title: WT  bone marrow lineage-negative cells replicate 3

city: shanghai

first: xuanhui

last: wu

state: shanghai

address: yueyang road 320

department: Institute of Nutrition

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Fastp(0.23.0) for sequencing data quality control and preprocessing
HISAT2(2.1.0) alignment program for mapping next-generation sequencing reads
HTSeq(0.10.0) for analysis of high-throughput sequencing data.
Gene set enrichment analysis was performed on GSEA_4.3.2 and visualization of differentially expressed genes was implemented by the pheatmap R package.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone Marrow

extract_protocol:
Lineage-negative cells cells from three WT and three  Abin1Q478H/Q478H mutation mice were purified by flow cytometry. Lineage-negative cells were then stained with Antibody Biotin CD3, Biotin CD45R,Biotin CD4, Biotin CD5 , Biotin CD8a Biotin ,Biotin CD19,Biotin CD11b,Biotin Ly-6G, Biotin TER-119, PE-Cy7 Streptavidin, and selected by beckman moflo Astrios EQ . Total RNAs from sorted lineage-negative bone marrow cells of WT and AbinQ478H/Q478H  mice at 5 months old were extracted with Trizol (9108, Takara). Each group had three independent samples. RNA samples were quantified using a Qubit 3.0 Fluorometer (Life Technologies, CA, USA), and RNA integrity was assessed using a 4200 TapeStation (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II mRNA Library Prep Kit following manufacturer's protocols.

value: Bone Marrow

value: bone marrow lineage-negative cells

value: primary cell

value: WT


title: Abin1Q478H/Q478H  bone marrow lineage-negative cells replicate 3

status: Public on Jan 08 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: Abin1Q478H/Q478H  bone marrow lineage-negative cells replicate 1


title: MA1710

city: Bloomington

first: Ellen

middle: D

last: Ketterson

state: IN

address: 1001 E. Third Street

country: USA

institute: Indiana University

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions v2.20.0.422).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.33 for all samples) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:25
Reads were mapped to the Junco genome using STAR (v2.7.2b) with the following parameters: --outSAMattributes All --outSAMunmapped Within --outReadsUnmapped Fastx --outFilterMultimapNmax 1 --seedSearchStartLmax 16 --quantMode GeneCounts --twopassMode Basic --outWigType wiggle --outWigStrand Unstranded --outWigNorm None --outSAMtype BAM SortedByCoordinate
Read counts for genes were generated with featureCounts from the subread package (v1.6.0) with the following parameters: -F SAF --fracOverlap 0.51 --primary -p -O -s 2 -Q 30 -T 30
Genome_build: dark_eyed_junco genome equivalent to genome on Ensemble and accessible here: ftp://ftp.ebi.ac.uk/pub/databases/ena/wgs/public/qzw/QZWM01.fasta.gz
Supplementary_files_format_and_content: Processed data files are tab-delimited files indicating the number of reads from a given sample (column) associated with a given gene (row)

organism: Junco hyemalis

source_name: feather

growth_protocol: We plucked the 6th, 4th, and 2nd rectrices from both left and right side of the tail (6 feathers total) from 6 Dark-eyed junco individuals to induce feather development. Developing feathers were collected 14 days later, by which time the length of the developing pin was approximately 1cm, and 1-1.5 cm long plumes were erupting from the tip of the pin. Feathers were collected by grabbing and pulling the developing pin at the base of the feather with curved forceps. The two 4th rectrices, which show incomplete pigmentation along the long axis were dissected on sterile culture dishes to separate the apigmented and the pigmented feather regions. The dissected samples were then immediately placed in a sterile 1.5ml centrifuge tube and flash-frozen on pulverized dry ice. The 6th and 2nd rectrices were flash-frozen without dissection as these feathers are either completely pigmented or apigmented. Feathers were then transferred to a -80C freezer until RNA extraction.

extract_protocol:
RNA was extracted using the Maxwell RSC automated nucleic acid extraction system (Promega, Madison, WI, USE; product number AS4500), using the Maxwell RSC simplyRNA Tissue kit (Promega, AS1340), following the manufacturer’s instructions. RNA was eluted in double-distilled water, and frozen at -80C.
RNA integrity was analyzed with Agilent Technologies 2200 Tape Station (Agilent Technologies). Input was quantified by using Qubit RNA BR Assay Kit. Samples were prepared using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina). Sequencing was performed using an Illumina NextSeq 500/550 Kits v2 reagents with 75 bp sequencing module.

tag: side

value: left

tag: position

value: 4th rectrix

tag: pigmentation

value: pigmented

tag: individual animal id

tag: rna extraction batch


title: BJ, BRD3RDBD1DBD2, replicate a

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description:
BET_normalizedCount42samples.xlsx
KH273a

data_processing:
Original image data file from high-throughput sequencing (Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The human refernce genome (assembly GRCH38, release 105) was indexed  using STAR (STAR version 2.7.3a) (runMode  genomeGenerate) on Cheaha supercomputer, and the read fragments of each FASTQ file was aligned to human reference genome using the STAR aligner (version 2.7.3a).
The BAM files were sorted and indexed using SAMtools (version 1.12), and the counting was achieved using HTSeq tools (Htseq-count).
The statistics and normalization of the RNA-seq were conducted using the DESeq2 software (version 1.30.1) on the Cheaha Rstudio server.
Assembly: GRCH38, release 105

organism: Homo sapiens

source_name: BJ

growth_protocol: Human iPS cells were cultured in standard feeder-free and serum-free chemically defined E8 media. Human fibroblast BJ cells were cultured in fibroblast media: DMEM: F12 media supplemented with 10% FBS and 5 ng/mL human bFGF

extract_protocol:
BJ fibroblast cells (ATCC, CRL-2522, foreskin fibroblasts) were cultured in six well plates at a density of 2 ´ 105 cells per well. At 24 hrs post seeding, the medium was removed and 2 mL fresh medium containing polybrene (final concentration=5 µg/mL) was added to the wells. The viruse preparations were then added into respective wells (day 0). At 18 hrs after virus addition, the virus-containing spent media were removed and fresh fibroblast medium was added. At 72 hrs after virus removal (on Day 4), the spent medium was removed and 1 mL of TRIzol (Invitrogen; Cat no. 15596018) was added directly to the each well. RNA was extracted following manufacturer’s protocol. After extraction, the RNA was further purified using Quick RNA Miniprep kit (Zymo Research; Cat. no. R1055) using manufacturer’s protocol.
Human mRNAs are captured via oligo(dT) beads. Non-stranded protocol was used. The purified mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization. In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.
The following samples were sequenced using DNA nanoball (DNB) technology, BJ48hS1, BJ48hS2, BJ48HS3, hESH1, hESH9, H1P43, H9P69S2.  mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. The obtained mRNA molecules were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. The cDNA fragments were amplified  with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and paired end 100 bases reads were generated in the way of sequenced by synthesis.

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of the indicated genes or BET mutants (MOI, OCT4, 8; SOX2, 5, KLF4, 5; and all others are 3). At 18 hours post transduction, virus-containing spent media were removed and RNAs were extracted 72 hours after virus removal using extraction protocols described.

value: BJ

value: foreskin fibroblasts

tag: treatment

value: lentiviral BRD3RDBD1DBD2


title: MA1709

value: 6th rectrix

value: apigmented


title: HCT116_TinT2_SP1_WT_2_rep1

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

library_source: genomic

data_processing:
FASTQ files of ATAC-seq data were processed by cutadapt for adapter removal. Trimmed reads were mapped against human genome (hg19) using bowtie2 aligner
Alignment files were filtered by sambamba tool for duplicates
Filtered mapping files were processed by MACS2 for peaks calling
DiffBind was used to identify the deferentially bound peaks between samples.
ATAC-seq profiles were generated using UCSC genome browser (hg19)
Genome_build: hg19

molecule: genomic DNA

source_name: Cell Line

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS (Gibco), penicillin and streptomycin (Gibco).

extract_protocol:
omni-ATAC-seq
ATAC seq library was prepared as described previously in PMID: 28846090. 50,000 cells were lysed for nuclei isolation. Transposition reaction was performed using Nextera DNA library preparation kit (NEB). Samples were amplified by eight PCR cycles for library preparation. Primer dimers and long DNA fragments were cleaned by AMPure XP beads purification step. DNA concentration was measured by Qubit fluorometric assay and library quality was determined by Bioanalyzer.

treatment_protocol: No treatment

tag: cancer type

value: colon cancer

value: untreated


title: MA1708

value: right


title: WT  bone marrow lineage-negative cells replicate 1


title: HCT116_TinT2_SP1_WT_1_rep1


title: DNA sample after immunoprecipitation with antibody Nr4a2

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

description: BV2 cell lines Nr4a2 samples was used as case

data_processing:
Data filtering : These reads were detected by SOAPnuke programs. Low-quality reads include three types, and the read which could be accord with anyone of the three types will be removed:    1) The ratio of N in whole read was over 10%;    2) Remove reads in which unknown bases are more than 10%;    3) The ratio of base whose quality was less than 20 was over 10%.
Clean data mapping: After filtering, the clean data was then mapped to the reference genome by Bowtie2
Peak-calling: MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.2.6) : The candidate peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value < 0.05
Specific peak region identifing: To determine the target genes of Nr4a2, the Model-based Analysis of ChIP-Seq (MACS) version 2.2.6 was used to identify the specific peak region. The region was defined as a peak with p-value < 0.05.
ChIP peak annotation: ChIP peak annotation by ChIPseeker, a R bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: wig files
Supplementary_files_format_and_content: peak text files

source_name: BV2 cell line

extract_protocol:
Nr4a2 ChIP assays were performed with 10^7 cells using SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, #9003) according to manufacturer’s instruction.
The libraries were constructed by Novogen (China) and sequenced on the Illumina HiSeq platform (Novogen, China).

