title: ds_gcn5_rep3

city: Utrecht

first: Aniek

last: Janssen

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Read QC (FastQC)
Sequence trimming (TrimGalore)
rRNA removal (SortMeRNA)
Mapping and read-group annotation (STAR)
Alignment-QC (RSeQC, Preseq)
PCR duplicate detection (Sambamba MarkDup)
Gene-expression/biotype quantification (featureCounts)
Gene-expression normalization (edgeR,DESeq2)
Transcript quantification (Salmon)
Variant calling (GATK4)
QC report (MultiQC,CustomQC)
Assembly: Drosophila_melanogaster. BDGP6.32
Supplementary files format and content: Tab delimited matrix with DeSeq2 feature counts

organism: Drosophila melanogaster

growth_protocol: cells were cultured in CCM3 medium supplemented by Antibiotic Antimycotic Solution

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy micro kit
Libraries were constructed using the TruSeq RNA stranded polyA kit according to manufacturers instructions

treatment_protocol: cells were transfectd with double stranded (ds) RNA against gene of interests: yellow as control, and target genes are elp3, gcn5 and nej for 5 days prior to RNA extraction

value: double stranded gcn5


title: ds_nej_rep1

status: Public on Aug 23 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: cell line

tag: treatment

value: double stranded nej


title: Vehicle 4

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

country: USA

institute: University of Chicago

data_processing:
Data was analyzed using Galaxy.
Reads were trimmed using trimmomatic. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel file with raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: islet

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: Mice were treated with vehicle or 30 mg/kg VLX-1005 SDD

tag: tissue

value: islet

tag: genotype

value: vehicle


title: Vehicle 3


title: M0 Vehicle 3

source_name: bone marrow derived macrophages

treatment_protocol: M0 or M1 macrophages were treated with vehicle or VLX-1005

value: bone marrow derived macrophages

tag: cell type

value: M0 macrophages


title: ds_gcn5_rep1


title: ds_elp3_rep2

value: double stranded elp3


title: ds_gcn5_rep2


title: Vehicle 1


title: Vehicle 2


title: ds_elp3_rep3


title: ds_elp3_rep1


title: RIP1-Tag5 wild type PNET tumor, mouse 3

city: Perth

first: Alistair

middle: R. R.

last: Forrest

state: WA

address: 6 Verdun Street, Nedlands

country: Australia

institute: Harry Perkins Institute of Medical Research, The University of Western Australia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq libraries were processed using Cell Ranger 2.1.1 with mm10-2.1.0 reference. Raw gene-barcode matrices from Cell Ranger output were used for downstream processing. Cells were distinguished from background noise using EmptyDrops. Outlier cells with high ratio of number of detected UMI to genes (> 3 median absolute deviations from median) were removed using Scater. Cells with less than 500 genes were excluded. Seurat v2 was used for sample integration and analysis.
Assembly: mm10
Supplementary files format and content: Matrices of raw gene by cell counts generated by Cell Ranger, in MTX format, from "raw_gene_bc_matrices" folder, not filtered.

source_name: PNET tumor

growth_protocol: autochthonous pancreatic neuroendocrine tumors from a transgenic mouse line (RIP1-Tag5) harvested from mice at 27 weeks of age

extract_protocol:
Tumors from 27 week-old RIP1-Tag5 mice were harvested and digested as previously described. Briefly, tumors were placed in FACS buffer (PBS, 1% FBS) on ice and minced using a scalpel. Tumors were digested under slow rotation in PBS containing 0.8 mg/ml dispase (Invitrogen), 0.2 mg/ml Collagenase P (Roche) and 0.1mg/ml DNAse I (Worthington Biochemical), at 37C for 20 min. Digestion was stopped with FBS and cells were resuspended in FACS buffer and viability assessed.
Single cell libraries were constructed from pooled tumors from three RIP1-Tag5 mice using the 10x Chromium 3’ v2 chemistry following the manufacturer’s protocol (10x Genomics).

treatment_protocol: untreated

value: PNET tumor

tag: strain

value: transgenic mouse line (RIP1-Tag5)

tag: age

value: 27 weeks


title: ds_yellow_rep3

value: double stranded yellow


title: 4sU labeling, 500µM, rep2, SLAMseq

city: Bethesda

first: Jun

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Raw sequencing data of SLAM-seq were first trimmed using cutadpt (v1.15) and then analyzed using SLAM-DUNK (v0.4.3) to map, filter and quantify reads containing T-to-C mutation.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files
Library strategy: SLAM-seq

source_name: lymph nodes

extract_protocol:
For single cell RNA sequencing, single cell suspension was prepared for 10X Genomics sample loading. For RNA-seq, RNA was extracted using RNeasy Mini Kit (Qiagen).
For NOTE-seq, Libraries were constructed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E) with serval additional steps detaied in the Method section. For regular 10xgenomics, libraries were constructed using  Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E). For SLAM-seq, 2 µg RNA were combined with 10 mM iodoacetamide (Sigma-Aldrich, St. Louis, MO, USA), 50 mM sodium phosphate buffer (pH 8.0) and 50% DMSO, followed by 15 min of incubation at 50°C. The reaction was stopped by adding 20 mM DTT, followed by RNA purification using 1.8X RNA beads (Aline Bioscience) and RNA elution with 11 µl nuclease-free water. Then, 500 ng RNA was subject to library construction using Quant-seq 3′ mRNA-Seq Library Prep Kit (Lexogen)
scRNA-seq and RNA-seq

value: lymph nodes

value: T lymphocytes


title: RIP1-Tag5 wild type PNET tumor, mouse 2

description: 10x Genomics


title: M0 Vehicle 2


title: ds_yellow_rep2


title: RIP1-Tag5 wild type PNET tumor, mouse 1

description: 10x Genomics


title: ds_nej_rep3


title: WT, MEF, rep2

city: Boston

first: Shengze

last: Yao

state: MA

address: 185 Cambridge St

department: Molbio

institute: Massachusetts General Hospital

description:
WT_MEF_rep2
MEF_RNA_counts.txt

data_processing:
The raw RNA-seq data underwent adaptor removal and trimming using trim_galore/cutadapt (versions 0.4.3/1.7.1). Subsequently, the RNA-seq data were mapped to three different genomes: C57BL/6J (mm10), M. musculus (mus), and M. castaneus (cas). Final mapping to reference mm10 genome was generated based on SNPs.Using Subread (version 2.0.2) featureCounts (Liao et al., 2014), counts per gene were computed. Additionally, deeptools were employed to generate bigwig files (rpkm-normalized) for forward or reverse strand, offering a comprehensive view of read coverage across the genomes.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: tab-delimited text for the raw counts

growth_protocol: Mouse embryonic stem cells (mESCs) were initially cultured on γ-irradiated MEF feeders using DMEM medium supplemented with high-glucose, 15% FBS, and LIF. To induce differentiation, ES cell colonies were dissociated with trypsin and transferred to a LIF-devoid medium, where they were maintained in suspension for 4 days to generate embryoid bodies (EBs). On the fourth day, the EBs were plated onto gelatin-coated dishes and allowed to further differentiate until harvested at specified time points. MEF cells were cultured separately in DMEM medium supplemented with high-glucose and 10% FBS.

extract_protocol:
For RNA-seq, total cellular RNA was extracted using TRIzol (Thermo Fisher). rRNA was subsequently removed from the extracted RNA using using the NEBNext rRNA Depletion Kit .
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs), which enabled the creation of strand-specific RNA-seq libraries

value: CAST/EiJ x 129S1

value: MEF

value: wild-type

tag: Sex

value: female

tag: time


title: VLX-1005 3


title: ds_yellow_rep1


title: VLX-1005 1


title: Seeded at stage 3_F3

city: Nishitokyo

first: Chikako

last: HONDA

state: Tokyo

address: Midoricho

country: Japan

institute: The University of Tokyo

data_processing:
The library was sequenced by paired-read 150bp mode of HiSeq X platform (Illumina, CA).
Generated reads were subjected to quality control using fastp 0.20.0 program (Chen et al., 2018: https://github.com/OpenGene/fastp). The cleaning procedure included, trimming ambiguity reads and adapters either 5ʹ or 3ʹ end of the reads and filtering reads with default parameters.
Trimmed sequence reads were aligned to the grape reference genome assembly (Vitis_vinifera.12X.dna_sm.toplevel.fa) from EnsemblPlants (https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-50) using Hisat2-2.2.1 (Kim et al., 2019) with default parameters.
mapped reads were counted for each gene by featureCounts (Liao et al., 2014) with default parameters using Vitis_vinifera.12X.50.gtf from EnsemblPlants as a gene annotation file.
Assembly: 12X
Supplementary files format and content: Comma Separated Values file includs raw counts for each Sample

organism: Vitis x labruscana x Vitis vinifera

source_name: Vitis labruscana Bailey × Vitis vinifera L.

extract_protocol:
Total RNA was manually extracted from grape berry skin and flesh, respectively, according to the method by Reid et al (2006) and then purified using a kit (NucleoSpin RNA Plant, MACHEREY-NAGEL, USA).
RNA-Seq library was prepared by the Lasy-seq v1.1 (Kamitaniet al., 2019), Sci.Rep., https://sites.google.com/view/lasy-seq/.

