title: wt_pH7_R2

city: Villeurbanne

first: Nathalie

last: Poussereau

address: 10, rue Dubois

country: France

institute: University Lyon1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.33 (parameters- LEADING:15 TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:36)
Trimmed sequence reads were mapped to Botrytis cinerea B05.10 (ASM14353v4 from NCBI) using STAR  (v2.6, parameters- --alignEndsType EndToEnd --outFilterMultimapScoreRange 0 --alignIntronMax 1)
Read count extraction was performed using featureCounts (Subread V2.0.2, parameters- -t exon -g gene_id)
Assembly: Botrytis cinerea B05.10 (ASM14353v4 from NCBI)
Supplementary files format and content: Comma-delimited csv file includes raw counts for each sample

organism: Botrytis cinerea B05.10

growth_protocol: Botrytis cinerea  B05.10 and the deletion DBcpacC mutant strain were maintained on solid sporulation medium

extract_protocol:
The mycelia were collected, frozen in liquid nitrogen and  lyophilized. Total RNA was extracted  using the RNeasy midi kit (Qiagen). RNA was then treated  by DNase (Ambion) and RNA quality was verified using the Bioanalyzer RNA 6000 Nano kit (Agilent).
1.5µg was sent to Fasteris SA (Switzerland) for transcriptome sequencing. Libraries for RNA-seq were constructed using the Illumina TruSeq Stranded mRNA library kit .

treatment_protocol: The B05.10 and DpacC strains were grown at 21°C on solid MANG medium for 3 days on the surface of cellophane membranes inoculated with 4-mm mycelial plugs. The membranes were then transferred for 4 h onto the surface of 2 ml of liquid Gamborg medium buffered at pH 5.0 or 7.0.

tag: biological replicate

value: wt

value: pH 7


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep4 (RNA-seq)

status: Public on Aug 20 2024

type: SRA

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

description: passage 27+9+8+5 (PXGL d27 5iLAF d11)

library_source: transcriptomic

data_processing:
Raw reads were aligned against the GRCh38 reference grenome using STAR.
Reads were filtered, sorted and marked for duplicates using samtools.
Features were obtained GENCODE reference annotation file v34 and raw counts were correponding to each feature was calculated using HTSEQ. TPM values were calculated using StringTie.
Differentially expressed genes were calculated using DESeq2. Raw counts were normalised for sequencing depth and library complexity using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data includes TPM values provided as a .txt file

molecule: polyA RNA

organism: Homo sapiens

source_name: Naïve human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were lysed in RNAzol RT reagent and total RNA was purified from cell extracts according to manufacturer's instructions.
mRNA containing polyA tail were enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module and libraries were prepared using the Swift RNA library kit or NEBNext Ultra II RNA Library Prep Kit according to respective manufacturers' instructions.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate or DMSO of equivalent v/v concentration, where specified.

tag: tissue

value: Naïve human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: ZIC3-/-; stable integration of 3x-Flag ZIC2 and M2rtTA ORFs clone 14

tag: treatment

value: Cultured in medium supplemented with 100ng/ml doxycycline for 72 hours


title: ZJ316_WT, rep2

city: Hangzhou

first: Xiangfeng

last: Chen

address: Xuezheng Street 18

country: China

institute: Zhejiang Gongshang University

data_processing:
Differentially expressed genes/transcripts are identified based on read counts data of transcripts obtained from gene expression analysis. Default parameters: p-adjust < 0.05 and |log2FC| >= 1, using BGI Cloud Platform (Dr.Tom) for online analysis, when the corrected P-value (P adjust) < 0.05, it is considered that there is a significant enrichment of this KEGG PATHWAY function.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: colon tissues

extract_protocol:
Excise the entire colon of each animal, rinse with PBS to remove fecal debris snap-frozen in liquid nitrogen, and store at -80 °C. RNA extraction kits were used to extract tissue RNA and reverse transcribed to cDNA for transcriptome sequencing.
Use the DNBSEQ platform

treatment_protocol: Animal model of ulcerative colitis was established by drinking 2.5% Dextran Sulfate Sodium (DSS). C57BL/6 male mice were randomly divided into 2 groups after a week of normal feeding and adaptive culture. Blank control group (C) (n=10): mice were fed normally until the end of the experiment. DSS colitis group (n=50): mice were fed with 2.5% DSS solution instead of pure water under normal diet conditions for 7 consecutive days, and DSS solution was changed every two days during this period to establish a mouse colitis model. After successful establishment of DSS colitis model, the colitis group was divided into 5 groups and treated with different interventions by gavage: PBS group (P): the mice were treated with PBS medium 200 μL/10 g by gavage every day for 5 weeks, until the end of the experiment. ZJ316 group (WT), ZJ316-KO (KO), ZJ316-COM (COM): the WT Lactobacillus plantarum ZJ316 bacteria, ZJ316-KO and ZJ316-COM suspension 200 μL/10 g (about 2.5×109 CFU/mL) was given by gavage respectively for 5 weeks, until the end of the experiment.

value: colon tissues

tag: strain

tag: Sex

value: male

value: WT


title: P2_2

city: Oslo

first: Ankush

last: Sharma

address: 3rd Floor,  Ullernchausseen 70

department: Department of Cancer Immunology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
processed data column: 4
Sample0004

data_processing:
Adaptors and low quality reads were removed using Trim Galore (v0.6.4).
The remaining high-quality reads were mapped to the Ensembl GRCh37.p75 using Salmon, in order to obtain gene expression estimates in the form of transcripts per million (TPM).
Assembly: Hg19/ GRCh37.p75
Supplementary files format and content: csv

source_name: follicular lymphoma, lymph node

extract_protocol:
Total RNA was extracted from fresh frozen tissue sections (follicular lymphoma) or from sorted B cell populations (tonsils), using Qiagen RNeasy Miniprep Kit according to manufacturer's guidelines. One ug of total RNA was used for the construction of sequencing libraries.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Hiseq4000 Intrument with 150bp paired end reads.

treatment_protocol: The tonsils were processed to single-cell suspension by mechanical mincing and stored in liquid nitrogen. The cells were thawed and rested in RPMI w/10% FCS at 37°C for at least 15 min before staining with the following antibodies: IgD-FITC (clone IA6-2), CD20-APC-H7 (clone L27), CD38-PerCP-Cy5.5 (clone HIT2) and CD27-APC (clone M-T271) from BD Biosciences, CD3-PE (clone UCHT1) from Dako. Live B-cell subsets were sorted on FACS Aria II (BD Biosciences): CD3-CD20+IgD+CD38-CD27- naive B cells, CD3-CD20+IgD-CD38-CD27+ memory B cells, and CD3-CD20++IgD-CD38+ GC B cells. The sorted cells were spun down and lysed in lysis buffer (RNeasy kit, Qiagen).

value: follicular lymphoma, lymph node

value: all cell types present in bulk

tag: genes mutated for this sample from patient


title: ZJ316_KO, rep3


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep3 (RNA-seq)

description: passage 27+9+8+5 (PXGL d27 5iLAF d11)


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep2 (RNA-seq)

description: passage 27+14+7+4 (PXGL d15 5iLAF d10)

value: ZIC3-/-; stable integration of 3x-Flag ZIC2 and M2rtTA ORFs clone 7


title: P14_2

description:
processed data column: 13
Sample0013


title: P14_1

description:
processed data column: 12
Sample0012


title: wt_pH5_R3

value: pH 5


title: P12_1

description:
processed data column: 11
Sample0011


title: ZJ316_KO, rep1


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep4 (RNA-seq)

description: passage 27+9+8+5 (PXGL d27 5iLAF d11)

value: Cultured in medium supplemented with DMSO for 72 hours


title: DSS, rep2


title: P11_2

description:
processed data column: 10
Sample0010


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, doxycycline 72h, rep1 (RNA-seq)

description: passage 27+14+8+3 (PXGL d11 5iLAF d10)

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: wt_pH7_R3


title: P41_1

description:
processed data column: 28
Sample0029

source_name: transformed follicular lymphoma, lymph node


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep3 (RNA-seq)

description: passage 27+9+8+5 (PXGL d27 5iLAF d11)


title: P11_1

description:
processed data column: 43
Sample0044


title: Control, rep3

value: water


title: ZJ316_WT, rep4


title: dpac_pH7_R2

value: deleted pac


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep2 (RNA-seq)

description: passage 27+14+7+4 (PXGL d15 5iLAF d10)


title: DSS, rep3


title: P10_1

description:
processed data column: 51
SampleP10_1


title: Control, rep2


title: dpac_pH7_R1

value: pH 7


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep1 (RNA-seq)

description: passage 27+14+8+3 (PXGL d11 5iLAF d10)

value: Naïve human embryonic stem cells


title: wt_pH5_R1

value: wt


title: P1_2

description:
processed data column: 2
Sample0002


title: DSS, rep1


title: Control, rep1


title: dpac_pH5_R3


title: dpac_pH5_R1


title: P1_1

description:
processed data column: 1
Sample0001


title: LL2_shNTRK_2

city: Winston Salem

first: Fei

last: Xing

state: NC

address: Main Medical center BLVD

department: Cancer Biology

country: USA

institute: Wake Forest School of Medicine

description: cell line

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC. We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: csv file of raw counts

extract_protocol:
RNAs were extracted from cancer cells or tumors using RNeasy Micro Kit (Qiagen, Germantown, USA Cat #74004)
Quality control analysis and quantification of the sequencing library were performed using the Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip

value: lung cancer


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep2 (RNA-seq)

description: passage 27+12+12+1 (collected 5 days post-nuclefection)

source_name: Primed human embryonic stem cells

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC3-/-ZIC5-/- clone 4

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA


title: LL2_shNTRK_3

description: cell line


title: dpac_pH7_R3


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep4 (RNA-seq)

description: passage 27+17+1 (collected 5 days post-nucleofection)

value: ZIC2-/-ZIC3-/- (done on ZIC3-/- clone 2)