tag: chip antibody


title: BJ, BRD3RDBD1, replicate c

description:
BET_normalizedCount42samples.xlsx
KH251c

value: lentiviral BRD3RDBD1


title: Abin1Q478H/Q478H  bone marrow lineage-negative cells replicate 2


title: HCT116_TinT2_SP1_KO_1_rep1

value: KO HCT116


title: MA1707


title: BJ, BRD3RDBD1, replicate b

description:
BET_normalizedCount42samples.xlsx
KH251b


title: HCT116_TinT2_SP1_WT_2_rep2


title: MA1706


title: “input” DNA sample that was not immuno-precipitated

description: BV2 cell lines  Input samples was used as control.

value: none (input)


title: BLM 146C>T TinT1 KO rep2

value: Melanoma

tag: clone

value: T TinT1 KO


title: BJ, BRD3RDBD1, replicate a

description:
BET_normalizedCount42samples.xlsx
KH251a


title: BJ GFP, replicate c

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
GFPc

value: WT + GFP

value: lentiviral GFP


title: BLM 146C>T TinT1 KO rep1


title: MA1705

value: 2nd rectrix


title: WT  bone marrow lineage-negative cells replicate 2

value: Bone Marrow

value: bone marrow lineage-negative cells

value: primary cell

value: WT


title: BLM 146C>T TinT1 WT rep2

value: T TinT1 WT


title: mmSC1

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

description: 3' end of DNA break

data_processing:
Library strategy: DEtail-seq
Illumina Casava1.7 software used for basecalling.
Duplicated reads which had same sequences for both forward and reverse reads were removed
Reads were aligned to the reference genome with Bowtie2 using --local settings
For visualization and split strand, we use bamCoverage from DeepTools (--binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse) to convert the aligned reads files (BAMs) including the second read in pairs to first single base bigWig files with 1bp bins. The option --filterRNAstrand forward means Crick strand and --filterRNAstrand reverse means Waston strand.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: sertoli cells (SC)

extract_protocol:
Testes from adult C57BL/6 mice were removed and decapsulated. The seminiferous tubules were tore into small pieces and incubated in 8 ml PBS containing 1 mg/ml collagenase (Sigma, C5138, St. Louis, MO, USA) and 1 mg/ml hyaluronidase (Sigma, H3506, St. Louis, MO) at 37°C for 6 min with gentle shaking. After pipetting, the dispersed seminiferous tubules and cells were incubated at 37°C for 5 min with gentle shaking. Then, the cells were collected by centrifugation at 200 × g for 5 min at 4°C, washed once with PBS, resuspended in 15 ml PBS containing 0.25% Trypsin and 1 mg/ml DNase I, and incubated at 37°C for 5 min with gentle shaking. Thereafter, the cells were collected and washed with PBS containing 0.5% BSA. After filtration through a 40 μm Nylon Cell Strainer, the cells were separated by sedimentation velocity at unit gravity at 4°C, using a 2–4% BSA gradient in PBS. The cell fractions were bottom-loaded in a volume of 300 ml. An aliquot of each fraction was examined by light microscope to assess cellular purity and cell type identity.
Each cell pellet was resuspended in 150 µl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 µl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 µl Solution 1 (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0, 5% β-mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was pre-warmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs were cut into small pieces (one agarose plug to 16~24 pieces), and expressed into 1 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5% β-mercaptoethanol, 10 µg/ml RNase A) and incubated at 37°C for overnight. Plugs were quickly washed three times with 1 ml TE buffer, and then washed five times with TE buffer incubated at 37°C for 6min (total 30min). Then plugs were expressed into 1ml Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and incubated at 54°C overnight. Plugs were finally washed six times with TE buffer and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.  The plugs were transferred to a PCR tube, and washed by 30 µl 1X Adaptase buffer (Swift, Accel-NGS, 10096) twice at room temperature, 10 min each time. Add 47 µl 1X Adaptase buffer and 3 µl Adaptase (Swift, Accel-NGS, 10096) to PCR tube, incubated with plugs at 37°C for 2 h. Removed buffer, and deactivated Adaptase in plugs by 98°C for 2 min. Purified DNA from plugs by Gel Extraction Kit (Qiagen, 28606). Sonicated DNA to 150~250 bp fragments by using Focused-ultrasonicator (Covaris, S220). The rest steps were following the manual of Accel-NGS 1S Plus DNA Library Kit (Swift, Accel-NGS, 10096). Briefly, denatured DNA fragments to ssDNA, and extended it to dsDNA. After purification, 2rd adaptor was ligated. After indexing PCR and purification, preparation of DEtail-seq library was finished. The DEtail-seq library was sequenced by NovaSeq 6000 (Illumina).

tag: strain


title: BJ GFP, replicate b

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
GFPb

value: BJ

value: foreskin fibroblasts


title: MA1704

value: left

value: pigmented


title: mmPac2

description: 3' end of DNA break

source_name: testicular cells at pachytene stage (Pac)


title: BJ GFP, replicate a

description:
BET_normalizedCount42samples.xlsx
BET_normalizedCount27samples.xlsx
GFPa


title: HCT116_TinT2_SP1_WT_1_rep2

value: colon cancer

value: untreated


title: MA1703

value: 4th rectrix

value: apigmented


title: mmPac1

description: 3' end of DNA break


title: BLM 146C TinT1 WT rep2

value: Melanoma

value: TinT1 WT


title: BLM 146C>T TinT1 WT rep1


title: MA1702


title: mmLZ2

description: 3' end of DNA break

source_name: testicular cells at leptotene/zygotene stages (L/Z)


title: BLM 146C TinT1 WT rep1


title: MA1701

value: 6th rectrix


title: hsTestis2

description: 3' end of DNA break

data_processing:
Illumina Casava1.7 software used for basecalling.
Duplicated reads which had same sequences for both forward and reverse reads were removed
Reads were aligned to the reference genome with Bowtie2 using --local settings
For visualization and split strand, we use bamCoverage from DeepTools (--binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse) to convert the aligned reads files (BAMs) including the second read in pairs to first single base bigWig files with 1bp bins. The option --filterRNAstrand forward means Crick strand and --filterRNAstrand reverse means Waston strand.
Genome_build: hg19

source_name: human testis

extract_protocol:
Human adult testis were subjected to a standard digestion procedure. Testes were washed twice in 1× HBSS and cut into small pieces. Then, tissues were digested with 1 mg/ml collagenase (Sigma, C5138, St. Louis, MO, USA) and 1 mg/ml hyaluronidase (Sigma, H3506, St. Louis, MO) at 37°C for 6 min with gentle shaking. After pipetting, the dispersed seminiferous tubules and cells were incubated at 37°C for 5 min with gentle shaking. The digestion was stopped by adding 10% FBS (Gibco,10082147). Single testicular cells were obtained by filtering through strainers with mesh size 70 µm (Fisher Scientific, 08–771–2) and 40 µm (Fisher Scientific, 08–771–1). The cells were pelleted by centrifugation at 600× g for 5 min, and washed twice with 1× PBS. Cell were re-suspended in 1× PBS ready for Detail-seq.
Each cell pellet was resuspended in 150 µl 50 mM EDTA pH 8.0 and allowed to thaw at 40°C. 498 µl LMP agarose (2% in 50 mM EDTA pH 8.0) was mixed with 102 µl Solution 1 (1 M sorbitol, 0.1 M sodium citrate, 60 mM EDTA pH 7.0, 5% β-mercaptoethanol and 1 mg/ml zymolyase 100T) and the mix was pre-warmed at 40°C before adding to the cells. The resuspended cells were pipetted into plug molds and chilled at 4°C for 30 min. Once solidified, the agarose plugs were cut into small pieces (one agarose plug to 16~24 pieces), and expressed into 1 ml of Solution 2 (0.45 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 7.5% β-mercaptoethanol, 10 µg/ml RNase A) and incubated at 37°C for overnight. Plugs were quickly washed three times with 1 ml TE buffer, and then washed five times with TE buffer incubated at 37°C for 6min (total 30min). Then plugs were expressed into 1ml Solution 3 (0.25 M EDTA pH 8.0, 0.01 M Tris-HCl pH 7.5, 1% SDS, 1 mg/ml proteinase K) and incubated at 54°C overnight. Plugs were finally washed six times with TE buffer and stored in plug storage solution (0.05 M EDTA pH 8.0, 50% glycerol) at -20°C until all plugs were ready to be processed for library preparation.  The plugs were transferred to a PCR tube, and washed by 30 µl 1X Adaptase buffer (Swift, Accel-NGS, 10096) twice at room temperature, 10 min each time. Add 47 µl 1X Adaptase buffer and 3 µl Adaptase (Swift, Accel-NGS, 10096) to PCR tube, incubated with plugs at 37°C for 2 h. Removed buffer, and deactivated Adaptase in plugs by 98°C for 2 min. Purified DNA from plugs by Gel Extraction Kit (Qiagen, 28606). Sonicated DNA to 150~250 bp fragments by using Focused-ultrasonicator (Covaris, S220). The rest steps were following the manual of Accel-NGS 1S Plus DNA Library Kit (Swift, Accel-NGS, 10096). Briefly, denatured DNA fragments to ssDNA, and extended it to dsDNA. After purification, 2rd adaptor was ligated. After indexing PCR and purification, preparation of DEtail-seq library was finished. The DEtail-seq library was sequenced by NovaSeq 6000 (Illumina).