value: flesh

value: Shine Muscat

value: seeded


title: WT, MEF, rep1

description:
WT_MEF_rep1
MEF_RNA_counts.txt


title: ds_nej_rep2

value: double stranded nej


title: Seeded at stage 3_S3

value: skin


title: Seeded at stage 4_S3


title: WT, ES, d14, rep2

description:
WT_ES_d14_rep2
ES_RNA_counts.txt

source_name: TST

value: TST

value: Differentiating mESC

value: day 14


title: RepE, MEF, rep1

description:
WT_RepE_rep1
MEF_RNA_counts.txt

value: Repeat E deletion


title: Seeded at stage 4_F3


title: Seeded at stage 1_F3


title: RepB, MEF, rep1

description:
WT_RepB_rep1
MEF_RNA_counts.txt

value: Repeat B deletion


title: Seeded at stage 4_S2


title: RepE, MEF, rep2

description:
WT_RepE_rep2
MEF_RNA_counts.txt


title: RepB, ES, d14, rep2

description:
RepB_ES_d14_rep2
ES_RNA_counts.txt


title: RepB, MEF, rep2

description:
WT_RepB_rep2
MEF_RNA_counts.txt


title: Seeded at stage 4_F2


title: RepB, ES, d14, rep1

description:
RepB_ES_d14_rep1
ES_RNA_counts.txt


title: Seeded at stage 3_S2


title: Seeded at stage 1_S3


title: MALE, ES, d14, rep1

description:
MALE_ES_d14_rep1
ES_RNA_counts.txt

value: male


title: Seeded at stage 3_F2


title: Seeded at stage 1_S2


title: Seeded at stage 1_F2


title: WT, ES, d7, rep1

description:
WT_ES_d7_rep1
ES_RNA_counts.txt

value: day 7


title: RepB, ES, d7, rep2

description:
RepB_ES_d7_rep2
ES_RNA_counts.txt


title: WT, ES, d14, rep1

description:
WT_ES_d14_rep1
ES_RNA_counts.txt


title: WT, ES, d7, rep2

description:
WT_ES_d7_rep2
ES_RNA_counts.txt


title: Seeded at stage 4_S1


title: RepB, ES, d7, rep1

description:
RepB_ES_d7_rep1
ES_RNA_counts.txt


title: Seeded at stage 3_F1


title: MALE, ES, d7, rep1

description:
MALE_ES_d7_rep1
ES_RNA_counts.txt


title: WT, ES, d4, rep2

description:
WT_ES_d4_rep2
ES_RNA_counts.txt

value: day 4


title: Seedless at stage 4_S3

value: seedless


title: RepB, ES, d4, rep1

description:
RepB_ES_d4_rep1
ES_RNA_counts.txt

value: CAST/EiJ x 129S1


title: Seeded at stage 1_S1


title: Seeded at stage 3_S1


title: Seeded at stage 1_F1


title: RepB, ES, d4, rep2

description:
RepB_ES_d4_rep2
ES_RNA_counts.txt


title: WT, ES, d4, rep1

description:
WT_ES_d4_rep1
ES_RNA_counts.txt

value: wild-type


title: MALE, ES, d7, rep2

description:
MALE_ES_d7_rep2
ES_RNA_counts.txt


title: MALE, ES, d4, rep2

description:
MALE_ES_d4_rep2
ES_RNA_counts.txt


title: Seedless at stage 3_F3


title: Seedless at stage 3_S3


title: MALE, ES, d14, rep2

description:
MALE_ES_d14_rep2
ES_RNA_counts.txt


title: Seedless at stage 4_F3


title: Seedless at stage 1_S3


title: MALE, ES, d4, rep1

description:
MALE_ES_d4_rep1
ES_RNA_counts.txt


title: WT, ES, d0, rep2

description:
WT_ES_d0_rep2
ES_RNA_counts.txt

value: mESC

value: female

value: day 0


title: Seedless at stage 1_F3

value: flesh

value: Shine Muscat


title: WT, ES, d0, rep1

description:
WT_ES_d0_rep1
ES_RNA_counts.txt


title: Seeded at stage 4_F1

value: seeded


title: Seedless at stage 4_S2

value: skin


title: RepB, ES, d0, rep2

description:
RepB_ES_d0_rep2
ES_RNA_counts.txt

value: TST


title: Seedless at stage 3_F2


title: Seedless at stage 4_F2


title: Seedless at stage 3_S2


title: MALE, ES, d0, rep2

description:
MALE_ES_d0_rep2
ES_RNA_counts.txt


title: RepB, ES, d0, rep1

description:
RepB_ES_d0_rep1
ES_RNA_counts.txt


title: MALE, ES, d0, rep1

description:
MALE_ES_d0_rep1
ES_RNA_counts.txt


title: Seedless at stage 1_F2


title: Seedless at stage 1_S2


title: Seedless at stage 4_S1


title: Seedless at stage 4_F1


title: RepE_MEF_Xist,rep2

library_source: genomic

data_processing:
The raw data underwent adaptor removal using trim_galore/cutadapt (versions 0.4.3/1.7.1). Subsequently, the trimmed reads were aligned to the genomes of Mus musculus (mus) and Mus castaneus (cas) using NovoAlign (version 4.03). These aligned reads were then mapped back to the reference mm10 genome using SNPs, resulting in the generation of a BAM file. To maintain uniform library sizes across the samples, random sampling with Samtools (version 1.11) was implemented. CHART coverage profiles were generated using DeepTools (version 3.1.2), resulting in the creation of bigwig files (rpkm-normalized).
To identify Xist CHART peaks on autosomes, reads from chromosome X (chrX) were initially excluded from the BAM file. Peak calling was performed using MACS2 (version 2.1) with default parameters. The resultant peak files from two replicates were merged using bedtools (version 2.30) intersect.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
Library strategy: CHART-SEQ

molecule: genomic DNA

extract_protocol:
For CHART-seq, 25 million cells underwent crosslinking with 1% formaldehyde, followed by additional crosslinking of nuclei with 3% formaldehyde. Chromatin was then sheared via sonication to produce fragments ranging from 2 to 4kb. Pre-clearing of the chromatin was performed using MyOne Streptavidin C1 beads. Subsequently, the pre-cleared chromatin was mixed with 36 pmol of either antisense (targeting Xist) or sense (used as a control) biotin-labeled probes, and captured using MyOne Streptavidin C1 beads. After washing the beads, DNA was eluted using RNase H. Eluted DNA was extracted via phenol-chloroform and further sheared to achieve fragments below 500 bp.
The library was generated using the NEBNext® Ultra™ II DNA Library Prep Kit.

value: MEF

tag: pull down_oligo

value: Antisense oligos to Xist


title: Seedless at stage 3_S1


title: Seedless at stage 1_F1


title: RepE_MEF_Sense,rep2

value: Repeat E deletion

value: Control sense oligos


title: RepE_MEF_Input,rep2


title: Seedless at stage 3_F1


title: Seedless at stage 1_S1


title: RepE_MEF_Xist,rep1


title: tissue,infiltrative,rep1

city: Fuzhou, Fujian, China

first: Jie

last: Liu

address: Shengli Clinical Medical College of Fujian Medical University, Department of Endoscopy, Fujian Provincial Hospital, Fuzhou, China

country: China

institute: Fujian Medical University

data_processing:
ROSE algorithm was programmed in Python (v3.9) to identify SEs. The data was visualized using IGV 2.14.1.
Assembly: hg38
Supplementary files format and content: bed, narrow peak
Library strategy: CUT&Tag

organism: Homo sapiens

source_name: gastric epithelial cell

extract_protocol:
Epi™ CUT and Tag Kit (Epibiotek, Guangzhou, China) was used to perform the CUT&Tag experiment with 5 steps: mixing the cell suspension with magnetic beads (10 μL ConA Beads and 1×105 cells), antibody binding (297 μL Wash Buffer, 3 μl 5% Digitonin, 12 μL 25× pAb Mix, and 3 μL antibody), incubation with Pa-Tn5 transposome, labeling (50 μL Tagmentation Buffer for 1 h at room temperature), library construction and sequencing.
Take 0.5 mL of Tn5 Buffer, add 5 μL of MgCl2 to formulate Tagmentation Buffer. 50 μL of Tagmentation Buffer was added to each tube, and incubated at 37°C for 1 h. After sample incubation, 1 μL of 10% SDS was added, and the sample was incubated at 55°C for 10 min, and purified with 1.8× DNA Clean Beads. Add 2× AmpliMix 25 uL, N5 Primer 2.5 μL, N7 Primer 2.5 μL to each tube. blow for more than 10 times to mix thoroughly, centrifuge. Stage 0, 72℃ 3 min/Stage 1, 98℃ 30 sec / Stage 2, 98℃ 15 sec, 60℃ 20 sec, 72℃ 8 sec, 14 Cycles / Stage 3, 72°C for 2 min. 1× DNA Clean Beads were used to purify the reaction after completion. The libraries were quality checked using Bioptic Qsep100 Analyzer to detect whether the library size distribution was in accordance with the theoretical size.

tag: disease

value: gastric cancer

value: gastric epithelial cell


title: RepE_MEF_Input,rep1


title: tissue,infiltrative,rep3


title: tissue,expanding,rep2


title: RepE_MEF_Sense,rep1


title: tissue,expanding,rep3


title: tissue,infiltrative,rep2


title: tissue,expanding,rep1


title: RepB_MEF_Xist,rep2

value: Repeat B deletion


title: RepB_MEF_Sense,rep2

value: CAST/EiJ x 129S1


title: skov3-fen-1um-9

city: Kunming

first: Xin

last: Wang

state: Yunnan

address: 519 Kunzhou Road,  Kunming, Yunnan, P. R. China

institute: Kunming Medical University, The Third Affiliated Hospital

description:
Gene expression of SKOV3 treated by FEN(1μM)
skov3-fen-1um-9

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: cell line

growth_protocol: All cells were incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from SKOV3 were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: SKOV3 cell line were treated by DMSO and FBZ for 48 hours

value: cell line

value: Ovarian cancer

value: FBZ for 48 hours


title: RepB_MEF_Input,rep2

value: female


title: skov3-fen-1um-8

description:
Gene expression of SKOV3 treated by FEN(1μM)
skov3-fen-1um-8


title: RepB_MEF_Xist,rep1


title: skov3-fen-1um-7

description:
Gene expression of SKOV3 treated by FEN(1μM)
skov3-fen-1um-7


title: skov3-DMSO-12

description:
Gene expression of SKOV3 treated by DMSO
skov3-DMSO-12

value: DMSO; Vehicle


title: RepB_MEF_Sense,rep1


title: skov3-DMSO-11

description:
Gene expression of SKOV3 treated by DMSO
skov3-DMSO-11


title: RepB_MEF_Input,rep1


title: skov3-DMSO-10

description:
Gene expression of SKOV3 treated by DMSO
skov3-DMSO-10


title: WT_ES_d14_Xist,rep2

value: Differentiating mESC

value: wild-type

value: day 14


title: WT_ES_d14_Input,rep2

value: TST


title: WT_ES_d14_Sense,rep2


title: TGF2207

city: Melbourne

first: antony

last: boynes

state: Victoria

address: Parkville

department: Ophthalmology

institute: University of Melbourne

data_processing:
Following the abundance estimates of transcripts generated by Salmon v1.8, the pseudocounts were mapped to the GRCh38 genome assembly using the tximport v1.22.0 package59. The gene count matrix was inputted as an DESeq2Dataset object using the DESeqDataSetFromTximport function, then the DESeq2Dataset object was normalised using the counts function to make fair gene expression comparisons between samples.
The normalised dataset was analysed with the DESeq2 v1.34.0 R package using rlog transformation.
Assembly: GRCh38 genome assembly
Supplementary files format and content: csv file contains raw counts for all samples
Supplementary files format and content: csv file contains differential expression analysis matrix

source_name: conjuctiva

growth_protocol: HTFs were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Sigma- Aldrich) containing Gibco Penicillin–Streptomycin– Glutamine (Thermo Fisher Scientific) and 10% fetal calf serum (FCS; Cytiva, Marlborough, MA) at 37°C with 5% CO2 in 50 mL and 160 mL cell culture flasks (Greiner Bio-One). Human Tenon’s Fibroblasts were passáged when flasks achieved 80% confluency by dissociating monolayers with a Trypsin-EDTA solution (0.25%; Sigma-Aldrich). Fibroblasts obtained on passáges 6 through 12, after initial cultures were established, were used. Phenotype verification of the cultured HTFs was achieved with the use of anti–fibroblast-specific protein 1 (S100A4) antibody (1:100; ABF32; Merck Millipore, Bayswater, VIC, Australia). HTFs (approx. 40,000 cells/well) were seeded onto coverslips in 6-well Nunc cell culture plates (Thermo Fisher Scientific).

extract_protocol:
RNA extraction was performed using illustra RNAspin Mini Kit (GE Healthcare Life Sciences), following manufacturer’s instructions. RNA concentration and quality were measured using SimpliNano (GE Healthcare Life Sciences). cDNA was synthesised by reverse transcription of RNA. RT-qPCR was performed using TaqManTM Fast Advanced Master Mix (4444554; Thermo Fisher Scientific, Lithuania) and Taqman gene expression assay probe for ACTA2 (Hs00426835_g1) and the housekeeping gene 18s rRNA control mix  (4318839; Applied Biosystems, Kingsland Grange, Woolston, Warrington, UK). RT-qPCR was performed on QuantStudio™ 7 Flex Real-Time PCR System (Thermo Fisher Scientific, Scoresby, VIC, Australia), following manufacturer’s instructions.
RNA was extracted using the Illustra RNAspin Mini Kit (GE Healthcare Life Sciences) according to manufacturer’s instructions. RNA quality was checked by bioanalyzer, followed by library construction using the TruSeq Stranded mRNA kit (Illumina) and sequenced using Novaseq 6000 (Illumina)

treatment_protocol: HTFs were serum-starved in DMEM with 1% FCS overnight in preparation for treatment. HTFs were then assigned to either the control (medium alone) or the TGFβ1 (10 ng/mL) treatment group. Following treatment, HTFs were fixed with 4% paraformaldehyde (PFA; P6148; Sigma-Aldrich, CA, USA) over a range of time-points (from Days 3-14).

