title: JGE07 (20 ug/mL dose)_rep3

description: Library name: T_9-3-3

value: extraction -> mix of Ethanol extracts of JGT (JGE07;20 ug/mL dose)_rep3


title: E2_HH2_AP_05

status: Public on Oct 24 2025

type: SRA

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

country: USA

institute: Boston Children's Hospital

description: Tomo-seq library

library_source: transcriptomic

data_processing:
Trimming of adapter sequences and poly(A) tails was performed using BBDuk (version 38.93)
Bam alignment files were indexed using samtools (version 1.10) and reads were counted with htseq-count (version 0.13.5) using a GTF file containing chicken gene annotations
Assembly: galGal6
Supplementary files format and content: raw counts for all the libraries, including the two AP replicates, the LR replicate, and the HH1-3 libraries

molecule: total RNA

organism: Gallus gallus

source_name: AP embryo #HH2E2

growth_protocol: Gastrula stage chicken embryos were obtained from fertilized eggs, dissected in Ringers solution, prepared for cryosectioning in O.C.T.

extract_protocol:
Total RNA for each section  was extracted with the kit RNAqueous®-Micro Kit (ThermoFisher #AM1931) following the manufacturers recommendations.
The RNA-seq libraries were prepared with the kit QuantSeq 3'mRNA-seq Library Prep Kit (FWD) for Illumina (Lexogen #K01596), following the manufacturers recommendations  for low input samples.
3'RNA-seq libraries

treatment_protocol: HH5 chicken embryos were cryosectioned into 100um sections following its antero-posterior or left-right axis. HH1, HH2 and HH3 embryos were hand dissected into equally distributed antero-posterior sections. Each section was collected for RNA extraction.

tag: developmental stage

tag: axis

value: antero-posterior

tag: tissue

value: embryo


title: MCTS1-V5 40S Sel-TCP-seq replicate 1

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

description: Library name: Sample 43

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts for each sample

organism: Homo sapiens

growth_protocol: HEK293T cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
RNA-seq extract protocol Total RNA was extracted from cell lysates with the use of a PureLink RNA Mini Kit (Thermo Fisher Scientific), and the quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent). Ribo-seq extract protocol cells were seeded at a density of 3.0 × 106 per 10-cm dish and cultured overnight to ensure subconfluence. The culture medium was removed, and the cells were immediately placed on ice, washed once with ice-cold PBS, and lysed with a lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 1% Triton X-100, and EDTA-free protease inhibitor cocktail] supplemented with cycloheximide (100 μg/ml). The lysates were incubated on ice for 10 min with TURBO DNase (Thermo Fisher Scientific) and then centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected, assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion [containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM dithiothreitol, and 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs. The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). Sel-TCP-seq extract protocol Cells were seeded at a density of 1.0 × 107 cells per 15-cm dish, with 8 dishes per assay, and were cultured overnight. The subconfluent cells were treated for 15 min at room temperature with crosslinking buffer [PBS containing 0.025% formaldehyde, 0.5 mM dithiobis(succinimidyl propionate) (DSP), 10 mM MgCl2, and 100 μg/ml cycloheximide], after which glycine was added to a final concentration of 125 mM and the cells were collected. The cells were washed twice with ice-cold PBS, lysed in a lysis buffer [50 mM HEPES-KOH (pH 7.5), 200 mM KCl, 10 mM MgCl2, 1% NP40, 100 μg/ml cycloheximide and cOmplete EDTA-free protease inhibitor cocktail (Roche)], and incubated for 10 min on ice. The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected, quantified for RNA concentration with a use of Nanodrop spectrophotometer (Thermo Fisher Scientific), incubated with RNase I (100 U per 120 μg of RNA, Thermo Fisher Scientific) at 5 min on ice. The samples were immediately loaded on a 15% to 50% sucrose gradient [containing 20 mM Tris-HCl (pH 7.5), 160 mM KCl, and 10 mM MgCl2] and centrifuged at 35,000 rpm (210,000 × g) for 5 h at 4°C in a SW41Ti rotor. The gradient was fractionated with the use of a TRIAX gradient-profiling system and AC-5700P microcollector. Polysome profiles were determined by measurement of absorbance at 260 nm. Dynabeads Protein G were conjugated with antibodies to V5 by incubation overnight at 4°C in lysis buffer supplemented with 0.5% bovine serum albumin, and they were washed three times with lysis buffer before use. Small portions of the 40S fractions were stored for TCP-seq, and the remaining samples were incubated with the beads for 90 min at 4°C for Sel-TCP-seq. The resulting immunoprecipitates were washed four times with a lysis buffer. 250 μl of de-crosslinking buffer [1% SDS, 10 mM EDTA, 10 mM Tris-HCl (pH 7.5), 5 mM DTT and 10 mM glycine], 750 μl of ISOGEN LS (Nippon Gene), and 200 μl of chloroform were added to the beads (Sel-TCP-seq) or 40S fractions (TCP-seq), which were then incubated for 45 min at 65°C before purification of RNA by precipitation with isopropanol.
RNA-seq library construction protocol For RNA-seq, after mRNA selection with the use of a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), libraries were prepared with the use of a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). For 3′ mRNA-seq, libraries were prepared from 1µg of the purified total RNA with the use of QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with UDI 12nt Set A1 for Illumina platform (Cat no.191.96, LEXOGEN). 16 cycles of PCR were used to amplify the library. The libraries were sequenced with a NovaSeq 6000 system (Novogene Japan). Ribo-seq library construction protocol The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina). Sel-TCP-seq library construction protcol Purified RNA was selected according to size in the range of 17 to 100 nt by electrophoresis in a 15% polyacrylamide and TBE-urea gel, and was then subjected to dephosphorylation, DNA linker ligation, and rRNA depletion with RiboZero Gold as described for the Ribo-seq protocol. RT was performed with the use of the SI-019 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The second linker (SI-018) was ligated by incubation overnight at 25°C with T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (New England Biolabs). The products were then amplified by PCR with the same primers as used for the Ribo-seq protocol, and those of the desired size were purified by electrophoresis through a 15% polyacrylamide nondenaturing gel. The libraries were sequenced with a NovaSeq 6000 system.

tag: cell line


title: JGE07 (500 ug/mL dose)_rep3

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: Library name: T_9-3-1

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 Rn6 Gene Transfer Format (GTF) file from UCSC browser
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: HEPG2 cells (ATCC HB-8065) were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S). Cultures were incubated at 37 °C in a humidified atmosphere with 5% CO2.

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: cell type

value: Hepatocyte

tag: treatment

value: extraction -> mix of Ethanol extracts of JGT (JGE07;500 ug/mL dose)_rep2


title: E2_HH2_AP_04

description: Tomo-seq library


title: eIF2D-V5 40S Sel-TCP-seq replicate 2

description: Library name: Sample 42


title: JGW04 (500 ug/mL dose)_rep1

description: Library name: T_3-1-4

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 Rn6 Gene Transfer Format (GTF) file from UCSC browser
Assembly: Rn6
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Rattus norvegicus

growth_protocol: PC12 cells (ATCC CRL-1721) were cultured on 100mm collagen I-coated culture dish (Coning BioCoat, Corning Inc., NY, USA) in DMEM containing 10% heat-inactivated horse serum (HS), 5% non-heat-inactivated FBS, and 1% P/S. For neuronal differentiation, cells were seeded onto collagen IV-coated multi-well plates (Coning BioCoat) and induced using differentiation medium (DM) composed of DMEM, 0.5% FBS, 100 ng/mL nerve growth factor (NGF; R&D systems, Minneapolis, MN, USA), 1% N2 plus media supplement (R&D systems), and 1% P/S. Media were partially exchanged on days 3 and 6 of differentiation, and neuronal morphology was monitored under phase-contrast microscopy (IX71, Olympus Corporation, Tokyo, Japan).

treatment_protocol: Drug treatment was conducted following IC20 determination using the WST-8 cell viability assay (Biomax, Guri, Republic of Korea). Each JGT extract prepared using hot water (JGW) or 70% ethanol (JGE) was tested at a maximum concentration of 500 μg/mL on  PC12

