title: eIF2D KO HEK293T #1 eIF2D(deltaWH)-V5 OE TCP-seq replicate 2

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

description: Library name: Sample 56

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

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.


title: SINC2

status: Public on Oct 24 2025

type: SRA

city: 南京

first: liang qingqing

middle: liang qingqing

last: liang qingqing

address: 栖霞区仙林大道163号南京大学仙林校区

country: China

institute: 南京市口腔医院

library_source: transcriptomic

data_processing: none provided

molecule: total RNA

organism: Rattus norvegicus

source_name: TMJ

extract_protocol: rna was harvested by using trizol

tag: tissue

value: TMJ

tag: cell line

value: primary chondrocyte

tag: cell type

tag: genotype

value: si-nc

tag: treatment


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

country: Japan

description: Library name: Sample 54

organism: Homo sapiens


title: ST2hi memory CD4, HDM, ATAC, rep1

city: Chiba-shi

first: Hiroyuki

last: Yagyu

state: Chiba

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

institute: Chiba University

library_source: genomic

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: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Lung

extract_protocol:
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 NovaSeq 6000 Sequencing System.

value: ST2hiCD44hiCD4+ T cells

tag: strain

value: BALB/c

value: wild-type

tag: sensitization

value: HDM

value: Lung


title: HSPCs, SC_mf, scRNAseq

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

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

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

description: 10× Genomics

library_source: transcriptomic single cell

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

source_name: Bone Marrow

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

value: Bone Marrow

value: HSPCs

value: Srsf2 mutated


title: ESC, CEBPa induced, 24h, sorted SSEA1-, clone 1

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_SSEA1_Low_24h

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

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

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: ST2hi memory CD4, HDM, ATAC, rep2


title: SIMS1

address: 栖霞区仙林大道163号南京大学仙林校区

value: si-ddx5+mechnical stress


title: HSPCs, SC_mdf, scRNAseq

description: 10× Genomics

value: Setd2 knockout and Srsf2 mutated


title: SIMS3

address: 栖霞区仙林大道163号南京大学仙林校区


title: HSPCs, SC_WT, scRNAseq

description: 10× Genomics

value: WT


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

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_Bulk_24h


title: SIMS2

address: 栖霞区仙林大道163号南京大学仙林校区


title: eIF2D KO HEK293T #1 eIF2D(deltaWH)-V5 OE TCP-seq replicate 1

description: Library name: Sample 55


title: ESC, CEBPa induced, 24h, sorted SSEA1-, clone 1, input

description: Library name: CEBPa_ChIP_CEBPaER_SSEA1_Low_24h_Input


title: ST2lo memory CD4, HDM, ATAC, rep2

value: ST2loCD44hiCD4+ T cells


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

description: Library name: Sample 53


title: ST2lo memory CD4, HDM, ATAC, rep1


title: ESC, CEBPa induced, 24h, sorted SSEA1+, clone 1, input

description: Library name: CEBPa_ChIP_CEBPaER_SSEA1_High_24h_Input


title: SINC1

address: 栖霞区仙林大道163号南京大学仙林校区

value: TMJ


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

description: Library name: CEBPa_ChIP_CEBPaER_Clone2_SSEA1_High_24h


title: SI3

address: 栖霞区仙林大道163号南京大学仙林校区

value: primary chondrocyte


title: eIF2D KO HEK293T #1 eIF2D-V5 OE TCP-seq replicate 1

description: Library name: Sample 51


title: ESC, CEBPa induced, 24h, sorted SSEA1+, clone 1

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_SSEA1_High_24h


title: Th2, input

description: input

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

source_name: Th2 cells

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

value: Th2 cells

tag: fatty acid

value: input

value: DMSO

tag: chip antibody


title: SI2

address: 栖霞区仙林大道163号南京大学仙林校区


title: SINC3

address: 栖霞区仙林大道163号南京大学仙林校区

value: si-nc


title: eIF2D KO HEK293T #1 eIF2D-V5 OE TCP-seq replicate 2

description: Library name: Sample 52


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

description: Library name: Sample 50


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

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_0h_Input


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

value: BALB/c

value: Linoleic

value: Atglistatin

value: PPARg


title: WT HEK293T empty TCP-seq replicate 2

description: Library name: Sample 48


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

value: Control


title: SI1

address: 栖霞区仙林大道163号南京大学仙林校区


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


title: memory CD4, nasal polyps, H3K27Ac, patient3

description: Library name: Polyp_3

data_processing:
ATAC-seq and CUT&Tag 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
Library strategy: CUT&Tag

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. The CUT&Tag assay was performed using the CUT&Tag Assay Kit (Cell Signaling Technology), according to the manufacturer’s protocol. A total of 1×10^5 sorted CD45RO+CD4+ T cells from nasal polyps and PBMCs of ECRS patients Th2 cells were subjected to CUT&Tag using an anti-H3K27Ac antibody (D5E4, Cell Signaling Technology).
Fragmented DNAs were purified using the QIAGEN MiniElute PCR Purification Kit and amplified using 8-10 PCR cycles based on the amplification curve. CUT&Tag DNA libraries were prepared using CUT&Tag Dual Index Primers and PCR Master Mix for Illumina Systems kit (Cell Signaling Technology) with 13 cycles of PCR amplification. 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: JGE08 (100 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_9-3-5

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

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).

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).

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: extraction -> mix of Ethanol extracts of JGT (JGE08;100 ug/mL dose)_rep3


title: MS2

address: 栖霞区仙林大道163号南京大学仙林校区

value: ms

value: mechnical stress


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

description: Library name: CEBPa_ChIP_CEBPaER_Clone1_0h

value: ESCs expressing CEBPa-ERT2


title: memory CD4, PBMCs, H3K27Ac, patient3

description: Library name: PBMC_3

source_name: PBMCs

value: PBMCs


title: NC3

address: 栖霞区仙林大道163号南京大学仙林校区

value: TMJ

value: primary chondrocyte

value: nc


title: JGE08 (20 ug/mL dose)_rep3

description: Library name: T_9-3-6

value: extraction -> mix of Ethanol extracts of JGT (JGE08;20 ug/mL dose)_rep3


title: WT HEK293T empty TCP-seq replicate 1

description: Library name: Sample 47


title: MS1

address: 栖霞区仙林大道163号南京大学仙林校区


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

description: Library name: Sample 49


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

value: Th2 cells

value: BALB/c

value: Linoleic

value: DMSO

value: RXRa


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: DND41,resistant,Micro-C

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 421 Curie Boulevard

department: Pathology

country: USA

institute: University of Pennsylvania

description: Library name: s02_241118_DND41_resistant_15U_20U_MicroC

data_processing:
Raw reads for each Micro-C 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

extract_protocol:
Micro-C was performed as previously described (Hsieh et al., 2020).
NEBNext Ultra II DNA library Prep Kit for Illumina (NEB cat# E7645S)

value: T-cell Acute Lymphoblatic Leukemia

value: GSI


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

value: Atglistatin

value: PPARg


title: NC2

address: 栖霞区仙林大道163号南京大学仙林校区


title: Th2, Oleic, DMSO, RXRa ChIP, rep1

value: Oleic


title: NC1

address: 栖霞区仙林大道163号南京大学仙林校区


title: DND41,parental,Micro-C

description: Library name: s03_241125_DND41_parental_15U_20U_MicroC

value: untreated


title: MS3

address: 栖霞区仙林大道163号南京大学仙林校区

value: ms

value: mechnical stress


title: JGE08 (500 ug/mL dose)_rep3

description: Library name: T_9-3-4

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE08;500 ug/mL dose)_rep3


title: JGE07 (500 ug/mL dose)_rep3

description: Library name: T_9-3-1

value: extraction -> mix of Ethanol extracts of JGT (JGE07;500 ug/mL dose)_rep3


title: Th2, Oleic, DMSO, RXRa ChIP, rep2

value: Th2 cells


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

value: BALB/c


title: JGE08 (20 ug/mL dose)_rep2

description: Library name: T_9-2-6

value: extraction -> mix of Ethanol extracts of JGT (JGE08;20 ug/mL dose)_rep2


title: hCO RF-treated with SH

city: New Haven

first: In-Hyun

last: Park

state: CT

address: 10 AMISTAD ST # 201B

department: Genetics

institute: Yale University

description: 10x Genomics

data_processing:
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
Assembly: hg19
Supplementary files format and content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: cortical organoids

growth_protocol: Human cortical organoids were cultured as performed previously (Xiang et al., 2017)

extract_protocol: Library was constructed by the manufacter's protocol (Chromium reagent 3' v2, 10X Genomics)

treatment_protocol: Human cortical organoids at day 70 were exposed to mobile phone radiofrequency.