value: testis


title: hsTestis1

description: 3' end of DNA break


title: mmSC2

description: 3' end of DNA break


title: mmLZ1

description: 3' end of DNA break


title: pilot_par_organoid_4

status: Public on Jan 07 2023

city: Worcester

first: Jan

last: Czerminski

state: MA

address: 55 Lake Ave N

department: Neurology

institute: UMass Medical School

data_processing:
Reads were mapped using HISAT2 (v2.0.5) to the GRCh37 reference (augmented with Tet and Puro transgenes) indexed with Ensembl 87 annotations
Strand-specific read counts per gene (Ensembl 87 annotations) for each sample were computed with featureCounts (subread v1.6.2)
Assembly: GRCh37
Supplementary files format and content: gzipped tab-delimited tables of read counts per gene per sample in pilot study and expanded study
Supplementary files format and content: fasta file with TET3G and PURO transgenes that were added to the reference genome for mapping

molecule: polyA RNA

source_name: par

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher) according to manufacturers instructions. RNA samples were cleared of contaminating genomic DNA by DNAse I (Roche) treatment for 1h at 37C.
RNA cleanup and DNAse I removal was performed using RNeasy MinElute columns (Qiagen) according to manufacturer's instructions. Clean RNA was assessed for quality on an Advanced Analytical Fragment Analyzer. All samples had an RQN > 7.5 and strand-specific sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

tag: study

value: pilot

tag: sample type

value: single organoid

tag: batch

value: par

value: iPSC-derived cerebral organoid

value: trisomic


title: pilot_par_organoid_2


title: org18_parA_rep1

source_name: parA

value: expanded

value: pooled organoids

value: parA


title: pilot_dis_organoid_8

source_name: dis

value: dis

value: disomic


title: pilot_dis_organoid_6


title: pilot_dis_organoid_7


title: pilot_dis_organoid_9


title: pilot_dis_organoid_10


title: pilot_par_organoid_5


title: org18_parA_rep2


title: org18_parB_rep1

source_name: parB

value: parB


title: org18_par_rep2


title: pilot_par_organoid_1


title: org18_disB_rep2

source_name: disB

value: disB


title: mTEChi, AireKO, rep4

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

description:
Aire_23
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

data_processing:
Sequence reads were trimmed to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Low-quality parts and adapter sequences were trimmed by fastp (v0.20.0)
Trimmed short reads were mapped to the mm10 genome using STAR (v2.7.3a) with a GTF file from EMBL-EBI (GRCm38.99)
Unmapped reads and reads mapped with low-quality scores (MAPQ < 5) were removed by SAMtools (v1.9)
Duplicated reads were filtered out using Picard Tools (v2.21.1)
Mapped reads on each gene were counted using htseq-count (v0.11.2) with --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Raw counts were normalized using edgeR package in R programming language
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for all samples
Supplementary files format and content: comma-separated values file includes edgeR normalized abundances for all samples

source_name: thymus

extract_protocol:
Mouse thymus was enzymatically  digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria directly into tubes containing TCL buffer (QIAGEN)
RNA-seq libraries were prepared by applying a RamDA-seq method for single-cell RNA-seq (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018) with some modifications. Specifically, RNA was isolated using RNAClean XP beads (x2.2 vol., Beckman Coulter) directly from the lysis buffer, and was eluted into 10 uL of water containing RNase inhibitor (4u/uL RNasinPlus RNase Inhibitor, Promega). The RNA was denatured by incubating at 65C for 5min, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 15min. Then cDNA was synthesized in 30uL of 1xRT Buffer containing RT Enzyme Mix (1.5uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (3.3uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 5uL of 10x NEB buffer2 (NEB), 1.25uL of dNTP mix (10mM each nt, NEB), 1.5uL of Klenow Fragment (3'→5' exo-, NEB), 5uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 7.25uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (x2 vol., Beckman Coulter) and quantified using Qubit (Qubit dsDNA HS Assay Kit, Invitrogen). Then ds-cDNA less than 1ng was applied for Tn5 tagmentation in a 25uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). DNA was purified using AMPure XP beads (x1.7 vol.) and amplified by 10~15 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.2 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

tag: tissue

value: thymus

value: MHCII-high epitherial cells

value: AireKO

tag: age

tag: Sex

value: male


title: org18_disB_rep1

tag: cell line

tag: cell type

tag: genotype


title: mTEChi, AireKO, rep3

description:
Aire_22
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz


title: mTEChi, AireKO, rep2

description:
Aire_21
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz


title: org18_disA_rep2

source_name: disA

value: disA


title: org18_disA_rep1


title: iHeps derived from PiZZ100 syngeneic MM iPSCs (Fluidigm_C1)

city: Boston

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

library_source: transcriptomic single cell

data_processing:
The sample was processed using the star trimmed pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: count matrix exported from the R seurat object (The cell IDs starting with c01-c10 belong to MM iPSCs, and the c11-c20 belongs to  ZZ iPSCs.)

source_name: PiZZ100 syngeneic MM iPSCs

extract_protocol:
Fluidigm C1 platform
C1 Single-Cell mRNA Seq
Fluidigm scRNA-seq

value: iHeps

tag: cell source

value: PiZZ100 syngeneic MM iPSCs

tag: sample collection


title: mTEChi, WT, rep6

description:
Aire_18
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: WT


title: org18_par_rep1

value: par

value: iPSC-derived cerebral organoid


title: org18_parB_rep2

value: expanded

value: trisomic


title: org18_dis_rep1

value: pooled organoids


title: org18_dis_rep2

value: dis


title: pilot_par_organoid_3

value: pilot

value: single organoid


title: iHeps derived from PiZZ100 syngeneic ZZ iPSCs (Fluidigm_C1)

source_name: PiZZ100 syngeneic ZZ iPSCs

value: PiZZ100 syngeneic ZZ iPSCs


title: mTEClo, AireKO, rep4

description:
Aire_12
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: thymus

value: MHCII-low epitherial cells


title: mTEClo, AireKO, rep3

description:
Aire_11
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: AireKO


title: org17_par_rep2


title: org17_parA_rep2

value: parA


title: org17_parB_rep1

value: parB


title: mTEClo, AireKO, rep1

description:
Aire_9
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: male


title: mTEChi, WT, rep7

description:
Aire_19
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: MHCII-high epitherial cells


title: org17_disB_rep2

value: disB

value: disomic


title: HeLa Fractionation Exp 6 Chrom Rep 2

city: Berlin

first: Jonathan

last: Alles

state: Berlin

address: Hannoversche Straße 28

department: Berlin Institute for Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbruck Center Berlin

data_processing:
Circular Consensus Sequence (CCS) reads were generated within the SMRT Link browser 5.0 (minimum full pass of three and minimum predicted accuracy of 90).
Once the raw data have been processed, the final CCS fastq files can be used directly as input for the FLAM-seq analysis pipeline, available at:    https://github.com/rajewsky-lab/FLAMAnalysis.
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Processed *_gene_polyA_length.csv files contain the extrac ted poly(A) tail length and sequence as well mapped gene locus for each read

source_name: HeLa Fractionation

growth_protocol: HeLa and HEK cells were cultured in DMEM medium containing 10% FBS at 37°C and 5% CO2

extract_protocol:
FLAM-seq library preparation was prepared according to (Legnini et al., 2019). In brief, polyadenylated RNA was isolated from total RNA using Illumina Truseq mRNA preparation kit. A GI tail was appended to selected mRNA using tailing reagents from USB poly(A) length assay kit. Tailed RNA was purified using 1.8x RNAClean beads. Tailed RNA was reverse transcribed using SMARTScribe Reverse Transcriptase Kit and isoTSO and RT primer 1 or 2. cDNA was purified using 0.6x Ampure XP beads and PCR amplified using PCR primer 1 or 2 and PCR Primer IIA using Advantage 2 DNA polymerase mix. FLAM-seq libraries were purified 2x using 0.6x Ampure XP beads. PacBio adapters addition and sequencing was performed according to standard procedures.A detailed protocol for the FLAM-seq method can be found at https://protocolexchange.researchsquare.com/article/pex-398/v1
FLAM-seq

value: HeLa S3

value: untreated

tag: fraction

value: chromatin

tag: pulldown reagent

tag: labeling time

tag: replicate

value: Rep 2


title: HeLa Fractionation Exp 6 Nuc Rep 2

tag: treatment

value: nucleoplasm


title: org17_disB_rep1

value: expanded

value: pooled organoids

value: iPSC-derived cerebral organoid


title: HeLa Fractionation Exp 6 Chrom Rep 1

value: Rep 1


title: org17_disA_rep1

value: disA


title: org17_disA_rep2


title: org17_parB_rep2

value: trisomic


title: org17_par_rep1

value: par


title: org17_dis_rep2

value: dis


title: HeLa Fractionation Exp 6 Cyto Rep 2

value: cytoplasm


title: HeLa Fractionation Exp 6 Cyto Rep 1


title: Pg infected 2

city: Yangsan-si

first: Yeongjoo

last: Kim

country: South Korea

institute: Pusan National University

data_processing:
Reads from the acquired raw RNA-Seq dataset were adapter and quality trimmed with default parameters with Trimmomatic.
Trimmed reads were aligned to Hg38 human genome reference with Hisat2 and raw counts were calculated using StringTie.
Read count data table was CPM-normalized and log2 transformed after low count removal.
Assembly: Hg38 primary assembly

source_name: brain

growth_protocol: HBEC-5i human brain microvascular endothelial cells were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA). The HBEC-5i cell line is an immortalized endothelial line described previously. The cells were grown in Vascular cell Basal medium (ATCC) supplemented with microvascular endothelial cell growth supplement (ATCC) and 1% penicillin-streptomycin (GIBCO, Waltham, MA, USA).