value: neuronal cell

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


title: eIF2D-V5 40S Sel-TCP-seq replicate 1

description: Library name: Sample 41


title: E2_HH2_AP_03

description: Tomo-seq library


title: JGE08 (100 ug/mL dose)_rep2

description: Library name: T_9-2-5

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep2


title: JGW02 (20 ug/mL dose)_rep3

description: Library name: T_2-3-6

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


title: JGE08 (500 ug/mL dose)_rep2

description: Library name: T_9-2-4

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep2


title: JGE08 (100 ug/mL dose)_rep3

description: Library name: T_9-3-5

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep3


title: E2_HH2_AP_02

description: Tomo-seq library


title: MCTS1 KO HEK293T #2 TCP-seq replicate 1

description: Library name: Sample 39


title: E1_HH3_AP_02

description: Tomo-seq library

source_name: AP embryo #HH3E1


title: JGW02 (500 ug/mL dose)_rep3

description: Library name: T_2-3-4

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


title: E2_HH2_AP_01

description: Tomo-seq library


title: MCTS1-V5 40S Sel-TCP-seq replicate 2

description: Library name: Sample 44


title: JGE07 (20 ug/mL dose)_rep2

description: Library name: T_9-2-3

value: extraction -> mix of Ethanol extracts of JGT (JGE07;20 ug/mL dose)_rep2


title: JGW02 (100 ug/mL dose)_rep3

description: Library name: T_2-3-5

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


title: JGE07 (100 ug/mL dose)_rep2

description: Library name: T_9-2-2

value: extraction -> mix of Ethanol extracts of JGT (JGE07;100 ug/mL dose)_rep2


title: JGW01 (20 ug/mL dose)_rep3

description: Library name: T_2-3-3

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


title: E1_HH2_AP_05

description: Tomo-seq library

source_name: AP embryo #HH2E1


title: MCTS1 KO HEK293T #1 TCP-seq replicate 1

description: Library name: Sample 37


title: E1_HH2_AP_04

description: Tomo-seq library


title: JGE07 (500 ug/mL dose)_rep2

description: Library name: T_9-2-1


title: JGE08 (20 ug/mL dose)_rep1

description: Library name: T_9-1-6

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep1


title: WT HEK293T TCP-seq replicate 4

description: Library name: Sample 36


title: JGW01 (500 ug/mL dose)_rep3

description: Library name: T_2-3-1

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


title: E1_HH2_AP_03

description: Tomo-seq library

value: antero-posterior


title: MCTS1 KO HEK293T #2 TCP-seq replicate 2

description: Library name: Sample 40


title: JGE08 (100 ug/mL dose)_rep1

description: Library name: T_9-1-5

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep1


title: JGE08 (500 ug/mL dose)_rep1

description: Library name: T_9-1-4

value: Hepatocyte

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep1


title: JGW02 (100 ug/mL dose)_rep2

description: Library name: T_2-2-5

value: neuronal cell

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


title: E1_HH2_AP_01

description: Tomo-seq library

value: embryo


title: eIF2D KO HEK293T #2 TCP-seq replicate 2

description: Library name: Sample 34


title: E1_HH2_AP_02

description: Tomo-seq library


title: eIF2D KO HEK293T #2 TCP-seq replicate 1

description: Library name: Sample 33


title: JGE07 (20 ug/mL dose)_rep1

description: Library name: T_9-1-3

value: extraction -> mix of Ethanol extracts of JGT (JGE07;20 ug/mL dose)_rep1


title: JGE07 (100 ug/mL dose)_rep1

description: Library name: T_9-1-2

value: extraction -> mix of Ethanol extracts of JGT (JGE07;100 ug/mL dose)_rep1


title: E2_HH1_AP_05

description: Tomo-seq library

source_name: AP embryo #HH1E2


title: JGW01 (20 ug/mL dose)_rep2

description: Library name: T_2-2-3

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


title: JGE07 (500 ug/mL dose)_rep1

description: Library name: T_9-1-1

value: extraction -> mix of Ethanol extracts of JGT (JGE07;500 ug/mL dose)_rep1


title: JGW01 (100 ug/mL dose)_rep2

description: Library name: T_2-2-2

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


title: eIF2D KO HEK293T #1 TCP-seq replicate 1

description: Library name: Sample 31


title: JGW01 (100 ug/mL dose)_rep3

description: Library name: T_2-3-2

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


title: MCTS1 KO HEK293T #1 TCP-seq replicate 2

description: Library name: Sample 38


title: E2_HH1_AP_04

description: Tomo-seq library


title: eIF2D KO HEK293T #1 TCP-seq replicate 2

description: Library name: Sample 32


title: E2_HH1_AP_03

description: Tomo-seq library


title: WT HEK293T TCP-seq replicate 2

description: Library name: Sample 30


title: JGE06 (20 ug/mL dose)_rep3

description: Library name: T_8-3-6

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep3


title: JGW01 (500 ug/mL dose)_rep2

description: Library name: T_2-2-1

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


title: JGW02 (20 ug/mL dose)_rep1

description: Library name: T_2-1-6

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


title: JGE06 (100 ug/mL dose)_rep3

description: Library name: T_8-3-5

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep3


title: E2_HH1_AP_02

description: Tomo-seq library

value: antero-posterior


title: WT HEK293T TCP-seq replicate 3

description: Library name: Sample 35


title: JGW02 (500 ug/mL dose)_rep2

description: Library name: T_2-2-4

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


title: E2_HH1_AP_01

description: Tomo-seq library


title: WT HEK293T TCP-seq replicate 1

description: Library name: Sample 29


title: JGE06 (500 ug/mL dose)_rep3

description: Library name: T_8-3-4

value: Hepatocyte

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep3


title: JGW02 (20 ug/mL dose)_rep2

description: Library name: T_2-2-6

value: neuronal cell

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


title: siDENR HEK293T #2 RNA-seq replicate 2

description: Library name: Sample 28

molecule: polyA RNA


title: JGW02 (100 ug/mL dose)_rep1

description: Library name: T_2-1-5

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


title: E1_HH1_AP_05

description: Tomo-seq library

source_name: AP embryo #HH1E1

value: embryo


title: JGW02 (500 ug/mL dose)_rep1

description: Library name: T_2-1-4

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


title: E1_HH1_AP_04

description: Tomo-seq library


title: siDENR HEK293T #2 RNA-seq replicate 1

description: Library name: Sample 27


title: JGE05 (100 ug/mL dose)_rep3

description: Library name: T_8-3-2

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;100 ug/mL dose)_rep3


title: siDENR HEK293T #2 Ribo-seq replicate 2

description: Library name: Sample 26

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts for each sample
Library strategy: Ribo-Seq


title: JGW01 (20 ug/mL dose)_rep1

description: Library name: T_2-1-3

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


title: JGE05 (500 ug/mL dose)_rep3

description: Library name: T_8-3-1

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;500 ug/mL dose)_rep3


title: JGW01 (100 ug/mL dose)_rep1

description: Library name: T_2-1-2

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


title: siDENR HEK293T #2 Ribo-seq replicate 1

description: Library name: Sample 25


title: E1_HH1_AP_02

description: Tomo-seq library


title: JGE06 (20 ug/mL dose)_rep2

description: Library name: T_8-2-6

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep2


title: siDENR HEK293T #1 RNA-seq replicate 2

description: Library name: Sample 24


title: JGW01 (500 ug/mL dose)_rep1

description: Library name: T_2-1-1

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


title: E1_HH1_AP_01

description: Tomo-seq library


title: JGE06 (100 ug/mL dose)_rep2

description: Library name: T_8-2-5

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep2


title: Aspirin_rep3

description: Library name: T_1-3-6


title: siDENR HEK293T #1 RNA-seq replicate 1

description: Library name: Sample 23


title: E1_LR_36

description: Tomo-seq library

source_name: LR embryo #E1

value: left-right


title: JGE05 (20 ug/mL dose)_rep3

description: Library name: T_8-3-3

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;20 ug/mL dose)_rep3


title: E1_LR_35

description: Tomo-seq library


title: Duloxetine_rep3

description: Library name: T_1-3-5


title: JGE05 (20 ug/mL dose)_rep2

description: Library name: T_8-2-3

value: mix-> extraction of Ethanol extracts of  Gamcho(GR)(JGE05;20 ug/mL dose)_rep2


title: E1_LR_34

description: Tomo-seq library


title: JGE06 (500 ug/mL dose)_rep2

description: Library name: T_8-2-4

value: Hepatocyte

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep2


title: Resveratrol_rep3

description: Library name: T_1-3-4

value: neuronal cell


title: siDENR HEK293T #1 Ribo-seq replicate 1

description: Library name: Sample 21


title: siDENR HEK293T #1 Ribo-seq replicate 2

description: Library name: Sample 22


title: siControl HEK293T RNA-seq replicate #2

description: Library name: Sample 20


title: JGE05 (100 ug/mL dose)_rep2

description: Library name: T_8-2-2

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;100 ug/mL dose)_rep2


title: E1_LR_33

description: Tomo-seq library


title: JGE05 (500 ug/mL dose)_rep2

description: Library name: T_8-2-1

value: mix-> extraction of Ethanol extracts of Gamcho(GR) (JGE05;500 ug/mL dose)_rep2


title: E1_HH1_AP_03

description: Tomo-seq library

value: antero-posterior

value: embryo


title: Amifostine_rep3

description: Library name: T_1-3-3


title: Non-treat(N.T)_rep3

description: Library name: T_1-3-1


title: E1_LR_32

description: Tomo-seq library


title: JGE06 (20 ug/mL dose)_rep1

description: Library name: T_8-1-6

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep1


title: siControl HEK293T Ribo-seq replicate #2

description: Library name: Sample 18


title: E1_LR_31

description: Tomo-seq library


title: JGE06 (100 ug/mL dose)_rep1

description: Library name: T_8-1-5

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep1


title: siControl HEK293T Ribo-seq replicate #1

description: Library name: Sample 17


title: Aspirin_rep2

description: Library name: T_1-2-6


title: E1_LR_30

description: Tomo-seq library


title: Duloxetine_rep2

description: Library name: T_1-2-5


title: JGE06 (500 ug/mL dose)_rep1

description: Library name: T_8-1-4

value: extraction -> mix of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep1


title: Resveratrol_rep2

description: Library name: T_1-2-4


title: MCTS1 KO HEK293T #2 RNA-seq replicate 2

description: Library name: Sample 16


title: MCTS1 KO HEK293T #2 RNA-seq replicate 1

description: Library name: Sample 15


title: JGE05 (20 ug/mL dose)_rep1

description: Library name: T_8-1-3

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;20 ug/mL dose)_rep1


title: JGE05 (100 ug/mL dose)_rep1

description: Library name: T_8-1-2

value: mix-> extraction of Ethanol extracts of  Gamcho(GR) (JGE05;100 ug/mL dose)_rep1


title: Non-treat(N.T)_rep2

description: Library name: T_1-2-1


title: siControl HEK293T RNA-seq replicate #1

description: Library name: Sample 19


title: JGE05 (500 ug/mL dose)_rep1

description: Library name: T_8-1-1

value: mix-> extraction of Ethanol extracts of Gamcho(GR) (JGE05;500 ug/mL dose)_rep1


title: E1_LR_26

description: Tomo-seq library


title: E1_LR_27

description: Tomo-seq library


title: MCTS1 KO HEK293T #2 Ribo-seq replicate 2

description: Library name: Sample 14


title: MCTS1 KO HEK293T #2 Ribo-seq replicate 1

description: Library name: Sample 13


title: JGE04 (20 ug/mL dose)_rep3

description: Library name: T_7-3-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep3


title: Aspirin_rep1

description: Library name: T_1-1-6


title: E1_LR_25

description: Tomo-seq library

value: left-right


title: JGE04 (100 ug/mL dose)_rep3

description: Library name: T_7-3-5

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep3


title: MCTS1 KO HEK293T #1 RNA-seq replicate 2

description: Library name: Sample 8


title: Duloxetine_rep1

description: Library name: T_1-1-5


title: MCTS1 KO HEK293T #1 RNA-seq replicate 1

description: Library name: Sample 7


title: Resveratrol_rep1

description: Library name: T_1-1-4


title: E1_LR_24

description: Tomo-seq library


title: JGE04 (500 ug/mL dose)_rep3

description: Library name: T_7-3-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep3


title: E1_LR_23

description: Tomo-seq library


title: JGE03 (20 ug/mL dose)_rep3

description: Library name: T_7-3-3

value: Hepatocyte

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep3


title: MCTS1 KO HEK293T #1 Ribo-seq replicate 2

description: Library name: Sample 6


title: E1_LR_28

description: Tomo-seq library


title: Amifostine_rep1

description: Library name: T_1-1-3

value: neuronal cell


title: Non-treat(N.T)_rep1

description: Library name: T_1-1-1


title: E1_LR_22

description: Tomo-seq library


title: Amifostine_rep2

description: Library name: T_1-2-3


title: E1_LR_29

description: Tomo-seq library


title: WT HEK293T RNA-seq replicate #2

description: Library name: Sample 4


title: HEK293_SOD1 OE_3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 32, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: kidney

growth_protocol: HEK293 cells (Cat# CRL-1573, ATCC) were maintained with DMEM (high glucose) (Cat# 6429-500ML, Sigma-Aldrich) containing 10% fetal bovine serum (Cat# 172012-500ML, Sigma-Aldrich) and 1% penicillin–streptomycin (Sigma-Aldrich, Cat# P4333-100ML). For cell passaging, HEK293 cells were treated with TrypLE Select Enzyme for 5 min at 37°C.