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep4 (ATAC-seq)

description: P27+9+8+5 (PXGL d27 5iLAF d11)

library_source: genomic

data_processing:
Raw reads were trimmed to 50bp using TrimGalore!
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Mitochondrial reads were removed prior to making coverage files and differential analysis.
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Assembly: GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were lysis in 50 ul ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2) supplemented with 0.1% Tween-20, 0.1% NP-40 and 0.01% digitonin, and incubated on ice for three minutes. Lysis  buffer was then diluted with 1 ml ATAC resuspension buffer supplemented with 0.1% Tween-20 and tubes were inverted three times. Nuclei were pelleted by centrifugation at 500g for 10 minutes at  4°C. Transposition reaction was carried out in 50 ul volume for each sample by resuspending nuclei in 25 ul 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20 DMF), 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20 and 5 ul H2O. Reactions were incubated at 37°C  for 30 minutes in a thermomixer with 1000 RPM mixing. Reactions were quenched with 5x volume of buffer PB and DNA was purified using the MinElute PCR purification kit (Qiagen). Libraries were next amplified using Illumina-compatible primers.
Libraries were constructed as described in Corces et al (2017) Nature Methods.

value: UCLA1 naive hESCs

value: ZIC3-/-; stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

value: Cultured in medium supplemented with 100ng/ml doxycycline for 72 hours


title: LL2_shNTRK_1

description: cell line


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep3 (RNA-seq)

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC3-/-ZIC5-/- clone 4)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: wt_pH7_R1


title: LL2_CNTRL_3

description: cell line

value: shCTRL


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep3 (RNA-seq)

description: passage 27+13+1 (collected 5 days post-nucleofection)


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep2 (ATAC-seq)

description: P27+14+7+4 (PXGL d15 5iLAF d10)


title: LL2_CNTRL_2

description: cell line


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep3 (RNA-seq)

value: ZIC3-/- clone 2

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep4 (RNA-seq)


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep1 (ATAC-seq)

description: P27+14+8+3 (PXGL d10 5iLAF d11)

value: Naïve human embryonic stem cells

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: LL2_CNTRL_1

description: cell line

value: lung cancer


title: UCLA1 primed hESC, ZIC2-/- (RNA-seq)

description: passage 31+10

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC2-/- clone 14


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep3 (ATAC-seq)

description: P27+9+8+5 (PXGL d27 5iLAF d11)

value: Human embryonic stem cells


title: scRNAlib_B6_2dpi_2, scRNAseq

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing , barcode processing , gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/7.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol
single cell gene expression RNA-seq

value: Lung

tag: time


title: scRNAlib_B6_Naive2, scRNAseq

description: 10x Genomics

value: Naive


title: LL2_E_PD_4

description: Tumor


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep4 (ATAC-seq)

description: P27+9+8+5 (PXGL d27 5iLAF d11)

value: UCLA1 naive hESCs

value: Cultured in medium supplemented with DMSO for 72 hours


title: scRNAlib_B6_2dpi_1, scRNAseq

description: 10x Genomics


title: scRNAlib_Tlr7KO_2dpi_2, scRNAseq

description: 10x Genomics


title: LL2_E_PD_2

description: Tumor


title: UCLA1 primed hESC, NT, rep2 (RNA-seq)

description: passage 27+9

value: WT clone 2

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep3 (ATAC-seq)

description: P27+9+8+5 (PXGL d27 5iLAF d11)

value: ZIC3-/-; stable integration of 3x-Flag ZIC2 and M2rtTA ORFs


title: LL2_E_PD_3

description: Tumor


title: LL2_E_PD_1

description: Tumor


title: UCLA1 primed hESC, NT, rep1 (RNA-seq)

description: passage 27+9

value: WT clone 1


title: scRNAlib_Tlr7KO_2dpi_1, scRNAseq

description: 10x Genomics


title: UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq (control for TRP 4h), rep2

data_processing:
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Deeptools was used to generate coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 or mTESR-plus medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs by plating of dissociated single cell suspension on 0.1% gelatin for 30 minutes prior to collection for experiments.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 min, and quenched with 0.14 M glycine for 10 min. Cells were then resuspended with 1 ml lysis buffer 1 (10 mM TrisHCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitors (Roche), 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1200g for 5 minutes at 4 °C. Nuclei were then resuspended with 1 ml lysis buffer 2 (10 mM TrisHCl pH 8.0, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitor, 1mM NaF, 1mM Na2VO3 and 1mM PMSF) and rotated 10 minutes at 4 °C. Nuclei were then pelleted and resuspended in 900 μl lysis buffer 3 (10 mM Tris-HCL pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), and chromatin was fragmented using the Covaris M220 sonicator. Chromatin was pre-cleared with ProtA/G beads for 2 hours at  4 °C. Antibodies were then added to pre-cleared lysates and incubated overnight with end-over-end shaking at 4 °C. Immunocomplexes were then immobiilzed on prot A/G beads, which were then washed 2×4 minutes with 500 μl Wash Buffer A (50 mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140 mM NaCl), 500 μl Wash Buffer B (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1 mM EDTA, 500 mM NaCl), and 500 μl TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). DNA was eluted in 100 μl elution buffer (50 mM TrisHCl pH 8.0, 1 mM EDTA, 1% SDS) after incubation at 65 °C for 10 minutes at 1400 rpm. The elute was collected, and the beads were subjected to a second round of elution with 150 μl elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250 μl with elution buffer. These samples were incubated 65 °C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15 μg of RNAse A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37 °C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56 °C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
Purified DNA was fragmented to 200 bp by sonication. Following this, libraires were prepared using the Swift DNA library kit or NEBNext Ultra II DNA Library Prep Kit, according to manufacturers' instructions.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate, 1 uM flavopiridol, 500 nM triptolide, 25 uM STM2457 or DMSO of equivalent v/v concentration, where specified for the appropriate period of time.

value: WT

value: Cultured in medium supplemented with DMSO for 4 hours

tag: antibody

value: anti-ZIC2 (Abcam ab150404)

tag: passage description

value: passage 36


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep2 (ATAC-seq)

description: P27+14+7+4 (PXGL d15 5iLAF d10)

value: Naïve human embryonic stem cells


title: UCLA1 primed hESC, TRP 4h, ZIC2 ChIP-seq, rep2

value: Primed human embryonic stem cells

value: Cultured in medium supplemented with 500 nM triptolide for 4 hours


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep4

value: UCLA1 primed hESCs

value: passage 30


title: UCLA1 primed hESC, Input, rep4

value: Human embryonic stem cells


title: LL2_PD_2

description: Tumor

value: lung cancer


title: CNLN35-3D-4

city: Strasbourg

first: Catherine

last: Leon

address: 10 rue Spielmann

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Alignment: Reads were mapped onto GRCm39 assembly of mouse genome using STAR 2.7.10b.
Quantification: Gene expression was quantified using HTSeq v0.13.5 (union mode) and Ensembl release 108 annotations.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values file containing raw read counts in each sample.

source_name: bone marrow

growth_protocol: Lineage-negative cells were sorted using negative magnetic depletion (StemCell kit), and grown for 3 days either in liquid medium or in hydrogel (methylcellulose 2%, Young modulus 30-60 Pa)

extract_protocol:
P2974
Cells were lysed and RNA extracted using Qiagen RNAseasy mini kit.
RNA-Seq libraries were generated from 150 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: Cells grown for 3 days were deposited onto a BSA 2-4% gradient to isolate the larger, mature megakaryocytes

value: bone marrow

value: Megakaryocyte

value: WT C57BL/6

value: culture milieu 3D methylcellulose


title: UCLA1 primed hESC, DMSO, Input (control for TRP 4h), rep2


title: CNLN34-Liq-4

value: culture milieu liquid


title: scRNAlib_B6_Naive1, scRNAseq

description: 10x Genomics

value: Lung

value: Naive


title: LL2_PD_3

description: Tumor


title: CNLN33-Liq-3


title: LL2_PD_1

description: Tumor


title: UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq (control for TRP 4h), rep1

value: WT

value: Cultured in medium supplemented with DMSO for 4 hours

value: passage 32


title: CNLN32-3D-3


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep3 (technical rep 2)

value: anti-ZIC2 (Abcam ab150404)

value: passage 27


title: UCLA1 primed hESC, DMSO, Input (control for TRP 4h), rep1

value: Primed human embryonic stem cells


title: UCLA1 primed hESC, IgG ChIP-seq, rep4

value: UCLA1 primed hESCs

value: anti-rabbit IgG (CST 2729)


title: UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep1 (ATAC-seq)

description: P27+14+8+3 (PXGL d10 5iLAF d11)