extract_protocol:
Total RNA from BEC cells of the control, Pg injection, and Fn injection groups was extracted and purified using TRIZol reagent in accordance with the manufacturer’s protocol. The eluted RNA purity and quantity of each sample were verified photometrically by optical density (OD) readings of the A260/280 nm ratio (Nanodrop 2000, Thermo Fisher Scientific, Waltham, MA, USA). The spectrophotometric ratio of A260/280 varied >1.80, and A260/230 values yield a ratio >2.0, so the isolated RNA could be regarded as pure.
NGS library construction was performed using ILLUMINA TruSeq RNA Library Kit.

treatment_protocol: The BEC cells were infected with a live P. gingivalis (strain 381) and F. nucleatum (Fusobacterium nucleatum subsp. polymorphumATCC 25586) at 500 MOI for 3h at 37℃ in 5% CO2. Then, the cells were washed with PBS and cultured in fresh media until harvest. Controls were subjected to the same media changes and wash conditions, without bacterial inoculation.

value: brain

value: microvascular endothelial cells

value: P.gingivalis infected


title: HeLa Fractionation Exp 5 Chrom Rep 1

value: HeLa S3


title: HeLa Fractionation Exp 6 Nuc Rep 1

value: untreated


title: Pg infected 3


title: org17_dis_rep1

value: disomic


title: Fn Infected 3

value: F.nucleatum infected


title: HeLa Fractionation Exp 5 Nuc Rep 2

value: nucleoplasm

value: Rep 2


title: org17_parA_rep1

value: expanded

value: pooled organoids

value: parA


title: HeLa Fractionation Exp 5 Chrom Rep 2

value: chromatin


title: Fn Infected 1


title: Normal Control 3

value: wild-type


title: HeLa Fractionation Exp 5 Nuc Rep 1

value: Rep 1


title: org16_parB_rep1

value: parB

value: iPSC-derived cerebral organoid

value: trisomic


title: Normal Control 2

value: brain

value: microvascular endothelial cells


title: Normal Control 1


title: HeLa Fractionation Exp 5 Cyto Rep 1

value: HeLa S3

value: cytoplasm


title: HeLa Fractionation Exp 5 Cyto Rep 2

value: untreated


title: org16_parA_rep2


title: org16_parB_rep2


title: org16_parA_rep1


title: Pg infected 1

value: P.gingivalis infected


title: Fn Infected 2

value: F.nucleatum infected


title: HeLa Fractionation Exp 4 Chrom Rep 2

value: Rep 2


title: mTEClo, AireKO, rep2

description:
Aire_10
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: thymus

value: MHCII-low epitherial cells

tag: strain

value: AireKO

value: male


title: org16_par_rep1

tag: study

value: expanded

value: pooled organoids

value: par


title: Microvesicles sample 7

city: Chicago

first: Xiaowei

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

description:
RNA-seq read counts combined from two sequencing runs
MV7

data_processing:
Raw sequence reads were mapped to the NCBI RefSeq transcriptome with Bowtie2 then normalized using the RPM method (reads per million reads) to get tRNA and yRNA reads. For miRNA analysis, the reads were aligned to miRBase human miRNAs with Blat. The aligned reads were then normalized to RPM counts (reads per million reads). For microbiome analysis, the reads were mapped using Kraken2 with standard Kraken2 reference database.
Assembly: NCBI RefSeq, miRBase
Supplementary files format and content: Tab-delimited text files containing normalized read count values for individual samples

source_name: Microvesicles

extract_protocol:
Total RNA was extracted from four saliva fractions by miRNeasy micro kit with the addition of glycogen and a second round of chloroform.
Small RNA libraries were prepared for sequencing using NEBNext small RNA-seq library preparation kit.

treatment_protocol:
RNAlater was added during saliva collection.
EXO and MV were isolated by differential ultracentrifugation according to the standard protocols.

value: Microvesicles

tag: disease state

value: healthy


title: Microvesicles sample 10

description:
RNA-seq read counts combined from two sequencing runs
MV10


title: Microvesicles sample 6

description:
RNA-seq read counts combined from two sequencing runs
MV6


title: org16_par_rep2

tag: sample type

tag: batch

value: iPSC-derived cerebral organoid

value: trisomic


title: Exosome sample 10

description:
RNA-seq read counts combined from two sequencing runs
EXO10

source_name: Exosome

tag: tissue

value: Exosome


title: Microvesicles sample 8

description:
RNA-seq read counts combined from two sequencing runs
MV8


title: Microvesicles sample 1

description:
RNA-seq read counts combined from two sequencing runs
MV1


title: HeLa Fractionation Exp 4 Chrom Rep 1

value: HeLa S3

value: chromatin

value: Rep 1


title: mTEChi, AireKO, rep1

description:
Aire_20
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: MHCII-high epitherial cells

tag: age

tag: Sex


title: HeLa Fractionation Exp 4 Nuc Rep 2

tag: cell line

value: untreated

value: nucleoplasm

value: Rep 2


title: Exosome sample 9

description:
RNA-seq read counts combined from two sequencing runs
EXO9


title: Exosome sample 8

description:
RNA-seq read counts combined from two sequencing runs
EXO8


title: org16_disB_rep1

value: disB

tag: cell type

tag: genotype

value: disomic


title: Exosome sample 6

description:
RNA-seq read counts combined from two sequencing runs
EXO6


title: HeLa Fractionation Exp 4 Cyto Rep 2

value: cytoplasm


title: EV-Depleted saliva sample 10

description:
RNA-seq read counts combined from two sequencing runs
EVD10

source_name: EV-Depleted saliva

value: EV-Depleted saliva


title: Exosome sample 1

description:
RNA-seq read counts combined from two sequencing runs
EXO1


title: org16_disA_rep2

value: expanded

value: pooled organoids

value: disA


title: Microvesicles sample 9

description:
RNA-seq read counts combined from two sequencing runs
MV9

value: Microvesicles

value: healthy


title: EV-Depleted saliva sample 9

description:
RNA-seq read counts combined from two sequencing runs
EVD9


title: HeLa Fractionation Exp 4 Cyto Rep 1


title: HeLa Fractionation Exp 3 Chrom Rep 2


title: EV-Depleted saliva sample 7

description:
RNA-seq read counts combined from two sequencing runs
EVD7


title: EV-Depleted saliva sample 6

description:
RNA-seq read counts combined from two sequencing runs
EVD6


title: EV-Depleted saliva sample 8

description:
RNA-seq read counts combined from two sequencing runs
EVD8


title: org16_dis_rep2

value: dis

value: iPSC-derived cerebral organoid


title: org16_disA_rep1


title: HeLa Fractionation Exp 3 Chrom Rep 1

value: HeLa S3

value: chromatin


title: org16_dis_rep1


title: HeLa Fractionation Exp 3 Nuc Rep 2


title: Cell-Free saliva sample 10

description:
RNA-seq read counts combined from two sequencing runs
CFS10

source_name: Cell-Free saliva

value: Cell-Free saliva


title: Cell-Free saliva sample 8

description:
RNA-seq read counts combined from two sequencing runs
CFS8


title: org15_parB_rep2

value: parB

value: trisomic


title: HeLa Fractionation Exp 3 Nuc Rep 1

value: untreated

value: nucleoplasm

value: Rep 1


title: EV-Depleted saliva sample 1

description:
RNA-seq read counts combined from two sequencing runs
EVD1


title: Cell-Free saliva sample 7

description:
RNA-seq read counts combined from two sequencing runs
CFS7


title: Exosome sample 7

description:
RNA-seq read counts combined from two sequencing runs
EXO7

value: Exosome


title: HeLa Fractionation Exp 4 Nuc Rep 1


title: org15_parB_rep1


title: Cell-Free saliva sample 6

description:
RNA-seq read counts combined from two sequencing runs
CFS6


title: HeLa Fractionation Exp 3 Cyto Rep 2

value: cytoplasm

value: Rep 2


title: org15_parA_rep1

value: expanded

value: pooled organoids

value: parA


title: org15_parA_rep2


title: Male_hPGCs_week_8_rep2

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
The sequencing quality of RNA-seq libraries were checked by FastQC (v0.11.5).
The adaptor sequences were removed by Flexbar (3.5.0) as specified by NEB (https://github.com/nebiolabs/nebnext-single-cell-rna-seq) with additional options (“--qtrim TAIL  --qtrim-format i1.8 -qt 20”) to remove low quality reads.
The pre-processed reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR (2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
Raw read counts per gene were extracted by the featureCounts function of the Subread package (1.6.2) using the default parameters.
Normalized read counts [log2(normalized counts +1)] and differentially expressed genes (absolute(log2(fold change)) > 2 and adjusted p-value < 0.05) were obtained using DEseq2 (1.26.0) in R (3.6.2) / Bioconductor (3.10.1).
Assembly: UCSC GRCh38/hg38
Supplementary files format and content: A tab-delimited text file containing raw read count per gene for all samples

source_name: human embryonic tissue

extract_protocol:
Cells were sorted directly into extraction buffer of PicoPure RNA Isolation Kit (Applied Biosystems) and RNA was extracted according to manufacturer’s protocol with on-column DNase I treatment (Qiagen 79254)
RNA-seq libraries were prepared from 3−10 ng of total RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England BioLabs) and by following providers’ instructions

value: human embryonic tissue

value: human PGC

value: Wild type


title: HeLa Fractionation Exp 3 Cyto Rep 1

value: HeLa S3


title: CI-Treated_HADF_D1

city: Pittsburgh

first: Chandan

middle: K

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Quality control, clustering and differential gene expression analysis were performed using Seurat v.3.1.1
Trajectory inference and pseudotime calculations were performed using Monocle v.1.10.1
Assembly: hg:38
Supplementary files format and content: barcode files
Supplementary files format and content: gene names file
Supplementary files format and content: count matrix file

source_name: cultured cells

growth_protocol: Primary human adult dermal fibroblasts (ATCC, Manassas, VA, cat. no. PCS-201-012) were expanded in fibroblast basal medium (ATCC cat. no. PCS-201-030) supplemented with fibroblast growth kit-serum-free (ATCC, cat. no. PCS-201-040) containing Penicillin-Streptomycin (10,000 U/mL) solution (GibcoTM/Life Technologies, Waltham, MA, cat. no. 15140122) at 37°C in humidified chamber consisting of 95% air and 5% CO2.