extract_protocol:
Total RNA was isolated from human respiratory organoids using ISOGENE (Cat# 319-90211, NIPPON GENE).
Library preparation was performed using an Illumina Stranded mRNA Prep Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions.

treatment_protocol: The plasmid vector was transfected into HEK293 cells using PEI Max (Cat# 24765-1, Polysciences).

value: kidney

value: Human embryonic kidney cells

tag: genotype

value: wild type

value: transfection of SOD1


title: JGE03 (100 ug/mL dose)_rep3

description: Library name: T_7-3-2

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep3


title: E1_LR_21

description: Tomo-seq library

value: embryo


title: JGE03 (500 ug/mL dose)_rep3

description: Library name: T_7-3-1

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep3


title: WT HEK293T RNA-seq replicate #1

description: Library name: Sample 3


title: HEK293_SOD1 OE_2


title: HEK293_SOD1 OE_1


title: JGE04 (100 ug/mL dose)_rep2

description: Library name: T_7-2-5

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep2


title: E1_LR_19

description: Tomo-seq library


title: JGE04 (20 ug/mL dose)_rep2

description: Library name: T_7-2-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep2


title: WT HEK293T Ribo-seq replicate #1

description: Library name: Sample 1


title: HEK293_clade IIb OPG175 OE_3

value: transfection of clade IIb OPG175


title: E1_LR_18

description: Tomo-seq library


title: JGE04 (500 ug/mL dose)_rep2

description: Library name: T_7-2-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep2


title: HEK293_clade IIb OPG175 OE_2


title: E1_LR_17

description: Tomo-seq library

value: left-right


title: 162200380CP

city: Guangzhou

first: Shaohua

last: Qu

state: Guangdong

address: No. 613, Huangpu West Avenue, Tianhe District, Guangzhou, Guangdong, P.R. China

country: China

institute: Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: GRCh38
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: normal tissue

extract_protocol:
The fresh breast tissue samples that from the breast cancer patients were collected and rapidly frozen in liquid nitrogen, and then stored in a -80 ℃ refrigerator. After the tissues were homogenized, total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries  for lncRNA-seq were prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reversetranscribed using fragmented RNA and dNTPs . RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments,sequencing adaptors were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR.

value: breast tissue


title: HEK293_clade IIb OPG175 OE_1


title: E1_LR_16

description: Tomo-seq library


title: JGE03 (500 ug/mL dose)_rep2

description: Library name: T_7-2-1

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep2


title: HEK293_clade I OPG175 OE_3

value: transfection of clade I OPG175


title: 162200350CP


title: 1622003500C

source_name: cancer tissue


title: MCTS1 KO HEK293T #1 Ribo-seq replicate 1

description: Library name: Sample 5


title: JGE03 (20 ug/mL dose)_rep2

description: Library name: T_7-2-3

value: Hepatocyte

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep2


title: E1_LR_20

description: Tomo-seq library


title: E1_LR_15

description: Tomo-seq library


title: HEK293_clade I OPG175 OE_2

value: kidney


title: WT HEK293T Ribo-seq replicate #2

description: Library name: Sample 2


title: E1_LR_14

description: Tomo-seq library


title: 162100370CP


title: JGE04 (20 ug/mL dose)_rep1

description: Library name: T_7-1-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep1


title: E1_LR_13

description: Tomo-seq library


title: HEK293_clade I OPG175 OE_1

value: Human embryonic kidney cells

value: wild type


title: JGE04 (100 ug/mL dose)_rep1

description: Library name: T_7-1-5

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep1


title: HEK293_control OE_3

value: transfection of control plasmid


title: 1621003700C


title: E1_LR_12

description: Tomo-seq library

value: embryo


title: 162100290CP


title: 1622003800C


title: HEK293_control OE_2


title: JGE04 (500 ug/mL dose)_rep1

description: Library name: T_7-1-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep1


title: JGE03 (100 ug/mL dose)_rep2

description: Library name: T_7-2-2

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep2


title: 1621002900C


title: E1_LR_11

description: Tomo-seq library


title: JGE03 (20 ug/mL dose)_rep1

description: Library name: T_7-1-3

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep1


title: E1_LR_10

description: Tomo-seq library


title: JGE03 (100 ug/mL dose)_rep1

description: Library name: T_7-1-2

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep1


title: 162100220CP


title: HEK293_control OE_1


title: JGE03 (500 ug/mL dose)_rep1

description: Library name: T_7-1-1

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep1


title: 1621002200C

value: breast tissue


title: E1_LR_09

description: Tomo-seq library

value: left-right


title: Granta519Cas9,Ctrl, Hi-C

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: Library name: s02_210618_Granta519Cas9_ctrl_Arima_HiC

library_source: genomic

data_processing:
Raw reads for each HiC sample were processed with Juicer (version 1.5.6) to obtain putative interactions with default parameters.
Assembly: hg19
Supplementary files format and content: .hic formatted file for juicebox viewing of contact matrices

molecule: genomic DNA

extract_protocol:
Arima HiC kit used per manufacture’s instructions
Accel-NGS 2S Plus DNA library kit

value: Mantle Cell Lymphoma

value: Ctrl


title: E1_LR_07

description: Tomo-seq library


title: JGE02 (100 ug/mL dose)_rep3

description: Library name: T_6-3-5

value: Hepatocyte

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep3


title: JGE02 (20 ug/mL dose)_rep3

description: Library name: T_6-3-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep3


title: E1_LR_08

description: Tomo-seq library


title: Granta519EBF1KIcl27,24hWO,RNAseq,rep3

description: Library name: s09_240415_Granta519cl27_24hdTAGWO_RNAseq_lib3_S9_R1.fastq.gz

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly using STAR
Assembly: hg19
Supplementary files format and content: .bw formatted file for genome browser viewing

extract_protocol:
RNeasy Plus Micro Kit (Qiagen #74034)
SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Clontech cat# 634873)


title: Granta519EBF1KIcl27,24hWO,RNAseq,rep2

description: Library name: s08_240415_Granta519cl27_24hdTAGWO_RNAseq_lib2_S8_R1.fastq.gz


title: 1621001800C


title: E1_LR_06

description: Tomo-seq library


title: JGE02 (500 ug/mL dose)_rep3

description: Library name: T_6-3-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep3


title: memory CD4, nasal polyps, ATAC, patient2

city: Chiba-shi

first: Hiroyuki

last: Yagyu

state: Chiba

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

institute: Chiba University

data_processing:
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: hg38
Supplementary files format and content: bigWig

source_name: nasal polyps

extract_protocol:
Freshly obtained nasal polyps were immediately minced and incubated in RPMI 1640 medium containing 1 mg/ml collagenase, 0.5 mg/ml hyaluronidase, and 0.2 mg/ml DNase I (Sigma-Aldrich). After incubation, nasal polyp mononuclear cells were purified by density gradient centrifugation using Percoll solution (GE Healthcare). PBMCs were isolated from peripheral blood using Ficoll-Paque Plus solution (GE Healthcare). 5×10^4 cells were pelleted, washed with 50 μl 1× PBS, and lysed with 50 μl lysis buffer. The nuclei were re-suspended in a 40 μl transposition reaction with 2 μl Tn5 transposase (Illumina) to tag and fragment the accessible chromatin at 37 °C for 30 min.
Fragmented DNAs were purified using the QIAGEN MiniElute PCR Purification Kit and amplified using 8-10 PCR cycles based on the amplification curve. The libraries were sequenced on an Illumina NextSeq 500 and NovaSeq 6000 Sequencing System.