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

value: Human embryonic stem cells

value: ZIC3-/-; stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

value: Cultured in medium supplemented with DMSO for 72 hours


title: CNLN31-Liq-2

value: bone marrow

value: Megakaryocyte

value: WT C57BL/6


title: ZJ316_WT, rep1

value: colon tissues

value: male


title: LL2_E_3

description: Tumor

value: lung cancer

value: Entrectinib


title: CNLN28-3D-1

value: culture milieu 3D methylcellulose


title: P10_2

description:
processed data column: 9
Sample0009

value: follicular lymphoma, lymph node

value: all cell types present in bulk


title: LL2_E_1

description: Tumor


title: UCLA1 primed hESC, TRP 4h, Input, rep1

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: WT

value: Cultured in medium supplemented with 500 nM triptolide for 4 hours

value: passage 32


title: CNLN30-3D-2


title: UCLA1 primed hESC, TRP 4h, Input, rep2

value: Human embryonic stem cells

value: passage 36


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep3 (technical rep 1)

value: anti-ZIC2 (Abcam ab150404)

value: passage 27


title: wt_pH5_R2

value: wt

value: pH 5


title: LL2_E_2

description: Tumor


title: CNLN29-Liq-1

value: bone marrow

value: Megakaryocyte

value: WT C57BL/6

value: culture milieu liquid


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, Input, rep2

value: ZIC2-/-ZIC3-/- (done on ZIC2-/- clone 8)

value: ZIC2-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC3

value: passage 62+8+1


title: TDP2seq_cKO_Mre11_rep1

city: New York

first: Meret

last: Arter

address: 430 E 67th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.
Top- and bottom-strand peaks were separately called as nucleotide positions with >3,000, >10 and >15 RPM of strand-specific read counts using averaged pUC19, E. coli, and S. cerevisiae TDP2-seq data, respectively. Positions with less read counts than those located at –1 and +1 positions on top and bottom strands, respectively, were not defined as peaks because those reads could be false-positively enriched due to incomplete fill-in of 5-prime overhangs at DNA ends before adaptor ligation.
Assembly: mm10, pUC19, ASM584v2, SacCer3
Supplementary files format and content: bigWig files contain read counts at positions of DNA double-strand break ends. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.
Supplementary files format and content: bed files contain peak locations. If only one file per experiment is submitted, peaks were determined based on average profiles of the two replicates.
Library strategy: TDP2-seq

source_name: Mus musculus

extract_protocol:
Testis cells from adult mice were obtained as described previously (ref. 1,2). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing. For in vitro SPO11 treated plasmid or genomic DNA samples, the treated DNA was mixed with wild type B6 (C57BL/6J) mouse testis cells right before plug formation to provide carrier DNA during library preparation. Plugs were treated with SDS, Proteinase K and RNAse as described previously (ref. 1,2). In-plug removal of covalently bound SPO11 using human TDP2 was performed as described with minor modifications (ref. 3). In brief, plugs were equilibrated in TDP2 buffer (0.05 M Tris-HCl pH 8, 0.15 M NaCl, 10 mM Mg2Cl, 0.5 mM Dithriothreitol, 30 μg/ml BSA, 2 mM ATP) and incubated with purified human TDP2 protein (490 pmol per plug, TopoGEN) at 37°C for 30 min according to the TopoGEN protocol. DNA ends were filled-in with T4 DNA polymerase (New England Biolabs) and ligated to biotinylated adaptors as described previously (ref. 1,2,4,5). To minimize the loss of small plasmid fragments through diffusion out of the plugs, the washing step after ligation of the first adaptor was reduced from overnight to 1h for samples containing plasmid DNA. After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously with minor modifications (ref. 1,2,4,5). For end repair after DNA shearing, NEBNext End repair Kit (New England Biolabs) was used. (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Kim et al., Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes. bioRxiv 2024.08.10.606181; https://doi.org/10.1101/2024.08.10.606181, (2024).(ref. 3) Gittens et al., A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nat Commun 10, 4846 (2019). (ref. 4) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 5) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina NextSeq 1000 sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequencing reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.

value: testis

value: cKO Mre11

tag: age

value: 16 weeks


title: UCLA1 primed hESC, Input, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: WT

value: passage 26


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, Input, rep1

value: Human embryonic stem cells


title: UCLA1 primed hESC, TRP 4h, ZIC2 ChIP-seq, rep1

value: Cultured in medium supplemented with 500 nM triptolide for 4 hours

value: anti-ZIC2 (Abcam ab150404)

value: passage 32


title: UCLA1 primed hESC, IgG ChIP-seq, rep3

value: anti-rabbit IgG (CST 2729)

value: passage 27


title: TDP2seq_cKO_Mre11_rep2

value: 5 weeks


title: dpac_pH5_R2

value: deleted pac

value: pH 5


title: LL2_IgG_3

description: Tumor

value: lung cancer

value: IgG


title: UCLA1 primed hESC, IgG ChIP-seq, rep2


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep2


title: Salmonella enterica serovar Typhimurium SL1344 500k mutant transposon library

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
reads were trimmed and quality filtered on their right (genomic sequence) ends using PRINSEQ with the command: prinseq-lite.pl -fastq stdin -out_good stdout -out_bad null -min_len 30 -trim_tail_right 2 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_window 3
Reads were filtered for 10 bases matching the expected transposon tag sequence, and filtered reads were then mapped against the appropriate reference genome and plasmid sequences, available at https://github.com/Gardner-BinfLab/EnTrI using the Bio-TraDIS pipeline with the following command line options:    bacteria_tradis -v --smalt_r 0 --smalt_k 8 --smalt_s 1 --smalt_y 0.9 -m 0 -f fastqs.txt -t TAAGAGACAG -r ref.fa
For each gene in each organism, we calculated an insertion index as a measure of gene essentiality. The insertion index is calculated as (ng/lg)(nG/lG) where ng is the number of unique insertion sites in the gene, lg is the length of the gene, nG is the number of insertion sites in the genome, and lG is the length of the genome. We calculated the insertion index for each gene after trimming 5% of the sequence from the 5’ end and 20% of the sequence from the 3’ end
To correct for biases in the insertion index, we used fitted values from a generalized additive model (GAM). For each genome, we fitted a GAM curve (using the MGCV package in R) with the formula y ~ s(x) to the distance vs. insertion index plot for distance normalization. The normalized insertion indices were calculated by dividing the insertion indices by the predicted insertion index from the GAM, then multiplying them by the average insertion index. The same procedure was repeated for G-C normalization.
We used the DBSCAN R package (25) to cluster the normalized insertion indices using the DBSCAN function with parameters minPts = 200 and eps = 0.05.
Supplementary files format and content: Ghomi_SI.xslx: essentiality scores for each gene in each organism
Supplementary files format and content: .plot files: read counts per genomic position

organism: Salmonella enterica subsp. enterica serovar Typhimurium

extract_protocol:
Qiagen Genomic-tip 100/G kit
~2 μg of genomic DNA was fragmented to a size of ~300 base-pairs using a Covaris Focused ultrasonicator (Covaris), followed by end repair using the NEBNext End Repair module (NEB), A-tailing using the NEBNext dA-Tailing module (NEB), and adapter ligation using the NEBNext Quick Ligation Module with a custom splinkerette adaptor (SplA5). PCR enrichment of fragments containing transposon sequence was then carried out using transposon- and adaptor-specific primers using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) for 10 to 20 cycles. PCR products were analyzed on an Agilent Bioanalyzer using a High Sensitivity DNA kit (Agilent Technologies), and by SYBR green qPCR (Kapa Biosystems). Sequencing was then performed on an Illumina HiSeq 2000 or MiSeq using transposon-specific primers and a custom dark-cycle sequencing protocol at the Wellcome Sanger Institute or the King Abdullah University of Science and Technology Bioscience Core Laboratory (Salmonella Typhimurium A130 and D23580). All custom adaptors, primers, and sequencing protocols are described in Barquist et al. "The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries" Bioinformatics 2016 and publicly available at  https://github.com/sanger-pathogens/Bio-Tradis/tree/master/recipes.
transposon insertion sequencing

value: transposon mutagenesis


title: Salmonella enterica serovar Typhimurium SL1344 1000k mutant transposon library

description:
Ghomi_SI.xslx
SL1344_9.plot


title: LL2_IgG_1

description: Tumor


title: cKO-3

city: Shanghai

first: Lian

last: Cui

state: China

address: 1278 Baode Road

institute: Shanghai Skin Disease Hospital

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4.
Assembly: mm39
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: Skin

extract_protocol:
RNA from the tail skin of the mice was extracted using TRIzol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V5 RNA-seq Library Prep Kit following manufacturer’s protocols.