extract_protocol:
Single cells were isolated from cultured cells (untreated HADF MI treated HADF cells at d1, d3, d5 and d7) and kept in 1XHBSS with 0.04%BSA until single cell cDNA synthesis. Single cells were encapsulated for NEXT GEMs preparation using barcoded beads and cDNA synthesis using the Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics).
library construction was done according to the manufacturer’s recommendations  (10X Genomics)

treatment_protocol: In vitro nanoelectroporation was conducted via 3D Nanochannel Electroporation (NEP) as described previously (Gallego-Perez et al., 2016). Briefly, the cells were first grown to full confluency overnight on the 3D NEP device. Subsequently, a pulsed electric field was used to deliver control (CI, 50nM) or miR-200b inhibitor (MI, 50nM) into the cells. The cells were then harvested 24 h after miRNA delivery, placed in EBM-2 basal medium (Lonza, cat. no. CC-3156) supplemented with EGM-2 MV SingleQuot kit components (Lonza, cat. no. CC-4147) and processed further for single cell RNA sequencing at diffrent time-points.

value: human adult dermal fibroblasts (HADF)

value: miRIDIAN microRNA hairpin inhibitor negative control; control inhibitor, CI

tag: timepoint


title: CI-Treated_HADF_D7


title: HeLa Fractionation Exp 2 Chrom Rep 2

tag: fraction

value: chromatin


title: Male_hPGCs_week_6_rep1


title: org15_par_rep1

source_name: par

value: par

value: iPSC-derived cerebral organoid

value: trisomic


title: Male_hPGCs_week_8_rep1


title: org15_par_rep2


title: HeLa Fractionation Exp 2 Chrom Rep 1

value: untreated

tag: pulldown reagent

value: Rep 1


title: Cell-Free saliva sample 9

description:
RNA-seq read counts combined from two sequencing runs
CFS9

value: Cell-Free saliva

value: healthy


title: Resetting_hPGCLCs_tt2iGoXAV_TBXT_KO_rep1

source_name: hESC-derived

value: hESC-derived

value: hPGCLC

value: TBXT knockout

value: hPGCLC differentiation


title: org16_disB_rep2

value: expanded

value: pooled organoids

value: disB

value: disomic


title: Resetting_hPGCLCs_tt2iGoXAV_TBXT_KO_rep2


title: org15_disB_rep1


title: Resetting_hPGCLCs_tt2iGoXAV_rep1

value: Wild type


title: Cell-Free saliva sample 1

description:
RNA-seq read counts combined from two sequencing runs
CFS1


title: HeLa Fractionation Exp 2 Nuc Rep 2

value: HeLa S3

value: nucleoplasm

tag: labeling time

value: Rep 2


title: Resetting_hPGCLCs_tt2iGoXAV_rep2


title: Resetting_precursors_tt2iGoXAV_passage_3_rep2

value: hPGCLC precursor

value: Resetting (tt2iGöXAV)


title: HeLa Fractionation Exp 2 Cyto Rep 2

value: untreated

value: cytoplasm

tag: replicate


title: org15_disA_rep2

value: disA

value: iPSC-derived cerebral organoid


title: Resetting_hPGCLCs_tt2iGoXAV_EOMES_KO_rep4

value: hESC-derived

value: hPGCLC

value: EOMES knockout

tag: treatment


title: Resetting_hPGCLCs_tt2iGoXAV_EOMES_KO_rep3

value: hPGCLC differentiation


title: HeLa Fractionation Exp 2 Cyto Rep 1

value: Rep 1


title: org15_dis_rep2

source_name: dis

value: expanded

value: pooled organoids

value: dis


title: Resetting_hPGCLCs_tt2iGoXAV_hindgut_day_25_rep3

value: co-cultured hPGCLC

value: Wild type

value: Hindgut co-culture


title: Resetting_hPGCLCs_tt2iGoXAV_EOMES_KO_rep1


title: org15_disA_rep1

value: disomic


title: Resetting_hPGCLCs_tt2iGoXAV_EOMES_KO_rep2


title: Resetting_hPGCLCs_tt2iGoXAV_TBXT_KO_rep3

value: TBXT knockout


title: HeLa Fractionation Exp 2 Nuc Rep 1

value: HeLa S3

value: untreated

value: nucleoplasm


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_35_rep4

value: ovarian somatic cells co-culture


title: org15_disB_rep2

value: disB

value: iPSC-derived cerebral organoid


title: org15_dis_rep1


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_35_rep3

value: hESC-derived


title: HeLa Fractionation Exp 1 Nuc Rep 1


title: Resetting_hPGCLCs_tt2iGoXAV_hindgut_day_25_rep1


title: Microvesicles sample 5

description:
RNA-seq read counts combined from two sequencing runs
MV5

value: Microvesicles

value: healthy


title: HeLa Fractionation Exp 1 Nuc Rep 2

value: Rep 2


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_35_rep2


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_35_rep1


title: HeLa Fractionation Exp 1 Chrom Rep 1

value: chromatin

value: Rep 1


title: HeLa Fractionation Exp 1 Cyto Rep 2

value: cytoplasm


title: Microvesicles sample 4

description:
RNA-seq read counts combined from two sequencing runs
MV4


title: Resetting_hPGCLCs_HENSM_TBXT_KO_rep3

value: hPGCLC

value: hPGCLC differentiation


title: Microvesicles sample 3

description:
RNA-seq read counts combined from two sequencing runs
MV3


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_25_rep2

value: co-cultured hPGCLC

value: Wild type


title: HeLa Fractionation Exp 1 Cyto Rep 1

value: HeLa S3


title: Resetting_precursors_tt2iGoXAV_ovarian_somatic_cells_day_25_rep1


title: Resetting_hPGCLCs_HENSM_TBXT_KO_rep2

value: TBXT knockout


title: Microvesicles sample 2

description:
RNA-seq read counts combined from two sequencing runs
MV2


title: Resetting_hPGCLCs_tt2iGoXAV_hindgut_day_25_rep2

value: Hindgut co-culture


title: HeLa Fractionation Exp 1 Chrom Rep 2

value: untreated


title: ISC3

city: Osaka

first: Akinobu

last: Suzuki

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Orthopaedic surgery

institute: Osaka Metropolitan University

data_processing:
Sequence data were mapped on the Rabbit genome (Apr. 2009 (Broad/oryCun2) ) using Tophat and analyzed by R.
Assembly: Apr. 2009 (Broad/oryCun2)

organism: Oryctolagus cuniculus

source_name: Ligamentum flavum

extract_protocol:
Total RNA was extracted with QIAzol Lysis Reagent and the RNeasy Plus Universal Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturers’ protocol. 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (San Diego, CA)  following manufacturer's protocols.

treatment_protocol: Eighteen-week-old male rabbits underwwent resection of the L3-4 supraspinal muscle and L2-3, L4-5 posterolateral fusion with instrumentation.