value: CD45RO+CD4+ T cells

value: nasal polyps

tag: Sex

value: male


title: E1_LR_05

description: Tomo-seq library

value: embryo


title: JGE01 (500 ug/mL dose)_rep3

description: Library name: T_6-3-1

value: mix-> extraction of Ethanol extracts of Jakyak (PR) (JGE01;500 ug/mL dose)_rep3


title: Granta519EBF1KIcl27,6hWO,RNAseq,rep3

description: Library name: s03_240415_Granta519cl27_6hdTAGWO_RNAseq_lib3_S3_R1.fastq.gz


title: E1_LR_04

description: Tomo-seq library


title: memory CD4, PBMCs, ATAC, patient2

source_name: PBMCs

value: PBMCs


title: Granta519EBF1KIcl27,24hWO,RNAseq,rep1

description: Library name: s07_240415_Granta519cl27_24hdTAGWO_RNAseq_lib1_S7_R1.fastq.gz


title: Granta519EBF1KIcl27,6hWO,RNAseq,rep2

description: Library name: s02_240415_Granta519cl27_6hdTAGWO_RNAseq_lib2_S2_R1.fastq.gz


title: JGE02 (20 ug/mL dose)_rep2

description: Library name: T_6-2-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep2


title: Granta519Cas9,EBF1-KO, Hi-C

description: Library name: s03_210618_Granta519Cas9_EBF1g7_Arima_HiC


title: E1_LR_03

description: Tomo-seq library


title: JGE02 (100 ug/mL dose)_rep2

description: Library name: T_6-2-5

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep2


title: memory CD4, nasal polyps, ATAC, patient1


title: memory CD4, PBMCs, ATAC, patient1


title: Granta519EBF1KIcl27,6hWO,RNAseq,rep1

description: Library name: s01_240415_Granta519cl27_6hdTAGWO_RNAseq_lib1_S1_R1.fastq.gz


title: JGE02 (500 ug/mL dose)_rep2

description: Library name: T_6-2-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep2


title: 162100180CP

value: breast tissue


title: Granta519EBF1KIcl27,24hr,RNAseq,rep3

description: Library name: s24_221115_Granta519EBF1KI_cl27_24hr_RNAseq_rep3_S8_R1.fastq.gz


title: Human_ECRS_Polyp_3

library_source: transcriptomic single cell

data_processing:
Sequenced reads from all samples were processed and aggregated using the Cell Ranger (v6.1.1) pipeline with GRCm38 as a reference.
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Nasal polyps

extract_protocol:
The lungs were dissociated using digestion buffer in C-tube (Miltenyi Biotec). After 30 min at 37 °C, the samples were treated with final GentleMACS dissociation. Cell suspensions were passed through a 70-μm cell strainer. Lung mononuclear cells were separated using Percoll solution (GE Healthcare). CD4+ or CD45+ cells were stained and freshly isolated using a FACSAria III cell sorter (BD Biosciences). For human samples, Freshly obtained nasal polyps were immediately minced and incubated in RPMI 1640 medium containing 1 mg/ml collagenase, 0.5 mg/ml hyaluronidase, and 0.2 mg/ml DNase I (Sigma-Aldrich). After incubation, nasal polyp mononuclear cells were purified by density gradient centrifugation using Percoll solution (GE Healthcare). PBMCs were isolated from peripheral blood using Ficoll-Paque Plus solution (GE Healthcare). CD4+ T cells were stained and sorted using a FACSAria III cell sorter (BD).
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: CD4+ T cells

tag: diagnosis

value: ECRS

value: Nasal polyps

value: female


title: E1_LR_02

description: Tomo-seq library

value: left-right


title: E1_LR_01

description: Tomo-seq library


title: JGE01 (100 ug/mL dose)_rep2

description: Library name: T_6-2-2

value: Hepatocyte

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;100 ug/mL dose)_rep2


title: Human_ECRS_Polyp_2


title: Granta519EBF1KIcl27,24hr,RNAseq,rep2

description: Library name: s23_221115_Granta519EBF1KI_cl27_24hr_RNAseq_rep2_S7_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE01 (20 ug/mL dose)_rep2

description: Library name: T_6-2-3

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;20 ug/mL dose)_rep2


title: Human_ECRS_Polyp_1

value: male


title: Granta519EBF1KIcl27,24hr,RNAseq,rep1

description: Library name: s22_221115_Granta519EBF1KI_cl27_24hr_RNAseq_rep1_S6_R1.fastq.gz


title: E2_AP_54

description: Tomo-seq library

source_name: AP embryo #E2

value: antero-posterior

value: embryo


title: E2_AP_53

description: Tomo-seq library


title: Granta519EBF1KIcl27,6hr,RNAseq,rep2

description: Library name: s11_221115_Granta519EBF1KI_cl27_6hr_RNAseq_rep2_S3_R1.fastq.gz


title: E2_AP_52

description: Tomo-seq library


title: Human_ECRS_PBMC_2

value: PBMCs


title: Granta519EBF1KIcl27,6hr,RNAseq,rep3

description: Library name: s12_221115_Granta519EBF1KI_cl27_6hr_RNAseq_rep3_S4_R1.fastq.gz


title: E2_AP_51

description: Tomo-seq library


title: JGE02 (100 ug/mL dose)_rep1

description: Library name: T_6-1-5

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep1


title: JGE02 (20 ug/mL dose)_rep1

description: Library name: T_6-1-6

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep1


title: Granta519EBF1KIcl27,6hr,RNAseq,rep1

description: Library name: s10_221115_Granta519EBF1KI_cl27_6hr_RNAseq_rep1_S2_R1.fastq.gz


title: Human_ECRS_PBMC_1


title: E2_AP_50

description: Tomo-seq library


title: JGE02 (500 ug/mL dose)_rep1

description: Library name: T_6-1-4

value: mix-> extraction of Ethanol extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep1


title: bCat_Lef1_HH5_3_AP3

description: Library name: bCat_Lef1_HH5_3_AP3

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal6 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Assembly: galGal6
Supplementary files format and content: bigwigs
Library strategy: CUT&RUN

source_name: whole embryo

growth_protocol: Gastrula stage chicken embryos were obtained from fertilized eggs and dissected in Ringers solution

extract_protocol:
Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.

treatment_protocol: HH5 chicken embryos were hand dissected into equally distributed antero-posterior sections. Position matching sections from 5 embryos were pooled  for CUT&RUN and library preparation.

value: whole embryo

tag: section

tag: antibody


title: Granta519EBF1KIcl27,0hr,RNAseq,rep3

description: Library name: s09_221115_Granta519EBF1KI_cl27_0hr_RNAseq_rep3_S1_R1.fastq.gz

value: untreated


title: bCat_Lef1_HH5_3_AP2

description: Library name: bCat_Lef1_HH5_3_AP2


title: E2_AP_49

description: Tomo-seq library


title: JGE01 (20 ug/mL dose)_rep1

description: Library name: T_6-1-3

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;20 ug/mL dose)_rep1


title: Granta519EBF1KIcl27,0hr,RNAseq,rep2

description: Library name: s08_221115_Granta519EBF1KI_cl27_0hr_RNAseq_rep2_S8_R1.fastq.gz


title: bCat_Lef1_HH5_3_AP1

description: Library name: bCat_Lef1_HH5_3_AP1


title: E2_AP_48

description: Tomo-seq library


title: JGE01 (500 ug/mL dose)_rep1

description: Library name: T_6-1-1

value: mix-> extraction of Ethanol extracts of Jakyak (PR) (JGE01;500 ug/mL dose)_rep1


title: bCat_Lef1_HH5_2_AP3

description: Library name: bCat_Lef1_HH5_2_AP3


title: E2_AP_46

description: Tomo-seq library


title: Granta519EBF1KIcl26,24hr,RNAseq,rep3

description: Library name: s21_221115_Granta519EBF1KI_cl26_24hr_RNAseq_rep3_S5_R1.fastq.gz


title: JGE01 (500 ug/mL dose)_rep2

description: Library name: T_6-2-1

value: mix-> extraction of Ethanol extracts of Jakyak (PR) (JGE01;500 ug/mL dose)_rep2


title: E2_AP_47

description: Tomo-seq library


title: Human_ECRS_PBMC_3

value: CD4+ T cells

value: ECRS

value: female


title: bCat_Lef1_HH5_2_AP2

description: Library name: bCat_Lef1_HH5_2_AP2


title: Granta519EBF1KIcl27,0hr,RNAseq,rep1

description: Library name: s07_221115_Granta519EBF1KI_cl27_0hr_RNAseq_rep1_S7_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE01 (100 ug/mL dose)_rep1

description: Library name: T_6-1-2

value: Hepatocyte

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;100 ug/mL dose)_rep1


title: E2_AP_44

description: Tomo-seq library

value: antero-posterior


title: JGW08 (500 ug/mL dose)_rep3

description: Library name: T_5-3-4

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep3


title: Granta519EBF1KIcl26,24hr,RNAseq,rep2

description: Library name: s20_221115_Granta519EBF1KI_cl26_24hr_RNAseq_rep2_S4_R1.fastq.gz


title: JGW08 (100 ug/mL dose)_rep3

description: Library name: T_5-3-5

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep3


title: E2_AP_45

description: Tomo-seq library

value: embryo


title: bCat_Lef1_HH5_2_AP1

description: Library name: bCat_Lef1_HH5_2_AP1


title: JGW08 (20 ug/mL dose)_rep3

description: Library name: T_5-3-6

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep3


title: bCat_Lef1_HH3_3_AP3

description: Library name: bCat_Lef1_HH3_3_AP3


title: Granta519EBF1KIcl26,24hr,RNAseq,rep1

description: Library name: s19_221115_Granta519EBF1KI_cl26_24hr_RNAseq_rep1_S3_R1.fastq.gz


title: Granta519EBF1KIcl26,6hr,RNAseq,rep3

description: Library name: s06_221115_Granta519EBF1KI_cl26_6hr_RNAseq_rep3_S6_R1.fastq.gz


title: Granta519EBF1KIcl26,6hr,RNAseq,rep2

description: Library name: s05_221115_Granta519EBF1KI_cl26_6hr_RNAseq_rep2_S5_R1.fastq.gz


title: E2_AP_42

description: Tomo-seq library


title: JGW07 (100 ug/mL dose)_rep3

description: Library name: T_5-3-2

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep3


title: E2_AP_43

description: Tomo-seq library


title: bCat_Lef1_HH3_3_AP1

description: Library name: bCat_Lef1_HH3_3_AP1

value: whole embryo


title: Granta519EBF1KIcl26,6hr,RNAseq,rep1

description: Library name: s04_221115_Granta519EBF1KI_cl26_6hr_RNAseq_rep1_S4_R1.fastq.gz


title: JGW07 (500 ug/mL dose)_rep3

description: Library name: T_5-3-1

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep3


title: E2_AP_41

description: Tomo-seq library


title: bCat_Lef1_HH3_2_AP3

description: Library name: bCat_Lef1_HH3_2_AP3


title: Granta519EBF1KIcl26,0hr,RNAseq,rep3

description: Library name: s03_221115_Granta519EBF1KI_cl26_0hr_RNAseq_rep3_S3_R1.fastq.gz