value: cortical organoids

tag: protection

value: Electromagnetic shield

value: Radiofreqnecy exposure


title: Granta519EBF1KI_cl97, 24hWO, Micro-C

description: Library name: s02_240918_Granta519EBF1KI_cl97_24hWO_25U_MicroC

value: Mantle Cell Lymphoma


title: JGE07 (100 ug/mL dose)_rep3

description: Library name: T_9-3-2

value: extraction -> mix of Ethanol extracts of JGT (JGE07;100 ug/mL dose)_rep3


title: Granta519EBF1KI_cl97, 6hWO, Micro-C

description: Library name: s01_240918_Granta519EBF1KI_cl97_6hWO_25U_MicroC


title: hCO RF-treated with AF

description: 10x Genomics

value: Aluminum foil


title: hCO RF-treated

description: 10x Genomics


title: JGE08 (500 ug/mL dose)_rep2

description: Library name: T_9-2-4

value: extraction -> mix of Ethanol extracts of JGT (JGE08;500 ug/mL dose)_rep2


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

value: Control

value: DMSO

value: RXRa


title: Granta519EBF1KI_cl97, 6hr, Micro-C

description: Library name: s03_231213_Granta519EBF1KI_cl97_6hr_25U_MicroC


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


title: Th2, Oleic, DMSO, PPARg ChIP, rep2

value: Oleic

value: PPARg


title: JGE08 (100 ug/mL dose)_rep2

description: Library name: T_9-2-5

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE08;100 ug/mL dose)_rep2


title: Granta519EBF1KI_cl97, 24hr, Micro-C

description: Library name: s02_230109_Granta519EBF1KI_cl97_24hr_25U_MicroC


title: hCO non-treated

description: 10x Genomics


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: 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: Th2, Linoleic, DMSO, PPARg ChIP, rep2

value: Th2 cells

value: BALB/c

value: Linoleic


title: Th2, Oleic, DMSO, PPARg ChIP, rep1


title: day80.H3K9me3.Rep2

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and ATAC-seq.

source_name: ES derived ventricular cardiomyocyte

extract_protocol: ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441).   Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the  links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf, Library preparation: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf.

value: ES derived ventricular cardiomyocyte

tag: differentiation time

value: H9 MLC2v:H2B

tag: matched input

value: day80.Input.Batch1.Rep2 in GSE116862

value: H3K9me3 (Abcam, Ab8898)


title: JGE07 (500 ug/mL dose)_rep2

description: Library name: T_9-2-1

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


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


title: day15.H3K9me3.Rep2

source_name: ES derived primitive cardiomyocite

value: ES derived primitive cardiomyocite

value: day15.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KI_cl27, 6hWO, Micro-C

description: Library name: s02_240711_Granta519EBF1KI_cl27_6hWO_MicroC

value: Mantle Cell Lymphoma


title: JGE08 (20 ug/mL dose)_rep1

description: Library name: T_9-1-6

value: extraction -> mix of Ethanol extracts of JGT (JGE08;20 ug/mL dose)_rep1


title: day15.H3K9me3.Rep1

value: day15.Input.Batch1.Rep1 in GSE116862


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

value: Control

value: DMSO

value: PPARg


title: day07.H3K9me3.Rep2

source_name: ES derived cardiac progenitor cells

value: ES derived cardiac progenitor cells

value: day07.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KI_cl27, 24hr, Micro-C

description: Library name: s40_221203_Granta519EBF1KI_cl27_24hr_MicroC


title: JGE08 (100 ug/mL dose)_rep1

description: Library name: T_9-1-5

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE08;100 ug/mL dose)_rep1


title: Granta519EBF1KI_cl27, 6hr, Micro-C

description: Library name: s42_221203_Granta519EBF1KI_cl27_6hr_MicroC


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

value: Th2 cells

value: BALB/c


title: Granta519EBF1KI_cl97, 0hr, Micro-C

description: Library name: s01_230109_Granta519EBF1KI_cl97_0hr_25U_MicroC

value: untreated


title: JGE08 (500 ug/mL dose)_rep1

description: Library name: T_9-1-4

value: extraction -> mix of Ethanol extracts of JGT (JGE08;500 ug/mL dose)_rep1


title: Mouse_control_lung_batch_2

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

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: CD45+ cells

value: wild-type

value: Lung

value: female


title: Granta519EBF1KI_cl27, 0hr, Micro-C

description: Library name: s38_221203_Granta519EBF1KI_cl27_0hr_MicroC

value: Mantle Cell Lymphoma


title: day80.H3K9me3.Rep1

value: ES derived ventricular cardiomyocyte

value: H9 MLC2v:H2B

value: day80.Input.Batch1.Rep1 in GSE116862

value: H3K9me3 (Abcam, Ab8898)


title: Granta519EBF1KIcl27,24hWO,SMC1ChIP,rep2

description: Library name: s16_240415_Granta519cl27_24hdTAGWO_SMC1_ChIP_rep2_S16_R1.fastq.gz

data_processing:
Reads from ChIP-seq were trimmed with Trim Galore and aligned to the Ensembl GRCh37.75 primary assembly using BWA.
Assembly: hg19
Supplementary files format and content: .bw formatted file for viewing on genome browser

extract_protocol:
ChIP-seq was performed as previously described (Zhou et al., 2022)
NEBNext Ultra II DNA library Prep Kit for Illumina (NEB cat# E7645S)


title: day07.H3K9me3.Rep1

value: ES derived cardiac progenitor cells

value: day07.Input.Batch1.Rep1 in GSE116862


title: Mouse_HDM_lung_batch_2


title: JGE07 (20 ug/mL dose)_rep1

description: Library name: T_9-1-3

value: neuronal cell

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


title: day05.H3K9me3.Rep2

source_name: ES derived cardiac mesoderm

value: ES derived cardiac mesoderm

value: day05.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KI_cl27, 24hWO, Micro-C

description: Library name: s01_240711_Granta519EBF1KI_cl27_24hWO_MicroC


title: Mouse_HDM_lung_batch_1

value: CD4+ T cells

value: BALB/c


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: Mouse_control_lung_batch_1

value: wild-type


title: Granta519EBF1KIcl27,24hWO,SMC1ChIP,rep1

description: Library name: s15_240415_Granta519cl27_24hdTAGWO_SMC1_ChIP_rep1_S15_R1.fastq.gz


title: day02.H3K9me3.Rep2

source_name: ES derived mesoderm

value: ES derived mesoderm

value: day02.Input.Batch1.Rep2 in GSE116862


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: Granta519EBF1KIcl27,24hWO,EBF1ChIP,rep2

description: Library name: s14_240415_Granta519cl27_24hdTAGWO_EBF1_ChIP_rep2_S14_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE06 (20 ug/mL dose)_rep3

description: Library name: T_8-3-6

value: extraction -> mix of Ethanol extracts of JGT (JGE06;20 ug/mL dose)_rep3


title: Granta519EBF1KIcl27,24hWO,EBF1ChIP,rep1

description: Library name: s13_240415_Granta519cl27_24hdTAGWO_EBF1_ChIP_rep1_S13_R1.fastq.gz


title: veh_FT3

first: Terry

last: Lin

state: CA

address: 10010 N Torrey Pines Rd, RBIO-P

department: RBIO

institute: Salk Institute

data_processing:
Sequencing library read quality was assessed using FastQC v0.11.5 (Babraham Bioinformatics, Cambridge, UK)
Libraries were individually mapped to the mm10 genome using STAR v2.5.3a
Gene expression levels were quantified across exons using HOMERv4.10 and mm10 UCSC genome annotation
Data normalization and differential gene expression was carried out via edgeR v3.26.7
Assembly: mm10
Supplementary files format and content: matrix table containing annotated raw counts in csv format

source_name: kidney

extract_protocol:
Total RNA was extracted from 30mg frozen kidney powder using TRIzol™ Reagent (ThermoFisher Scientific)
500ng of total RNA was used to prepare libraries using TruSeq Stranded mRNA kit (Illumina)

value: kidney

value: TRF


title: day05.H3K9me3.Rep1

value: H9 MLC2v:H2B

value: day05.Input.Batch1.Rep1 in GSE116862

value: H3K9me3 (Abcam, Ab8898)


title: JGE06 (500 ug/mL dose)_rep3

description: Library name: T_8-3-4

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE06;500 ug/mL dose)_rep3


title: Granta519EBF1KIcl27,24hWO,YY1ChIP,rep2

description: Library name: s10_240701_Granta519cl27_24hWO_YY1_ChIP_rep2_S10_R1.fastq.gz


title: veh_FT2


title: veh_FT1


title: day00.H3K9me3.Rep2

source_name: Embryonic stem cell

value: Embryonic stem cell

value: day00.Input.Batch1.Rep2 in GSE116862


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: Granta519EBF1KIcl27,6hWO,YY1ChIP,rep2

description: Library name: s08_240701_Granta519cl27_6hWO_YY1_ChIP_rep2_S8_R1.fastq.gz


title: Granta519EBF1KIcl27,6hWO,YY1ChIP,rep1

description: Library name: s07_240701_Granta519cl27_6hWO_YY1_ChIP_rep1_S7_R1.fastq.gz


title: day80.H3K4me3.Rep2

value: ES derived ventricular cardiomyocyte

value: day80.Input.Batch1.Rep2 in GSE116862

value: H3K4me3 (Millipore, 04-745)