value: Ligamentum flavum

tag: strain

value: New Zealand white rabbit

value: 70 weeks old

value: Male

value: ISC load


title: Exosome sample 5

description:
RNA-seq read counts combined from two sequencing runs
EXO5

value: Exosome

value: healthy


title: ISC2


title: Resetting_hPGCLCs_HENSM_rep2

value: hESC-derived


title: Resetting_hPGCLCs_HENSM_TBXT_KO_rep1


title: HeLa Splicing Inhibition PlaB Rep 1

source_name: HeLa Nuclei Splicing Inhibition

value: 100 nM Pladienolide B 3 h

value: nuclei

value: 3 h

value: Rep 1


title: Exosome sample 4

description:
RNA-seq read counts combined from two sequencing runs
EXO4


title: ISC1


title: Fused3

value: Fused


title: HeLa Splicing Inhibition Ctrl Rep 2

value: HeLa S3

value: Rep 2


title: HeLa Splicing Inhibition Ctrl Rep 1


title: Exosome sample 2

description:
RNA-seq read counts combined from two sequencing runs
EXO2


title: Resetting_hPGCLCs_HENSM_EOMES_KO_rep4

value: hPGCLC

value: EOMES knockout

value: hPGCLC differentiation


title: Exosome sample 3

description:
RNA-seq read counts combined from two sequencing runs
EXO3


title: EV-Depleted saliva sample 5

description:
RNA-seq read counts combined from two sequencing runs
EVD5

value: EV-Depleted saliva


title: Resetting_hPGCLCs_HENSM_EOMES_KO_rep3


title: Resetting_hPGCLCs_HENSM_EOMES_KO_rep2


title: HeLa SLAM 180 min 4SU Rep 1

source_name: HeLa SLAM-seq

value: 500 uM 4-thiouridine 180 min

value: whole cell

value: 180 min


title: EV-Depleted saliva sample 4

description:
RNA-seq read counts combined from two sequencing runs
EVD4


title: Fused1

value: Ligamentum flavum

value: New Zealand white rabbit

value: 70 weeks old

value: Male


title: Resetting_hPGCLCs_HENSM_rep1

value: hESC-derived

value: Wild type


title: HeLa SLAM 90 min 4SU Rep 2

value: 500 uM 4-thiouridine 90 min

value: 90 min


title: EV-Depleted saliva sample 3

description:
RNA-seq read counts combined from two sequencing runs
EVD3

value: healthy


title: Cotrol2

value: Sham operation


title: HeLa Splicing Inhibition PlaB Rep 2

value: HeLa S3

value: 100 nM Pladienolide B 3 h

value: nuclei

value: 3 h

value: Rep 2


title: Fused2

value: Fused


title: Resetting_hPGCLCs_HENSM_hindgut_day_25_rep3

value: co-cultured hPGCLC

value: Hindgut co-culture


title: EV-Depleted saliva sample 2

description:
RNA-seq read counts combined from two sequencing runs
EVD2

value: EV-Depleted saliva


title: HeLa SLAM 0 min 4SU Rep 2

value: untreated

value: whole cell

value: 0 min


title: Cell-Free saliva sample 5

description:
RNA-seq read counts combined from two sequencing runs
CFS5

value: Cell-Free saliva


title: Resetting_hPGCLCs_HENSM_hindgut_day_25_rep2

value: hESC-derived

value: Wild type


title: Mouse Brain Fractionation Cyto Rep 2

source_name: Mouse Brain Fractionation

value: brain

value: cytoplasm


title: HeLa SLAM 180 min 4SU Rep 2

value: HeLa S3

value: 500 uM 4-thiouridine 180 min

value: 180 min


title: HeLa SLAM 90 min 4SU Rep 1

value: 500 uM 4-thiouridine 90 min

value: 90 min

value: Rep 1


title: HeLa SLAM 0 min 4SU Rep 1


title: Cell-Free saliva sample 4

description:
RNA-seq read counts combined from two sequencing runs
CFS4

value: healthy


title: Cell-Free saliva sample 3

description:
RNA-seq read counts combined from two sequencing runs
CFS3


title: Mouse Brain Fractionation Cyto Rep 1


title: Peri-gastrulation_hPGCLCs_PreME_TBXT_KO_rep3

value: hPGCLC

value: TBXT knockout

value: hPGCLC differentiation


title: HEK 4SU PD 5 90 min PD

source_name: HEK Pulldown

value: Flp-In T-REx 293 cell line

value: 1 mM 4-thiouridine 90 min

value: whole cell

value: MyOne Streptavidin C1 beads


title: Control3

value: Ligamentum flavum

value: New Zealand white rabbit

value: 70 weeks old

value: Male

value: Sham operation


title: Mouse Brain Fractionation Nuclei Rep 2

value: brain

value: untreated

value: nuclei

value: Rep 2


title: Cell-Free saliva sample 2

description:
RNA-seq read counts combined from two sequencing runs
CFS2

value: Cell-Free saliva

value: healthy


title: HEK 4SU PD 5 45 min PD

value: 1 mM 4-thiouridine 45 min

value: 45 min

value: Rep 1


title: Peri-gastrulation_hPGCLCs_PreME_TBXT_KO_rep2

value: hESC-derived

value: hPGCLC

value: TBXT knockout

value: hPGCLC differentiation


title: HEK 4SU PD 8 20 min SN

value: Flp-In T-REx 293 cell line

value: 1 mM 4-thiouridine 20 min

value: whole cell

value: MyOne Streptavidin C1 beads

value: 20 min


title: Mouse Brain Fractionation Nuclei Rep 1

value: brain

value: untreated


title: Peri-gastrulation_hPGCLCs_PreME_TBXT_KO_rep1


title: Cotrol1

value: Ligamentum flavum

value: New Zealand white rabbit

value: 70 weeks old

value: Male

value: Sham operation


title: Peri-gastrulation_hPGCLCs_PreME_hindgut_day_25_rep3

value: co-cultured hPGCLC

value: Wild type

value: Hindgut co-culture


title: HEK 4SU PD 8 20 min PD

value: Rep 1


title: 24: DIF_siRSL24D1_RESCUE_R3

city: LYON

first: Mathieu

last: GABUT

address: 28 rue laennec

department: Cancer Initiation and Tumor cell Identity

country: France

institute: Cancer Research Centre of Lyon, Inserm U1052

description: siRSL24D1 RA +Dox R3

data_processing:
Raw sequencing reads were aligned on the murin genome (mm38) with STAR (v2.7.8a), with the annotation of known genes from gencode vM25.
Gene expression was quantified using Salmon (1.4.0),the murin genome (grchm38) , and the annotation of protein coding genes from gencode vM25
Assembly: GRCh38
Supplementary files format and content: txt file with normalized expression (log2(TPM+1)) from salmon for each sample

growth_protocol: CGR8 cells were seeded in 6 well plates pre-coated with 0.2% gelatin and cultivated in DMEM media containing 10% of FBS (ESC quality) and exogenous LIF.

extract_protocol:
Cells were harvested in 1ml of TRIzol reagent and total RNA was extracted according to manufacturer’s instructions. RNA was quantified and integrity was mesured by optic density using a 2100 BioAnalyzer
Libraries were prepared with the TrueSeq poly-A+ kit from Illumina

treatment_protocol: Cells were transfected with siRNAs and collected after 72h for total RNA extraction or seeded for RA (retinoic acid) induced differentiation. After 4 days of 10 nM RA treatment, cells were collected and total RNA extracted.

tag: vector

value: siRSL24D1+ FBS+RA+Dox

value: mouse embryonic stem cell line


title: Notch_Inhibition 3

city: NYC

first: Nicole

last: Dubois

state: NY

address: 1740 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using STAR 2.5.0a aligner with parameters --outSAMtype BAM   SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000
Removed duplicates using Picard MarkDuplicates 1.112(1930) with parameters REMOVE_DUPLICATES=true , ASSUME_SORTED=true, VALIDATION_STRINGENCY=SILENT, CREATE_INDEX=true
Counted the raw reads using HTSeq 0.6.0
Performed differential expression analysis using DESeq2
Genome_build: hg19, gencode.v19
Supplementary_files_format_and_content: htseq-count

source_name: Day 30 hESC-derived cardiomyocytes; DAPT treated day 5-6 to inhibit Notch signaling

extract_protocol:
Zymo Research RNA microprep
Ribo Zero

tag: differentiation protocol

value: hESCs differentiated as embryoid bodies until day 30

value: hESCs harboring a ROSA26-driven NOTCH1 ICD-ER fusion

value: Day 30 hESC-derived cardiomyocytes


title: Ctrl_Fibroblast

source_name: Day 30 hESC-derived fibroblasts; control

value: Day 30 hESC-derived fibroblasts

value: control


title: Peri-gastrulation_hPGCLCs_PreME_hindgut_day_25_rep2

value: hESC-derived


title: Peri-gastrulation_hPGCLCs_PreME_rep2

value: hPGCLC

value: hPGCLC differentiation


title: Notch_Inhibition 1


title: Peri-gastrulation_hPGCLCs_PreME_rep1


title: HEK 4SU PD 8 15 min PD

value: Flp-In T-REx 293 cell line

value: 1 mM 4-thiouridine 15 min

value: whole cell

value: MyOne Streptavidin C1 beads

value: 15 min


title: 21: DIF_siControl_RESCUE_R3

description: siControl RA +Dox R3

value: siControl + FBS+RA+Dox


title: Notch_Induction 3

source_name: Day 30 hESC-derived cardiomyocytes; 4OHT treated day 5-6 to induce Notch signaling


title: 22: DIF_siRSL24D1_RESCUE_R1

description: siRSL24D1 RA +Dox R1


title: Peri-gastrulation_hPGCLCs_PreME_hindgut_day_25_rep1

value: co-cultured hPGCLC

value: Wild type

value: Hindgut co-culture


title: HEK 4SU PD 8 15 min SN

value: Rep 1


title: HEK 4SU PD 8 10 min SN

value: 1 mM 4-thiouridine 10 min

value: 10 min


title: 20: DIF_siControl_RESCUE_R2

description: siControl RA +Dox R2

value: mouse embryonic stem cell line


title: HEK 4SU PD 8 0 min SN

value: untreated

value: 0 min


title: 18: DIF_siRSL24D1_nores_R3

description: siRSL24D1 RA -Dox R3

value: siRSL24D1 + FBS+RA


title: HEK 4SU PD 8 10 min PD


title: Notch_Inhibition 2

value: hESCs differentiated as embryoid bodies until day 30

value: hESCs harboring a ROSA26-driven NOTCH1 ICD-ER fusion

value: Day 30 hESC-derived cardiomyocytes


title: 19: DIF_siControl_RESCUE_R1

description: siControl RA +Dox R1


title: Notch_Induction 1


title: Capacitating_hPGCLCs_rep3

value: hESC-derived

value: hPGCLC

value: hPGCLC differentiation


title: Capacitating_hPGCLCs_rep2


title: 17: DIF_siRSL24D1_nores_R2

description: siRSL24D1 RA -Dox R2


title: Capacitating_hPGCLCs_rep1


title: Ctrl_CM 3

source_name: Day 30 hESC-derived cardiomyocytes; control

value: control


title: Resetting_hPGCLCs_HENSM_EOMES_KO_rep1

value: EOMES knockout


title: HEK293FT_AptaChC-seq_RBPJ_rep2

city: Hefei

first: Xucong

last: Teng

address: No. 96, Jinzhai Road

department: Hefei National Laboratory of Physical Science at Microscale

institute: University of Science and Technology of China

description: RBPJ aptamer conjugated BAMEA-Tn5 was used.