value: conjuctiva

value: human tenons fibroblast


title: WT_ES_d14_Xist,rep1

value: Antisense oligos to Xist


title: WT_ES_d14_Sense,rep1

value: Control sense oligos


title: CX2207

value: control


title: WT_ES_d14_Input,rep1


title: TGF2203


title: TGF2202


title: CX2202


title: RepB_ES_d14_Xist,rep2


title: RepB_ES_d14_Sense,rep2


title: RepB_ES_d14_Xist,rep1


title: RepB_ES_d14_Input,rep2


title: i3N, iGC186 rep1

city: Baltimore

first: Shuying

last: Sun

state: MD

address: Hunterian 205

department: Physiology

institute: jhmi

data_processing:
Raw reads were trimmed using trim-galore (0.6.7) and aligned to human genome and transcriptome (hg38) using HISAT2 (version 2.2.1)
Cleaned reads were mapped to human GRCh38/hg38
The number of reads mapped to GENCODE (https://www.gencodegenes.org/, version 38) annotated genes were counted using subread (version 2.0.1).
HISAT2-aligned BAMs were used as input to rMATS (version 4.1.1) for alternative splicing analysis using GRCh38 reference genome
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file with splicing junction counts betwwen two groups

growth_protocol: Classic Neuronal Medium

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher), and RNA concentrations were determined with the Qubit RNA HS Assay Kit on a Qubit 4.0 Fluorometer
Libraries were prepared according to protocol accompanying the NEBNext® Ultra™ II Directional RNA Library Prep Kit (Cat. No. E7765) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Day 10 neuron

value: (GGGGCC)186 overexpression


title: i3N, iGC186 rep3


title: RepB_ES_d14_Input,rep1

value: CAST/EiJ x 129S1

value: Repeat B deletion


title: i3N, iGC186 rep2


title: RepB_ES_d14_Sense,rep1


title: i3N, iGC2 rep3

value: (GGGGCC)2 overexpression


title: MALE_ES_d14_Xist,rep2

value: male


title: i3N, iGC2 rep2


title: MALE_ES_d14_Sense,rep2


title: 45-iPS, day 8, 10X 3' v.3.1

city: Seattle

first: Sergei

last: Doulatov

state: Washington

address: 1959 NE Pacific St K259

institute: University of Washington

description: 10X Genomics 3' v.3.1

data_processing:
For sci-RNA-seq, the Brotman Baty Institute used an internal pipeline similar to the one found in http://dx.doi.org/10.17504/protocols.io.9yih7ue; briefly, processing was done using Python 3.7.7, TrimGalore v.0.6.4, CutAdapt v.1.18, single-end trimming mode, a quality Phred score cutoff of 20 and the default maximum trimming error rate, followed by alignment to Homo sapiens GRCh38 using STAR v.2.6.1d, followed by filtering using samtools v.1.9, followed by removal of duplicates and gene assignment using bedtools v.2.27.1 and bamtools v.2.5.1, followed by the removal of doublets using scrublet v.0.2.1.  For 10X sc-RNA-seq, FASTQ files for the iPS-derived EB sample were processed using CellRanger v.4.0.0 to align reads to the GRCh38-2020-A reference genome.
Assembly: GRCh38
Supplementary files format and content: compressed tab seperated value files, compressed matrix files, comma seperated value files

source_name: CD34+, CD43+ or CD45+ embryoid body cells

extract_protocol:
For cell isolation for sci-RNA-seq or 10x sc-RNA-seq, whole embryoid bodies were collected, incubated in 2mg/ml Collagenase B in IMDM for 2 hours with trituration every 30min, followed by incubation in 2ml Gentle Cell dissociation reagent for 15min, followed by rapid trituration for manual dissociation, followed by filtration through a 70μM filter and resuspension in 3% FBS in PBS. For sci-RNA-seq, cells were then resuspended in a cell lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) followed by gentle pipetting, followed by filtration of the resulting nuclei through a 70μM strainer and incubation in 4% paraformaldehyded in 1.25X PBS for 15min with gentle inversion every 5min, followed by resuspension in a nuclei suspension buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1% SUPERase In RNAse Inhibitor) and flash freezing in liquid nitrogen. For 10X sc-RNA-seq, cells were sorted for CD34+, CD43+ or CD45+ cells into 50% FBS using FACS (Aria III).
For sci-RNA-seq, the samples were submitted to the Brotman Baty Institute for processing following a similar protocol to the one published in http://dx.doi.org/10.17504/protocols.io.9yih7ue. For 10X sc-RNA-seq, the manufacturer's protocol for library construction was followed.
10X 3' sc-RNA-seq

value: iPSC


title: i3N, iGC2 rep1


title: MALE_ES_d14_Xist,rep1


title: 8365-19, Antigen positive B cells

city: Nashville

first: Ivelin

last: Georgiev

state: TN

address: 11475 MRB IV 2213 Garland Ave

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

description: 10X VDJ-seuquencing with enrichment for BCR sequences. Processed file contains contigs processed by Cell Ranger.

library_source: other

data_processing:
For paired HC/LC files: LIBRA-seq bioinformatic pipeline was used, with IMGT-HighV quest used to annotate sequences in filtered_contig fasta files.
For filtered contig FASTA files, raw FASTQ files were aligned and flitered with Cell Ranger 3.1.0.
Assembly: GRCh38 7.0 (10X Genomics)
Supplementary files format and content: Paired_HC_LC tab separated files contains aligned sequences from the VDJ and antigen barcode sequencing, with annotations and UMI counts for each antigens. This file is generated by the LIBRA-seq bioinformatic pipeline.
Supplementary files format and content: Filtered contig fastsa files contain aligned contigs filtered by Cell Ranger VDJ pipeline.

molecule: other

source_name: B cell

extract_protocol:
PBMCs were mixed with barcoded antigens, then antigen specific B cells were sorted from human PBMCs using the standard LIBRA-seq pipeline (Shiakolas & Setliff et al., Cell 2019).
Cells were distributed into microfluidic droplets containing unique cell-specific oligonucleotides using the 10X Genomics Chromium Controller. cDNA libraires from single cells were further amplified with BCR enrichment primers using the 10X Genomics VDJ protocol.
LIBRA-seq

value: B cell

value: Healthy


title: 8365-13, Antigen positive B cells


title: 8365-9, Antigen positive B cells


title: CX2203


title: MALE_ES_d14_Sense,rep1

value: Differentiating mESC

value: wild-type


title: 8365-6, Antigen positive B cells


title: 8365-8, Antigen positive B cells


title: MALE_ES_d14_Input,rep1

value: day 14


title: WT_ES_d7_Sense,rep2

value: TST

value: female

value: day 7


title: WT_ES_d7_Xist,rep1

value: Antisense oligos to Xist


title: 8365-2, Antigen positive B cells


title: WT_ES_d7_Sense,rep1

value: Control sense oligos


title: 8365-5, Antigen positive B cells


title: WT_ES_d7_Xist,rep2


title: 8365-3, Antigen positive B cells


title: RepB_ES_d7_Xist,rep2


title: 8365-1, Antigen positive B cells

description: 10X VDJ-sequencing with enrichment for BCR sequences, with corresponding sequencing of antigen barcode olignonucleotides (hash) for the same cells. Processed file contains contigs processed by Cell Ranger for BCR VDJ data, along with a paired heavy and light chain CSV containing annotated sequences for each cell (mapped by cellular barcodes).


title: MALE_ES_d14_Input,rep2


title: i3N, shSRRM2 rep3

value: Day 14 neuron

value: SRRM2 shRNA


title: i3N, shSRRM2 rep2


title: RepB_ES_d7_Sense,rep2

value: CAST/EiJ x 129S1


title: WT_ES_d7_Input,rep1


title: Early and late senescence 50 days

city: Chuncheon

first: Prakash

last: Basnet

state: Gangwon-do

address: Department of Agriculture and Life Industry, Kangwon National University, Bldg. Asangwan Rm.424, 1 K

department: Agriculture and Life Industries

country: South Korea

institute: Kangwon National University

data_processing:
Trimmomatic v0.36
Trimmomatic sliding window (4:20)
HITSAT2 v2.1.0
String Tie v1.3.4d
DESeq V1.36.0 (for DEGs analysis)
Assembly: Glycine max Wm82.a2. v1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Glycine max

source_name: Leaf

growth_protocol: Plants were grown in greenhouse for 50 and 95 days under normal condition

extract_protocol:
The leaves from 50 and 95 days after sowing (DAS) ES and LS plants were sampled and harvested immediately in frozen liquid nitrogen (N) for RNA isolation using Genall Ribospin. Illumina Nova SeqHigh-trhroughput platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: 50 days senescence variation


title: RepB_ES_d7_Input,rep2

value: Repeat B deletion


title: i3N, shSRRM2 rep1


title: untreated U937 cells (differentiated)

type: RNA

city: Geesthacht

first: Krathika

last: Bhat

address: Max-Planck-Str. 1

country: Germany

institute: Helmholtz Zentrum Hereon

description:
control
SAMPLE 1

data_processing:
The Ct values were provided by the software. For the normalization, five housekeeping genes were used: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes as follows: deltaCt = (Ct_Target − Ct_HKG)]
Fold change was calculated using the normalized values as follows: Fold change = 2^(-deltadeltaCt), where deltadeltaCt = deltaCt_test - deltaCt_control
Fold Change worksheet reports test/control (i.e., LPS-treated/untreated) ratios.
Matrix normalized worksheet reports normalized signal (against housekeeping genes) i.e. deltaCt. deltaCt = (Ct_Target − Ct_HKG)].  Ct_HKG is the geometric mean of the Ct values for the five HK genes ACTB, B2M, GAPDH, HPRT1, RPLP0.

label: SYBR Green

source_name: monocyte cell line-derived macrophages

label_protocol: RT-qPCR was carried out using RT² Profiler™ PCR Array for Human Cytokines & Chemokines (330231 PAHS-150ZD-2, Qiagen). The cDNA input per array well was 12.5 ng. The reaction sequence involved the following steps: 95 °C for 3 min, 40 cycles of 95 °C for 20 s and 60 °C for 50 s.

growth_protocol: 500,000 U937 cells/mL added to wells of 6WP in 3 mL RPMI-1640+10% FBS  medium. The cells were differentiated by exposing them to 10 ng/mL PMA for 48 h. The medium was replaced with MEM+10% FBS

extract_protocol: After 24 h, RNA was extracted using QuickRNA microprep kit (R1051, Zymo Research) and cDNA was synthesized using RevertAid kit (K1691, ThermoFisher) using 2000 ng total RNA.

treatment_protocol: After 24 h in MEM+10% FBS medium, the medium in the wells was replaced with either fresh MEM + 10%FBS or medium with 10 ng/mL LPS + 5 ng/mL IFNgamma.

value: monocyte cell line-derived macrophages

value: no stimulant


title: LPS+IFNgamma treated U937 cells (differentiated)

description:
test
SAMPLE 2

value: 10 ng/mL LPS + 5 ng /mL IFNgamma


title: seedling, ein2lhp1_27_rep2

city: Austin

first: Zhengyao

last: Shao

state: TX

address: 2506 Speedway, NMS 5.324

department: MBS

institute: University of Texas at Austin

description:
diff_ein2lhp1_27vs21.csv
featureCounts_results_ein2lhp1_27vs21.txt

data_processing:
Paired-end raw fastq data were evaluated with FastQC and low-quality reads were removed with Trim Galore (Babraham Institute).
The trimmed and filtered reads were then mapped to the Arabidopsis reference genome (TAIR10) with STAR.
Mapped reads were counted by featureCounts (Subread 2.0.1) and differentially regulated genes were identified using R package DESeq2.
Assembly: TAIR10
Supplementary files format and content: bw files for IGV visuaization
Supplementary files format and content: raw featureCounts and DESeq2 results and summarized DEGS and their log2FC

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis seeds were first surface-sterilized with solution containing 50% bleach and 0.01% Triton X-100 for 10 minutes, washed with sterile distilled water for four times, sown on Murashige and Skoog (MS) medium plates containing 1% sucrose and 1% phytoblend agar and stratified for three days at 4°C in the dark.

extract_protocol:
RNA extraction was conducted following the manufacturer’s recommendation using the RNeasy Plant Kit (Qiagen) with DNase I digestion and clean up (Qiagen, RNeasy Mini Kit (250)).
Libraries were generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770), with 1μg RNA as input, following the manufacturer’s instructions.