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: Granta519EBF1KIcl27,24hWO,YY1ChIP,rep1

description: Library name: s09_240701_Granta519cl27_24hWO_YY1_ChIP_rep1_S9_R1.fastq.gz


title: day80.H3K4me3.Rep1

value: day80.Input.Batch1.Rep1 in GSE116862


title: veh_FT4


title: JGE06 (20 ug/mL dose)_rep2

description: Library name: T_8-2-6

value: extraction -> mix of Ethanol extracts of JGT (JGE06;20 ug/mL dose)_rep2


title: veh_FA3

value: adlib


title: day15.H3K4me3.Rep2

value: ES derived primitive cardiomyocite

value: day15.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KIcl27,24hr,YY1ChIP,rep2

description: Library name: s06_240701_Granta519cl27_24hdTAG_YY1_ChIP_rep2_S6_R1.fastq.gz

value: Mantle Cell Lymphoma


title: veh_FA1

value: kidney


title: veh_FA4


title: day15.H3K4me3.Rep1

value: H9 MLC2v:H2B

value: day15.Input.Batch1.Rep1 in GSE116862


title: JGE06 (100 ug/mL dose)_rep2

description: Library name: T_8-2-5

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE06;100 ug/mL dose)_rep2


title: day02.H3K9me3.Rep1

value: ES derived mesoderm

value: day02.Input.Batch1.Rep1 in GSE116862

value: H3K9me3 (Abcam, Ab8898)


title: day07.H3K4me3.Rep2

value: ES derived cardiac progenitor cells

value: day07.Input.Batch1.Rep2 in GSE116862


title: day00.H3K9me3.Rep1

value: Embryonic stem cell

value: day00.Input.Batch1.Rep1 in GSE116862


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: JGE06 (100 ug/mL dose)_rep3

description: Library name: T_8-3-5

value: extraction -> mix of Ethanol extracts of JGT (JGE06;100 ug/mL dose)_rep3


title: fan_FT7

value: TRF


title: Granta519EBF1KIcl27,6hr,YY1ChIP,rep2

description: Library name: s04_240701_Granta519cl27_6hdTAG_YY1_ChIP_rep2_S4_R1.fastq.gz


title: fan_FT6


title: day07.H3K4me3.Rep1

value: day07.Input.Batch1.Rep1 in GSE116862

value: H3K4me3 (Millipore, 04-745)


title: veh_FA2

value: kidney

value: adlib


title: JGE06 (500 ug/mL dose)_rep2

description: Library name: T_8-2-4

value: extraction -> mix of Ethanol extracts of JGT (JGE06;500 ug/mL dose)_rep2


title: day05.H3K4me3.Rep2

value: ES derived cardiac mesoderm

value: H9 MLC2v:H2B

value: day05.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KIcl27,24hr,YY1ChIP,rep1

description: Library name: s05_240701_Granta519cl27_24hdTAG_YY1_ChIP_rep1_S5_R1.fastq.gz

value: Mantle Cell Lymphoma


title: Granta519EBF1KIcl27,6hr,YY1ChIP,rep1

description: Library name: s03_240701_Granta519cl27_6hdTAG_YY1_ChIP_rep1_S3_R1.fastq.gz


title: fan_FT5


title: Granta519EBF1KIcl27,0hr,YY1ChIP,rep1

description: Library name: s01_240701_Granta519cl27_0hr_YY1_ChIP_rep1_S1_R1.fastq.gz

value: untreated


title: JGE05 (500 ug/mL dose)_rep2

description: Library name: T_8-2-1

value: neuronal cell

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


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: fan_FT1


title: Granta519EBF1KIcl27,24hWO,CTCFChIPseq,rep2

description: Library name: s10_240610_Granta519EBF1KI_cl27_24hWO_CTCF_CHIPseq_rep2_S10_R1.fastq.gz


title: day05.H3K4me3.Rep1

value: day05.Input.Batch1.Rep1 in GSE116862


title: fan_FA7


title: JGE06 (20 ug/mL dose)_rep1

description: Library name: T_8-1-6

value: extraction -> mix of Ethanol extracts of JGT (JGE06;20 ug/mL dose)_rep1


title: Granta519EBF1KIcl27,0hr,YY1ChIP,rep2

description: Library name: s02_240701_Granta519cl27_0hr_YY1_ChIP_rep2_S2_R1.fastq.gz


title: Granta519EBF1KIcl27,24hWO,CTCFChIPseq,rep1

description: Library name: s09_240610_Granta519EBF1KI_cl27_24hWO_CTCF_CHIPseq_rep1_S9_R1.fastq.gz


title: day00.H3K4me3.Rep2

value: Embryonic stem cell

value: day00.Input.Batch1.Rep2 in GSE116862


title: day02.H3K4me3.Rep1

value: ES derived mesoderm

value: day02.Input.Batch1.Rep1 in GSE116862


title: Granta519EBF1KIcl27,6hWO,CTCFChIPseq,rep2

description: Library name: s08_240610_Granta519EBF1KI_cl27_6hWO_CTCF_CHIPseq_rep2_S8_R1.fastq.gz


title: JGE06 (500 ug/mL dose)_rep1

description: Library name: T_8-1-4

value: extraction -> mix of Ethanol extracts of JGT (JGE06;500 ug/mL dose)_rep1


title: fan_FA2

value: kidney

value: adlib


title: Granta519EBF1KIcl27,6hWO,CTCFChIPseq,rep1

description: Library name: s07_240610_Granta519EBF1KI_cl27_6hWO_CTCF_CHIPseq_rep1_S7_R1.fastq.gz


title: day00.H3K4me3.Rep1

value: day00.Input.Batch1.Rep1 in GSE116862

value: H3K4me3 (Millipore, 04-745)


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: fan_FA1


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: Granta519EBF1KIcl27,24hr,CTCFChIPseq,rep2

description: Library name: s06_240610_Granta519EBF1KI_cl27_24hdTAG_CTCF_CHIPseq_rep2_S6_R1.fastq.gz

value: Mantle Cell Lymphoma


title: day80.H3K4me1.Rep2

value: ES derived ventricular cardiomyocyte

value: H9 MLC2v:H2B

value: day80.Input.Batch1.Rep2 in GSE116862

value: H3K4me1 (Abcam, ab8895)


title: JGE05 (100 ug/mL dose)_rep1

description: Library name: T_8-1-2

value: neuronal cell

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


title: Granta519EBF1KIcl27,24hr,CTCFChIPseq,rep1

description: Library name: s05_240610_Granta519EBF1KI_cl27_24hdTAG_CTCF_CHIPseq_rep1_S5_R1.fastq.gz


title: day80.H3K4me1.Rep1

value: day80.Input.Batch1.Rep1 in GSE116862


title: day02.H3K4me3.Rep2

value: ES derived mesoderm

value: day02.Input.Batch1.Rep2 in GSE116862


title: PHX3174, Input, Rep2

city: Kobe

first: Hiroki

last: Shibuya

state: Hyogo

address: 2-2-3 Minatojima-minamimachi

department: BDR

institute: RIKEN institute

data_processing:
The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5' end that serves as a unique molecular identifier (UMI) after sequencing primers are ligated to the 3' end of cDNA molecules. Therefore, eCLIP reads begin with the UMI, and, in the first step of analysis, UMIs were pruned from read sequences using umi_tools (v0.5.1).
All non-repeat mapped reads were mapped to the C. elegans genome (ce11) using STAR (v2.6.0c). PCR duplicates were removed using umi tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Overlapping reads that were not mapped to an annotated transcript were merged using bedtools (v2.26.0), and these regions were used, along with annotated transcript regions, for peak calling. Peaks were identified within eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper).
Assembly: C. elegans genome (ce11)
Supplementary files format and content: BigWig

organism: Caenorhabditis elegans

growth_protocol: C. eleganswere grownand maintainedat 20°Con10 cm agar plates seeded with OP50 E. coli.