data_processing:
[Trimming] Raw reads were trimmed with Trim Galore (version: 0.4.4).
[Read alignment] Trimmed reads were filtered for repeat elements using sequences obtained from RepBase (v26.08) with bowtie2 (v.2.3.5.1). Then reads were aligned with bowtie2 (v.2.3.5.1) using -I 25 -X 500 -N 1 -L 25 and samtools (v1.10).
[Deduplication] BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[Genome coverage] Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
[Peak calling] Peaks were called using MACS2 callpeak using parameters --nomodel --nolambda -q 0.05
Assembly: hg19
Supplementary files format and content: Normalized genomic tracks in BigWig format

source_name: human cell line

growth_protocol: HEK293FT cells, HEK293FT-FOXM1-Knockout cells, MCF-7 cells and MCF-10A cells were obtained from National Infrastructure of Cell Line Resource (NICLR, China). The cell lines were checked free of mycoplasma contamination by PCR. Their species origins were confirmed with PCR. The identity of the cell line was authenticated with STR profiling (FBI, CODIS). All the results can be viewed on the website (http://cellresource.cn). HEK293FT cells, HEK293FT-FOXM1-Knockout cells, MCF-7 cells were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Macklin) at 37 °C/5% CO2. MCF-10A cells were maintained in MCF-10A culture medium(Procell).

extract_protocol:
AptaChC-seq
The cells were fixed using 0.5% PFA for 2 min at RT, and then quenched by 0.125 M glycine for 2 min at RT. The fixed cells were washed with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine) for 3 times and resuspended in wash buffer. Next, 5K-100K cells were immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at RT for 10 min. The beads-bound cells were incubated in 50 μl of blocking buffer (wash buffer with 2 mM EDTA, 0.1% BSA, 100 nM random ssDNA and 0.05% digitonin) at RT by rotating for 20 min. Then the blocking buffer was removed. The incubated cells were then resuspended with 100 ul of Tn5 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine and 0.01% Digitonin) with 100 nM BAMEA-Tn5 and incubated at room temperature for 0.5 hour by rotating. Then the BAMEA-Tn5 buffer was removed. BAMEA-Tn5-bound cells were washed with 500 ul of Tn5 buffer twice, followed by tagmentation in 25 ul of tagmentation buffer (Tn5 buffer with 10 mM MgCl2) at 37℃ for 0.5 hour. Then 25 uL of 100 nM MEB-Tn5 in 20 mM HEPES pH 7.5 was added to the mixture and further incubated for 0.5 h. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. Then the DNA fragments were extracted by streptavidin magnetic beads.
Purified genomic DNA from AptaChC-seq were mixed with the universal i5 primer and barcoded i7 primer, and amplified with 5X Ampli PCR Mix (Novoprotein, Shanghai). The library PCR products were cleaned up with DNA Clean Beads (Vazyme, Nanjing).
OTHER：AptaChC-seq

value: HEK293FT cell line


title: 23: DIF_siRSL24D1_RESCUE_R2

description: siRSL24D1 RA +Dox R2

value: siRSL24D1+ FBS+RA+Dox


title: Resetting_hPGCLCs_HENSM_hindgut_day_25_rep1

value: co-cultured hPGCLC

value: Wild type

value: Hindgut co-culture


title: Notch_Induction 2


title: Ctrl_CM 2


title: 16: DIF_siRSL24D1_nores_R1

description: siRSL24D1 RA -Dox R1

value: mouse embryonic stem cell line


title: Peri-gastrulation_hPGCLCs_4i_TBXT_KO_rep3

value: TBXT knockout


title: Ctrl_CM 1


title: HEK293FT_AptaChC-seq_RELA_rep2

description: RELA aptamer conjugated BAMEA-Tn5 was used.


title: 15: DIF_siControl_nores_R3

description: siControl RA -Dox R3

value: siControl + FBS+RA


title: HEK 4SU PD 8 0 min PD

value: Flp-In T-REx 293 cell line

value: untreated

value: whole cell

value: MyOne Streptavidin C1 beads

value: 0 min

value: Rep 1


title: Hematopoietic Mesoderm 1

data_processing:
Illumina Casava1.8 software used for basecalling
RNA-seq reads were aligned to the mm10 genome assembly using STAR 2.5.0a_alpha aligner with parameters --outSAMtype BAM   SortedByCoordinate, --outSAMstrandField intronMotif, --outSAMattributes All
Removed duplicates using Picard MarkDuplicates 1.112(1930) with parameters REMOVE_DUPLICATES=true , ASSUME_SORTED=true, VALIDATION_STRINGENCY=SILENT, CREATE_INDEX=true
Counted the raw reads using HTSeq 0.6.0
Performed differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: htseq-count

source_name: Embryonic Hematopoietic mesoderm (KDR+)

extract_protocol:
Agilent Absolutely RNA nanoprep kit
NuGEN Ovation Ultralow V2 and RNA-seq system V2

tag: developmental stage

tag: mouse line

value: Embryonic Hematopoietic mesoderm (KDR+)


title: 13: DIF_siControl_nores_R1

description: siControl RA -Dox R1


title: Peri-gastrulation_hPGCLCs_4i_TBXT_KO_rep1

tag: tissue

value: hESC-derived

value: hPGCLC

value: hPGCLC differentiation


title: Hematopoietic Mesoderm 2


title: Peri-gastrulation_hPGCLCs_4i_hindgut_day_25_rep1


title: Peri-gastrulation_hPGCLCs_4i_hindgut_day_25_rep2


title: Peri-gastrulation_hPGCLCs_4i_TBXT_KO_rep2


title: HEK293FT_AptaChC-seq_RBPJ_rep1

value: HEK293FT cell line


title: MCF-10A_ATAC-seq_rep2

extract_protocol:
standard ATAC-seq protocol(Nat Methods 2017, 14 (10), 959-962.)
ATAC-seq
The cells were fixed using 0.5% PFA for 2 min at RT, and then quenched by 0.125 M glycine for 2 min at RT. The fixed cells were washed with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine) for 3 times and resuspended in wash buffer. Next, 5K-100K cells were immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at RT for 10 min. The beads-bound cells were incubated in 50 μl of blocking buffer (wash buffer with 2 mM EDTA, 0.1% BSA, 100 nM random ssDNA and 0.05% digitonin) at RT by rotating for 20 min. Then the blocking buffer was removed. The incubated cells were then resuspended with 100 ul of Tn5 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine and 0.01% Digitonin) with 100 nM BAMEA-Tn5 and incubated at room temperature for 0.5 hour by rotating. Then the BAMEA-Tn5 buffer was removed. BAMEA-Tn5-bound cells were washed with 500 ul of Tn5 buffer twice, followed by tagmentation in 25 ul of tagmentation buffer (Tn5 buffer with 10 mM MgCl2) at 37℃ for 0.5 hour. Then 25 uL of 100 nM MEB-Tn5 in 20 mM HEPES pH 7.5 was added to the mixture and further incubated for 0.5 h. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. Then the DNA fragments were extracted by streptavidin magnetic beads.
Purified genomic DNA from AptaChC-seq were mixed with the universal i5 primer and barcoded i7 primer, and amplified with 5X Ampli PCR Mix (Novoprotein, Shanghai). The library PCR products were cleaned up with DNA Clean Beads (Vazyme, Nanjing).
OTHER：AptaChC-seq

value: MCF-10A cell line


title: Endoderm 3

source_name: Embryonic endoderm (EPCAM+)

value: Embryonic endoderm (EPCAM+)


title: 14: DIF_siControl_nores_R2

description: siControl RA -Dox R2


title: MCF-10A_AptaChC-seq_FOXM1_rep2

description: FOXM1 aptamer conjugated BAMEA-Tn5 was used.