value: Skin


title: UCLA1 primed hESC, Input, rep1

value: Primed human embryonic stem cells

value: passage 22


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, H2AK119ub ChIP-seq, rep1

value: UCLA1 primed hESCs

value: ZIC2-/-ZIC3-/- (done on ZIC2-/- clone 8)

value: ZIC2-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC3

value: anti-H2AK119ub (CST 8240)

value: passage 62+8+1


title: UCLA1 primed hESC, WT +sgNT, Input, rep2

value: Human embryonic stem cells

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA

value: passage 68+1


title: LL2_IgG_2

description: Tumor


title: Salmonella enterica serovar Typhimurium SL1344 250k mutant transposon library


title: UCLA1 primed hESC, IgG ChIP-seq, rep1

value: anti-rabbit IgG (CST 2729)


title: cKO-1


title: Salmonella enterica serovar Typhimurium SL1344 100k mutant transposon library


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep1

value: anti-ZIC2 (Abcam ab150404)


title: Ctrl-3


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, H2AK119ub ChIP-seq, rep2


title: Salmonella enterica serovar Typhimurium SL1344 50k mutant transposon library


title: UCLA1 primed hESC, WT +sgNT, H2AK119ub ChIP-seq, rep1


title: Ctrl-2


title: cKO-2


title: AJC002 primed hiPSC, Input, rep1

source_name: Primed human induced pluripotent stem cells

value: AJC002 primed hiPSCs

value: passage 25


title: AJC002 primed hiPSC, IgG ChIP-seq, rep1

value: Primed human induced pluripotent stem cells


title: UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep2 (ATAC-seq)

description: P27+19+3 (PXGL d12 5iLAF d10)

source_name: Reverting human embryonic stem cells

value: Reverting human embryonic stem cells

value: UCLLA1 reverting hESCs


title: Ctrl-1

value: Skin


title: AJC002 primed hiPSC, ZIC2 ChIP-seq, rep1


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, Input, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC3-/-ZIC5-/- clone 4

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 reverting hESC, NT, 5iLAF d6, rep2 (ATAC-seq)

description: P27+19+3 (PXGL d12 5iLAF d10)


title: UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep1 (ATAC-seq)

description: P27+18+3 (PXGL d12 5iLAF d10)


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, Input, rep1

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC3-/-ZIC5-/- clone 12)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: B12-IP_D3_cKO

data_processing:
*library strategy: MeRIP-seq
Sequence reads were trimmed for adaptor/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to mm10 using STAR software
Read count extraction were performed using featurecount
m6A peaks were called using Metpeak
Assembly: mm10
Supplementary files format and content: BigWig data

source_name: Epidermis

extract_protocol:
RNA from the epidermis of the mice was extracted using TRIzol.
MeRIP (NBE, Cat. E1610S, lot 10176803); The ULI-MeRIP sample library was prepared using the SMARTer Stranded Total RNA-Seq Kit v2 following the manufacturer's guidelines. Input RNA, fragmented and IP-extracted, underwent fragmentation and reverse transcription into cDNA. Total RNA from embryos was fragmented according to the manufacturer's protocol. Subsequently, libraries of IP and input (or total RNA) samples were amplified through 15–19 cycles and 14–15 cycles, respectively.

value: Epidermis

tag: strain background


title: B12-input_D3_cKO


title: mNET-seq_Tyr1P_DRB_15min

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Assembly: hg38
Supplementary files format and content: bigwig files: genome-coverage files for all samples
Library strategy: mNET-seq

molecule: nuclear RNA

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% foetal bovine serum, 100 U/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine at 37°C with 5% CO2

extract_protocol:
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin.
Libraries were prepared according to the protocol of TruSeq Small RNA Library Preparation Kit (Illumina) for mNET-seq.

treatment_protocol: HeLa cells were treated with 90 μM Madrasin, 1 μM PlaB, 100 μM DRB, or with DMSO, the resuspension vehicle, for 15 or 30 minutes.

tag: mnet-seq antibody

value: Anti-phospho-RNAPII (Tyr1) Antibody, clone 3D12, MABE350, Merck Millipore

value: HeLa

value: Epithelial cell

value: Wild type

value: DRB 15 minutes, 100 μM


title: B11-input_D3_WT


title: UCLA1 primed hESC, WT +sgNT, Input, rep1

value: Human embryonic stem cells

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA

value: passage 68+1


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, Input, rep1

value: ZIC3-/-ZIC5-/- clone 12


title: mNET-seq_Tyr1P_DMSO

value: DMSO


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, H3K27me3 ChIP-seq, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC3-/-ZIC5-/- clone 4)

value: anti-H3K27me3 (CST 9733)


title: mNET-seq_Thr4P_DRB_15min

value: RNA Pol II CTD phospho Thr4 antibody (mAb) 6D7, 61361, Active Motif


title: mNET-seq_Thr4P_DMSO


title: UCLA1 primed hESC, WT +sgNT, H2AK119ub ChIP-seq, rep2

value: anti-H2AK119ub (CST 8240)


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep2 (ATAC-seq)

description: P27+12+11+1 (collected 5 days post-nuclefection)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, H3K27me3 ChIP-seq, rep2

value: ZIC3-/-ZIC5-/- clone 4

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep1 (ATAC-seq)

description: P27+12+7+1 (collected 5 days post-nuclefection)


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, Input, rep2


title: B10-input_D3_cKO

value: Epidermis


title: UCLA1 primed hESC, Input, rep3

value: passage 27


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep3 (ATAC-seq)

value: Human embryonic stem cells


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep3 (ATAC-seq)


title: mNET-seq_Ser7P_DMSO

value: RNA pol II CTD phospho Ser7 antibody (mAb) 4E12, 61087, Active Motif

value: HeLa

value: Epithelial cell

value: Wild type


title: UCLA1 reverting hESC, NT, 5iLAF d6, rep1 (ATAC-seq)

description: P27+18+3 (PXGL d12 5iLAF d10)

value: Reverting human embryonic stem cells

value: UCLLA1 reverting hESCs

value: WT


title: B9-IP_D3_WT


title: B9-input_D3_WT


title: mNET-seq_Ser5P_PlaB_30min

value: Anti-Phospho RNA Polymerase II CTD (Ser5) mAb, MABI0603, MBL International

value: Pladienolide B 30 minutes, 1 μM


title: mNET-seq_Ser2P_PlaB_30min

value: Anti-Phospho RNA Polymerase II CTD (Ser2) mAb, MABI0602, MBL International


title: mNET-seq_Ser5P_DRB_15min

value: DRB 15 minutes, 100 μM


title: UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep2 (ATAC-seq)

description: P27+18+1 (collected 5 days post-nucleofection)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC5-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: HEK-1-IP

data_processing:
Sequence reads were trimmed for adaptor/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to hg38 using STAR software
Read count extraction were performed using featurecount
m6A peaks were called using Metpeak
Assembly: hg38
Supplementary files format and content: BigWig data

source_name: Primary human epidermal keratinocyte

extract_protocol:
RNA from the HEKa was extracted using TRIzol.
The ULI-MeRIP sample library was prepared using the SMARTer Stranded Total RNA-Seq Kit v2 following the manufacturer's guidelines. Input RNA, fragmented and IP-extracted, underwent fragmentation and reverse transcription into cDNA. Total RNA from embryos was fragmented according to the manufacturer's protocol. Subsequently, libraries of IP and input (or total RNA) samples were amplified through 15–19 cycles and 14–15 cycles, respectively.
MeRIP-seq

value: Primary human epidermal keratinocyte


title: HEK-2-IP


title: HEK-2-input


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep2 (ATAC-seq)

description: P27+17+1 (collected 5 days post-nucleofection)

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: B8-IP_D3_cKO

value: Epidermis


title: UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep1 (ATAC-seq)

description: P27+15+1 (collected 5 days post-nucleofection)

value: Human embryonic stem cells


title: B10-IP_D3cKO


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, H3K27me3 ChIP-seq, rep1

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC3-/-ZIC5-/- clone 12)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2

value: anti-H3K27me3 (CST 9733)


title: B7-input_D3_WT


title: B8-input_D3_cKO


title: mNET-seq_Ser2P_DMSO

value: HeLa

value: Epithelial cell

value: Wild type

value: DMSO


title: HEK-1-input


title: mNET-seq_Ser2P_DRB_15min


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep1 (ATAC-seq)

description: P27+16+1 (collected 5 days post-nucleofection)


title: B11-IP_D3_WT


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep1 (ATAC-seq)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA


title: mNET-seq_PolII_PlaB_30min

value: Anti-RNA Polymerase II CTD mAb, MABI0601, MBL International

value: Pladienolide B 30 minutes, 1 μM


title: AD-MSC, NA treat, Day 21

city: Seoul

first: Jae Hoon

last: Song

address: 201 Songpa-daero, Songpa-gu

country: South Korea

institute: ENCell Co., Ltd.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample
Supplementary files format and content: Cells were treated nervonic acid during adipogenic differentiation period.

source_name: Adipose tissue

growth_protocol: AD-MSCs were maintained in MEM-a supplemented with 10% fetal bovine serum (FBS) and 0.5% gentamicin in humidifed atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Adipogenic differentiation was proceeded over 90% confluency in adipogenic differentiation condition following manufacturer's instruction.