extract_protocol:
Five 10 cm dishes of C. elegans were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation and snap frozen. C. elegans was then lysed and treated with RNase I to fragment RNAs.
Sigma monoclonal anti-FLAG M2 antibody (cat # F1804-1MG)or Sheep Anti-Mouse IgG (ThermoFisher Scientific, cat# 11202D) was pre-coupled to Dynabeads M-280, added to the lysate, and incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder being magnetically separated and washed with lysis buffer only. eCLIP was performed by excising the area from ~60 kDa to ~135 kDa, and RNA adapter ligation, IP-western blot, reverse transcription, DNA adapter ligation, and PCR amplification were performed.

tag: sample type

value: whole organism


title: PHX3174, Input, Rep1


title: Granta519EBF1KIcl27,6hr,CTCFChIPseq,rep2

description: Library name: s04_240610_Granta519EBF1KI_cl27_6hdTAG_CTCF_CHIPseq_rep2_S4_R1.fastq.gz


title: day15.H3K4me1.Rep2

value: ES derived primitive cardiomyocite

value: day15.Input.Batch1.Rep2 in GSE116862


title: day15.H3K4me1.Rep1

value: day15.Input.Batch1.Rep1 in GSE116862


title: fan_FA5

value: kidney

value: adlib


title: JGE04 (20 ug/mL dose)_rep3

description: Library name: T_7-3-6

value: mix-> extraction of Ethanol extracts of JGT (JGE04;20 ug/mL dose)_rep3


title: N2, Input, Rep1

value: WT


title: Granta519EBF1KIcl27,6hr,CTCFChIPseq,rep1

description: Library name: s03_240610_Granta519EBF1KI_cl27_6hdTAG_CTCF_CHIPseq_rep1_S3_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE04 (100 ug/mL dose)_rep3

description: Library name: T_7-3-5

value: mix-> extraction of Ethanol extracts of JGT (JGE04;100 ug/mL dose)_rep3


title: PHX3174, control_IgG, eCLIP


title: day07.H3K4me1.Rep2

value: ES derived cardiac progenitor cells

value: H9 MLC2v:H2B

value: day07.Input.Batch1.Rep2 in GSE116862


title: JGE06 (100 ug/mL dose)_rep1

description: Library name: T_8-1-5

value: neuronal cell

value: extraction -> mix of Ethanol extracts of JGT (JGE06;100 ug/mL dose)_rep1


title: JGE04 (500 ug/mL dose)_rep3

description: Library name: T_7-3-4

value: mix-> extraction of Ethanol extracts of JGT (JGE04;500 ug/mL dose)_rep3


title: day07.H3K4me1.Rep1

value: day07.Input.Batch1.Rep1 in GSE116862

value: H3K4me1 (Abcam, ab8895)


title: Granta519EBF1KIcl27,0hr,CTCFChIPseq,rep2

description: Library name: s02_240610_Granta519EBF1KI_cl27_0hr_CTCF_CHIPseq_rep2_S2_R1.fastq.gz

value: untreated


title: PHX3174, FLAG, eCLIP

value: whole organism


title: JGE04 (20 ug/mL dose)_rep2

description: Library name: T_7-2-6

value: mix-> extraction of Ethanol extracts of JGT (JGE04;20 ug/mL dose)_rep2


title: N2, FLAG, eCLIP


title: day05.H3K4me1.Rep2

value: ES derived cardiac mesoderm

value: day05.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KIcl27,0hr,CTCFChIPseq,rep1

description: Library name: s01_240610_Granta519EBF1KI_cl27_0hr_CTCF_CHIPseq_rep1_S1_R1.fastq.gz


title: Granta519EBF1KIcl27,6hWO,SMC1ChIPseq,rep2

description: Library name: s16_240427_Granta519cl27_6hWO_SMC1_ChIP_rep2_S16_R1.fastq.gz


title: JGE04 (100 ug/mL dose)_rep2

description: Library name: T_7-2-5

value: mix-> extraction of Ethanol extracts of JGT (JGE04;100 ug/mL dose)_rep2


title: N2, Rep2

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT 2 software. HISAT 2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Assembly: WBcel235 (GCA_000002985.3)
Supplementary files format and content: BigWig

source_name: asynchronized worm culture

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen) from worms homogenized with TissueLyser II (QIAGEN), followed by purification with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
After rRNA subtraction, RNA-seq libraries were prepared by Novogene and sequenced using Illumina Novaseq 6000 (PE150). For cDNA synthesis, isolated RNA was treated with DNase I (Invitrogen) at 37°C for 30 min, the enzyme was inactivated at 65°C for 10 min, and reverse transcription was performed using a random hexamer with SuperScript III First-Strand Synthesis System (Invitrogen) according to the manufacturer's instruction.

value: WT


title: day05.H3K4me1.Rep1

value: day05.Input.Batch1.Rep1 in GSE116862


title: Granta519EBF1KIcl27,6hWO,SMC1ChIPseq,rep1

description: Library name: s15_240427_Granta519cl27_6hWO_SMC1_ChIP_rep1_S15_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE04 (500 ug/mL dose)_rep2

description: Library name: T_7-2-4

value: mix-> extraction of Ethanol extracts of JGT (JGE04;500 ug/mL dose)_rep2


title: N2, Rep1


title: day02.H3K4me1.Rep2

value: ES derived mesoderm

value: H9 MLC2v:H2B

value: day02.Input.Batch1.Rep2 in GSE116862


title: JGE05 (500 ug/mL dose)_rep1

description: Library name: T_8-1-1

value: neuronal cell

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


title: JGE04 (20 ug/mL dose)_rep1

description: Library name: T_7-1-6

value: mix-> extraction of Ethanol extracts of JGT (JGE04;20 ug/mL dose)_rep1


title: day02.H3K4me1.Rep1

value: day02.Input.Batch1.Rep1 in GSE116862

value: H3K4me1 (Abcam, ab8895)


title: PHX4686, FLAG, eCLIP, Rep2

description: asynchronized worm culture

data_processing:
The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5' end that serves as a unique molecular identifier (UMI) after sequencing primers are ligated to the 3' end of cDNA molecules. Therefore, eCLIP reads begin with the UMI, and, in the first step of analysis, UMIs were pruned from read sequences using umi_tools (v0.5.1).
All non-repeat mapped reads were mapped to the C. elegans genome (ce11) using STAR (v2.6.0c). PCR duplicates were removed using umi tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Overlapping reads that were not mapped to an annotated transcript were merged using bedtools (v2.26.0), and these regions were used, along with annotated transcript regions, for peak calling. Peaks were identified within eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper).
Assembly: C. elegans genome (ce11)
Supplementary files format and content: BigWig, Bed file

extract_protocol:
Five 10 cm dishes of C. elegans were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation and snap frozen. C. elegans was then lysed and treated with RNase I to fragment RNAs.
Sigma monoclonal anti-FLAG M2 antibody (cat # F1804-1MG)was pre-coupled to Dynabeads M-280, added to the lysate, and incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder being magnetically separated and washed with lysis buffer only. eCLIP was performed by excising the area from ~60 kDa to ~135 kDa, and RNA adapter ligation, IP-western blot, reverse transcription, DNA adapter ligation, and PCR amplification were performed.

value: whole organism

value: dkc-1(syb4686[gfp::3xFLAG::dkc-1]) III


title: JGE04 (100 ug/mL dose)_rep1

description: Library name: T_7-1-5

value: mix-> extraction of Ethanol extracts of JGT (JGE04;100 ug/mL dose)_rep1


title: Granta519EBF1KIcl27,24hr,EBF1ChIPseq,rep2

description: Library name: s52_221207_Granta519EBF1KI_cl27_24hr_EBF1_CHIPseq_rep2_S16_R1.fastq.gz


title: Granta519EBF1KIcl27,6hWO,EBF1ChIPseq,rep1

description: Library name: s13_240427_Granta519cl27_6hWO_EBF1_ChIP_rep1_S13_R1.fastq.gz


title: JGE04 (500 ug/mL dose)_rep1

description: Library name: T_7-1-4

value: mix-> extraction of Ethanol extracts of JGT (JGE04;500 ug/mL dose)_rep1


title: N2, FLAG, eCLIP, Rep2

description: asynchronized worm culture


title: PHX4686, FLAG, eCLIP, Rep1

description: asynchronized worm culture


title: day00.H3K4me1.Rep1

value: Embryonic stem cell

value: day00.Input.Batch1.Rep1 in GSE116862


title: day00.H3K4me1.Rep2

value: day00.Input.Batch1.Rep2 in GSE116862


title: day80.H3K27me3.Rep2

value: ES derived ventricular cardiomyocyte

value: day80.Input.Batch1.Rep2 in GSE116862

value: H3K27me3 (Active Motif, AM61017)