value: untreated


title: E2_AP_40

description: Tomo-seq library


title: bCat_Lef1_HH3_2_AP2

description: Library name: bCat_Lef1_HH3_2_AP2


title: JGW08 (20 ug/mL dose)_rep2

description: Library name: T_5-2-6

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep2


title: Granta519EBF1KIcl26,0hr,RNAseq,rep2

description: Library name: s02_221115_Granta519EBF1KI_cl26_0hr_RNAseq_rep2_S2_R1.fastq.gz


title: E2_AP_39

description: Tomo-seq library


title: JGW08 (100 ug/mL dose)_rep2

description: Library name: T_5-2-5

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep2


title: bCat_Lef1_HH3_2_AP1

description: Library name: bCat_Lef1_HH3_2_AP1


title: Granta519EBF1KIcl26,0hr,RNAseq,rep1

description: Library name: s01_221115_Granta519EBF1KI_cl26_0hr_RNAseq_rep1_S1_R1.fastq.gz


title: JGW07 (20 ug/mL dose)_rep3

description: Library name: T_5-3-3

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep3


title: bCat_Lef1_HH3_AP3

description: Library name: bCat_Lef1_HH3_AP3


title: E2_AP_37

description: Tomo-seq library


title: Granta519Cas9,EBF1-KO, RNAseq, rep3

description: Library name: s12_210730_Granta519_EBF1g7_RNAseq_rep3_S12_R1.fastq.gz


title: bCat_Lef1_HH3_3_AP2

description: Library name: bCat_Lef1_HH3_3_AP2


title: bCat_Lef1_HH3_AP2

description: Library name: bCat_Lef1_HH3_AP2


title: Granta519Cas9,EBF1-KO, RNAseq, rep2

description: Library name: s11_210730_Granta519_EBF1g7_RNAseq_rep2_S11_R1.fastq.gz


title: E2_AP_36

description: Tomo-seq library


title: JGW07 (100 ug/mL dose)_rep2

description: Library name: T_5-2-2

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep2


title: bCat_Lef1_HH3_AP1

description: Library name: bCat_Lef1_HH3_AP1


title: Granta519Cas9,EBF1-KO, RNAseq, rep1

description: Library name: s10_210730_Granta519_EBF1g7_RNAseq_rep1_S10_R1.fastq.gz


title: E2_AP_35

description: Tomo-seq library


title: JGW07 (500 ug/mL dose)_rep2

description: Library name: T_5-2-1

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep2


title: G. sulfurreducens PCA, DB_C, biol rep 3

city: East Lansing

first: Morgen

last: Clark

state: Michigan

address: 567 Wilson Rd

department: Microbiology, Genetics, & Immunology

institute: Michigan State University

description:
Library name: Sample 6
Column name in counts_per_million_all_samples.xlsx: DB_C_CPM

data_processing:
bcl-convert (v4.2.4, Illumina) was used for demulitplexing, quality control, and adapter trimming
HISAT2 (v2.2.0) was used for read mapping
featureCounts (v2.0.1, Subread) was used for read quantification
In R4 (v4.0.2), reads were normalized using edgeR's (v1.14.5) Trimmed Means of M values (TMM)
The glmQLFTest in edgeR (v1.14.5) was used for differential expression analysis
Assembly: RefSeq: GCF_000007985.2
Supplementary files format and content: counts_per_million_all_samples.xlsx
Supplementary files format and content: raw_counts_all_samples.tsv

organism: Geobacter sulfurreducens

source_name: Geobacter sulfurreducens

growth_protocol: 10-mL cultures were grown at 35℃ to mid-exponential phase and transferred three times before harvesting from mid-exponential phase for RNA extraction

extract_protocol:
Transcription was stopped using 1mL of 5% water-saturated phenol in ethanol before RNA extraction using a Qiagen Rneasy kit
Libraries were prepared using Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) following the manufacturer's protocols.

treatment_protocol: NB or DB medium, both with 15 mM acetate and 40 mM fumarate

value: Geobacter sulfurreducens

tag: strain

value: PCA


title: E2_AP_34

description: Tomo-seq library


title: G. sulfurreducens PCA, DB_B, biol rep 2

description:
Library name: Sample 5
Column name in counts_per_million_all_samples.xlsx: DB_B_CPM


title: Granta519Cas9,Ctrl, RNAseq, rep2

description: Library name: s08_210730_Granta519_ctrl_RNAseq_rep2_S8_R1.fastq.gz

value: Mantle Cell Lymphoma

value: Ctrl


title: JGW08 (100 ug/mL dose)_rep1

description: Library name: T_5-1-5

value: Hepatocyte

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep1


title: E2_AP_33

description: Tomo-seq library

value: antero-posterior

value: embryo


title: Granta519Cas9,Ctrl, RNAseq, rep1

description: Library name: s07_210730_Granta519_ctrl_RNAseq_rep1_S7_R1.fastq.gz


title: E2_AP_32

description: Tomo-seq library


title: E2_AP_38

description: Tomo-seq library


title: JGW08 (500 ug/mL dose)_rep1

description: Library name: T_5-1-4

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep1


title: JGW08 (500 ug/mL dose)_rep2

description: Library name: T_5-2-4

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep2


title: JGW07 (20 ug/mL dose)_rep2

description: Library name: T_5-2-3

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep2


title: Granta519EBF1KIcl97,24hWO,RNAseq,rep3

description: Library name: s12_240415_Granta519cl97_24hdTAGWO_RNAseq_lib3_S12_R1.fastq.gz


title: G. sulfurreducens PCA, NB_C, biol rep 3

description:
Library name: Sample 3
Column name in counts_per_million_all_samples.xlsx: NB_C_CPM


title: G. sulfurreducens PCA, NB_B, biol rep 2

description:
Library name: Sample 2
Column name in counts_per_million_all_samples.xlsx: NB_B_CPM


title: E2_AP_31

description: Tomo-seq library


title: JGW07 (20 ug/mL dose)_rep1

description: Library name: T_5-1-3

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep1


title: E2_AP_30

description: Tomo-seq library


title: JGW07 (100 ug/mL dose)_rep1

description: Library name: T_5-1-2

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep1


title: G. sulfurreducens PCA, NB_A, biol rep 1

description:
Library name: Sample 1
Column name in counts_per_million_all_samples.xlsx: NB_A_CPM


title: E2_AP_29

description: Tomo-seq library


title: Granta519Cas9,Ctrl, RNAseq, rep3

description: Library name: s09_210730_Granta519_ctrl_RNAseq_rep3_S9_R1.fastq.gz


title: METTL3 KO Rescue with METTL3 human myoblast, DM6d, repeat2

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

institute: University of Georgia

description: Library name: METTL3RES_DM6d_2

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

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


title: Granta519EBF1KIcl97,6hWO,RNAseq,rep3

description: Library name: s06_240415_Granta519cl97_6hdTAGWO_RNAseq_lib3_S6_R1.fastq.gz


title: JGW07 (500 ug/mL dose)_rep1

description: Library name: T_5-1-1

value: extraction -> mix of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep1


title: JGW08 (20 ug/mL dose)_rep1

description: Library name: T_5-1-6

value: extraction -> mix of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep1


title: E2_AP_28

description: Tomo-seq library


title: METTL3 KO Rescue with METTL3 human myoblast, DM6d, repeat1

description: Library name: METTL3RES_DM6d_1


title: JGW06 (20 ug/mL dose)_rep3

description: Library name: T_4-3-6

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep3


title: G. sulfurreducens PCA, DB_A, biol rep 1

description:
Library name: Sample 4
Column name in counts_per_million_all_samples.xlsx: DB_A_CPM

value: Geobacter sulfurreducens

value: PCA


title: Granta519EBF1KIcl97,6hWO,RNAseq,rep2

description: Library name: s05_240415_Granta519cl97_6hdTAGWO_RNAseq_lib2_S5_R1.fastq.gz

value: Mantle Cell Lymphoma


title: METTL3 KO human myoblast, DM6d, repeat2

description: Library name: METTL3KO_DM6d_2


title: JGW06 (100 ug/mL dose)_rep3

description: Library name: T_4-3-5

value: Hepatocyte

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep3


title: E2_AP_26

description: Tomo-seq library

value: antero-posterior

value: embryo


title: E2_AP_25

description: Tomo-seq library


title: JGW06 (500 ug/mL dose)_rep3

description: Library name: T_4-3-4

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep3


title: Granta519EBF1KIcl97,24hWO,RNAseq,rep2

description: Library name: s11_240415_Granta519cl97_24hdTAGWO_RNAseq_lib2_S11_R1.fastq.gz


title: METTL3 KO human myoblast, DM6d, repeat1

description: Library name: METTL3KO_DM6d_1


title: METTL3 KO Rescue with METTL3 human myoblast, DM2d, repeat2

description: Library name: METTL3RES_DM2d_2


title: Granta519EBF1KIcl97,24hWO,RNAseq,rep1

description: Library name: s10_240415_Granta519cl97_24hdTAGWO_RNAseq_lib1_S10_R1.fastq.gz


title: Granta519EBF1KIcl97,24hr,RNAseq,rep3

description: Library name: s24_221126_Granta519EBF1KI_cl97_24hr_RNAseq_rep3_S24_R1.fastq.gz


title: JGW05 (100 ug/mL dose)_rep3

description: Library name: T_4-3-2

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


title: METTL3 KO Rescue with METTL3 human myoblast, DM2d, repeat1

description: Library name: METTL3RES_DM2d_1


title: Granta519EBF1KIcl97,24hr,RNAseq,rep1

description: Library name: s22_221126_Granta519EBF1KI_cl97_24hr_RNAseq_rep1_S22_R1.fastq.gz


title: E2_AP_23

description: Tomo-seq library


title: Granta519EBF1KIcl97,24hr,RNAseq,rep2

description: Library name: s23_221126_Granta519EBF1KI_cl97_24hr_RNAseq_rep2_S23_R1.fastq.gz


title: JGW05 (20 ug/mL dose)_rep3

description: Library name: T_4-3-3

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


title: Granta519EBF1KIcl97,6hr,RNAseq,rep3

description: Library name: s12_221126_Granta519EBF1KI_cl97_6hr_RNAseq_rep3_S12_R1.fastq.gz