value: Adipose tissue

value: Mesenchymal stem cell

value: WT

value: Adipogenic differentiation


title: B6-input_D6_cKO


title: UCLA1 primed hESC, ZIC5-/- +sgNT, rep1 (ATAC-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC5-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: m5-stm2457-2-input

data_processing:
*library strategy: MeRIP-seq
Sequence reads were trimmed for adaptor/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to hg38 using STAR software
Read count extraction were performed using featurecount
m6A peaks were called using Metpeak
Assembly: hg38
Supplementary files format and content: BigWig data

source_name: HaCaT cell

extract_protocol:
RNA from the HaCaT cells was extracted using TRIzol.
MeRIP (NBE, Cat. E1610S, lot 10176803); The ULI-MeRIP sample library was prepared using the SMARTer Stranded Total RNA-Seq Kit v2 following the manufacturer's guidelines. Input RNA, fragmented and IP-extracted, underwent fragmentation and reverse transcription into cDNA. Total RNA from embryos was fragmented according to the manufacturer's protocol. Subsequently, libraries of IP and input (or total RNA) samples were amplified through 15–19 cycles and 14–15 cycles, respectively.

value: HaCaT cell

value: Keratinocyte

value: M5 and STM2457 treatment


title: m5-stm2457-2-ip


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep2 (ATAC-seq)

value: Human embryonic stem cells

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: AD-MSC, NA treat, Day 14


title: B5-IP_D6_WT

value: Epidermis


title: B5-input_D6_WT


title: m5-stm2457-1-ip


title: AD-MSC, NA treat, Day 7


title: AD-MSC, control, Day 7


title: B4-IP_D6_cKO


title: B6-IP_D6_cKO


title: B4-input_D6_cKO


title: UCLA1 primed hESC, WT +sgZIC2, rep2 (ATAC-seq)

description: P42+1 (collected 5 days post-nucleofection)

value: WT primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: m5-dmso-2-input

value: M5 and DMSO treatment


title: UCLA1 primed hESC, WT +sgZIC2, rep1 (ATAC-seq)

description: P31+1 (collected 5 days post-nucleofection)


title: B3-IP_D6_WT


title: UCLA1 primed hESC, ZIC5-/- +sgNT, rep2 (ATAC-seq)


title: AD-MSC, control, Day 21


title: ps-4-input

source_name: skin

extract_protocol:
RNA from the skin tissue of the healthy donors or patients with psoriasis or atopic dermatitis was extracted using TRIzol.
MeRIP (NBE, Cat. E1610S, lot 10176803);  The ULI-MeRIP sample library was prepared using the SMARTer Stranded Total RNA-Seq Kit v2 following the manufacturer's guidelines. Input RNA, fragmented and IP-extracted, underwent fragmentation and reverse transcription into cDNA. Total RNA from embryos was fragmented according to the manufacturer's protocol. Subsequently, libraries of IP and input (or total RNA) samples were amplified through 15–19 cycles and 14–15 cycles, respectively.

value: skin

value: patient with psoriasis


title: m5-dmso-1-ip


title: B2-IP_D6_WT


title: UCLA1 primed hESC, WT +sgNT, rep2 (ATAC-seq)

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: ps-3-ip


title: m5-stm2457-1-input


title: UCLA1 primed hESC, WT +sgZIC2, rep3 (ATAC-seq)


title: mNET-seq_Ser7P_DRB_15min

value: RNA pol II CTD phospho Ser7 antibody (mAb) 4E12, 61087, Active Motif

value: HeLa

value: Epithelial cell

value: Wild type

value: DRB 15 minutes, 100 μM


title: B3-input_D6_WT


title: ps-3-input


title: B7-IP_D3_WT


title: pbs-stm2457-2-ip

value: PBS and STM2457 treatment


title: B2-input_D6_WT


title: ps-2-ip


title: pbs-stm2457-2-input

value: HaCaT cell


title: UCLA1 primed hESC, WT +sgNT, rep1 (ATAC-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: WT


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, H3K27me3 ChIP-seq, rep1

value: Human embryonic stem cells

value: ZIC3-/-ZIC5-/- clone 12

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA

value: anti-H3K27me3 (CST 9733)


title: B1-IP_D6_cKO

value: Epidermis


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep2 (RNA-seq)

description: passage 27+12+10+1 (collected 5 days post-nuclefection)

extract_protocol:
Cells were lysed in RNAzol RT reagent and total RNA was purified from cell extracts according to manufacturer's instructions.
mRNA containing polyA tail were enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module and libraries were prepared using the Swift RNA library kit or NEBNext Ultra II RNA Library Prep Kit according to respective manufacturers' instructions.

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC3-/-ZIC5-/- clone 12)

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: ps-2-input

value: skin

value: patient with psoriasis


title: B1-input_D6_cKO


title: pbs-stm2457-1-ip

value: Keratinocyte


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep1 (RNA-seq)

description: passage 27+12+7+1 (collected 5 days post-nucleofection)


title: m5-dmso-1-input

value: M5 and DMSO treatment


title: ps-1-ip


title: ICELL8.NCBP2OE.NCM

city: Beijing

first: Wang

last: Li

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

data_processing:
Adapters in paired-end reads were filtered by the Cutadapt program (v1.8.1) with parameters: -m 20 --trim-n --max-n 0.7 -q 20. Clean reads were then mapped to the mm10 reference genome with the STAR aligner (v2.5.2b) and alignments were assigned to the GENCODE annotation (vM25) by the featureCounts program (v2.0.0). Cell filtering and clustering were conducted with the R Seurat package (v4.0.1). The dataset was trimmed of cells expressing fewer than 500 genes or more than 10000 genes. Reads from mitochondrial genes were removed to control the extremely high mitochondrial RNA percentage. Both t-SNE and UMAP were then used for two-dimensional visualization.
Assembly: mm10
Supplementary files format and content: Seurat object

source_name: heart

extract_protocol:
scRNA-seq libraries were generated using the ICELL8 single-cell system (Takara Bio, Japan). Briefly, isolated cells were stained with ReadyProbes® Cell Viability Imaging Kit (Thermo Fisher Scientific, R37610) according to the manufacturer’s instructions. The cells were counted after PBS washing. A cell suspension of 2.0×103 cells/ml was transferred to the SmartChipTM MultiSample NanoDispenser (Takara Bio, MSND) for single-cell preparation. Dispensed cells were then imaged on the imaging station, and live single cells were selected based on Hoechst+PI- staining. The reverse transcription and first-step amplification were performed on a Chip Cycler (Bio-Rad), followed by cDNA purification and size selection with Agencourt AMPure XP beads (Beckman Coulter, A63880). One nanogram of purified cDNA was used to generate a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1024), and then sequenced on the NovaSeq 6000 platform (Illumina) using the 150 bp paired-end sequencing protocol.
One nanogram of purified cDNA was used to generate a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1024)
NovaSeq 6000 platform (Illumina) using the 150 bp paired-end sequencing protocol.

tag: developmental stage

value: adult

value: heart

value: non CM

value: wild type

value: NCBP2 overexpression


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep2 (ATAC-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs


title: n-4-ip

value: healthy control


title: ICELL8.GFP.OE.NCM

value: GFP overexpression


title: pbs-dmso-2-input

value: HaCaT cell

value: PBS and DMSO treatment


title: UCLA1 primed hESC, WT +sgNT, rep3 (ATAC-seq)

value: Human embryonic stem cells

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep2 (RNA-seq)

description: passage 27+16+1 (collected 5 days post-nucleofection)

data_processing:
Raw reads were aligned against the GRCh38 reference grenome using STAR.
Reads were filtered, sorted and marked for duplicates using samtools.
Features were obtained GENCODE reference annotation file v34 and raw counts were correponding to each feature was calculated using HTSEQ. TPM values were calculated using StringTie.
Differentially expressed genes were calculated using DESeq2. Raw counts were normalised for sequencing depth and library complexity using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data includes TPM values provided as a .txt file

value: ZIC2-/-ZIC5-/- (done on ZIC5-/- clone 8)

value: ZIC5-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: ICELL8.NCBP2OE.CM

value: CM


title: UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep3 (RNA-seq)

description: passage 27+15+1 (collected 5 days post-nucleofection)

value: ZIC2-/-ZIC5-/- (done on ZIC5-/- clone 6)


title: ICELL8.GFP.OE.CM

value: adult

value: heart


title: n-3-ip

value: skin


title: UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep1 (RNA-seq)

description: passage 27+14+1 (collected 5 days post-nucleofection)


title: pbs-dmso-1-ip

value: Keratinocyte


title: pbs-dmso-1-input


title: RNA-seq_neonatal_FB_shPTBP1.2

data_processing:
After sequencing, adapters in the RNA-seq reads were trimmed by the Cutadapt program (v1.8.1). Clean reads were then collected and aligned to the mouse reference genome (mm10 version).
Differentially expressed isoforms and genes were identified by the RSEM package (v1.3.1) or DEseq2 package (v1.38.3) according to the alignments. Alternative splicing events were identified and quantified by the rMATS software (v4.1.2).
Assembly: mm10
Supplementary files format and content: alignments in bigWig format

extract_protocol:
Total RNA was extracted from mouse ventricular cardiomyocytes using the GeneJet RNA Purification Kit (Thermo Scientific, K0732).
RNAs from different samples performed quality control using 2100 Bioanalyzer, and RNAs passed quality control constructed libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB #E7760L) for sequencing.