title: N2, FLAG, eCLIP, Rep1

description: asynchronized worm culture

value: WT


title: Granta519EBF1KIcl27,8hr,EBF1ChIPseq,rep2

description: Library name: s50_221207_Granta519EBF1KI_cl27_8hr_EBF1_CHIPseq_rep2_S14_R1.fastq.gz

value: Mantle Cell Lymphoma


title: Granta519EBF1KIcl27,24hr,EBF1ChIPseq,rep1

description: Library name: s51_221207_Granta519EBF1KI_cl27_24hr_EBF1_CHIPseq_rep1_S15_R1.fastq.gz


title: JGE02 (20 ug/mL dose)_rep3

description: Library name: T_6-3-6

value: neuronal cell

value: mix-> extraction of Ethanol extracts of JGT (JGE02;20 ug/mL dose)_rep3


title: JGE02 (100 ug/mL dose)_rep3

description: Library name: T_6-3-5

value: mix-> extraction of Ethanol extracts of JGT (JGE02;100 ug/mL dose)_rep3


title: PHX4686, GFP-FLAG-DKC-1, Input, Rep2

description: asynchronized worm culture


title: day80.H3K27me3.Rep1

value: H9 MLC2v:H2B

value: day80.Input.Batch1.Rep1 in GSE116862


title: Granta519EBF1KIcl27,8hr,EBF1ChIPseq,rep1

description: Library name: s49_221207_Granta519EBF1KI_cl27_8hr_EBF1_CHIPseq_rep1_S13_R1.fastq.gz


title: JGE02 (500 ug/mL dose)_rep3

description: Library name: T_6-3-4

value: mix-> extraction of Ethanol extracts of JGT (JGE02;500 ug/mL dose)_rep3


title: PHX4686, GFP-FLAG-DKC-1, Input, Rep1

description: asynchronized worm culture

value: whole organism

value: dkc-1(syb4686[gfp::3xFLAG::dkc-1]) III


title: Granta519EBF1KIcl27,6hWO,EBF1ChIPseq,rep2

description: Library name: s14_240427_Granta519cl27_6hWO_EBF1_ChIP_rep2_S14_R1.fastq.gz


title: day15.H3K27me3.Rep2

value: ES derived primitive cardiomyocite

value: day15.Input.Batch1.Rep2 in GSE116862


title: N2, Input, Rep2

description: asynchronized worm culture


title: JGE01 (20 ug/mL dose)_rep3

description: Library name: T_6-3-3

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;20 ug/mL dose)_rep3


title: Granta519EBF1KIcl27,6hr,EBF1ChIPseq,rep1

description: Library name: s47_221207_Granta519EBF1KI_cl27_6hr_EBF1_CHIPseq_rep1_S11_R1.fastq.gz


title: day15.H3K27me3.Rep1

value: day15.Input.Batch1.Rep1 in GSE116862


title: JGE01 (100 ug/mL dose)_rep3

description: Library name: T_6-3-2

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;100 ug/mL dose)_rep3


title: N2, Input, Rep1

description: asynchronized worm culture


title: day07.H3K27me3.Rep1

value: ES derived cardiac progenitor cells

value: day07.Input.Batch1.Rep1 in GSE116862


title: HH5Multiome_GEX

city: Boston

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: scRNA-seq library

data_processing:
Demultiplexing, cellranger-arc pipeline (version 2.0.0)
Upon generation of the UMI count matrix via cellranger-arc’s count function, downstream processing was performed using Seurat (version 4.3.0) and Signac (version 1.8.0). In addition to cellranger’s initial cell quality filtering
Assembly: galGal6
Supplementary files format and content: .txt file displaying cell barcodes with UMAP embeddings, sample of origin, and cluster assignment

organism: Gallus gallus

source_name: HH5 whole embryo

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

extract_protocol: After enzymatic dissociation, embryos were processed using the 10x Multiome protocol

tag: developmental stage

tag: axis

value: antero-posterior


title: JGE02 (20 ug/mL dose)_rep2

description: Library name: T_6-2-6

value: mix-> extraction of Ethanol extracts of JGT (JGE02;20 ug/mL dose)_rep2


title: day05.H3K27me3.Rep2

value: ES derived cardiac mesoderm

value: day05.Input.Batch1.Rep2 in GSE116862

value: H3K27me3 (Active Motif, AM61017)


title: JGE01 (500 ug/mL dose)_rep3

description: Library name: T_6-3-1

value: neuronal cell

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


title: HH5Multiome_ATAC

description: scATAC-seq library


title: Granta519EBF1KIcl27,0hr,EBF1ChIPseq,rep2

description: Library name: s46_221207_Granta519EBF1KI_cl27_0hr_EBF1_CHIPseq_rep2_S10_R1.fastq.gz

value: Mantle Cell Lymphoma

value: untreated


title: Granta519EBF1KIcl27,6hr,SMC1ChIP,rep1

description: Library name: s24_230103_Granta519EBF1KI_cl27_6hr_SMC1_ChIP_rep1_S24_R1.fastq.gz


title: HH2antEpi_XAV_3

description: ATAC-seq library

data_processing:
Trimming of Nextera adapter sequences was performed using cutadapt (version 3.4) using the following parameters: “-a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”. Trimmed reads were aligned to the galGal6 chicken reference genome using bowtie2 (version 2.4.4) with the following arguments: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000”.
Bam alignment files were indexed using samtools (version 1.10), followed by marking of duplicate reads using Picard’s (version 2.26.2) MarkDuplicates function. Duplicate reads were then removed using samtools view with the following arguments: “-F 1804 -f 2”. Peaks were called with macs2 (version 2.2.7.1) using the parameters: “-f BAMPE -g 1e9 -q 0.05 --call-summits”
Assembly: galGal6
Supplementary files format and content: bigwigs were generated from Bam files using DeepTools’ bamCoverage function (version 3.5.1) with the following arguments: “--binSize 5 --normalizeUsing RPKM --extendReads”. Reads in peaks were counted using DiffBind (version 3.4.11).

source_name: HH2 anterior Epiblast

growth_protocol: HH2 stage chicken embryos were obtained from fertilized eggs. The anterior epiblast of 3 embryos per sample were dissected in Ringers solution and cultured as described bellow.

extract_protocol: After enzymatic tissue dissociation cells were processed using the OMNI-ATAC-Seq protocol (Corces et al., 2017)

treatment_protocol: After dissection, samples were transfered to 96-well plates covered with fibronectnin and cultured for 24h in the presence of 10uM CHIR99021, 10uM XAV or, as a control, DMSO.

tag: tissue

value: anterior epiblast

value: XAV 10 uM


title: JGE02 (100 ug/mL dose)_rep2

description: Library name: T_6-2-5

tag: cell line

value: mix-> extraction of Ethanol extracts of JGT (JGE02;100 ug/mL dose)_rep2


title: Granta519EBF1KIcl27,24hr,SMC1ChIP,rep1

description: Library name: s23_230103_Granta519EBF1KI_cl27_24hr_SMC1_ChIP_rep1_S23_R1.fastq.gz

tag: cell type


title: JGE02 (500 ug/mL dose)_rep2

description: Library name: T_6-2-4

value: mix-> extraction of Ethanol extracts of JGT (JGE02;500 ug/mL dose)_rep2


title: day05.H3K27me3.Rep1

tag: genotype

value: H9 MLC2v:H2B

value: day05.Input.Batch1.Rep1 in GSE116862


title: day02.H3K27me3.Rep2

value: ES derived mesoderm

value: day02.Input.Batch1.Rep2 in GSE116862


title: Granta519EBF1KIcl27,6hr,SMC1ChIP,rep2

description: Library name: s22_230103_Granta519EBF1KI_cl27_6hr_SMC1_ChIP_rep2_S22_R1.fastq.gz

tag: treatment


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: Granta519EBF1KIcl27,6hr,EBF1ChIPseq,rep2

description: Library name: s48_221207_Granta519EBF1KI_cl27_6hr_EBF1_CHIPseq_rep2_S12_R1.fastq.gz


title: HH2antEpi_XAV_1

description: ATAC-seq library


title: day02.H3K27me3.Rep1

value: day02.Input.Batch1.Rep1 in GSE116862


title: Granta519EBF1KIcl27,24hr,SMC1ChIP,rep2

description: Library name: s21_230103_Granta519EBF1KI_cl27_24hr_SMC1_ChIP_rep2_S21_R1.fastq.gz


title: day00.H3K27me3.Rep2

value: Embryonic stem cell

value: day00.Input.Batch1.Rep2 in GSE116862


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: HH2antEpi_DMSO_3

description: ATAC-seq library

value: DMSO


title: Granta519EBF1KIcl27,0hr,SMC1ChIP,rep2

description: Library name: s20_230103_Granta519EBF1KI_cl27_0hr_SMC1_ChIP_rep2_S20_R1.fastq.gz