treatment_protocol: After stratification, plated seeds on MS medium were grown at 21°C in SD. Five-day-old green seedlings in each indicated genetic background grown in 21°C SD were shifted to warm temperature (27°C) from ZT4 for four hours till ZT8 in SD condition.

value: seedling


title: seedling, ein2lhp1_27_rep1


title: 8365-4, Antigen positive B cells

value: B cell

value: Healthy


title: RepB_ES_d7_Xist,rep1

value: TST

value: Differentiating mESC


title: i3N, shSON rep3

value: SON shRNA


title: seedling, lhp1_27_rep2

description:
diff_lhp1_27vs21.csv
featureCounts_results_lhp1_27vs21.txt


title: RepB_ES_d7_Sense,rep1

value: female

value: day 7


title: Early and late senescence 95 days

value: 95 days senescence variation


title: WT_ES_d7_Input,rep2

value: wild-type


title: RepB_ES_d7_Input,rep1

value: CAST/EiJ x 129S1


title: seedling, lhp1_27_rep1


title: i3N, shSON rep1

value: Day 14 neuron


title: i3N, shSON rep2


title: MALE_ES_d7_Xist,rep2

value: Antisense oligos to Xist

value: male


title: MSC-iPS, day 21, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

data_processing:
For sci-RNA-seq, the Brotman Baty Institute used an internal pipeline similar to the one found in http://dx.doi.org/10.17504/protocols.io.9yih7ue; briefly, processing was done using Python 3.7.7, TrimGalore v.0.6.4, CutAdapt v.1.18, single-end trimming mode, a quality Phred score cutoff of 20 and the default maximum trimming error rate, followed by alignment to Homo sapiens GRCh38 using STAR v.2.6.1d, followed by filtering using samtools v.1.9, followed by removal of duplicates and gene assignment using bedtools v.2.27.1 and bamtools v.2.5.1, followed by the removal of doublets using scrublet v.0.2.1.  For 10X sc-RNA-seq, FASTQ files for the iPS-derived EB sample were processed using CellRanger v.4.0.0 to align reads to the GRCh38-2020-A reference genome.
Assembly: GRCh38
Supplementary files format and content: compressed tab seperated value files, compressed matrix files, comma seperated value files
Library strategy: single-cell combinatorial indexing RNA-seq (sci-RNA-seq)

source_name: whole embryoid body

extract_protocol:
For cell isolation for sci-RNA-seq or 10x sc-RNA-seq, whole embryoid bodies were collected, incubated in 2mg/ml Collagenase B in IMDM for 2 hours with trituration every 30min, followed by incubation in 2ml Gentle Cell dissociation reagent for 15min, followed by rapid trituration for manual dissociation, followed by filtration through a 70μM filter and resuspension in 3% FBS in PBS. For sci-RNA-seq, cells were then resuspended in a cell lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) followed by gentle pipetting, followed by filtration of the resulting nuclei through a 70μM strainer and incubation in 4% paraformaldehyded in 1.25X PBS for 15min with gentle inversion every 5min, followed by resuspension in a nuclei suspension buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1% SUPERase In RNAse Inhibitor) and flash freezing in liquid nitrogen. For 10X sc-RNA-seq, cells were sorted for CD34+, CD43+ or CD45+ cells into 50% FBS using FACS (Aria III).
For sci-RNA-seq, the samples were submitted to the Brotman Baty Institute for processing following a similar protocol to the one published in http://dx.doi.org/10.17504/protocols.io.9yih7ue. For 10X sc-RNA-seq, the manufacturer's protocol for library construction was followed.

value: whole embryoid body

value: MSC-iPS

value: iPSC


title: MSC-iPS, day 21, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: MSC-iPS, day 14, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, ein3eil1_27_rep1

description:
diff_ein3eil1_27vs21.csv
featureCounts_results_ein3eil1_27vs21.txt

value: seedling


title: MSC-iPS, day 18, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N,shScramble rep3

value: shScramble


title: MALE_ES_d7_Sense,rep2

value: Control sense oligos


title: MSC-iPS, day 18, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N,shScramble rep2


title: i3N,shScramble rep1


title: seedling, ein2_27_rep2

description:
diff_ein2_27vs21.csv
featureCounts_results_ein2_27vs21.txt


title: MSC-iPS, day 14, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: MALE_ES_d7_Input,rep2


title: seedling, ein2_27_rep1


title: MALE_ES_d7_Xist,rep1


title: i3N, GR, heavy, 3min, rep3

data_processing:
The raw reads from fastq files were first processed by default quality-filter using Trimmomatic-0.38
Cleaned reads were mapped to human GRCh38/hg38 and quantified by RSEM
Assembly: GRCh38/hg38
Supplementary files format and content: tab deliminated normalized read counts for each sample

value: GR

tag: fraction

value: polyA RNA associated with >7 ribos

value: harringtonine 3 min


title: MSC-iPS, day 11, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: MALE_ES_d7_Sense,rep1

value: Differentiating mESC


title: i3N, GFP, heavy, 3min, rep3

value: GFP


title: seedling, ein3eil1_27_rep2


title: MALE_ES_d7_Input,rep1

value: day 7


title: seedling, wt_27_rep1

description:
diff_wt_27vs21.csv
featureCounts_results_wt_27vs21.txt


title: MSC-iPS, day 8, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, ein2lhp1_21_rep1


title: WT_ES_d4_Xist,rep2

value: TST

value: wild-type

value: female

value: day 4


title: i3N, GFP, heavy, 0min, rep3

value: Day 14 neuron

value: harringtonine 0 min


title: MSC-iPS, day 7, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: whole embryoid body

value: MSC-iPS


title: i3N, GR, med, 3min, rep3

value: polyA RNA associated with 3-7 ribos


title: MSC-iPS, day 11, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: iPSC


title: i3N, GFP, med, 3min, rep3


title: i3N, GR, med, 0min, rep3


title: seedling, lhp1_21_rep1

value: seedling


title: WT_ES_d4_Sense,rep2

value: CAST/EiJ x 129S1

value: Control sense oligos


title: WT_ES_d4_Xist,rep1

value: Antisense oligos to Xist


title: 45-iPS, day 21, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, lhp1_21_rep2


title: WT_ES_d4_Input,rep2

value: Differentiating mESC


title: MSC-iPS, day 8, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, wt_27_rep2


title: MSC-iPS, day 7, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N, GR, heavy, 0min, rep3

value: GR

value: polyA RNA associated with >7 ribos


title: i3N, GFP, med, 0min, rep3

value: GFP


title: 45-iPS, day 21, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, ein2lhp1_21_rep2


title: WT_ES_d4_Input,rep1

value: TST

value: wild-type


title: seedling, ein3eil1_21_rep1


title: 45-iPS, day 18, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N, GR, heavy, 3min, rep2

value: harringtonine 3 min


title: 45-iPS, day 18, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: seedling, ein3eil1_21_rep2


title: WT_ES_d4_Sense,rep1

value: female

value: day 4


title: RepB_ES_d4_Xist,rep2

value: Repeat B deletion


title: seedling, ein2_21_rep2


title: i3N, GFP, heavy, 3min, rep2

value: Day 14 neuron


title: 45-iPS, day 14, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: whole embryoid body


title: RepB_ES_d4_Sense,rep2


title: i3N, GR, heavy, 0min, rep2

value: harringtonine 0 min


title: seedling, wt_21_rep2

value: seedling


title: i3N, GR, med, 3min, rep2

value: polyA RNA associated with 3-7 ribos


title: 45-iPS, day 11, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: iPSC


title: 45-iPS, day 14, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: 45-iPS, day 11, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N, GFP, heavy, 0min, rep2


title: RepB_ES_d4_Xist,rep1

value: CAST/EiJ x 129S1

value: Antisense oligos to Xist


title: seedling, wt_21_rep1


title: Shhcre;Lonp1, lung, E13.5, rep4, bulk RNA-seq

city: San Diego

first: Le

last: Xu

state: CA

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

data_processing:
For bulk RNA-seq, FASTQ files were aligned to the mouse reference genome (mm10) by using Bowtie2 (Langmead and Salzberg, 2012) with default settings. Differential gene expression analysis was performed using Cufflinks (Trapnell et al., 2010). Heatmaps were generated by ggplot2 (version 3.3.2).
For scRNA-seq, Cell Ranger (version 3.0.2) was used to initially align the raw reads onto the mouse reference genome (mm10) and generate the feature-barcode matrix. Next, R package Seurat (version 4.0) (Hao et al., 2021) was used to perform data quality control, normalization, scaling, principal components analysis (PCA) and the canonical correlation analysis (CCA) based data integration. Briefly, to filter out low-quality cells or doublets, cells with fewer than 200 or more than 4,000 unique features, or more than 15% mitochondrial contents were removed from further analysis. Then "LogNormalize" was used to normalize the feature expression. A total of 2,000 top variable features were identified by function FindVariableFeatures and kept for PCA. Top 20 significant components were chosen to conduct dimensional reduction by uniform manifold approximation and projection (UMAP) with default parameters. The expression features of marker genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: mouse mm10
Supplementary files format and content: For bulk RNA-seq, gene expression matrix.
Supplementary files format and content: For scRNA-seq, h5 files from cellranger.

growth_protocol: Embryos used in this study were harvested from time-mated mice, counting noon the day when the vaginal plug was found as E0.5. All mice were in B6 background or have been back crossed to B6 background for at least 3 generations. Littermates were used as controls in all experiments. All mice were housed in facilities accredited by American Association for Accreditation of Laboratory Animal Care (AAALAC) at University of California San Diego. All animal husbandry and experiments were approved by Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Total RNA from embryonic or adult lungs were extracted by using Trizol (Invitrogen) and RNeasy Micro RNA extraction kit (Qiagen).
For bulk RNAseq, cDNA libraries were constructed by using Illumina TruSeq RNA Library Prep Kit V2 (Illumina). For scRNA, single cell libraries were generated from sorted epithelial cells by using Chromium Single Cell 3’ v3 kit (10X Genomics).

treatment_protocol: Tamoxifen dissolved in corn oil was administrated intraperitoneally at the dose of 50 mg/kg. Three times in every other day.

value: whole lung cells


title: RepB_ES_d4_Sense,rep1

value: Differentiating mESC

value: Control sense oligos


title: RepB_ES_d4_Input,rep1

value: TST


title: Shhcre;Lonp1, lung, E13.5, rep3, bulk RNA-seq


title: i3N, GR, med, 0min, rep2

value: GR


title: 45-iPS, day 8, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: Shhcre;Lonp1, lung, E13.5, rep2, bulk RNA-seq


title: MALE_ES_d4_Xist,rep2

value: wild-type

value: male


title: i3N, GFP, med, 0min, rep2

value: GFP


title: RepB_ES_d4_Input,rep2

value: Repeat B deletion

value: female

value: day 4


title: 45-iPS, day 7, replicate 2, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: whole embryoid body


title: seedling, ein2_21_rep1

value: seedling


title: MALE_ES_d4_Sense,rep2


title: Shhcre;Lonp1, lung, E13.5, rep1, bulk RNA-seq


title: MALE_ES_d4_Input,rep2


title: control, lung, E13.5, rep3, bulk RNA-seq


title: 45-iPS, day 8, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a


title: i3N, GR, heavy, 0min, rep1

value: Day 14 neuron

value: polyA RNA associated with >7 ribos

value: harringtonine 0 min


title: MALE_ES_d4_Input,rep1

value: CAST/EiJ x 129S1


title: i3N, GFP, heavy, 0min, rep1


title: HEK293T_ChIPseq_CTCF_dTAG_rep3

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

data_processing:
ChIP-seq reads were mapped to the hg38 mouse reference genome assembly using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The bigwig coverage tracks were generated using the “bamCoverage” function from the deepTools.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format.