value: neonatal

value: FB

value: wild type


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep2 (RNA-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC2-/-ZIC3-/- (done on ZIC3-/- clone 20)

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: pbs-stm2457-1-input

value: HaCaT cell

value: PBS and STM2457 treatment


title: RNA-seq_neonatal_FB_shPTBP1.1


title: HeLa cells, shControl,  rep3

first: hongqin

last: liu

address: 230 Haike Road, Zhangjiang Hi-Tech Park

department: SLST

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Uterus; cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium  supplemented with 10% fetal bovine serum , 1% penicillin-streptomycin and 5% CO2 in 37 °C.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Uterus; cervix

value: HeLa

value: epithelial cell

value: WT


title: n-2-ip

value: healthy control


title: UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep1 (RNA-seq)

value: Human embryonic stem cells

value: ZIC3-/-ZIC5-/- clone 12

value: ZIC3- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep1 (RNA-seq)

description: passage 27+11+1 (collected 5 days post-nucleofection)


title: n-2-input

value: skin


title: HeLa cells, shControl,  rep1


title: UCLA1 primed hESC, ZIC5-/- +sgNT, rep3 (RNA-seq)

value: ZIC5-/- clone 6

value: ZIC5-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: RNA-seq_neonatal_FB_shNT.2

value: neonatal

value: heart

value: FB

value: wild type

value: shNT


title: AD-MSC, control, Day 14

value: Adipose tissue

value: Mesenchymal stem cell

value: Adipogenic differentiation


title: RNA-seq_neonatal_FB_shNT.1


title: pbs-dmso-2-ip

value: HaCaT cell

value: Keratinocyte

value: PBS and DMSO treatment


title: HeLa cells, shZBTB17, shRNA#3, rep3

value: Uterus; cervix

value: HeLa

value: epithelial cell

value: ZBTB17 knockdown


title: RNA-seq_neonatal_FB_shNCBP2.2


title: UCLA1 primed hESC, ZIC5-/- +sgNT, rep1 (RNA-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC5-/- clone 8


title: HeLa cells, shZBTB17, shRNA#2, rep2


title: n-1-input

value: skin

value: healthy control


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep2 (RNA-seq)

value: ZIC3-/- clone 20

value: ZIC3-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: ad-4-ip

value: patient with atopic dermatitis (AD)


title: HeLa cells, shZBTB17, shRNA#2, rep1


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep1  (RNA-seq)


title: HeLa cells, shControl,  rep2

value: WT


title: RNA-seq_neonatal_FB_shG3BP1.2

value: neonatal

value: heart

value: FB

value: wild type


title: HeLa cells, shZBTB17, shRNA#1, rep3

value: Uterus; cervix

value: HeLa


title: ad-4-input


title: RNA-seq_neonatal_FB_shG3BP1.1


title: UCLA1 primed hESC, ZIC3-/- +sgNT, rep1 (ATAC-seq)

extract_protocol:
Cells were lysis in 50 ul ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2) supplemented with 0.1% Tween-20, 0.1% NP-40 and 0.01% digitonin, and incubated on ice for three minutes. Lysis  buffer was then diluted with 1 ml ATAC resuspension buffer supplemented with 0.1% Tween-20 and tubes were inverted three times. Nuclei were pelleted by centrifugation at 500g for 10 minutes at  4°C. Transposition reaction was carried out in 50 ul volume for each sample by resuspending nuclei in 25 ul 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20 DMF), 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20 and 5 ul H2O. Reactions were incubated at 37°C  for 30 minutes in a thermomixer with 1000 RPM mixing. Reactions were quenched with 5x volume of buffer PB and DNA was purified using the MinElute PCR purification kit (Qiagen). Libraries were next amplified using Illumina-compatible primers.
Libraries were constructed as described in Corces et al (2017) Nature Methods.


title: ps-4-ip

value: patient with psoriasis


title: m5-dmso-2-ip

value: HaCaT cell

value: Keratinocyte

value: M5 and DMSO treatment


title: RNA-seq_neonatal_FB_shNCBP2.1


title: n-1-ip


title: HeLa cells, shZBTB17, shRNA#1, rep2

value: epithelial cell

value: ZBTB17 knockdown


title: UCLA1 primed hESC, WT +sgZIC2, rep1 (RNA-seq)

description: passage 31+1 (collected 5 days post-nucleofection)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: WT primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: ad-3-ip

value: skin

value: patient with atopic dermatitis (AD)


title: RNA-seq_neonatal_FB_PTBP1-OE.2

value: neonatal

value: heart

value: Ptbp1 OE


title: HeLa cells, shZBTB17, shRNA#1, rep1

value: Uterus; cervix


title: RNA-seq_neonatal_FB_PTBP1-OE.1

value: FB

value: wild type


title: UCLA1 primed hESC, WT +sgNT, rep2 (RNA-seq)

description: passage 35+1 (collected 5 days post-nucleofection)

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: ad-2-ip


title: mNET-seq, Ser5P, Madrasin 30 minutes

extract_protocol:
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin. Nuclear RNAs were purified following cellular fractionation for 3'seq.
Libraries were prepared according to the protocol of TruSeq Small RNA Library Preparation Kit (Illumina) for mNET-seq.

treatment_protocol: HeLa cells were treated with 90 μM Madrasin or with DMSO, the resuspension vehicle, for 30 minutes.

value: Anti-Phospho RNA Polymerase II CTD (Ser5) mAb, MABI0603, MBL International

value: HeLa

value: epithelial

value: Wild-type

value: Madrasin 30 minutes, 90 μM


title: UCLA1 primed hESC, WT +sgNT, rep1 (RNA-seq)

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells


title: mNET-seq_Ser5P_DMSO

value: DMSO


title: RNA-seq_neonatal_FB_NCBP2-OE.1

value: neonatal

value: Ncbp2 OE


title: ad-1-ip

value: skin

value: patient with atopic dermatitis (AD)


title: UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Input, rep2

source_name: Naïve human embryonic stem cells

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 min, and quenched with 0.14 M glycine for 10 min. Cells were then resuspended with 1 ml lysis buffer 1 (10 mM TrisHCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitors (Roche), 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1200g for 5 minutes at 4 °C. Nuclei were then resuspended with 1 ml lysis buffer 2 (10 mM TrisHCl pH 8.0, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitor, 1mM NaF, 1mM Na2VO3 and 1mM PMSF) and rotated 10 minutes at 4 °C. Nuclei were then pelleted and resuspended in 900 μl lysis buffer 3 (10 mM Tris-HCL pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), and chromatin was fragmented using the Covaris M220 sonicator. Chromatin was pre-cleared with ProtA/G beads for 2 hours at  4 °C. Antibodies were then added to pre-cleared lysates and incubated overnight with end-over-end shaking at 4 °C. Immunocomplexes were then immobiilzed on prot A/G beads, which were then washed 2×4 minutes with 500 μl Wash Buffer A (50 mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140 mM NaCl), 500 μl Wash Buffer B (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1 mM EDTA, 500 mM NaCl), and 500 μl TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). DNA was eluted in 100 μl elution buffer (50 mM TrisHCl pH 8.0, 1 mM EDTA, 1% SDS) after incubation at 65 °C for 10 minutes at 1400 rpm. The elute was collected, and the beads were subjected to a second round of elution with 150 μl elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250 μl with elution buffer. These samples were incubated 65 °C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15 μg of RNAse A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37 °C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56 °C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
Purified DNA was fragmented to 200 bp by sonication. Following this, libraires were prepared using the Swift DNA library kit or NEBNext Ultra II DNA Library Prep Kit, according to manufacturers' instructions.

value: Naïve human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

value: passage 26+11+8


title: UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq, rep2

value: anti-Flag M2 (Sigma F3165)


title: UCLA1 primed hESC, WT +sgZIC2, rep2 (RNA-seq)

value: WT primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC2


title: UCLA1 primed hESC, ZIC5-/- +sgNT, rep2 (RNA-seq)

value: ZIC5-/- clone 8

value: ZIC5-deficient primed  hESCs electroporated with Cas9 and non-target sgRNA


title: mNET-seq, total pol II, Madrasin 30 minutes

value: Anti-RNA Polymerase II CTD mAb, MABI0601, MBL International

value: HeLa

value: epithelial

value: Wild-type

value: Madrasin 30 minutes, 90 μM


title: RNA-seq_neonatal_FB_GFP.2

value: neonatal

value: heart

value: FB

value: wild type

value: GFP OE


title: ad-1-input

value: skin

value: patient with atopic dermatitis (AD)


title: RNA-seq_neonatal_FB_GFP.1


title: UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Input, rep1

value: Naïve human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 2

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

value: passage 26+11+8


title: ps-1-input

value: patient with psoriasis


title: AB5E1 ALI7, patient 5

city: Reims

first: Valérian

last: Dormoy

address: 45 rue Cognacq-Jay

institute: Université de Reims Champagne-Ardenne

description:
340t
340_5E1

data_processing:
Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.
Quality control of raw sequence data was performed using FastQC (version 0.11.5).
Head bases were trimmed for adaptor sequences, and low-complexity or low-quality sequence was removed with Trimmomatic (version 0.39).
The remaining sequences were mapped to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.1.1) with stringent parameters generating bam format.
The quality of alignment was checked using metrics provided by qualimap (version 2.2.1) and low quality alignments removed.
Raw counts were obtained using htseq-count (version 0.6.1).
Raw counts were normalized using a scalling factor based on median gene expression across the samples and filtered to exclude genes with fewer than 5 counts across the samples.
Assembly: hg38
Supplementary files format and content: matrix including normalized counts for each sample

source_name: lung

growth_protocol: After the proliferation phase, isolated airway epithelial cells were cultured in Pneumacult-ALI for 7 days

extract_protocol:
Total RNA was purified from frozen primary tumor cell pellets with RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s specifications.
Libraries are prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1µg total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing.
Sequencing is then carried out on Paired End 100b reads of Illumina NovaSeq.

