: Kenji

last: Chamoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

description:
Library name: Sample3
10x Genomics

library_source: other

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1.
Assembly: GRCm39
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: feature_reference.csv
Supplementary files format and content: filtered_contig_annotations.csv
Supplementary files format and content: multi.csv
Library strategy: CITE-seq

molecule: protein

source_name: Tumor

extract_protocol:
Tumor sample from MC38 tumor-bearing mice (n=20 mice) on day14 were pooled and digested. From the tumor digestions, CD8+ TILs were enriched by Manual MACS Magnetic Separators according to the manufacturer’s instructions. They were subsequently stained with appropriately diluted MitoTracker Deep Red and MitoTracker Green for 30 minutes in a 37 °C CO2 incubator. After washing with 2% FCS in PBS twice, cells were stained with Zombie Violet and Fc-blocked by anti-CD16/32 antibody, and then stained with a mixture of appropriately diluted fluorescent-labeled and oligo-conjugated antibodies targeting cell surface antigens for 12 minutes at 4°C. Cells were washed with 2% FCS in PBS twice, filtered through a 40-μm cell strainer before sorting. Viable single PD1- CD45.2+ CD8a+ cells and D1, D2, D3 subsets of PD1+ CD45.2+ CD8a+ cells were sorted using FACSMelody. To identify each subset in scRNA-seq, the sorted cells’ Fc receptor was blocked by anti-CD16/32 antibody and stained with oligonucleotide-labelled Hashatag 1 antibody for PD1− population, Hashtag 4 antibody for D1, Hashtag 5 antibody for D2 and Hashtag 6 antibody for D3. After incubation for 30 minutes at 4 °C, each cell subsets were washed three times with 2% FCS in PBS and pooled.
Library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2, 10x Genomics). Briefly, pooled samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel bead-in-emulsions (GEMs). Inside the GEMs, mRNA was reverse-transcribed into barcoded cDNA. Barcoded antibody-derived tags (ADTs) from the cell surface were also captured and reverse-transcribed in parallel. During this reverse transcription step, the Illumina Read 1 (R1) primer binding site was incorporated into both cDNA and ADT sequences. After breaking the emulsions, the pooled barcoded cDNA and ADTs were purified using Silane DynaBeads, followed by PCR amplification. Size selection was then performed using SPRIselect reagent to isolate cDNA and ADT fragments of appropriate lengths for downstream library preparation, including TCR profiling (V(D)J), gene expression (GEX), and cell surface protein tags. During library construction, Illumina R2 primer binding sites, paired-end adapter sequences (P5 and P7), and sample indices were added to enable multiplexed paired-end sequencing on an Illumina platform.

value: Tumor

value: CD8+ T cells

value: No

tag: library type

value: ADT


title: CD8+ T cells in MC38 tumor, GEX

description:
Library name: Sample2
10x Genomics

value: GEX


title: wt, 10DAG, input, Rep1


title: HSPCs, md1, RNA-seq


title: HSPCs, mx2, RNA-seq

value: WT


title: wt, 48HAI, H3K27me3, Rep2

source_name: imbibbed seed

value: imbibed seed

value: 48 HAI

value: H3K27me3 (Millipore #07-449)


title: RB030_kidney

description: Library name: RB030_kidney

value: Kidney

value: control


title: CD8+ T cells in MC38 tumor, VDJ

description:
Library name: Sample1
10x Genomics

value: VDJ


title: HSPCs, mx1, RNA-seq

value: Bone Marrow

value: HSPCs


title: wt, 48HAI, H3K27me3,  Rep1

value: wt


title: ESC, CEBPa induced, 24h, clone 1, input

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_Bulk_24h_Input

data_processing:
Raw reads were trimmed using TrimGalore (Cutadapt version 0.4.2_dev). Reads were then aligned to the mm10 genome using bowtie2 (version 2.2.4) with default parameters. Samtools (version 1.9) were used to convert sam files to bam files which were then sorted and indexed using samtools view, sort, and index respectively. Non-primary and supplementary alignments, alongside reads with a MAPQ < 10 were filtered out using the samtools view -F 2304 -b -q 10 command. Read duplicates were detected and removed via the MarkDuplicates command of Picard-tools (https://broadinstitute.github.io/picard/, version 2.3.0). Deeptools bamCoverage (version 3.0.1) was employed to generate bigwig track files for visualization with the following options used:
binSize 1 normalizeUsing RPKM effectiveGenomeSize 2150570000 extendReads 147.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
For chromatin immunoprecipitations, 10 million cells were collected and crosslinked in 1% formaldehyde under rotation for 10 min, followed by glycine-mediated quenching. After the centrifuge, the cell pellet was re-suspended in SDS lysis buffer for 15 min and sonicated for 18 cycles of 30 sec on, and 30 sec off using the Bioruptor Pico (Diagenode). The supernatant was incubated with protein A magnetic beads (10002D, Invitrogen) pre-coupled with CEBPa antibody (8718, Cell Signaling) at 4℃ overnight. The next day, DNA was collected after sequentially washing and elution, followed by Proteinase K treatment and de-crosslinking.
Libraries were prepared using the DNA Library Prep for Illumina kit (E7370, NEB) and amplified by Multiplex Oligos for Illumina kit (E6440, E6442, E6444, E6446, NEB). Libraries were sequenced on the NextSeq2000 instrument (Illumina), obtaining at least 40 million reads per sample.

value: ESCs expressing CEBPa-ERT2

value: tamoxifen


title: wt, 48HAI, input


title: ESC, CEBPa induced, 24h, sorted SSEA1-, clone 2

description: Library name: CEBPa_ChIP_CEBPaER_Clone2_SSEA1_Low_24h