title: Granta519EBF1KIcl27,0hr,EBF1ChIPseq,rep1

description: Library name: s45_221207_Granta519EBF1KI_cl27_0hr_EBF1_CHIPseq_rep1_S9_R1.fastq.gz


title: HH2antEpi_DMSO_2

description: ATAC-seq library


title: day07.H3K27me3.Rep2

value: ES derived cardiac progenitor cells

value: day07.Input.Batch1.Rep2 in GSE116862

value: H3K27me3 (Active Motif, AM61017)


title: JGE01 (100 ug/mL dose)_rep2

description: Library name: T_6-2-2

value: neuronal cell

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


title: day00.H3K27me3.Rep1

value: day00.Input.Batch1.Rep1 in GSE116862


title: JGE02 (100 ug/mL dose)_rep1

description: Library name: T_6-1-5

value: mix-> extraction of Ethanol extracts of JGT (JGE02;100 ug/mL dose)_rep1


title: HH2antEpi_DMSO_1

description: ATAC-seq library

value: anterior epiblast


title: JGE02 (20 ug/mL dose)_rep1

description: Library name: T_6-1-6

value: mix-> extraction of Ethanol extracts of JGT (JGE02;20 ug/mL dose)_rep1


title: Granta519EBF1KIcl27,24hr,H3K27me3ChIP,rep2

description: Library name: s18_230103_Granta519EBF1KI_cl27_24hr_H3K27me3_ChIP_rep2_S18_R1.fastq.gz

value: Mantle Cell Lymphoma


title: day80.ATAC.Rep1

extract_protocol: ATAC-seq was performed on 50,000 cells as described previously with minor modifications (Buenrostro et al. 2013). Cell suspensions were thawed at 37°C and pelleted for 5 min at 500 g at 4°C. Cell pellets were resuspended in 250 µl permeabilization buffer (5 % BSA, 0.2 % IGEPAL-CA630, 1mM DTT and cOMplete EDTA-free protease inhibitor cocktail (Roche) in PBS) and incubated on an overhead shaker for 5 min at 4°C, followed by centrifugation for 5 min at 500 g. Pellet was resupended in 25 µl tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM K-acetate, 11 mM Mg-acetate, 17.6 % DMF) and counted on a hemocytometer.  40K nuclei were used for tagmentation and the reaction volume was adjusted to 19 µl using tagmentation buffer. After addition of 1 µl Tn5 transposomes (Illumina) tagmentation was performed at 37°C for 60 min with shaking (500 rpm). Next, samples were purified using MinElute columns (Qiagen), PCR-amplified for 9 cycles with NEBNext® High-Fidelity 2X PCR Master Mix (NEB, 72°C 5 min, 98°C 30 s,[ 98°C 10 s, 63°C 30 s, 72°C 60 s] x cycles, 72°C ∞). Amplified libraries were purified using MinElute columns (Qiagen) and Ampure XP Bead (Beckmann Coulter).

value: ES derived ventricular cardiomyocyte

value: H9 MLC2v:H2B


title: Granta519EBF1KIcl27,24hr,H3K27me3ChIP,rep1

description: Library name: s17_230103_Granta519EBF1KI_cl27_24hr_H3K27me3_ChIP_rep1_S17_R1.fastq.gz


title: HH2antEpi_XAV_2

description: ATAC-seq library

value: XAV 10 uM


title: JGE02 (500 ug/mL dose)_rep1

description: Library name: T_6-1-4

value: mix-> extraction of Ethanol extracts of JGT (JGE02;500 ug/mL dose)_rep1


title: HH2antEpi_CHIR_2

description: ATAC-seq library

value: CHIR 10 uM


title: Granta519EBF1KIcl27,24hr,H3K4me1ChIP,rep2

description: Library name: s16_230103_Granta519EBF1KI_cl27_24hr_H3K4me1_ChIP_rep2_S16_R1.fastq.gz


title: day15.ATAC.Rep2

value: ES derived primitive cardiomyocite


title: HH2antEpi_CHIR_1

description: ATAC-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: Granta519EBF1KIcl27,24hr,H3K4me1ChIP,rep1

description: Library name: s15_230103_Granta519EBF1KI_cl27_24hr_H3K4me1_ChIP_rep1_S15_R1.fastq.gz


title: day15.ATAC.Rep1


title: Granta519EBF1KIcl27,24hr,H3K27acChIP,rep2

description: Library name: s14_230103_Granta519EBF1KI_cl27_24hr_H3K27ac_ChIP_rep2_S14_R1.fastq.gz


title: H3K27ac_HH3_AP6

description: C&R library

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: HH3 embryo

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: antero-posterior

tag: antibody


title: JGE01 (100 ug/mL dose)_rep1

description: Library name: T_6-1-2

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


title: day07.ATAC.Rep2

value: ES derived cardiac progenitor cells


title: day07.ATAC.Rep1


title: JGE01 (500 ug/mL dose)_rep1

description: Library name: T_6-1-1

value: neuronal cell

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


title: Granta519EBF1KIcl27,24hr,H3K27acChIP,rep1

description: Library name: s13_230103_Granta519EBF1KI_cl27_24hr_H3K27ac_ChIP_rep1_S13_R1.fastq.gz


title: Granta519EBF1KIcl27,0hr,SMC1ChIP,rep1

description: Library name: s19_230103_Granta519EBF1KI_cl27_0hr_SMC1_ChIP_rep1_S19_R1.fastq.gz

value: untreated


title: day05.ATAC.Rep2

value: ES derived cardiac mesoderm


title: H3K27ac_HH3_AP4

description: C&R library


title: Granta519EBF1KIcl27,6hr,H3K27me3ChIP,rep2

description: Library name: s12_230103_Granta519EBF1KI_cl27_6hr_H3K27me3_ChIP_rep2_S12_R1.fastq.gz


title: day80.ATAC.Rep2


title: JGW08 (20 ug/mL dose)_rep3

description: Library name: T_5-3-6

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


title: HH2antEpi_CHIR_3

description: ATAC-seq library

value: anterior epiblast


title: day05.ATAC.Rep1


title: H3K27ac_HH3_AP3

description: C&R library


title: JGW08 (500 ug/mL dose)_rep3

description: Library name: T_5-3-4

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


title: H3K27ac_HH3_AP2

description: C&R library


title: JGW07 (20 ug/mL dose)_rep3

description: Library name: T_5-3-3

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


title: day02.ATAC.Rep2

value: ES derived mesoderm

value: H9 MLC2v:H2B


title: Granta519EBF1KIcl27,6hr,H3K4me1ChIP,rep2

description: Library name: s10_230103_Granta519EBF1KI_cl27_6hr_H3K4me1_ChIP_rep2_S10_R1.fastq.gz

value: Mantle Cell Lymphoma


title: H3K27ac_HH3_AP1

description: C&R library


title: Granta519EBF1KIcl27,6hr,H3K27me3ChIP,rep1

description: Library name: s11_230103_Granta519EBF1KI_cl27_6hr_H3K27me3_ChIP_rep1_S11_R1.fastq.gz


title: day02.ATAC.Rep1


title: JGW07 (100 ug/mL dose)_rep3

description: Library name: T_5-3-2

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


title: Granta519EBF1KIcl27,6hr,H3K4me1ChIP,rep1

description: Library name: s09_230103_Granta519EBF1KI_cl27_6hr_H3K4me1_ChIP_rep1_S9_R1.fastq.gz


title: H3K27ac_HH2_AP5

description: C&R library

source_name: HH2 embryo


title: day00.ATAC.Rep1

value: Embryonic stem cell


title: Granta519EBF1KIcl27,6hr,H3K27acChIP,rep2

description: Library name: s08_230103_Granta519EBF1KI_cl27_6hr_H3K27ac_ChIP_rep2_S8_R1.fastq.gz


title: day00.ATAC.Rep2


title: H3K27ac_HH3_AP5

description: C&R library


title: H3K27ac_HH2_AP4

description: C&R library


title: JGW07 (500 ug/mL dose)_rep3

description: Library name: T_5-3-1

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


title: H3K27ac_HH2_AP3

description: C&R library

value: antero-posterior


title: Granta519EBF1KIcl27,6hr,H3K27acChIP,rep1

description: Library name: s07_230103_Granta519EBF1KI_cl27_6hr_H3K27ac_ChIP_rep1_S7_R1.fastq.gz


title: JGW08 (20 ug/mL dose)_rep2

description: Library name: T_5-2-6

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


title: JGW08 (100 ug/mL dose)_rep2

description: Library name: T_5-2-5

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


title: JGW08 (100 ug/mL dose)_rep3

description: Library name: T_5-3-5

value: neuronal cell

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


title: H3K27ac_HH2_AP2

description: C&R library


title: Granta519EBF1KIcl27,0hr,H3K27me3ChIP,rep2

description: Library name: s06_230103_Granta519EBF1KI_cl27_0hr_H3K27me3_ChIP_rep2_S6_R1.fastq.gz

value: untreated


title: poly(A) RNAseq eRF1-dTAG mESCs, biological replicate B

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description: B6291_1 RNAseq_counts.csv

data_processing:
Basecalls performed using CASAVA version 1.4
sequenced reads were trimmed for adapter sequence using cutadapt. The resulting reads with a length between 20 and 35nt were retained for mapping by HISAT2 (v2.1.0).
Assembly: mm10
Supplementary files format and content: csv files containing the counts (in counts per million reads) for each sample

molecule: polyA RNA

growth_protocol: All the mESCs used in this study were cultured on 0.5% gelatin-coated tissue culture plates in the 2i + Lif medium (DMEM/F-12, 2% FBS, 2mM L-Glutamine, 0.1mM MEM NEAA, 1% Penicillin-Streptomycin, 0.1 mM β-mercaptoethanol and 1000 U/mL mLIF, 1 x N2N27, 3 uM CHIR99021 and 1 uM PD0325901).