growth_protocol: Human Embryonic Kidney 293T ZNF143-FKBP12F36V cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS), Penicillin/Streptomycin, and 5% glutamine at 37°C with 5% CO2. HEK293T ZNF143-FKBP12F36V cells were grown to approximately 80-90% confluence in 10 cm dishes.

extract_protocol:
Formaldehyde (final concentration 1%, Electron Microscopy Sciences) was added directly to the plates containing 10 mL of media and incubated for 10 minutes at 37°C in the incubator to fix the cells. The reaction was then quenched by adding 0.125M glycine (final concentration) to the plates, swirling, and incubating for an additional 10 minutes at 37°C. The plates were washed once with 10 mL and then with 5 mL of ice‐cold PBS containing protease inhibitors (cOmplete Roche, Sigma‐Aldrich). Subsequently, the cells were scraped into 5 mL of ice‐cold PBS containing protease inhibitors and transferred to a 15 mL tube. The process was repeated to collect all the cells, and the pellet was transferred to a 1.5 mL tube and stored at -80°C after snap freezing in liquid nitrogen. For ChIP, the frozen pellets were thawed on ice for 10 minutes. The cells were then lysed by resuspending in 1 mL of cold sonication buffer per 1 x 108 cells (0.5% SDS, 0.01M EDTA, 50mM Tris-HCl pH 8.0, and 1X protease inhibitors). The lysate was divided to obtain approximately 200 to 300 μL per tube and sonicated for 15 sec ON, 15 sec OFF, for 30 minutes at 25% amplitude using a Qsonica sonicator. The samples were then spun at ~17000x g in a mini centrifuge for 10 minutes at 4°C, and the supernatant was collected. The supernatant was diluted (at least 5 times) to achieve a concentration of one million cells per 200 μL lysate to reduce SDS concentration with ChIP dilution buffer containing protease inhibitors (0.01% SDS, 1.2mM EDTA, 16.68 mM Tris–HCl pH 8.0, 167mM NaCl, 1.1% Triton X-100, and 1X protease inhibitors). Four million cell equivalents of cell lysate were aliquoted, and appropriate amounts of antibody were added (4 μL of anti‐CTCF antibody (3418S, Cell Signalling, 91ng/μl) or 18μL of anti-ZNF143 antibody (16618-1-AP, Proteintech, 500 ng/µl)). The samples were incubated overnight with rotation at 4°C. The immune complex was collected by incubating with 40 μL Protein A + Protein G beads (Dynabeads Protein A and Protein G, Invitrogen) on a rotisserie at 4°C for 90 minutes. The beads were washed once each with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 150mM NaCl, 20mM Tris HCl pH 8.0), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH8.0), LiCl immune complex buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.0), and then with 1x TE (10mM Tris-HCl, 1mM EDTA pH8.0), all containing 1x protease inhibitors. To elute the immunoprecipitated complexes, 150 μL of elution buffer (10mM Tris-HCl pH 8.0, 300mM NaCl, 55mM EDTA, 0.5% SDS) was added, followed by 1 μL RNAse A, and incubated at 37°C for 10 minutes. This was followed by the addition of 5 μL Proteinase K and overnight incubation at 65°C. The DNA was purified after removing the beads with a MinElute PCR purification kit (Qiagen), and eluted DNA in a 52 μL elution buffer provided in the kit.
ChIP‐seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) index primers, following the manufacturer's protocols. Libraries were assessed on a TapeStation and Qubit and sequenced on Illumina NextSeq 500 generating paired-end reads.

treatment_protocol: The cells were treated with 0.5 μM dTAGV-1 for 30 minutes, or no treatment for control.

value: ZNF143 tagged with an inducible degron tag

tag: antibody

value: CTCF (3418S, Cell Signaling)


title: P14 CD8+ T cell d15 after LCMV Arm RNA

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: University of Lausanne

description:
Arm_d15RNA
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V2.1.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen

extract_protocol:
Spleens were smashed, lymphocytes were washed and stained with flow cytometry antibodies. Live transferred cells were then sorted by FACS based on their CD8, CD44 and CD45 markers
Library was performed according to the manufacturer's instructions (single cell 3' V2 protocol, 10x Genomics)

value: Spleen

value: T lymphocyte

value: Mixed sample (WT,KO)


title: P14 CD8+ T cell d15 after LCMV Arm CMO

description:
Arm_d15CMO
10X Genomics


title: 45-iPS, day 7, replicate 1, sci-RNA-seq

description: sci-RNA-seq, 3-level, RNA3-028-a

value: iPSC


title: HEK293T_ChIPseq_CTCF_dTAG_rep2


title: i3N, GR, med, 3min, rep1

value: GR

value: polyA RNA associated with 3-7 ribos

value: harringtonine 3 min


title: i3N, GR, heavy, 3min, rep1


title: WT_ES_d0_Xist,rep2

value: TST

value: mESC

value: wild-type

value: Antisense oligos to Xist

value: female

value: day 0


title: control, lung, E13.5, rep2, bulk RNA-seq

value: whole lung cells


title: i3N, GFP, med, 3min, rep1

value: Day 14 neuron

value: GFP


title: control, lung, E13.5, rep1, bulk RNA-seq


title: WT_ES_d0_Sense,rep2

value: CAST/EiJ x 129S1

value: Control sense oligos


title: MALE_ES_d4_Sense,rep1

value: Differentiating mESC

value: male

value: day 4


title: HEK293T_ChIPseq_CTCF_Untreated_rep3

value: ZNF143 tagged with an inducible degron tag

value: Untreated

value: CTCF (3418S, Cell Signaling)


title: i3N, GR, med, 0min, rep1

value: GR

value: polyA RNA associated with 3-7 ribos

value: harringtonine 0 min


title: WT_ES_d0_Input,rep2

value: TST

value: mESC

value: wild-type


title: CIA+JAKi synovial cells scRNA-seq

city: Tokyo

first: Noriko

last: Komatsu

address: 7-3-1, Hongo, Bunkyo-ku

institute: The Univ of Tokyo

data_processing:
Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.).
Assembly: mm10
Supplementary files format and content: The processed data files include barcodes, tsv; features, tsv; matrix, mtx

source_name: synovium

extract_protocol:
Fresh synovial tissue was dissociated in type II collagenase solution (Worthington, 4 mg/mL) at 37 °C for 1 hour with frequent shaking. After the first 30-min incubation, cell suspensions were carefully homogenized by a series of 18G, 21G and 25G needles until the cell suspension passed through the needles smoothly. After digestion, cells were collected by centrifugation and the cell pellet was then treated with ACK buffer (Sigma) to lyse the red blood cells, and then filtered using 100-μm cell strainers to remove the tissue debris to get the single-cell suspensions.
Sequencing libraries were generated using a 10x Genomics Single-cell 3' Solution (v.3) kit and then subjected to Illumina sequencing (HiSeq 4000)

treatment_protocol: CIA mice were administrated a JAK inhibitor (JAKi), upadacitinib (Selleck, 12mg/kg) by oral gavage twice a day from d7 to d21 after the 2nd immunization.  Single-cell RNA-seq was performed on knee joint synovial cells of 6 CIA+JAKi mice) day 21 after 2nd immunization with a target output of 3,000 cells, then captured with the 10x Genomics Chromium system.

tag: disease state

value: collagen-induced arthritis (CIA)

value: synovium

value: synovial cells

value: treated with upadacitinib


title: i3N, GFP, med, 0min, rep1

value: Day 14 neuron

value: GFP


title: i3N, GR, input, 3min, rep3

value: polyA RNA

value: harringtonine 3 min


title: HEK293T_ChIPseq_CTCF_Untreated_rep1

value: ZNF143 tagged with an inducible degron tag


title: WT_ES_d0_Xist,rep1

value: CAST/EiJ x 129S1

value: Antisense oligos to Xist

value: female

value: day 0


title: KO_31D_50PM_Rep6

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Gene expression from Drosophila body representing Cdk5a Knock Out collected at 31 Days Old (50 Percent Mortality)

hyb_protocol: Fragmented cRNA were hybridized to the DroGene-1_0-st GeneChip then stained and washed via fluidics station according to Affymetrix guidelines.

scan_protocol: GeneChips were scanned using a GeneArray Scanner according to Affymetrix guidelines, producing 1 CEL file per sample.

data_processing: Gene expression data was generated from each CEL file using the Transcriptome Analysis Console (TAC) software (ThermoFisher Scientific).

label: biotin

label_protocol: Biotinylated cRNA were prepared from isolated RNA then fragmented according to the Affymetrix recommended protocol for hybridization to the DroGene-1_0-st GeneChip.

growth_protocol: Flies were grown to the ages described then frozen.  After, bodies were dissected away from heads and homogenized in Lysis Binding Mix (MagMAX mirVana total RNA isolation kit) using a Bullet Blendor Storm 24.

extract_protocol: RNA was isolated using the MagMAX mirVana total RNA isolation kit and KingFisher Apex purification system with 96 Deep-well head.

value: Oregon R

value: Body

value: 31 Days Old (50 Percent Mortality)

value: Cdk5a Knock Out


title: i3N, GFP, input, 3min, rep3


title: HEK293T_ChIPseq_ZNF143_Proteintech_dTAG_rep4

description:
ZNF143_Proteintech_dTAG_30min.rpgc.bw
ZNF143_Proteintech_dTAG_30min_peaks.bed

value: ZNF143 (16618-1-AP, Proteintech)


title: HEK293T_ChIPseq_CTCF_Untreated_rep2

value: Untreated

value: CTCF (3418S, Cell Signaling)


title: WT_ES_d0_Sense,rep1

data_processing:
The raw data underwent adaptor removal using trim_galore/cutadapt (versions 0.4.3/1.7.1). Subsequently, the trimmed reads were aligned to the genomes of Mus musculus (mus) and Mus castaneus (cas) using NovoAlign (version 4.03). These aligned reads were then mapped back to the reference mm10 genome using SNPs, resulting in the generation of a BAM file. To maintain uniform library sizes across the samples, random sampling with Samtools (version 1.11) was implemented. CHART coverage profiles were generated using DeepTools (version 3.1.2), resulting in the creation of bigwig files (rpkm-normalized).
To identify Xist CHART peaks on autosomes, reads from chromosome X (chrX) were initially excluded from the BAM file. Peak calling was performed using MACS2 (version 2.1) with default parameters. The resultant peak files from two replicates were merged using bedtools (version 2.30) intersect.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
Library strategy: CHART-SEQ

value: TST

value: mESC

value: wild-type

value: Control sense oligos


title: RepB_ES_d0_Xist,rep2

value: Repeat B deletion


title: i3N, GR, input, 0min, rep3

value: Day 14 neuron

value: GR

value: polyA RNA

value: harringtonine 0 min


title: KO_31D_50PM_Rep5

source_name: Drosophila body representing Cdk5a Knock Out collected at 31 Days Old (50 Percent Mortality)


title: WT_ES_d0_Input,rep1

value: CAST/EiJ x 129S1

value: female

value: day 0


title: KO_31D_50PM_Rep4

value: Oregon R

value: Body

value: 31 Days Old (50 Percent Mortality)


title: HEK293T_ChIPseq_CTCF_dTAG_rep1

value: ZNF143 tagged with an inducible degron tag


title: HEK293T_ChIPseq_ZNF143_Proteintech_dTAG_rep3

value: ZNF143 (16618-1-AP, Proteintech)


title: KO_31D_50PM_Rep3

value: Cdk5a Knock Out


title: RepB_ES_d0_Sense,rep2

value: TST

value: mESC


title: KO_31D_50PM_Rep2


title: KO_31D_50PM_Rep1


title: HEK293T_ChIPseq_ZNF143_Proteintech_dTAG_rep2


title: i3N, GR, input, 3min, rep2

value: harringtonine 3 min


title: i3N, GFP, med, 3min, rep2

value: GFP

value: polyA RNA associated with 3-7 ribos


title: MALE_ES_d4_Xist,rep1

value: Differentiating mESC

value: wild-type

value: Antisense oligos to Xist

value: male

value: day 4


title: i3N, GFP, input, 3min, rep2

value: Day 14 neuron

value: polyA RNA


title: RepB_ES_d0_Xist,rep1

value: CAST/EiJ x 129S1

value: Repeat B deletion

value: female

value: day 0


title: KO_23D_Rep6

description: Gene expression from Drosophila body representing Cdk5a Knock Out collected at 23 Days Old