title: E2_AP_24

description: Tomo-seq library


title: E2_AP_22

description: Tomo-seq library


title: METTL3 KO human myoblast, DM2d, repeat2

description: Library name: METTL3KO_DM2d_2


title: JGW05 (500 ug/mL dose)_rep3

description: Library name: T_4-3-1

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


title: JGW06 (20 ug/mL dose)_rep2

description: Library name: T_4-2-6

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep2


title: JGW06 (100 ug/mL dose)_rep2

description: Library name: T_4-2-5

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep2


title: METTL3 KO Rescue with METTL3 human myoblast, GM, repeat2

description: Library name: METTL3RES_GM_2

value: Skeletal muscle

value: Human myoblast

value: immortalized cell line

value: GM


title: METTL3 KO human myoblast, DM2d, repeat1

description: Library name: METTL3KO_DM2d_1


title: E2_AP_21

description: Tomo-seq library


title: Granta519EBF1KIcl97,6hWO,RNAseq,rep1

description: Library name: s04_240415_Granta519cl97_6hdTAGWO_RNAseq_lib1_S4_R1.fastq.gz


title: Granta519EBF1KIcl97,6hr,RNAseq,rep1

description: Library name: s10_221126_Granta519EBF1KI_cl97_6hr_RNAseq_rep1_S10_R1.fastq.gz


title: E2_AP_27

description: Tomo-seq library


title: METTL3 KO Rescue with METTL3 human myoblast, GM, repeat1

description: Library name: METTL3RES_GM_1


title: JGW06 (500 ug/mL dose)_rep2

description: Library name: T_4-2-4

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep2


title: E2_AP_19

description: Tomo-seq library


title: JGW05 (20 ug/mL dose)_rep2

description: Library name: T_4-2-3

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


title: Granta519EBF1KIcl97,0hr,RNAseq,rep3

description: Library name: s09_221126_Granta519EBF1KI_cl97_0hr_RNAseq_rep3_S9_R1.fastq.gz

value: Mantle Cell Lymphoma

value: untreated


title: Granta519EBF1KIcl97,0hr,RNAseq,rep2

description: Library name: s08_221126_Granta519EBF1KI_cl97_0hr_RNAseq_rep2_S8_R1.fastq.gz


title: JGW05 (100 ug/mL dose)_rep2

description: Library name: T_4-2-2

value: Hepatocyte

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


title: METTL3 KO human myoblast, GM, repeat1

description: Library name: METTL3KO_GM_1


title: E2_AP_18

description: Tomo-seq library

value: antero-posterior

value: embryo


title: JGW05 (500 ug/mL dose)_rep2

description: Library name: T_4-2-1

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


title: single cell CRISPR screen CROP-Seq libray, transcriptome sub libraries-2

description: Library name: CROP_Seq_Transcriptome_2

value: WT


title: Granta519EBF1KIcl97,0hr,RNAseq,rep1

description: Library name: s07_221126_Granta519EBF1KI_cl97_0hr_RNAseq_rep1_S7_R1.fastq.gz


title: E2_AP_17

description: Tomo-seq library


title: E2_AP_16

description: Tomo-seq library


title: Granta519EBF1KIcl97,6hr,RNAseq,rep2

description: Library name: s11_221126_Granta519EBF1KI_cl97_6hr_RNAseq_rep2_S11_R1.fastq.gz


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

description: Library name: CROP_Seq_CRISPR


title: JGW06 (100 ug/mL dose)_rep1

description: Library name: T_4-1-5

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep1


title: Granta519EBF1KIcl29,24hr,RNAseq,rep2

description: Library name: s20_221126_Granta519EBF1KI_cl29_24hr_RNAseq_rep2_S20_R1.fastq.gz


title: E2_AP_15

description: Tomo-seq library


title: JGW06 (500 ug/mL dose)_rep1

description: Library name: T_4-1-4

value: extraction -> mix of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep1


title: E2_AP_20

description: Tomo-seq library


title: Granta519EBF1KIcl29,24hr,RNAseq,rep1

description: Library name: s19_221126_Granta519EBF1KI_cl29_24hr_RNAseq_rep1_S19_R1.fastq.gz


title: E2_AP_14

description: Tomo-seq library


title: JGW05 (20 ug/mL dose)_rep1

description: Library name: T_4-1-3

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


title: D5 human myoblast, DM6d, repeat1

description: Library name: D5_DM6d_1

value: Skeletal muscle

value: DMD


title: Granta519EBF1KIcl29,6hr,RNAseq,rep3

description: Library name: s06_221126_Granta519EBF1KI_cl29_6hr_RNAseq_rep3_S6_R1.fastq.gz


title: E2_AP_13

description: Tomo-seq library


title: JGW05 (100 ug/mL dose)_rep1

description: Library name: T_4-1-2

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


title: D5 human myoblast, DM2d, repeat2

description: Library name: D5_DM2d_2

value: Human myoblast

value: immortalized cell line


title: METTL3 KO human myoblast, GM, repeat2

description: Library name: METTL3KO_GM_2

value: GM


title: Granta519EBF1KIcl29,6hr,RNAseq,rep2

description: Library name: s05_221126_Granta519EBF1KI_cl29_6hr_RNAseq_rep2_S5_R1.fastq.gz

value: Mantle Cell Lymphoma


title: E2_AP_12

description: Tomo-seq library


title: JGW05 (500 ug/mL dose)_rep1

description: Library name: T_4-1-1

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


title: Granta519EBF1KIcl29,6hr,RNAseq,rep1

description: Library name: s04_221126_Granta519EBF1KI_cl29_6hr_RNAseq_rep1_S4_R1.fastq.gz


title: D5 human myoblast, DM2d, repeat1

description: Library name: D5_DM2d_1


title: E2_AP_11

description: Tomo-seq library


title: Granta519EBF1KIcl29,24hr,RNAseq,rep3

description: Library name: s21_221126_Granta519EBF1KI_cl29_24hr_RNAseq_rep3_S21_R1.fastq.gz


title: JGW04 (20 ug/mL dose)_rep3

description: Library name: T_3-3-6

value: Hepatocyte

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep3


title: Granta519EBF1KIcl29,0hr,RNAseq,rep2

description: Library name: s02_221126_Granta519EBF1KI_cl29_0hr_RNAseq_rep2_S2_R1.fastq.gz

value: untreated


title: D5 human myoblast, GM, repeat1

description: Library name: D5_GM_1


title: E2_AP_09

description: Tomo-seq library

value: antero-posterior

value: embryo


title: E2_AP_10

description: Tomo-seq library


title: D5 human myoblast, GM, repeat2

description: Library name: D5_GM_2


title: JGW04 (100 ug/mL dose)_rep3

description: Library name: T_3-3-5

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep3


title: D5 human myoblast, DM6d, repeat2

description: Library name: D5_DM6d_2


title: JGW04 (500 ug/mL dose)_rep3

description: Library name: T_3-3-4

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep3


title: Granta519EBF1KIcl29,0hr,RNAseq,rep1

description: Library name: s01_221126_Granta519EBF1KI_cl29_0hr_RNAseq_rep1_S1_R1.fastq.gz


title: D1 human myoblast, DM6d, repeat1

description: Library name: D1_DM6d_1


title: O

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

data_processing:
Reads were mapped to the human GRCh38.p13 (hg38, obtained from Ensembl) genome and annotated with Ensemble 104 using nf-co pipeline (version 2.0: https://nf-co.re/rnaseq/2.0, utilizing STAR alignment and featureCounts quantification).
Assembly: hg38 (GRCh38.13)
Supplementary files format and content: table-delimited text file includes raw counts for each sample

growth_protocol: Human MDA-MB-231 cells were cultured in high glucose DMEM 4.5 g/L (11995073, Gibco) with 10% Fetal Bovine Serum (FBS; 16140071, Gibco) and 1% penicillin/streptomycin (P/S; 10,000 U/mL; 15140122, Gibco). Cells were incubated at 37°C with 5% CO2 and 100% humidity unless otherwise stated.

extract_protocol:
cells were washed 1X with 10 mL of 1X PBS and incubated with 5 mL of TrypLETM Express Enzyme (12604013, Thermo Fisher Scientific) at 5% CO2 and 37°C. After cells were fully detached, 5 mL of DMEM were added to each flask, and cells were collected into 15 mL tubes and centrifuged for 5 min at 0.3g. Cell pellets were resuspended in 1 mL of 1X PBS and centrifuged once again for 5 min at 0.3g. Finally, cell pellets were resuspended in 300 μL of TRIzolTM Reagent (15596026, Life Technologies) and incubated for 5 min. 300 μL of 100% ethanol was added to each tube and total RNA was extracted with Direct-zol RNA Miniprep Plus kit (R2070, Zymo Research).
20 ng of RNA per sample were subjected to Illumina TruSeq Stranded mRNA Library Prep Kit (20020594, Illumina) and TruSeq RNA Single Indexes Set A (20020492, Illumina) for RNA-seq on the Illumina NextSeq500 using the NextSeq 500/550 High Output Kit v2.5 (75Cycles) (20024906, Illumina).

treatment_protocol: Cells (500,000) were plated into T75 flasks and allowed to reach 70-80% confluence using cell culture medium with pHe=7.4. At that point, cells were washed with 2.5 mL of cell culture media with pH of 7.4, 6.7 or 6.4, and then incubated with media of prescribed pH for 24 h.