treatment_protocol: antibody directed against sonic hedgehog ligand (AB5E1)

value: lung

tag: individual

value: patient 5

value: bronchial airway epithelial cells

value: F

tag: smoking status

value: smoker

value: AB5E1 ALI7


title: mNET-seq, total pol II, DMSO 30 minutes

value: Anti-RNA Polymerase II CTD mAb, MABI0601, MBL International

value: HeLa

value: epithelial

value: Wild-type

value: DMSO 30 minutes


title: Control Male GD18 Gonocytes 3

city: Laval

first: Geraldine

last: Delbes

address: 531 Boul des Prairies

department: Biology

institute: INRS Centre Armand-Frappier Santé Biotechnologie

data_processing:
Raw reads were cleaned from remaining adaptor sequences and low-quality nucleotides using Trimmomatics 0.36 and a minimum sequencing quality of 30.
Reads longer than 30 bp were then aligned to the converted and unconverted reference genome  (ensembl/release99/fasta/rattus_norvegicus/) using Bowtie2   as implemented in the Bismark 0.19.0 program.
Based on read alignments with converted and unconverted genomes,DNA methylation was extracted by Bismark 0.19.0 program,
Assembly: ensembl/release99/fasta/rattus_norvegicus/
Supplementary files format and content: tab-delimited text files include DNA methylation values and count for each Sample
Supplementary files format and content: Excel file of DMRs with annotations PMID: 37283046 (data from previous published work)

organism: Rattus norvegicus

source_name: Germ cell

growth_protocol: Transgenic Sprague-Dawley rats expressing germ cell-specific GFP (GCS-EGFP) were housed on a 12L:12D cycle and were fed with commercial food (Teklad global 18% protein, Envigo, Madison, WI) and tap water ad libitum.

extract_protocol:
Genomic DNA  were extracted from FACS-sorted germ cells using QIAamp DNA micro kit (QIAgen, Toronto, Ontario, Canada).
Methyl-Seq capture libraries were prepared using the Rat SureSelectXT Methyl-Seq Target Enrichment Panels kit (Agilent) as described in the SureSelectXT Methyl-Seq target Enrichment System for Illumina Multiplexed Sequencing protocol (Agilent, Version E0, April 2018).

treatment_protocol: Two females were caged with one male overnight and vaginal smears were done the following day to identify sperm-positive females. That day was counted as gestational day 0 (GD0) and females were separated into two groups (n=5/group) randomly: one fed a control diet (18%kcal from fat) and the other fed a HFD (45% kcal from fat)

tag: tissue

value: Germ cell

value: Sprague-Dawley

value: Male

value: GFP-GCS

value: Gonocytes

tag: diet

value: Control


title: n-4-input

value: skin

tag: cell line

value: healthy control


title: ad-2-input

value: patient with atopic dermatitis (AD)


title: RNA-seq_neonatal_FB_G3BP1-OE.1

value: neonatal

value: heart

tag: cell type

value: FB

tag: genotype

value: wild type

value: G3bp1 OE


title: Control Male GD18 Gonocytes 4

tag: strain


title: RNA-seq_neonatal_FB_NCBP2-OE.2

tag: treatment

value: Ncbp2 OE


title: AB5E1 ALI7, patient 4

description:
293t
293_5E1

value: lung

value: patient 4

value: bronchial airway epithelial cells

tag: Sex

value: M

value: former smoker

value: AB5E1 ALI7


title: UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq, rep1

value: Naïve human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 2

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

value: anti-Flag M2 (Sigma F3165)

value: passage 26+11+8


title: n-3-input

value: skin

value: healthy control


title: RNA-seq_neonatal_EC_shNT.2

value: neonatal

value: heart

value: EC

value: wild type

value: shNT


title: UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep4

source_name: Primed human embryonic stem cells

value: Primed human embryonic stem cells

value: WT

value: anti-H3K27me3 (CST 9733)

value: passage 26+12


title: UCLA1 primed hESC, NT control, Input, rep4

value: UCLA1 primed hESCs


title: Control Male GD18 Gonocytes 1

value: Germ cell

value: Sprague-Dawley

value: Male

value: GFP-GCS

value: Gonocytes

value: Control


title: RNA-seq_neonatal_EC_shNT.1


title: CTL ALI7, patient 4

description:
293c
293_CTL

value: lung

value: patient 4

value: bronchial airway epithelial cells

value: M

value: former smoker

value: CTL ALI7


title: HFD female GD16 Gonocytes 3

value: female

value: high-fat diet


title: UCLA1 primed hESC, NT control, Input, rep2

value: Primed human embryonic stem cells

value: Human embryonic stem cells

value: WT

value: passage 27+9


title: RNA-seq_neonatal_EC_shNCBP2.2

value: neonatal

value: heart

value: EC

value: wild type


title: ad-3-input

value: skin

value: patient with atopic dermatitis (AD)


title: UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep2

value: UCLA1 primed hESCs

value: anti-H3K27me3 (CST 9733)


title: HFD female GD16 Gonocytes 2

value: Germ cell

value: Sprague-Dawley

value: GFP-GCS

value: Gonocytes


title: CTL ALI7, patient 3

description:
285c
285_CTL

value: lung

value: patient 3

value: bronchial airway epithelial cells

value: F

value: smoker

value: CTL ALI7


title: CTL ALI7, patient 5

description:
340c
340_CTL

value: patient 5


title: AB5E1 ALI7, patient 3

description:
285t
285_5E1

value: AB5E1 ALI7


title: UCLA1 primed hESC, H2AK119ub ChIP-seq, rep2

value: Primed human embryonic stem cells

value: Human embryonic stem cells

value: WT

value: anti-H2AK119ub (CST 8240)

value: passage 27+9


title: UCLA1 primed hESC, NT control, Input, rep3

value: UCLA1 primed hESCs

value: passage 26+12


title: HFD female GD16 Gonocytes 1

value: Germ cell

value: Sprague-Dawley

value: female

value: GFP-GCS

value: high-fat diet


title: Control Male GD18 Gonocytes 2

value: Male

value: Gonocytes

value: Control


title: CTL ALI7, patient 2

description:
284c
284_CTL

value: lung

value: patient 2

value: bronchial airway epithelial cells

value: M

value: former smoker

value: CTL ALI7


title: RNA-seq_neonatal_FB_G3BP1-OE.2

value: neonatal

value: heart

value: FB

value: wild type

value: G3bp1 OE


title: RNA-seq_neonatal_EC_NCBP2-OE.2

value: EC

value: Ncbp2 OE


title: RNA-seq_neonatal_EC_NCBP2-OE.1


title: HFD male GD16 Gonocytes 4

value: Germ cell

value: Sprague-Dawley

value: male

value: GFP-GCS

value: high-fat diet


title: UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep3

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: WT

value: anti-H3K27me3 (CST 9733)

value: passage 26+12


title: RNA-seq_neonatal_EC_GFP.2

value: neonatal

value: heart

value: GFP OE


title: UCLA1 primed hESC, NT control, Input, rep1

value: passage 27+9


title: HFD male GD16 Gonocytes 2

value: Gonocytes


title: CTL ALI7, patient 1

description:
279c
279_CTL

value: lung

value: patient 1

value: bronchial airway epithelial cells

value: F

value: non-smoker

value: CTL ALI7


title: RNA-seq_neonatal_EC_GFP.1

value: EC

value: wild type


title: RNA-seq_neonatal_EC_shNCBP2.1


title: RNA-seq_neonatal_EC_G3BP1-OE.2

value: G3bp1 OE


title: UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep1

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: WT


title: AB5E1 ALI7, patient 2

description:
284t
284_5E1

value: patient 2

value: M

value: former smoker

value: AB5E1 ALI7


title: HFD male GD16 Gonocytes 1

value: Germ cell

value: Sprague-Dawley

value: male

value: GFP-GCS

value: Gonocytes

value: high-fat diet


title: RNA_CAL27_la_2

first: Fengyang

last: Jing

address: xueyuan road #38

institute: Peking university

data_processing:
Raw data of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
total RNA was used as input material for the RNA sample preparations.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