value: Oregon R

value: Body

value: 23 Days Old

value: Cdk5a Knock Out


title: RepB_ES_d0_Input,rep2

value: TST

value: mESC


title: KO_23D_Rep4

source_name: Drosophila body representing Cdk5a Knock Out collected at 23 Days Old


title: i3N, GR, input, 0min, rep2

value: GR

value: harringtonine 0 min


title: i3N, GFP, input, 0min, rep3

value: GFP


title: i3N, GFP, input, 0min, rep2


title: RepB_ES_d0_Input,rep1


title: KO_23D_Rep5


title: i3N, GR, input, 3min, rep1

value: harringtonine 3 min


title: RepB_ES_d0_Sense,rep1

value: Control sense oligos


title: HEK293T_ChIPseq_ZNF143_Proteintech_Untreated_rep2

description:
ZNF143_Proteintech_Untreated.rpgc.bw
ZNF143_Proteintech_Untreated_peaks.bed

value: ZNF143 tagged with an inducible degron tag

value: Untreated

value: ZNF143 (16618-1-AP, Proteintech)


title: HEK293T_ChIPseq_ZNF143_Proteintech_Untreated_rep1


title: MALE_ES_d0_Xist,rep2

value: CAST/EiJ x 129S1

value: wild-type

value: Antisense oligos to Xist

value: male


title: i3N, GFP, input, 3min, rep1

value: Day 14 neuron

value: polyA RNA


title: MALE_ES_d0_Sense,rep2

value: day 0


title: KO_23D_Rep3

value: Oregon R

value: Body

value: 23 Days Old

value: Cdk5a Knock Out


title: HEK293T_ChIPseq_ZNF143_Proteintech_Untreated_rep4


title: i3N, GR, input, 0min, rep1

value: GR

value: harringtonine 0 min


title: KO_10D_Rep6

description: Gene expression from Drosophila body representing Cdk5a Knock Out collected at 10 Days Old

value: 10 Days Old


title: KO_23D_Rep1


title: HEK293T_ChIPseq_ZNF143_Proteintech_Untreated_rep3

value: ZNF143 tagged with an inducible degron tag


title: sample ID: L00230, NonNBS, immunohistochemistry: NonGCB

city: Łódź

first: Jędrzej

last: Chrzanowski

state: łódzkie

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Raw data with adapter sequences or low-quality sequences were filtered using SOAPnuke software with filter parameters “-n 0.03 -l 20 -q 0.4 -A 0.28”.
After base calling FASTQ files were preprocessed with fastp version 0.20.1 and next aligned to the human reference genome (GRCh38.p13) with STAR version 2.7.10a.
The standard alignment protocol was followed, with homo sapiens Ensembl version 104 GTF annotation file. Read counts were analyzed using HTSeq version 0.13.5.
Read counts were normalized to the trimmed mean of M values (TMM) as implemented in the edgeR 3.12 package.
The ComBat normalization method (using Python implementation, doi: 10.1101/2020.03.17.995431v2), was used to correct the batch effects observed by day of RNA isolation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lymphocytes

extract_protocol:
RNeasy FFPE Mini Kit (Cat. #: 73504, Qiagen, Germany) with Deparaffinization Solution (Cat. #: 19093, Qiagen, Germany) was used to isolated RNA material from Formalin-Fixed Paraffin-Embedded (FFPE) samples
The RNAseq procedure was performed with the usage of SureSelect XT RNA Direct Human All Exon V6+UTR (Agilent, Technologies, California, USA) and NextSeq™ 500/550 High Output Kit v2.5 (300 Cycles; Illumina, California, USA) in accordance with the protocol provided by the manufacturer.

value: lymphocytes

value: FFPE

value: NonNBS

value: NonGCB


title: MALE_ES_d0_Input,rep2

first: Shengze

last: Yao

address: 185 Cambridge St

institute: Massachusetts General Hospital

extract_protocol:
For CHART-seq, 25 million cells underwent crosslinking with 1% formaldehyde, followed by additional crosslinking of nuclei with 3% formaldehyde. Chromatin was then sheared via sonication to produce fragments ranging from 2 to 4kb. Pre-clearing of the chromatin was performed using MyOne Streptavidin C1 beads. Subsequently, the pre-cleared chromatin was mixed with 36 pmol of either antisense (targeting Xist) or sense (used as a control) biotin-labeled probes, and captured using MyOne Streptavidin C1 beads. After washing the beads, DNA was eluted using RNase H. Eluted DNA was extracted via phenol-chloroform and further sheared to achieve fragments below 500 bp.
The library was generated using the NEBNext® Ultra™ II DNA Library Prep Kit.

value: CAST/EiJ x 129S1

value: mESC

value: wild-type


title: sample ID: L00229, NonNBS, immunohistochemistry: GCB

value: GCB


title: i3N, GFP, input, 0min, rep1

value: Day 14 neuron

value: GFP

value: polyA RNA


title: KO_23D_Rep2

city: Bethesda

value: Oregon R

value: Body

value: 23 Days Old


title: MALE_ES_d0_Xist,rep1

city: Boston

value: Antisense oligos to Xist

value: male

value: day 0


title: MALE_ES_d0_Sense,rep1

value: Control sense oligos


title: Input, rep2

city: Chengdu

first: Zhihong

last: Xue

state: Sichuan

address: No. 20, 3rd section, South Renmin Road

institute: Sichuan University

data_processing:
Untrimmed sequencing reads were first analyzed for quality control by fastqc solfware(v0.11.9). The adaptor sequence and low-quality reads were then trimmed off using trim_galore solfware(v0.6.7)
Ribosome RNAs were removed from trimmed reads using SortMeRNA solfware(v)
Reads without ribosome RNAs were mapped to hg38 reference genome using STAR solfware(v2.7.1a) as default parameters
Raw readcounts were calculated using FeatureCounts solfware（v2.0.1）.The raw readcounts were normalized by the FPKM method.
Assembly: hg38
Supplementary files format and content: Comma-Separated Values CSV files include FPKM values or raw counts for each Sample

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% newborn calf serum (NBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were isolated using the Trizol Reagent. We incubated 75ul HARD-AP beads with  50ug the total RNAs of HEK293 cells for 2 hours.After washing and eluting the samples，we got the HARD-AP samples. The total RNAs were the Input sample.
RNA sequencing libraries were prepared from 2μg of input RNAs or HARD-AP purified RNAs with the following modification. We removed ribosomal RNA using Epicentre Ribo-Zero™ rRNA Removal Kit (Human). Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. Using RNA as a template and random oligonucleotides as primers, synthesize the first strand of cDNA, then use RNaseH to degrade the RNA strand, and in the DNA polymerase I system, use dNTP with dUTP instead of dTTP as raw material to synthesize the second strand of cDNA .Purify the double-stranded cDNA, then perform double-end repair and introduce the "A" base at the 3'end and connect the sequencing adapter. At this time, USER enzyme (NEB, USA) was added to degrade the second strand of cDNA containing U. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina)

value: Human embryonic kidney cell

value: WT

value: Input


title: sample ID: L00233, NonNBS, immunohistochemistry: GCB

value: lymphocytes

value: FFPE

value: NonNBS


title: KO_10D_Rep5

source_name: Drosophila body representing Cdk5a Knock Out collected at 10 Days Old

value: 10 Days Old

value: Cdk5a Knock Out


title: Input, rep1


title: sample ID: L00228, NBS, immunohistochemistry: No data

value: NBS

value: No data


title: MALE_ES_d0_Input,rep1

value: CAST/EiJ x 129S1

value: mESC

value: wild-type


title: sample ID: L00226, NonNBS, immunohistochemistry: GCB

value: GCB


title: HARD-AP, rep2

value: HARD-AP


title: Multiplexed_Library_3

city: Mainz

first: Wolfram

last: Ruf

address: Langenbeckstrasse 1

institute: CTH Mainz

description:
See Demultiplex File Supplementary File Demultiplexing.pdf for sample tag information.
H14_EKDL220000172-1a_HWVNFDSX2_L3

data_processing:
The Rhapsody pipeline was used to map the fastq files and generate count matrixes
Assembly: gencodevM19-20181206.gtf | GRCm38-PhiX-gencodevM19-20181206.tar.gz
Supplementary files format and content: The Comma Seperated Value (.csv) files contain the count matrixes per sample

source_name: Heart

extract_protocol:
CD45+ cells were isolated from the infarcted myocardium by enzymatic digestion with the Multi Tissue Dissociation Kit 2 (#130-110-203, Miltenyi Biotec) using the gentle MACS dissociator (#130-093-235, Miltenyi Biotec). After homogenization, suspensions were passed through 70 μm cell strainer and resuspended in cell isolation buffer. Dead cells were eliminated with dead cell removal microbeads (#130-090-101, Miltenyi Biotec) followed by positive selection on anti-CD45 microbeads (#130-052-301, Miltenyi Biotec). Counts of viable cells were measured on the automated cell counter of the BD Rhapsody platform. Samples, which passed the viability test, were tagged for the identification of biological replicates after pooling and sequencing. After washing sample tagged cells, we repeated cell counts and viability testing and loaded up to 30,000 cells on a cartridge to achieve single cell isolation
Library construction and quality control were done according to the Rhapsody pipeline

value: Heart

value: Cd45+ selected

value: multiplexed sample:F7fl/fl CX3CR1Cre and F7fl/fl WT


title: sample ID: L00224, NonNBS, immunohistochemistry: GCB


title: KO_10D_Rep4

value: Oregon R

value: Body


title: KO_10D_Rep3


title: KO_10D_Rep1


title: KO_10D_Rep2


title: HARD-AP, rep1

value: Human embryonic kidney cell

value: WT


title: HEK293T_ChIPseq_ZNF143_Proteintech_dTAG_rep1

value: ZNF143 tagged with an inducible degron tag

value: ZNF143 (16618-1-AP, Proteintech)


title: Multiplexed_Library_2

description:
See Demultiplex File Supplementary File Demultiplexing.pdf for sample tag information.
H13_EKDL220000171-1a_HWVNFDSX2_L1


title: sample ID: L00222, NonNBS, immunohistochemistry: NonGCB

value: lymphocytes

value: FFPE

value: NonNBS

value: NonGCB


title: Multiplexed_Library_1

description:
See Demultiplex File Supplementary File Demultiplexing.pdf for sample tag information.
F7_d3_S1


title: SO_2_5_IU

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

description: 100bp read length

data_processing:
For Bulk RNA-seq analysis: FASTQ files were pseudoaligned, and DEGs were determined using DESeq. DEGs were then plotted as Principal Component Analysis and heat maps through BioJupies.  For single cell RNA-seq analysis: CellRanger was used to align the sequencing data. Scanpy was used to as a secondary data analysis. The generated loom files were read in as anndata objects and concatenated into a master anndata object. Preprocessing and quality control were performed similarly to the methods described in Scanpys clustering tutorial.
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq data: transcripts per million (TPM) values were exported into .csv files. For single cell RNA-seq data: .h5ad files were exported following standard codes in Scanpy tutorial.

source_name: oviduct

growth_protocol: Oviductal tissues were collected from adult C57BL6/J mice and stored in pairs (one pair of oviducts per animal) at 0.5, 1.5, 2.5, and 3.5 dpc/dpp of natural fertilization and pseudopregnancy, respecitvely. For 0.5 dpc/dpp tissue, female mice were placed for mating at 21:00h. For 1.5, 2.5, and 3.5 dpc/dpp, female mice were placed for mating between 5-6 p.m.