extract_protocol:
After RNase1 digestion of cell lysate, 80S ribosomes were isolated by sucrose density gradient. Then the ribosome protected fragments were isolated via 15% UREA-PAGE gel.
Ribosome profiling (small RNA-seq)

treatment_protocol: 1hr 500nM dTAG-13

value: mESCs

value: Wild-type


title: poly(A) RNAseq eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate B

description: B6291D_1 RNAseq_counts.csv

value: 1hr 500nM dTAG-13


title: Granta519EBF1KIcl27,0hr,H3K27me3ChIP,rep1

description: Library name: s05_230103_Granta519EBF1KI_cl27_0hr_H3K27me3_ChIP_rep1_S5_R1.fastq.gz


title: H3K27ac_HH2_AP1

description: C&R library


title: JGW08 (500 ug/mL dose)_rep2

description: Library name: T_5-2-4

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


title: poly(A) RNAseq eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate A

description: A6291D_1 RNAseq_counts.csv


title: Granta519EBF1KIcl27,0hr,H3K4me1ChIP,rep2

description: Library name: s04_230103_Granta519EBF1KI_cl27_0hr_H3K4me1_ChIP_rep2_S4_R1.fastq.gz


title: JGW07 (20 ug/mL dose)_rep2

description: Library name: T_5-2-3

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


title: H3K27ac_HH1_AP5

description: C&R library

source_name: HH1 embryo


title: Granta519EBF1KIcl27,0hr,H3K4me1ChIP,rep1

description: Library name: s03_230103_Granta519EBF1KI_cl27_0hr_H3K4me1_ChIP_rep1_S3_R1.fastq.gz


title: H3K27ac_HH1_AP4

description: C&R library


title: poly(A) RNAseq eRF1-dTAG mESCs, biological replicate A

description: A6291_1 RNAseq_counts.csv


title: JGW07 (500 ug/mL dose)_rep2

description: Library name: T_5-2-1

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


title: H3K27ac_HH1_AP3

description: C&R library


title: Granta519EBF1KIcl27,0hr,H3K27acChIP,rep2

description: Library name: s02_230103_Granta519EBF1KI_cl27_0hr_H3K27ac_ChIP_rep2_S2_R1.fastq.gz


title: JGW08 (20 ug/mL dose)_rep1

description: Library name: T_5-1-6

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


title: ribosome profiling eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate A

description: 6291_1A riboseq_counts.csv

molecule: cytoplasmic RNA


title: H3K27ac_HH1_AP2

description: C&R library


title: Granta519EBF1KIcl27,0hr,H3K27acChIP,rep1

description: Library name: s01_230103_Granta519EBF1KI_cl27_0hr_H3K27ac_ChIP_rep1_S1_R1.fastq.gz

value: Mantle Cell Lymphoma


title: ribosome profiling eRF1-dTAG mESCs, biological replicate B

description: 6291_0B riboseq_counts.csv


title: Granta519, SMC1, HiChIP

description: Library name: S01_211207_Granta519Cas9_SMC1_HiChIP

data_processing:
Raw reads for each HiChIP sample were processed with HiC-Pro to obtain putative interactions with default parameters.
Assembly: hg19
Supplementary files format and content: .hic formatted file for juicebox viewing of contact matrices
Library strategy: HiChIP

extract_protocol:
HiChIP was performed as previously described (Petrovic et al., 2019).
NEBNext Ultra II DNA library Prep Kit for Illumina (NEB cat# E7645S)


title: JGW08 (100 ug/mL dose)_rep1

description: Library name: T_5-1-5

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


title: H3K27ac_HH1_AP1

description: C&R library


title: Granta519, EBF1_MP, HiChIP

description: Library name: S02_210917_Granta519Cas9_EBF1_MP_HiCHIP


title: H3K27ac_HH5_AP7

description: C&R library

source_name: HH5 embryo


title: Granta519, EBF1_RG, HiChIP

description: Library name: S01_210917_Granta519Cas9_EBF1_RG_HiCHIP


title: ribosome profiling eRF1-dTAG mESCs, biological replicate A

description: 6291_0A riboseq_counts.csv


title: JGW08 (500 ug/mL dose)_rep1

description: Library name: T_5-1-4

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


title: JGW07 (100 ug/mL dose)_rep1

description: Library name: T_5-1-2

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


title: JGW07 (20 ug/mL dose)_rep1

description: Library name: T_5-1-3

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


title: ribosome profiling Gcn2 knockout eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate B

description: 5702_1A riboseq_counts.csv

value: Gcn2 knockout


title: ribosome profiling Gcn2 knockout eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate A

description: 5702_1A riboseq_counts.csv


title: ribosome profiling eRF1-dTAG mESCs treated with 1hr 500nM dTAG-13, biological replicate B

description: 6291_1B riboseq_counts.csv


title: H3K27ac_HH5_AP6

description: C&R library

value: antero-posterior


title: ribosome profiling Gcn2 knockout eRF1-dTAG mESCs untreated, biological replicate B

description: 5702_0B riboseq_counts.csv


title: H3K27ac_HH5_AP5

description: C&R library


title: H3K27ac_HH5_AP4

description: C&R library


title: ribosome profiling Gcn2 knockout eRF1-dTAG mESCs untreated, biological replicate A

description: 5702_0A riboseq_counts.csv


title: JGW07 (500 ug/mL dose)_rep1

description: Library name: T_5-1-1

value: neuronal cell

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


title: JGW07 (100 ug/mL dose)_rep2

description: Library name: T_5-2-2

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


title: Granta519cl27,72hr,ATACseq,rep2

description: Library name: s44_230103_Granta519EBF1KI_cl27_72hr_ATACseq_rep2_S20_R1.fastq.gz

data_processing:
Reads from ATAC-seq experiments were trimmed with Trim Galore and aligned to the Ensembl GRCh37.75 primary assembly using BWA
Assembly: hg19
Supplementary files format and content: .bw formatted file for genome browser viewing

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro, 2013)
Illumina Nextera DNA Library Prep Kit (cat# FC-121-1030)


title: Granta519cl27,72hr,ATACseq,rep3

description: Library name: s45_230103_Granta519EBF1KI_cl27_72hr_ATACseq_rep3_S21_R1.fastq.gz


title: Granta519cl27,72hr,ATACseq,rep1

description: Library name: s43_230103_Granta519EBF1KI_cl27_72hr_ATACseq_rep1_S19_R1.fastq.gz


title: JGW06 (20 ug/mL dose)_rep3

description: Library name: T_4-3-6

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).