value: Oral Squamous Cell Carcinoma

value: 10mM lactate for 24 hours


title: RNA_CAL27_la_3


title: RNA_CAL27_la_1


title: Control Female GD16 Gonocytes 2

value: Female

value: Control


title: UCLA1 primed hESC, ZIC2-/-, Input, rep3

data_processing:
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Deeptools was used to generate coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: ZIC2-/- clone 7

value: passage 27+9


title: UCLA1 primed hESC, H2AK119ub ChIP-seq, rep1

value: Human embryonic stem cells

value: WT

value: anti-H2AK119ub (CST 8240)


title: UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep3

value: anti-H3K27me3 (CST 9733)


title: RNA-seq_neonatal_EC_G3BP1-OE.1

value: neonatal

value: heart

value: EC

value: wild type

value: G3bp1 OE


title: RNA_CAL27_3

value: Oral Squamous Cell Carcinoma


title: Control Female GD16 Gonocytes 1

value: Germ cell

value: Sprague-Dawley

value: GFP-GCS

value: Gonocytes


title: RNA-seq_neonatal_CM_shPTBP1.3

value: CM


title: HFD male GD16 Gonocytes 3

value: male

value: high-fat diet


title: UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC2-/- clone 5

value: passage 27+9


title: AB5E1 ALI7, patient 1

description:
279t
279_5E1

value: lung

value: patient 1

value: bronchial airway epithelial cells

value: F

value: non-smoker

value: AB5E1 ALI7


title: RNA-seq_neonatal_CM_shPTBP1.2

value: neonatal

value: heart

value: wild type


title: Control Male GD16 Gonocytes 4

value: Germ cell

value: Sprague-Dawley

value: Male

value: GFP-GCS

value: Gonocytes

value: Control


title: RNA_CAL27_2

value: Oral Squamous Cell Carcinoma


title: RNA_CAL27_1


title: RNA-seq_neonatal_CM_shPTBP1.1

value: CM


title: Control Male GD16 Gonocytes 3


title: UCLA1 primed hESC, ZIC2-/-, Input, rep1

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC2-/- clone 1

value: passage 26+12


title: RNA-seq_neonatal_CM_shNT.3

value: shNT


title: CUTTAG_CAL27_la

data_processing:
Raw data  of fastq format were firstly processed using fastp (version 0.20.0)
clean data were obtained by removing reads containing adapter, reads containingploy-N and low-quality reads.All the downstream analyses were based on the clean data.
Index of the reference genome was built using BWA[3] (v0.7.12) and clean reads were aligned to the reference genome using BWA mem -k 32 -T 30 -t 4 -M.
These reads were filtered for high quality (MAPQ ≥ 13),we removed reads that were not paired and with PCR duplicates. Only uniquely mapped and de-duplicated reads were used for further analysis.
Peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include narrow peaks for each Sample
Library strategy: CUT&Tag

extract_protocol:
Take out the cryovial and shake it in 37°C water to quickly thaw it within 1-2min.Cells were centrifuged for 5 min at 600×g at 4 ℃ Cell activity was detected with LUNA-FL and counted.
The cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin.The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation

value: 10mM lactate for 24 hours

value: pan-lactyllysine (PTM-Bio,PTM-1401RM)


title: Control Female GD16 Gonocytes 3

value: Female


title: RNA-seq_neonatal_CM_shNT.2

value: neonatal

value: heart

value: wild type


title: CUTTAG_CAL27


title: UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep1

value: anti-H3K27me3 (CST 9733)


title: Control Male GD16 Gonocytes 2

value: Germ cell

value: Sprague-Dawley

value: Male

value: GFP-GCS

value: Gonocytes


title: RNA-seq_neonatal_CM_shNT.1

value: CM


title: UCLA1 primed hESC, ZIC2-/-, Input, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC2-/- clone 5

value: passage 27+9


title: WT Pancreas_Mist1 line_repl 3

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

institute: University of Western Ontario

description: Batch 3

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mouse genome mm10 and sorted by coordinate using STAR 2.7.9a
Gene counts were generated using the featureCounts function of the Subread aligner v2.0.3
Subsequent differential expression analysis was performed using the DESeq2 v1.38.3
Assembly: mm10
Supplementary files format and content: tab delimited format (txt) includes raw counts for each sample in each line (Ptf1a line and Mist1 line)
Supplementary files format and content: tab delimited format (txt) includes differentially expressed genes (DESeq2) for the KRAS samples from each line (Ptf1a line and Mist1 line) compared to their corresponding WT

source_name: Pancreas

extract_protocol:
RNA was isolated from pancreatic tissue 22 days after initial TX gavage using Trizol (ThermoFisher Scientific, 15596018) and the PureLink RNA mini kit (ThermoFisher Scientific, 12183018A)
Illumina NextSeq High Output 150 cycle sequencing kit was used for library making following rRNA reduction.

value: Pancreas

value: WT

value: Tamoxifen oral gavage


title: FSK3

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

institute: Fudan University

description: FSK treatment

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination. And After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2.
Then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Rnor_6.0.
Supplementary_files_format_and_content: Excel files include FPKM values and raw gene counts for every gene and every sample

growth_protocol: C6 Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Yeasen),100 units/ml penicillin, and 100 μg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37°C。

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C6 Cells were treated with DMSO or FSK for 24 hours

value: rat glioma cells

value: treated with FSK for 24 hours


title: RNA-seq_neonatal_CM_shNCBP2.3

value: neonatal

value: heart

value: wild type


title: RNA-seq_neonatal_CM_shNCBP2.2


title: WT Pancreas_Mist1 line_repl 2

description: Batch 3


title: WT Pancreas_Mist1 line_repl 1

description: Batch 3


title: ATAC_CAL27

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.0)
clean data were obtained by removing reads containing adapter, reads containingploy-N and low-quality reads.
Index of the reference genome was built using BWA(v0.7.12) and clean reads were aligned to the reference genome using BWA mem.
These reads were filtered for high quality (MAPQ ≥ 13),we removed reads that were not paired and with PCR duplicates. Only uniquely mapped and de-duplicated reads were used for further analysis.
Peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits--nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for alldata sets.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include narrow peaks for each Sample

extract_protocol:
Take out the cryovial and shake it in 37℃ water,Cells were centrifuged and it was counted with LUNA-FL.Live cells undergo a series of treatments and nucleus was collected.
the nucleus pellet was resuspended in the Tn5 transposase reaction mix.It was incubated at 37℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition.After the PCR reaction, libraries were purified with the AMPure beads.

value: Oral Squamous Cell Carcinoma


title: ATAC_CAL27_la

value: 10mM lactate for 24 hours


title: 10x_8_VDJ

city: Heidelberg

first: Anna

last: Obraztsova

address: Im Neuenheimer Feld 280

department: B Cell Immunology

institute: German Cencer Research Center (DKFZ)

description:
This sample also has reads produced with NextSeq 2000
VDJ-enriched RNA
VDJ (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains BCR transcript

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.
Library strategy: VDJ-seq

source_name: Plasmablasts and S+ and CD71+ B cells, VDJ

extract_protocol:
S-reacitve B cells (S+), activated B cells (CD71+) and plasmablasts (CD27+CD38+) were isolated from PBMC samples by fluorescence-activated cell sorting (FACS). Sorted single cells were captured using Chromium controller (10x Genomics) according to the Chromium Single Cell 5’ Reagent Kit (CG000330 Rev C) protocols.
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping

value: PBMC

value: B cell

value: 2 doses of BNT162b2

tag: library type

value: VDJ


title: FSK1

description: FSK treatment


title: 10x_8_GEX

description:
This sample also has reads produced with NextSeq 2000
polyA RNA
GEX (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains transcript

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.

source_name: Plasmablasts and S+ and CD71+ B cells, GEX

value: GEX


title: FSK2

description: FSK treatment


title: RNA-seq_neonatal_CM_shNCBP2.1

value: CM


title: KRAS Pancreas_Mist1 line_repl 3

description: Batch 3


title: RNA-seq_neonatal_CM_shG3BP1.3


title: 10x_8_CSP

description:
This sample also has reads produced with NextSeq 2000
Cell surface protein (CSP)
CSP library: read1 file contains cell barcode and UMI; read2 file contains hashtag or antigen DNA barcode

library_source: other

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.
Library strategy: CITE-seq

molecule: protein

source_name: Plasmablasts and S+ and CD71+ B cells, CSP

value: CSP


title: KRAS Pancreas_Mist1 line_repl 2

description: Batch 3

value: Pancreas


title: DMSO2

description: DMSO treatment

value: treated with DMSO for 24 hours


title: DMSO3

description: DMSO treatment


title: RNA-seq_neonatal_CM_shG3BP1.2


title: KRAS Pancreas_Mist1 line_repl 1

description: Batch 3

value: Tamoxifen oral gavage


title: Control Male GD16 Gonocytes 1

value: Germ cell

value: Sprague-Dawley

value: Male

value: GFP-GCS

value: Gonocytes

value: Control


title: 10x_7_VDJ

description:
VDJ-enriched RNA
VDJ (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains BCR transcript


title: RNA-seq_neonatal_CM_shG3BP1.1

value: neonatal

value: heart

value: wild type


title: 10x_7_GEX

description:
polyA RNA
GEX (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains transcript

value: PBMC

value: B cell

value: 2 doses of BNT162b2