extract_protocol:
Oviducts were dissected and kept in 1 mL Leibovitz-15 + 1% fetal bovine serum (FBS). Then, oviducts were sectioned into two regions (Infundibulum + Ampulla (IA), Isthmus + Uterotubal Junction (IU). Tissue samples were placed in a sterile Eppendorf tube and flash-frozen in liquid N2. Samples were stored at -80°C for later RNA extraction. The oviducts were collected at the same time points as their dpc counterparts for DPP samples. Total RNA were extracted utilizing the RNeasy Micro Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions. DNA digestion was performed with all samples using a Qiagen RNase-free DNase Set (1500 K units). RNA was then shipped to the University of California San Diego (UCSD) for quality control, library preparation, and sequencing. RNA integrity (RIN) was verified using TapeStation for a minimum RIN value of 7. RNA from this study has an average RIN of 9.04. For singe cell-RNA seq analysis: Another set of mice was used for single-cell isolations and scRNA-seq analysis. Mating and tissue collection protocols were similar to bulk RNA isolation described above, with the exception that female mice were superovulated using the protocol described previously (73) to ensure sufficient numbers of female mice at each time point could be harvested for single cell isolation and library preparation within the same day (n= 3-4 mice/group). Superovulation was performed by intraperitoneal injection of 5 IU pregnant mare serum gonadotropin (PMSG, Prospect HOR-272, East Brunswick, NJ). Forty-eight hrs after PMSG injection, females were injected with 5 IU of human chorionic gonadotropin (hCG, Prospect HOR-250). Immediately after the hCG injection, females were placed in fertile male cages for mating. Oviducts were collected at 0.5, 1.5, and 2.5 dpc and dissected into IA and IU regions before single-cell isolation. For the control group, oviducts were collected 16 hrs post hCG injection. Trypsin-EDTA (0.25%, MilliporeSigma, T4049) was used for oviductal cell isolation.
For Bulk RNA-seq analysis: RNA libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina Inc., San Diego, CA). For single-cell RNA-seq analysis: The final cell concentration was targeted for 8,000 cells/run. Cell singlets were captured for the library preparation using 10X Chromium Controller and Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA). Libraries generated were then evaluated for quality using Fragment Analyzer (Agilent, Santa Clara, CA).
For Bulk RNA-seq analysis: Libraries were sequenced using the Illumina NovaSeqS4 platform with a read depth of 25M reads/sample (n=3/region/timepoint), paired-end, and 100bp read length. For single cell RNA-seq analysis:  Libraries were sequenced using Illumina HiSeq4000 at the University of Oregon, targeting 400 million reads/run, paired-end, and 100 bp read length.

value: oviduct

tag: region

value: isthmus and uterotubal junction

tag: timepoint

value: Superovulated 2.5 dpc


title: WT_58D_50PM_Rep6

description: Gene expression from Drosophila body representing Wild Type collected at 58 Days Old (50 Percent Mortality)

value: 58 Days Old (50 Percent Mortality)

value: Wild Type


title: sample ID: 966, NBS, immunohistochemistry: NonGCB

value: NBS


title: SO_2_5_IA

description: 100bp read length

value: infundibulum and ampulla

value: wild-type


title: WT_58D_50PM_Rep4

source_name: Drosophila body representing Wild Type collected at 58 Days Old (50 Percent Mortality)

value: Oregon R

value: Body


title: WT_58D_50PM_Rep3


title: SO_1_5_IU

description: 100bp read length

value: Superovulated 1.5 dpc


title: SO_1_5_IA

description: 100bp read length


title: sample ID: 95559, NBS, immunohistochemistry: NonGCB


title: sample ID: 350, NBS, immunohistochemistry: GCB

value: GCB


title: sample ID: L00221, NonNBS, immunohistochemistry: GCB


title: sample ID: 3390, NBS, immunohistochemistry: GCB


title: SO_0_5_IU

description: 100bp read length

value: Superovulated 0.5 dpc


title: WT_58D_50PM_Rep5


title: sample ID: L00220, NonNBS, immunohistochemistry: GCB

value: lymphocytes


title: SO_0_5_IA

description: 100bp read length


title: WT_58D_50PM_Rep1


title: sample ID: LAO9869, NonNBS, immunohistochemistry: NonGCB

value: FFPE


title: sample ID: 26183, NBS, immunohistochemistry: GCB


title: SO_Estrus_IU

description: 100bp read length

value: Superovulated estrus


title: SO_Estrus_IA

description: 100bp read length


title: sample ID: LAO6667, NonNBS, immunohistochemistry: GCB

value: NonNBS


title: sample ID: LAL9609, NonNBS, immunohistochemistry: GCB


title: 3.5 dpp, IU, Rep3

description: 100bp read length

value: oviduct

value: 3.5 days of pseudopregnancy (0.5 dpp)


title: WT_41D_Rep4

description: Gene expression from Drosophila body representing Wild Type collected at 41 Days Old

value: 41 Days Old


title: WT_41D_Rep3

source_name: Drosophila body representing Wild Type collected at 41 Days Old


title: 3.5 dpp, IU, Rep2

description: 100bp read length

value: isthmus and uterotubal junction


title: sample ID: LAJ2682, NonNBS, immunohistochemistry: GCB


title: WT_58D_50PM_Rep2

value: 58 Days Old (50 Percent Mortality)

value: Wild Type


title: WT_41D_Rep2


title: sample ID: LAI0151, NonNBS, immunohistochemistry: GCB


title: 3.5 dpp, IA, Rep3

description: 100bp read length

value: infundibulum and ampulla


title: WT_41D_Rep6


title: 3.5 dpp, IU, Rep1

description: 100bp read length

value: wild-type


title: sample ID: LAH2392, NonNBS, immunohistochemistry: NonGCB

value: NonGCB


title: WT_41D_Rep1

value: Oregon R

value: Body


title: sample ID: LAB7012, NonNBS, immunohistochemistry: NonGCB


title: sample ID: 52386, NBS, immunohistochemistry: NonGCB

value: NBS


title: WT_20D_Rep5

description: Gene expression from Drosophila body representing Wild Type collected at 20 Days Old

value: 20 Days Old


title: WT_20D_Rep6

source_name: Drosophila body representing Wild Type collected at 20 Days Old


title: 3.5 dpp, IA, Rep2

description: 100bp read length


title: 3.5 dpp, IA, Rep1

description: 100bp read length


title: sample ID: 37525, NBS, immunohistochemistry: NonGCB

value: lymphocytes


title: 2.5 dpp, IU, Rep3

description: 100bp read length

value: 2.5 days of pseudopregnancy (0.5 dpp)


title: 2.5 dpp, IU, Rep2

description: 100bp read length


title: sample ID: 381844, NonNBS, immunohistochemistry: NonGCB

value: FFPE


title: WT_20D_Rep4


title: 2.5 dpp, IU, Rep1

description: 100bp read length


title: WT_20D_Rep2


title: 2.5 dpp, IA, Rep3

description: 100bp read length


title: WT_20D_Rep1


title: sample ID: NG9, NonNBS, immunohistochemistry: NonGCB

value: NonNBS


title: sample ID: 314005c, NonNBS, immunohistochemistry: GCB

value: GCB


title: WT_20D_Rep3


title: sample ID: NG8, NonNBS, immunohistochemistry: NonGCB


title: 2.5 dpp, IA, Rep2

description: 100bp read length

value: oviduct


title: WT_10D_Rep6

description: Gene expression from Drosophila body representing Wild Type collected at 10 Days Old

value: 10 Days Old


title: i3N, GFP, heavy, 3min, rep1

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher), and RNA concentrations were determined with the Qubit RNA HS Assay Kit on a Qubit 4.0 Fluorometer
Libraries were prepared according to protocol accompanying the NEBNext® Ultra™ II Directional RNA Library Prep Kit (Cat. No. E7765) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Day 14 neuron

value: GFP

value: polyA RNA associated with >7 ribos

value: harringtonine 3 min


title: WT_10D_Rep5

source_name: Drosophila body representing Wild Type collected at 10 Days Old

value: Wild Type


title: WT_10D_Rep4


title: sample ID: NG14, NonNBS, immunohistochemistry: NonGCB

value: NonGCB


title: 2.5 dpp, IA, Rep1

description: 100bp read length

value: infundibulum and ampulla

value: wild-type


title: WT_41D_Rep5

value: Oregon R

value: Body

value: 41 Days Old


title: 1.5 dpp, IU, Rep3

description: 100bp read length

value: isthmus and uterotubal junction

value: 1.5 days of pseudopregnancy (0.5 dpp)


title: sample ID: NG13, NonNBS, immunohistochemistry: NonGCB

value: lymphocytes

value: FFPE

value: NonNBS


title: Ly19_Setd1BC_H3K4Me3

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Libraries were then sequenced on a HiSeq 2500 System as 50-bp single-end runs.
ChIP-seq reads were aligned to Homo sapiens (hg38) using Bowtie2 with default parameters, following adapter trimming by Trimmomatic.
Analysis was conducted using only high-quality and uniquely mapped reads, with a mapping quality (MAPQ) threshold of ≥ 20.
Peak calling for ChIP-seq reads was performed against Input reads using the Genrich peak caller which considered replicate consistency.
Peak annotation was done using the HOMER package. DESeq2 R package was employed to identify differentially enriched H3K4me3 peaks between the SETD1B KO and control samples.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cell line

growth_protocol: OCILY19 cells were maintained in RPMI supplemented with 10% Fetal bovine serum (FBS) and glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
3–5×107 cells were crosslinked with 1% paraformaldehyde at room temperature for 15 min and sonicated to generate chromatin fragments of 200–600bp. Fragmented chromatin was then immunoprecipitated overnight with one microgram of H3K4me3 antibody (#ab8580; Abcam) incubated overnight at 4 °C. Enriched DNA was isolated by Dynabeads Protein A (#10001D, Thermo Fisher Scientific) and subsequent reverse cross-linking and purification.
ChIP–seq libraries were prepared from 1–5 ng ChIP DNA according to the instructions of the TruSeq ChIP Library Preparation Kit (#IP-202-1012, Illumina). Libraries were  sequenced on a HiSeq 2500 System as 50-bp single-end runs.

value: Cell line

tag: chip antibody

value: H3K4me3 antibody (#ab8580; Abcam)


title: sample ID: NG11, NonNBS, immunohistochemistry: NonGCB

tag: cell line


title: sample ID: NG10, NonNBS, immunohistochemistry: NonGCB

tag: treatment


title: sample ID: NG12, NonNBS, immunohistochemistry: NonGCB


title: Ly19_ctrlSetd1bC_H3K4me3_chip2

tag: tissue


title: 1.5 dpp, IU, Rep1

description: 100bp read length

value: oviduct

tag: genotype


title: 1.5 dpp, IA, Rep3

description: 100bp read length


title: Ly19_ctrl_H3k4me3


title: 1.5 dpp, IU, Rep2

description: 100bp read length


title: Ly19_Setd1BC_input


title: WT_10D_Rep1

value: 10 Days Old


title: WT_10D_Rep3


title: 1.5 dpp, IA, Rep2

description: 100bp read length


title: sample ID: G7, NonNBS, immunohistochemistry: GCB

tag: cell type

value: GCB


title: 1.5 dpp, IA, Rep1

description: 100bp read length

tag: strain


title: sample ID: G6, NonNBS, immunohistochemistry: GCB


title: Ly19_ctrl_input


title: Ly19_ctrl_H3K4me3_chip2


title: WT_10D_Rep2

tag: age

value: Wild Type


title: OCILY8_sgSETD1BKO_3

description:
Ly8_sgSETD1BKO1_IGO_10565_6
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx

data_processing:
The Casava v.1.8 software (Illumina) was used for base calling.
Libraries were validated using the 2100 Bioanalyzer Instrument and the Quant-iT dsDNA HS Assay Kit (Q33120, Thermo Fisher Scientific).
Adaptor sequences trimmed using Trimmomatic.
RNA-seq reads were mapped to the Homo sapiens (hg38) genome assembly using HISAT2.
Sequencing reads were assigned to genes by featureCounts in Rsubread package in Bioconductor.
Differentially expressed mRNAs between SETD1B KO and control were identified, and FDR (Benjamini–Hochberg) was estimated, using DEseq2
Assembly: hg38
Supplementary files format and content: counts.xlsx is an excel contains raw gene counts for each sample, the first column containing gene name
Supplementary files format and content: sig.deseq2_expr.xlsx contains normalized count values for genes, the last column containing the gene name. Genes with no reads were excluded

growth_protocol: OCILY8 cells were maintained in RPMI supplemented with 10% Fetal bovine serum (FBS) and glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini kit (Quiagen). RNA size, concentration, and integrity were verified using a 2100 Bioanalyzer Instrument (Agilent Technologies).
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA sample kits according to the manufacturer’s protocol.