value: Triple negative breast cancer

value: WT

value: PH = 6.4, Repeat 4


title: E2_AP_07

description: Tomo-seq library


title: JGW03 (100 ug/mL dose)_rep3

description: Library name: T_3-3-2

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep3


title: E2_AP_08

description: Tomo-seq library


title: D1 human myoblast, DM2d, repeat2

description: Library name: D1_DM2d_2

value: Skeletal muscle

value: DMD


title: JGW03 (20 ug/mL dose)_rep3

description: Library name: T_3-3-3

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep3


title: E2_AP_06

description: Tomo-seq library


title: N

value: PH = 6.9, Repeat 4


title: D1 human myoblast, DM2d, repeat1

description: Library name: D1_DM2d_1

value: Human myoblast

value: immortalized cell line


title: D1 human myoblast, DM6d, repeat2

description: Library name: D1_DM6d_2


title: JGW03 (500 ug/mL dose)_rep3

description: Library name: T_3-3-1

value: Hepatocyte

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep3


title: M

value: PH = 7.4, Repeat 4


title: Granta519EBF1KIcl29,0hr,RNAseq,rep3

description: Library name: s03_221126_Granta519EBF1KI_cl29_0hr_RNAseq_rep3_S3_R1.fastq.gz

value: Mantle Cell Lymphoma

value: untreated


title: L

value: PH = 6.4, Repeat 3


title: E2_AP_05

description: Tomo-seq library

value: antero-posterior

value: embryo


title: D1 human myoblast, GM, repeat2

description: Library name: D1_GM_2

value: GM


title: JGW04 (20 ug/mL dose)_rep2

description: Library name: T_3-2-6

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep2


title: E2_AP_04

description: Tomo-seq library


title: D1 human myoblast, GM, repeat1

description: Library name: D1_GM_1


title: JGW04 (100 ug/mL dose)_rep2

description: Library name: T_3-2-5

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep2


title: K

value: Triple negative breast cancer

value: WT

value: PH = 6.9, Repeat 3


title: J

value: PH = 7.4, Repeat 3


title: K1 human myoblast, DM6d, repeat2

description: Library name: K1_DM6d_2

value: Skeletal muscle

value: Human myoblast


title: E2_AP_02

description: Tomo-seq library


title: JGW03 (20 ug/mL dose)_rep2

description: Library name: T_3-2-3

value: Hepatocyte

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep2


title: E2_AP_03

description: Tomo-seq library


title: K1 human myoblast, DM6d, repeat1

description: Library name: K1_DM6d_1

value: immortalized cell line


title: I

value: PH = 6.4, Repeat 2


title: JGW03 (100 ug/mL dose)_rep2

description: Library name: T_3-2-2

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep2


title: K1 human myoblast, DM2d, repeat2

description: Library name: K1_DM2d_2


title: E2_AP_01

description: Tomo-seq library


title: K1 human myoblast, DM2d, repeat1

description: Library name: K1_DM2d_1


title: G

value: PH = 7.4, Repeat 2


title: E1_AP_45

description: Tomo-seq library

source_name: AP embryo #E1

value: antero-posterior


title: K1 human myoblast, GM, repeat2

description: Library name: K1_GM_2


title: C

value: PH = 6.4, Repeat 1


title: E1_AP_44

description: Tomo-seq library

value: embryo


title: JGW04 (20 ug/mL dose)_rep1

description: Library name: T_3-1-6

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;20 ug/mL dose)_rep1


title: JGW04 (100 ug/mL dose)_rep1

description: Library name: T_3-1-5

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;100 ug/mL dose)_rep1


title: K1 human myoblast, GM, repeat1

description: Library name: K1_GM_1

value: GM


title: B

value: Triple negative breast cancer

value: WT

value: PH = 6.9, Repeat 1


title: JGW04 (500 ug/mL dose)_rep1

description: Library name: T_3-1-4

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep1


title: E1_AP_43

description: Tomo-seq library


title: JGW04 (500 ug/mL dose)_rep2

description: Library name: T_3-2-4

value: mix-> extraction of Water extracts of JGT (PR:GR=1:2;500 ug/mL dose)_rep2


title: A

value: PH = 7.4, Repeat 1


title: A17 human myoblast, DM6d, repeat2

description: Library name: A17_DM6d_2

value: Skeletal muscle

value: Human myoblast


title: E1_AP_42

description: Tomo-seq library


title: JGW03 (20 ug/mL dose)_rep1

description: Library name: T_3-1-3

value: Hepatocyte

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;20 ug/mL dose)_rep1


title: JGW03 (100 ug/mL dose)_rep1

description: Library name: T_3-1-2

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;100 ug/mL dose)_rep1


title: E1_AP_41

description: Tomo-seq library

value: antero-posterior


title: A17 human myoblast, DM2d, repeat2

description: Library name: A17_DM2d_2

value: immortalized cell line


title: A17 human myoblast, DM6d, repeat1

description: Library name: A17_DM6d_1


title: ESC, CEBPa induced, 72h, sorted SSEA1-, clone 2

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

description: Library name: CEBPaER_Clone2_SSEA1_Low_72h

data_processing:
Reads were mapped using STAR (standard options) and the Ensembl mouse genome annotation version. Gene expression was quantified using STAR (–quantMode GeneCounts). Sample scaling and statistical analysis were performed using the R package DESeq2 (R 3.3.2 and Bioconductor 3.0). The statistical power of gene expression variation at any given time point was identified using the nbinomLRT test. Log2-vsd (variance stabilized DESeq2) counts were used for further analysis unless stated otherwise.
Assembly: mm10
Supplementary files format and content: DESeq2 normalized counts

organism: Mus musculus

source_name: ESCs expressing CEBPa-ERT2

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:
Two clones were used for RNA sequencing as biological replicates. Total RNA was extracted using RNeasy Mini Kit (74104, Qiagen)
Libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (20020595, Illumina) and assessed using Bioanalyzer DNA 1000 (5067-1504, Agilent). Libraries were sequenced on a HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