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


title: JGW06 (100 ug/mL dose)_rep3

description: Library name: T_4-3-5

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


title: Granta519cl27,48hr,ATACseq,rep3

description: Library name: s42_230103_Granta519EBF1KI_cl27_48hr_ATACseq_rep3_S18_R1.fastq.gz


title: JGW06 (500 ug/mL dose)_rep3

description: Library name: T_4-3-4

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


title: H3K27ac_HH5_AP2

description: C&R library


title: H3K27ac_HH5_AP3

description: C&R library


title: H3K27ac_HH5_AP1

description: C&R library


title: BatchC_Vehicle_rep2

description: Library name: C1-2-2

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.

value: Hepatocyte


title: BatchC_Vehicle_rep3

description: Library name: C1-3-2


title: JGW05 (20 ug/mL dose)_rep3

description: Library name: T_4-3-3

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

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


title: bCat_Lef1_HH5_AP3

description: C&R library


title: BatchC_non-treat_rep2

description: Library name: C1-2-1


title: Granta519cl27,24hr,ATACseq,rep3

description: Library name: s36_221120_Granta519EBF1KI_cl27_24hr_ATACseq_rep3_S36_R1.fastq.gz


title: Granta519cl27,48hr,ATACseq,rep1

description: Library name: s40_230103_Granta519EBF1KI_cl27_48hr_ATACseq_rep1_S16_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: bCat_Lef1_HH5_AP2

description: C&R library


title: BatchC_Vehicle_rep1

description: Library name: C1-1-2


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: bCat_Lef1_HH5_AP1

description: C&R library


title: JGW06 (20 ug/mL dose)_rep2

description: Library name: T_4-2-6

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


title: Granta519cl27,24hr,ATACseq,rep2

description: Library name: s35_221120_Granta519EBF1KI_cl27_24hr_ATACseq_rep2_S35_R1.fastq.gz

value: Mantle Cell Lymphoma


title: E1_ATAC_AP07

description: ATAC-seq library

source_name: AP embryo ATAC #E1

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


title: BatchC_non-treat_rep1

description: Library name: C1-1-1


title: Granta519cl27,24hr,ATACseq,rep1

description: Library name: s34_221120_Granta519EBF1KI_cl27_24hr_ATACseq_rep1_S34_R1.fastq.gz


title: Granta519cl27,8hr,ATACseq,rep3

description: Library name: s33_221120_Granta519EBF1KI_cl27_8hr_ATACseq_rep3_S33_R1.fastq.gz


title: BatchC_non-treat_rep3

description: Library name: C1-3-1


title: BatchB_Vehicle_rep3

description: Library name: B1-3-2


title: BatchB_non-treat_rep3

description: Library name: B1-3-1


title: Granta519cl27,48hr,ATACseq,rep2

description: Library name: s41_230103_Granta519EBF1KI_cl27_48hr_ATACseq_rep2_S17_R1.fastq.gz


title: JGW06 (100 ug/mL dose)_rep2

description: Library name: T_4-2-5

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


title: Granta519cl27,8hr,ATACseq,rep2

description: Library name: s32_221120_Granta519EBF1KI_cl27_8hr_ATACseq_rep2_S32_R1.fastq.gz


title: JGW06 (500 ug/mL dose)_rep2

description: Library name: T_4-2-4

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


title: E1_ATAC_AP06

description: ATAC-seq library


title: E1_ATAC_AP05

description: ATAC-seq library


title: E1_ATAC_AP04

description: ATAC-seq library


title: BatchB_non-treat_rep2

description: Library name: B1-2-1


title: BatchB_Vehicle_rep2

description: Library name: B1-2-2


title: Granta519cl27,8hr,ATACseq,rep1

description: Library name: s31_221120_Granta519EBF1KI_cl27_8hr_ATACseq_rep1_S31_R1.fastq.gz


title: JGW05 (100 ug/mL dose)_rep2

description: Library name: T_4-2-2

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


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: E1_ATAC_AP03

description: ATAC-seq library

value: antero-posterior


title: JGW05 (20 ug/mL dose)_rep2

description: Library name: T_4-2-3

value: neuronal cell

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


title: BatchB_non-treat_rep1

description: Library name: B1-1-1


title: BatchA_Vehicle_rep3

description: Library name: A1-3-2


title: E1_ATAC_AP01

description: ATAC-seq library


title: Granta519cl27,0hr,ATACseq,rep3

description: Library name: s27_221120_Granta519EBF1KI_cl27_0hr_ATACseq_rep3_S27_R1.fastq.gz

value: untreated


title: E2_HH3_AP_06

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

source_name: AP embryo #HH3E2

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.

value: embryo


title: JGW06 (20 ug/mL dose)_rep1

description: Library name: T_4-1-6

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


title: Granta519cl27,6hr,ATACseq,rep1

description: Library name: s28_221120_Granta519EBF1KI_cl27_6hr_ATACseq_rep1_S28_R1.fastq.gz


title: BatchA_non-treat_rep3

description: Library name: A1-3-1


title: Granta519cl27,0hr,ATACseq,rep1

description: Library name: s25_221120_Granta519EBF1KI_cl27_0hr_ATACseq_rep1_S25_R1.fastq.gz


title: Granta519cl27,0hr,ATACseq,rep2

description: Library name: s26_221120_Granta519EBF1KI_cl27_0hr_ATACseq_rep2_S26_R1.fastq.gz


title: JGW06 (500 ug/mL dose)_rep1

description: Library name: T_4-1-4

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


title: BatchA_Vehicle_rep2

description: Library name: A1-2-2

value: Hepatocyte


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: BatchA_non-treat_rep2

description: Library name: A1-2-1


title: E2_HH3_AP_04

description: Tomo-seq library


title: Granta519cl27,24hWO,ATAC,rep3

description: Library name: s09_240417_Granta519cl27_24hWO_ATAC_rep3_S9_R1.fastq.gz


title: BatchB_Vehicle_rep1

description: Library name: B1-1-2


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: E2_HH3_AP_03

description: Tomo-seq library


title: Granta519cl27,6hr,ATACseq,rep2

description: Library name: s29_221120_Granta519EBF1KI_cl27_6hr_ATACseq_rep2_S29_R1.fastq.gz


title: Granta519cl27,6hr,ATACseq,rep3

description: Library name: s30_221120_Granta519EBF1KI_cl27_6hr_ATACseq_rep3_S30_R1.fastq.gz


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: E1_ATAC_AP02

description: ATAC-seq library


title: Granta519cl27,24hWO,ATAC,rep2

description: Library name: s08_240417_Granta519cl27_24hWO_ATAC_rep2_S8_R1.fastq.gz


title: BatchA_non-treat_rep1

description: Library name: A1-1-1


title: E2_HH3_AP_02

description: Tomo-seq library


title: JGW06 (100 ug/mL dose)_rep1

description: Library name: T_4-1-5

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


title: E2_HH3_AP_05

description: Tomo-seq library


title: Granta519cl27,24hWO,ATAC,rep1

description: Library name: s07_240417_Granta519cl27_24hWO_ATAC_rep1_S7_R1.fastq.gz

value: Mantle Cell Lymphoma


title: JGE01 (20 ug/mL dose)_rep3

description: Library name: R6-3-3

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;20 ug/mL dose)_rep3


title: E2_HH3_AP_01

description: Tomo-seq library


title: JGW04 (100 ug/mL dose)_rep3

description: Library name: T_3-3-5

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


title: Granta519cl27,6hWO,ATAC,rep2

description: Library name: s02_240417_Granta519cl27_6hWO_ATAC_rep2_S2_R1.fastq.gz


title: JGW04 (500 ug/mL dose)_rep3

description: Library name: T_3-3-4

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


title: JGE01 (100 ug/mL dose)_rep3

description: Library name: R6-3-2

value: mix-> extraction of Ethanol extracts of Jakyak (PR)(JGE01;100 ug/mL dose)_rep3


title: E1_HH3_AP_05

description: Tomo-seq library

source_name: AP embryo #HH3E1

value: antero-posterior


title: Granta519cl27,6hWO,ATAC,rep1

description: Library name: s01_240417_Granta519cl27_6hWO_ATAC_rep1_S1_R1.fastq.gz


title: JGW06 (20 ug/mL dose)_rep1

description: Library name: R4-1-6

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


title: JGW04 (20 ug/mL dose)_rep2

description: Library name: T_3-2-6

value: neuronal cell

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


title: E1_HH3_AP_04

description: Tomo-seq library

value: embryo


title: Trichostatin A_rep3

description: Library name: R1-1-4

value: Trichostatin A_rep2


title: BatchA_Vehicle_rep1

description: Library name: A1-1-2


title: JGW04 (100 ug/mL dose)_rep2

description: Library name: T_3-2-5

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


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

description: Library name: Sample 46

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

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.


title: E1_HH3_AP_03

description: Tomo-seq library


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

description: Library name: Sample 45


title: JGW04 (500 ug/mL dose)_rep2

description: Library name: T_3-2-4

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


title: JGE08 (500 ug/mL dose)_rep3

description: Library name: T_9-3-4

value: Hepatocyte

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


title: JGW04 (20 ug/mL dose)_rep3

description: Library name: T_3-3-6

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


title: JGW04 (20 ug/mL dose)_rep1

description: Library name: T_3-1-6

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


title: Granta519cl27,6hWO,ATAC,rep3

description: Library name: s03_240417_Granta519cl27_6hWO_ATAC_rep3_S3_R1.fastq.gz

value: Mantle Cell Lymphoma


title: E1_HH3_AP_01

description: Tomo-seq library


title: JGW04 (100 ug/mL dose)_rep1

description: Library name: T_3-1-5

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


title: E1_HH3_AP_06

description: Tomo-seq library