value: Lymphoma

value: SETD1B knockout


title: 0.5 dpp, IU, Rep1

description: 100bp read length

value: wild-type

value: 0.5 days of pseudopregnancy (0.5 dpp)


title: sample ID: G5, NonNBS, immunohistochemistry: GCB


title: 0.5 dpp, IU, Rep3

description: 100bp read length


title: 0.5 dpp, IU, Rep2

description: 100bp read length


title: sample ID: G4, NonNBS, immunohistochemistry: GCB


title: sample ID: G3, NonNBS, immunohistochemistry: GCB


title: OCILY8_sgSETD1BKO_2

description:
Ly8_sgSETD1BKO1_IGO_10565_5
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx


title: 0.5 dpp, IA, Rep3

description: 100bp read length

value: infundibulum and ampulla


title: OCILY8_sgNTC1_3

description:
Ly8_sgNTC1_IGO_10565_3
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx

value: WT


title: sample ID: G2, NonNBS, immunohistochemistry: GCB


title: sample ID: G1, NonNBS, immunohistochemistry: GCB


title: sample ID: 16, NonNBS, immunohistochemistry: GCB


title: 0.5 dpp, IA, Rep2

description: 100bp read length


title: 0.5 dpp, IA, Rep1

description: 100bp read length


title: 4sU labeling, scRNA-seq, sti_J

first: Jun

last: Lyu

address: 37 Convent Drive

institute: National cancer institute

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Raw sequencing data of SLAM-seq were first trimmed using cutadpt (v1.15) and then analyzed using SLAM-DUNK (v0.4.3) to map, filter and quantify reads containing T-to-C mutation.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files

source_name: Jurkat T Clone E6-2

extract_protocol:
For single cell RNA sequencing, single cell suspension was prepared for 10X Genomics sample loading. For RNA-seq, RNA was extracted using RNeasy Mini Kit (Qiagen).
For NOTE-seq, Libraries were constructed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E) with serval additional steps detaied in the Method section. For regular 10xgenomics, libraries were constructed using  Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E). For SLAM-seq, 2 µg RNA were combined with 10 mM iodoacetamide (Sigma-Aldrich, St. Louis, MO, USA), 50 mM sodium phosphate buffer (pH 8.0) and 50% DMSO, followed by 15 min of incubation at 50°C. The reaction was stopped by adding 20 mM DTT, followed by RNA purification using 1.8X RNA beads (Aline Bioscience) and RNA elution with 11 µl nuclease-free water. Then, 500 ng RNA was subject to library construction using Quant-seq 3′ mRNA-Seq Library Prep Kit (Lexogen)
scRNA-seq and RNA-seq

value: Jurkat T Clone E6-2


title: OCILY8_sgNTC1_1

description:
Ly8_sgNTC1_IGO_10565_1
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx


title: OCILY19_sgSETD1BKO_3

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgSETD1BKO1_IGO_10565_6

value: KMT2D+SETD1B double mutant


title: sample ID: 15, NonNBS, immunohistochemistry: No data

value: lymphocytes

value: No data


title: 4sU labeling, scRNA-seq, unsti_J

source_name: Jurkat T Clone E6-1

value: Jurkat T Clone E6-1


title: 3.5 dpc, IU, Rep2

description: 100bp read length

value: isthmus and uterotubal junction

value: 3.5 days post coitus (0.5 dpc)


title: 3.5 dpc, IA, Rep3

description: 100bp read length

value: oviduct


title: OCILY19_sgSETD1BKO_2

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgSETD1BKO1_IGO_10565_5

value: Cell line


title: OCILY19_sgSETD1BKO_1

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgSETD1BKO1_IGO_10565_4


title: no 4sU labeling, scRNA-seq, SNP background for Jurkat

description: Barnyard

source_name: Jurkat T cell Clone E6-1 and NIH3T3

value: Jurkat T cell Clone E6-1 and NIH3T3


title: 3.5 dpc, IA, Rep2

description: 100bp read length


title: OCILY19_sgNTC1_3

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgNTC1_IGO_10565_3

value: KMT2D mutant


title: 4sU labeling, scRNA-seq,eHAP

source_name: eHAP

value: eHAP


title: 3.5 dpc, IA, Rep1

description: 100bp read length


title: OCILY19_sgNTC1_2

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgNTC1_IGO_10565_2

value: Lymphoma


title: 2.5 dpc, IU, Rep3

description: 100bp read length

value: wild-type

value: 2.5 days post coitus (0.5 dpc)


title: no 4sU labeling, scRNA-seq


title: OCILY8_sgSETD1BKO_1

description:
Ly8_sgSETD1BKO1_IGO_10565_4
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx

value: SETD1B knockout


title: OCILY8_sgNTC1_2

description:
Ly8_sgNTC1_IGO_10565_2
LY8_RNAseq_counts.xlsx
LY8_RNAseq.sig.dseq2_Expr.xlsx

value: WT


title: OCILY19_sgNTC1_1

description:
LY19_RNAseq.sig.dseq2_Expr.xlsx
LY19_RNAseq_counts.xlsx
Ly19_sgNTC1_IGO_10565_1


title: Tb_HAp_long_3, Day 21

city: London

first: Jishizhan

last: Chen

address: 10 Pond St

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

data_processing:
Quality checked by FastQC v.0.11.9
Trimmed the adapters, poorly expressed or nonexpressed genes via the Trimmomatic v.0.38.0 with following parameters: PE; ILLUMINACLIP: TruSeq3-PE.fa: 2:30:10; LEADING: 3; TRAILING: 3; SLIDINGWINDOW: 4:15; MINLEN: 50.
After that, the HISAT2 v.2.2.1 was utilised to map sequences to the UCSC Homo sapiens GRCh38 reference.
The table of read counts with Entrez gene IDs was generated using the featureCounts v.2.0.1.
Assembly: hg38
Supplementary files format and content: Tabular files of read counts for each Sample.

source_name: bone marrow-derived mesenchymal stem cells

growth_protocol: hBMSCs were cultured in the Mesenchymal Stem Cell Osteogenic Differentiation Medium (MODM, ScienCell, Carlsbad, US) in humidified atmosphere with 5% CO2 at 37C for 21 days.

extract_protocol:
Total RNA extraction was performed using a Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, US), according to the manufacturer’s protocol.
The RNA-Seq was carried out at the UCL Genomics facility. RNA concentration was measured on a Nanodrop spectrometer and 500 ng of RNA was used for cDNA synthesis and library preparation using the Kapa mRNA HyperPrep assay (Roche, Basel, Switzerland) and xGen UDI-UMI adapters (Integrated DNA Technology, Shanghai, China) , according to the manufacturer’s protocol. Sequencing of these libraries was performed on the NextSeq 2000 (Illumina, San Diego, US) P2 flow-cell with 56bp paired-end reads.

treatment_protocol: hBMSCs were culture on coated coverslips. Different groups were set up based on the coating substrates, which are hydroxyapatite nanorods (HAp NRs) with or without 4 mol% terbium (Tb) doping, in short- or long-range ordered patterns (fixed by PDMS). The coverslips coated with only PDMS were utilised as the control.

value: PDMS + long-range ordered Tb-HAp


title: Tb_HAp_long_2, Day 21

value: bone marrow-derived mesenchymal stem cells


title: 2.5 dpc, IU, Rep1

description: 100bp read length


title: Tb_HAp_long_1, Day 21


title: 2.5 dpc, IU, Rep2

description: 100bp read length


title: 3.5 dpc, IU, Rep3

description: 100bp read length


title: DB_N3_VDJ

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

description:
Clonotype_allsamples.csv
GEX_allsamples.csv
MetaData_allsamples.csv

data_processing:
The Illumina control software HCS HD 3.4.0.38 and the real-time analysis program RTA v2.7.7 were used.
bcl2fastq2 v2.20 was used to demultiplex samples and generate reads.
Reads were aligned to GRCh38 genome assembly using cellranger v3.0.2.
Counting data of reference gene expression levels and clonotypes were generated by cellranger v3.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: clonotype assignment
Supplementary_files_format_and_content: expression data
Supplementary_files_format_and_content: meta data assignment

source_name: T lymphocytes

growth_protocol: Cells were stimulated weekly with LMP2-pulsed dendritic cells and cultured in complete media. Cells were counted and viability checked using a Hemocytometer and Trypan Blue.

extract_protocol:
FACS-sorted LMP2 multimer-positive cells were harvested. The targeted cell recovery was set at 6000 cells and RNA was isolated using 10X Genomics reagents.
Libraries were prepared using the kits Chromium Next GEM Single Cell 5' Kit v2 and Chromium Single Cell Human TCR Amplification Kit (10x Genomics inc.). Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The 10X Single cells 5’ libraries were sequenced on Illumina HiSeq 4000 PE28x98 while the 10X Single Cells VDJ (Human T) libraries were sequenced on Illumina HiSeq 4000 PE150.

treatment_protocol: Cells were treated or not with anti-PD-L1 and anti-TIM3 antibodies.

tag: lmp2 specificity

value: positive

tag: days in culture

value: PD-L1/TIM3 double blockade


title: Tb_HAp_short_3, Day 21

value: PDMS + short-range ordered Tb-HAp


title: 3.5 dpc, IU, Rep1

description: 100bp read length

value: isthmus and uterotubal junction


title: DB_N2_VDJ


title: DB_N1_VDJ


title: Tb_HAp_short_2, Day 21


title: 2.5 dpc, IA, Rep2

description: 100bp read length

value: infundibulum and ampulla


title: 2.5 dpc, IA, Rep3

description: 100bp read length

value: oviduct


title: DB_N3_SC


title: Tb_HAp_short_1, Day 21


title: DB_N2_SC


title: 1.5 dpc, IU, Rep3

description: 100bp read length

value: 1.5 days post coitus (0.5 dpc)


title: 2.5 dpc, IA, Rep1

description: 100bp read length


title: HAp_long_3, Day 21

value: PDMS + long-range ordered HAp


title: DB_N1_SC


title: 1.5 dpc, IU, Rep2

description: 100bp read length


title: Ctrl_N3_VDJ

value: Untreated


title: HAp_long_2, Day 21


title: HAp_long_1, Day 21


title: 1.5 dpc, IU, Rep1

description: 100bp read length


title: HAp_short_3, Day 21

value: PDMS + short-range ordered HAp


title: 1.5 dpc, IA, Rep3

description: 100bp read length


title: Ctrl_N1_VDJ


title: 1.5 dpc, IA, Rep2

description: 100bp read length


title: Ctrl_N2_VDJ


title: 1.5 dpc, IA, Rep1

description: 100bp read length


title: Ctrl_N3_SC


title: HAp_short_2, Day 21


title: Control_3, Day 21

value: PDMS


title: Ctrl_N2_SC


title: Ctrl_N1_SC


title: 0.5 dpc, IU, Rep3

description: 100bp read length

value: wild-type

value: 0.5 days post coitus (0.5 dpc)


title: 0.5 dpc, IU, Rep2

description: 100bp read length


title: 0.5 dpc, IU, Rep1

description: 100bp read length


title: Control_1, Day 21