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

value: ESCs expressing CEBPa-ERT2

value: tamoxifen

tag: time


title: H

value: PH = 6.9, Repeat 2


title: ESC, CEBPa induced, 72h, sorted SSEA1-, clone 1

description: Library name: CEBPaER_Clone1_SSEA1_Low_72h


title: E1_AP_46

description: Tomo-seq library

value: embryo


title: JGW03 (500 ug/mL dose)_rep2

description: Library name: T_3-2-1

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep2


title: JGW03 (500 ug/mL dose)_rep1

description: Library name: T_3-1-1

value: mix-> extraction of Water extracts of JGT (PR:GR=1:1;500 ug/mL dose)_rep1


title: ESC, CEBPa induced, 72h, sorted SSEA1+, clone 2

description: Library name: CEBPaER_Clone2_SSEA1_High_72h


title: E1_AP_40

description: Tomo-seq library


title: A17 human myoblast, GM, repeat2

description: Library name: A17_GM_2

value: WT

value: GM


title: JGW02 (20 ug/mL dose)_rep3

description: Library name: T_2-3-6

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep3


title: E1_AP_39

description: Tomo-seq library


title: E1_AP_38

description: Tomo-seq library


title: ESC, CEBPa induced, 72h, sorted SSEA1+, clone 1

description: Library name: CEBPaER_Clone1_SSEA1_High_72h


title: JGW02 (100 ug/mL dose)_rep3

description: Library name: T_2-3-5

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep3


title: A17 human myoblast, GM, repeat1

description: Library name: A17_GM_1

value: Skeletal muscle


title: ESC, CEBPa induced, 48h, sorted SSEA1-, clone 2

description: Library name: CEBPaER_Clone2_SSEA1_Low_48h


title: JGW02 (500 ug/mL dose)_rep3

description: Library name: T_2-3-4

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep3


title: A15 human myoblast, DM6d, repeat2

description: Library name: A15_DM6d_2

value: Human myoblast


title: E1_AP_36

description: Tomo-seq library


title: ESC, CEBPa induced, 48h, sorted SSEA1-, clone 1

description: Library name: CEBPaER_Clone1_SSEA1_Low_48h


title: ESC, CEBPa induced, 48h, sorted SSEA1+, clone 2

description: Library name: CEBPaER_Clone2_SSEA1_High_48h


title: JGW01 (20 ug/mL dose)_rep3

description: Library name: T_2-3-3

value: Hepatocyte

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


title: E1_AP_35

description: Tomo-seq library

value: antero-posterior


title: JGW01 (100 ug/mL dose)_rep3

description: Library name: T_2-3-2

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


title: ESC, CEBPa induced, 48h, sorted SSEA1+, clone 1

description: Library name: CEBPaER_Clone1_SSEA1_High_48h

value: ESCs expressing CEBPa-ERT2


title: ESC, CEBPa non-induced, 0h, clone 2

description: Library name: CEBPaER_Clone2_0h


title: E1_AP_34

description: Tomo-seq library


title: JGW01 (500 ug/mL dose)_rep3

description: Library name: T_2-3-1

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


title: E1_AP_33

description: Tomo-seq library


title: JGW02 (20 ug/mL dose)_rep2

description: Library name: T_2-2-6

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep2


title: A15 human myoblast, DM2d, repeat1

description: Library name: A15_DM2d_1

value: immortalized cell line


title: A17 human myoblast, DM2d, repeat1

description: Library name: A17_DM2d_1


title: A15 human myoblast, GM, repeat2

description: Library name: A15_GM_2


title: Trophoblast stem cells, biological replicate 2

description: Library name: TSC_Rep2_0h

source_name: Trophoblast stem cells

value: Trophoblast stem cells


title: E1_AP_31

description: Tomo-seq library

value: embryo


title: A15 human myoblast, GM, repeat1

description: Library name: A15_GM_1

value: WT


title: ESC, CEBPa non-induced, 0h, clone 1

description: Library name: CEBPaER_Clone1_0h


title: JGW02 (100 ug/mL dose)_rep2

description: Library name: T_2-2-5

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep2


title: JGW02 (500 ug/mL dose)_rep2

description: Library name: T_2-2-4

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep2


title: A16 human myoblast, DM6d, repeat2

description: Library name: A16_DM6d_2


title: Trophoblast stem cells, biological replicate 1

description: Library name: TSC_Rep1_0h


title: E1_AP_30

description: Tomo-seq library


title: E1_AP_37

description: Tomo-seq library


title: A15 human myoblast, DM2d, repeat2

description: Library name: A15_DM2d_2


title: A16 human myoblast, DM6d, repeat1

description: Library name: A16_DM6d_1


title: A15 human myoblast, DM6d, repeat1

description: Library name: A15_DM6d_1


title: JGW01 (20 ug/mL dose)_rep2

description: Library name: T_2-2-3

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


title: ESC, CEBPa induced, 72h, clone 2

description: Library name: CEBPaER_Clone2_72h

value: tamoxifen


title: JGW01 (100 ug/mL dose)_rep2

description: Library name: T_2-2-2

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


title: E1_AP_29

description: Tomo-seq library


title: A16 human myoblast, DM2d, repeat2

description: Library name: A16_DM2d_2

value: Skeletal muscle

value: Human myoblast


title: ESC, CEBPa induced, 72h, clone 1

description: Library name: CEBPaER_Clone1_72h


title: E1_AP_28

description: Tomo-seq library


title: A16 human myoblast, DM2d, repeat1

description: Library name: A16_DM2d_1


title: JGW02 (20 ug/mL dose)_rep1

description: Library name: T_2-1-6

value: Hepatocyte

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;20 ug/mL dose)_rep1


title: E1_AP_27

description: Tomo-seq library

value: antero-posterior


title: E1_AP_32

description: Tomo-seq library


title: JGW02 (100 ug/mL dose)_rep1

description: Library name: T_2-1-5

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;100 ug/mL dose)_rep1


title: A16 human myoblast, GM, repeat2

description: Library name: A16_GM_2

value: GM


title: ESC, CEBPa induced, 48h, clone 1

description: Library name: CEBPaER_Clone1_48h

value: ESCs expressing CEBPa-ERT2


title: E1_AP_26

description: Tomo-seq library


title: ESC, CEBPa induced, 24h, clone 2

description: Library name: CEBPaER_Clone2_24h


title: A16 human myoblast, GM, repeat1

description: Library name: A16_GM_1

value: immortalized cell line


title: CHAMP1 RES human myoblast, DM6d, repeat3

description: Library name: CHAMP1RES_DM6d_3

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).
Assembly: Hg38
Supplementary files format and content: Raw count from featurecounts output

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.


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

description: Library name: CEBPaER_Clone1_24h


title: JGW01 (20 ug/mL dose)_rep1

description: Library name: T_2-1-3

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


title: E1_AP_24

description: Tomo-seq library

data_processing:
Trimming of adapter sequences and poly(A) tails was performed using BBDuk (version 38.93)
Bam alignment files were indexed using samtools (version 1.10) and reads were counted with htseq-count (version 0.13.5) using a GTF file containing chicken gene annotations
Assembly: galGal6
Supplementary files format and content: raw counts for all the libraries, including the two AP replicates, the LR replicate, and the HH1-3 libraries

value: embryo


title: JGW02 (500 ug/mL dose)_rep1

description: Library name: T_2-1-4

value: mix-> extraction of Water extracts of JGT (PR:GR=2:1;500 ug/mL dose)_rep1


title: CHAMP1 RES human myoblast, DM6d, repeat2

description: Library name: CHAMP1RES_DM6d_2


title: E1_AP_25

description: Tomo-seq library


title: E1_AP_23

description: Tomo-seq library


title: ESC, CEBPa induced, 12h, clone 1

description: Library name: CEBPaER_Clone1_12h


title: CHAMP1 KO human myoblast, DM6d, repeat3

description: Library name: CHAMP1KO_DM6d_3


title: JGW01 (500 ug/mL dose)_rep2

description: Library name: T_2-2-1

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


title: CHAMP1 RES human myoblast, DM6d, repeat1

description: Library name: CHAMP1RES_DM6d_1


title: Embryonic stem cells, biological replicate 2

description: Library name: ESC_Rep2_0h

source_name: Embryonic stem cells

value: Embryonic stem cells


title: E1_AP_22

description: Tomo-seq library


title: E1_AP_21

description: Tomo-seq library


title: ESC, CEBPa induced, 12h, clone 2

description: Library name: CEBPaER_Clone2_12h


title: CHAMP1 KO human myoblast, DM6d, repeat2

description: Library name: CHAMP1KO_DM6d_2


title: Vorinostat_rep3

description: Library name: T_1-3-6


title: JGW01 (100 ug/mL dose)_rep1

description: Library name: T_2-1-2

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


title: E1_AP_20

description: Tomo-seq library


title: Embryonic stem cells, biological replicate 1

description: Library name: ESC_Rep1_0h


title: ESC, CEBPa induced, 48h, clone 2

description: Library name: CEBPaER_Clone2_48h

value: tamoxifen


title: Wortmannin_rep3

description: Library name: T_1-3-5


title: JGW01 (500 ug/mL dose)_rep1

description: Library name: T_2-1-1

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


title: CHAMP1 KO human myoblast, DM6d, repeat1

description: Library name: CHAMP1KO_DM6d_1

value: Skeletal muscle


title: Hippocampus Visudyne

city: Taipei city

first: Gilbert

middle: Aaron

last: Lee

address: 250 Wu-Hsing Street,

country: Taiwan

institute: Taipei Medical University

data_processing:
Differentially expressed genes (DEGs) were identified using DESeq2 (version 1.28.0) (Love et al., 2014).
Supplementary files format and content: CSV file includes  differential expressed gene profile of Visudyne vs. saline treatment

source_name: hippocampus

extract_protocol:
We prepared a sequencing library from purified RNA by using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s recommendations.
The quality of the library was assessed on the Agilent Bioanalyzer 2100 and Real-Time PCR systems. The qualified libraries were then sequenced on the Illumina NovaSeq 6000 platform, with 150 bp paired-end reads. The bases with low quality and sequences from adapters in raw data were removed using fastp (version 0.20.0) (Chen et al., 2018). The filtered reads were aligned to the reference genomes by using HISAT2 (version 2.1.0) (Kim et al., 2019). FeatureCounts (version 2.0.1) in the Subread package was applied for gene abundance quantification (Liao et al., 2014).

treatment_protocol: Hippocampus RNA were harvested from mice treated with saline or Visudyne treatment 24 hour post-cerebral ischemia reperfusion

value: hippocampus

value: WT

value: Visudyne


title: E1_AP_19

description: Tomo-seq library

value: antero-posterior


title: Trichostatin A_rep2

description: Library name: T_1-3-4

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 Rn6 Gene Transfer Format (GTF) file from UCSC browser
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

value: Hepatocyte

value: Trichostatin A_rep2


title: E1_AP_18

description: Tomo-seq library


title: CHAMP1 RES human myoblast, DM2d, repeat2

description: Library name: CHAMP1RES_DM2d_2

value: Human myoblast


title: Hippocampus Visudyne RL


title: Wortmannin_rep2

description: Library name: T_1-2-5


title: Hippocampus Visudyne R2


title: Vorinostat_rep2

description: Library name: T_1-2-6


title: E1_AP_17

description: Tomo-seq library


title: Hippocampus Saline L

value: Saline


title: CHAMP1 KO human myoblast, DM2d, repeat3

description: Library name: CHAMP1KO_DM2d_3

value: immortalized cell line


title: Hippocampus Saline R


title: E1_AP_16

description: Tomo-seq library

value: embryo


title: Trichostatin A_rep1

description: Library name: T_1-2-4

value: Trichostatin A_rep1


title: Vorinostat_rep1

description: Library name: T_1-1-6


title: E1_AP_15

description: Tomo-seq library


title: Hippocampus Saline U


title: CHAMP1 KO human myoblast, DM2d, repeat2

description: Library name: CHAMP1KO_DM2d_2


title: E1_AP_14

description: Tomo-seq library


title: Wortmannin_rep1

description: Library name: T_1-1-5


title: E1_AP_13

description: Tomo-seq library


title: saline and Visudyen treatment scRNAseq

description: BD Rhapsody Express system

data_processing:
Whole-transcriptome FASTQ files were then processed using the standard Rhapsody WTA Analysis Pipeline (version 1.9.1; BD Biosciences) on Seven Bridges (https://www.sevenbridges.com). The genes were identified through alignment against the GRCm38 genome reference.
For all the analyses, we used recursive substitution error correction, and multiplets and undetermined cells were excluded from the analysis. For further analysis, molecule count tables were input into the plugin Seurat (version 4.0.4) by using SEQGEQ (BD Bioscience).
Supplementary files format and content: CSV file

source_name: brain

extract_protocol:
Labeled single cells and Cell Capture Beads were loaded into mciro-well cartridges  (BD Biosciences, cat# 633733; and cartridge reagent kit, BD biosciences, cat# 633731). Then cell were lysed, and released mRNA were captured by Cell Capture Beads.  Retrieved mRNA were performing reverse transcription and treatment with Exonuclease I (BD biosciences, cat# 633773)
cDNA libraries were prepared for sequencing by using the BD Rhapsody WTA Amplification kit (BD biosciences, cat# 633801) according to the manufacturer’s instructions. The final libraries were multiplexed for paired-end (150-bp) sequencing on the HiSeq 2500 sequencer (Illumina, USA).

treatment_protocol:
We used the BD Rhapsody Express system to perform single-cell RNA-Seq (scRNA-Seq) analysis on brain-infiltrating leukocytes in saline and Visudyen treated mice.
We sequentially labeled CD45+-sorted live brain–infiltrating leukocytes through single-cell labeling on the BD Single-Cell Multiplexing Kit (BD Biosciences, #633781, USA) and BD AbSeq Ab-Oligos (AbSeq Oligo antimouse CD3, CD4, CD8, NKp46, CD11b, and CD11c) reagents, according to the manufacturer’s protocol.

value: immune cells

value: brain

tag: age

value: 8 weeks old


title: E1_AP_12

description: Tomo-seq library

extract_protocol:
Total RNA for each section  was extracted with the kit RNAqueous®-Micro Kit (ThermoFisher #AM1931) following the manufacturers recommendations.
The RNA-seq libraries were prepared with the kit QuantSeq 3'mRNA-seq Library Prep Kit (FWD) for Illumina (Lexogen #K01596), following the manufacturers recommendations  for low input samples.
3'RNA-seq libraries


title: CHAMP1 RES human myoblast, DM2d, repeat3

description: Library name: CHAMP1RES_DM2d_3


title: CHAMP1 RES human myoblast, GM, repeat2

description: Library name: CHAMP1RES_GM_2

value: GM


title: CHAMP1 RES human myoblast, GM, repeat3

description: Library name: CHAMP1RES_GM_3


title: CHAMP1 KO human myoblast, DM2d, repeat1

description: Library name: CHAMP1KO_DM2d_1