title: 12: ESC_siRSL24D1_RESCUE_R3

description: siRSL24D1 48h +Dox R3

value: siRSL24D1+ FBS/LIF+Dox


title: Endoderm 2


title: MCF-10A_ATAC-seq_rep1


title: 11: ESC_siRSL24D1_RESCUE_R2

description: siRSL24D1 48h +Dox R2

value: mouse embryonic stem cell line


title: Peri-gastrulation_hPGCLCs_4i_ovarian_somatic_cells_day_35_rep2

value: co-cultured hPGCLC

value: Wild type

value: ovarian somatic cells co-culture


title: 10: ESC_siRSL24D1_RESCUE_R1

description: siRSL24D1 48h +Dox R1


title: Peri-gastrulation_hPGCLCs_4i_ovarian_somatic_cells_day_35_rep1


title: MCF-10A_AptaChC-seq_FOXM1_rep1


title: Hematopoietic Mesoderm 3


title: Endoderm 1


title: HEK293FT_AptaChC-seq_RELA_rep1


title: MCF-7_ATAC-seq_rep2

value: MCF-7 cell line


title: Peri-gastrulation_hPGCLCs_4i_rep2


title: MCF-7_ATAC-seq_rep1


title: Peri-gastrulation_hPGCLCs_4i_rep1


title: Cardiac mesoderm, Foxa2Cre:YFP- 3

source_name: Embryonic non-ventricular cardiac mesoderm


title: Cardiac mesoderm, Foxa2Cre:YFP- 2

value: Embryonic non-ventricular cardiac mesoderm


title: Resetting_precursors_tt2iGoXAV_passage_3_rep1

value: hPGCLC precursor

value: Resetting (tt2iGöXAV)


title: Cardiac mesoderm, Foxa2Cre:YFP- 1


title: Cardiac mesoderm, Foxa2Cre:YFP+ 3

source_name: Embryonic ventricular cardiac mesoderm

value: Embryonic ventricular cardiac mesoderm


title: 6: ESC_siRSL24D1_nores_R3

description: siRSL24D1 48h -Dox R3

value: siRSL24D1+ FBS/LIF


title: Resetting_precursors_tt2iGoXAV_passage_1_rep2

value: hESC-derived


title: 5: ESC_siRSL24D1_nores_R2

description: siRSL24D1 48h -Dox R2


title: Cardiac mesoderm, Foxa2Cre:YFP+ 2


title: MCF-7_AptaChC-seq_FOXM1_rep2


title: Naive_hESCs_tt2iGoXAV_rep2

value: hESC


title: HEK293FT-FOXM1-Knockout_AptaChC-seq_FOXM1_rep2

value: HEK293FT cell line with FOXM1 gene knockdown


title: Cardiac mesoderm, Foxa2Cre:YFP+ 1


title: Resetting_precursors_tt2iGoXAV_passage_1_rep1


title: 4: ESC_siRSL24D1_nores_R1

description: siRSL24D1 48h -Dox R1


title: 3: ESC_siControl_nores_R3

description: siControl 48h -Dox R3

value: siControl + FBS/LIF


title: 9: ESC_siControl_RESCUE_R3

description: siControl 48h +Dox R3

value: siControl + FBS/LIF+Dox


title: 8: ESC_siControl_RESCUE_R2

description: siControl 48h +Dox R2


title: 2: ESC_siControl_nores_R2

description: siControl 48h -Dox R2


title: HEK293FT_CUT&Tag_NegativeIgG_rep2

description: Rabbit negative control IgG was used.

extract_protocol:
standard CUT&Tag protocol (Nat Protoc 2020, 15 (10), 3264-3283.)
CUT&Tag
The cells were fixed using 0.5% PFA for 2 min at RT, and then quenched by 0.125 M glycine for 2 min at RT. The fixed cells were washed with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine) for 3 times and resuspended in wash buffer. Next, 5K-100K cells were immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at RT for 10 min. The beads-bound cells were incubated in 50 μl of blocking buffer (wash buffer with 2 mM EDTA, 0.1% BSA, 100 nM random ssDNA and 0.05% digitonin) at RT by rotating for 20 min. Then the blocking buffer was removed. The incubated cells were then resuspended with 100 ul of Tn5 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine and 0.01% Digitonin) with 100 nM BAMEA-Tn5 and incubated at room temperature for 0.5 hour by rotating. Then the BAMEA-Tn5 buffer was removed. BAMEA-Tn5-bound cells were washed with 500 ul of Tn5 buffer twice, followed by tagmentation in 25 ul of tagmentation buffer (Tn5 buffer with 10 mM MgCl2) at 37℃ for 0.5 hour. Then 25 uL of 100 nM MEB-Tn5 in 20 mM HEPES pH 7.5 was added to the mixture and further incubated for 0.5 h. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. Then the DNA fragments were extracted by streptavidin magnetic beads.
Purified genomic DNA from AptaChC-seq were mixed with the universal i5 primer and barcoded i7 primer, and amplified with 5X Ampli PCR Mix (Novoprotein, Shanghai). The library PCR products were cleaned up with DNA Clean Beads (Vazyme, Nanjing).
OTHER：AptaChC-seq

value: HEK293FT cell line


title: Resetting_precursors_HENSM_rep2

value: Resetting (HENSM)


title: HEK293FT_CUT&Tag_NegativeIgG_rep1

description: Rabbit negative control IgG was used.


title: HEK293FT-FOXM1-Knockout_AptaChC-seq_FOXM1_rep1


title: 1: ESC_siControl_nores_R1

description: siControl 48h -Dox R1

value: mouse embryonic stem cell line


title: HEK293FT_AptaChC-seq_NegativeAptamer_rep2

description: Random ssDNA conjugated BAMEA-Tn5 was used.


title: 7: ESC_siControl_RESCUE_R1

description: siControl 48h +Dox R1


title: Resetting_precursors_HENSM_rep1


title: MCF-7_AptaChC-seq_FOXM1_rep1


title: Peri-gastrulation_precursors_PreME_rep2

value: PreME differentiation


title: Thrombopoietin hMSCs, biological rep4

type: RNA

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description: Gene expression data from human Mesenchymal Stem Cells (hMSCs)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G System

data_processing:
The data were analyzed with Transcriptome Analysis Console 4.0 (TAC) using Affymetrix default analysis settings and global scaling as normalization method. Gene Level was calculated using SST-RMA algoritm. The number of genes measured in the Clariom S array as probesets is 21448 and the array includes also  other 5741 probesets of control (in total 27189 probesets).
Gene Level - SST-RMA. Genome Version: hg38 (Homo sapiens)

label: biotin

source_name: human Mesenchymal Stem/Stromal Cells (hMSCs)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: MSCs were isolated from bone marrow (BM) from 4 healthy donors and seeded at 1X106 MNC/cm2 on culture flasks with DMEM + 10%SBF +1% Penicillin/Streptomycin. Cultured until 3rd passage at 37ºC, 5% CO2 in incubator.

extract_protocol: RNA was isolated and purified using RNeasy Kit, it was performed according to the manufacturer's instructions.

treatment_protocol: Eltrombopag was dissolved in sterile water at a concentration of 10 mM. MSCs were cultured with EP in a final concentration of (15μM-50μM) during 24 hours, whereas control cells were incubated with the same media without the Eltrombopag for the same periods.

value: bone marrow

value: Thrombopoietin


title: Eltrombopag 50uM hMSCs, biological rep4

value: human Mesenchymal Stem/Stromal Cells (hMSCs)

value: Eltrombopag 50uM


title: Peri-gastrulation_precursors_PreME_rep1

source_name: hESC-derived

value: hPGCLC precursor

value: Wild type


title: mTEChi, WT, rep3

description:
Aire_15
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

source_name: thymus

value: thymus

value: MHCII-high epitherial cells

value: WT

tag: age

value: male


title: mTEChi, WT, rep5

description:
Aire_17
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

tag: Sex

value: female


title: HEK293FT_ATAC-seq_rep1


title: mTEChi, WT, rep4

description:
Aire_16
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz


title: HEK293FT_CUT&Tag_FOXM1_rep3

description: Rabbit anti-FOXM1 antibody was used.


title: Naive_hESCs_tt2iGoXAV_rep1

value: hESC-derived

tag: cell line

value: hESC

value: Resetting (tt2iGöXAV)


title: Primed_hESCs_E8_rep2

tag: cell type


title: HEK293FT_ATAC-seq_rep2

value: HEK293FT cell line


title: Control hMSCs (no drug), biological rep4

value: Control


title: Eltrombopag 15uM hMSCs, biological rep4

value: Eltrombopag 15uM


title: HEK293FT_CUT&Tag_FOXM1_rep2

description: Rabbit anti-FOXM1 antibody was used.


title: mTEChi, WT, rep1

description:
Aire_13
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

tag: genotype


title: Capacitating_precursors_rep2

value: Capacitation (N2B27XAV)


title: HEK293FT_CUT&Tag_FOXM1_rep1

description: Rabbit anti-FOXM1 antibody was used.


title: Primed_hESCs_E8_rep1


title: Capacitating_precursors_rep1


title: mTEClo, WT, rep8

description:
Aire_8
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: MHCII-low epitherial cells


title: HEK293FT_AptaChC-seq_NegativeAptamer_rep1


title: HEK293FT_AptaChC-seq_FOXM1_rep2


title: mTEClo, WT, rep7

description:
Aire_7
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz


title: Thrombopoietin hMSCs, biological rep3

value: bone marrow

value: human Mesenchymal Stem/Stromal Cells (hMSCs)

value: Thrombopoietin


title: HEK293FT_AptaChC-seq_FOXM1_rep1


title: Peri-gastrulation_precursors_4i_rep1

value: hPGCLC precursor

value: Wild type


title: mTEClo, WT, rep6

description:
Aire_6
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: thymus


title: Eltrombopag 50uM hMSCs, biological rep3

value: Eltrombopag 50uM


title: non-metastasis 4

city: Jinan

first: Jing

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60掳C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarrays (8*60K) for 17 hours at 65掳C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37掳C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were scanned using an Agilent Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um . Dye channel was set to Green and Green PMT is set to 100%.

data_processing: The generated image files were analyzed using Agilent Feature Extraction Software (v 11.0.1.1). Using GemeSpring v12.1 software(Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: non-metastasis 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA Extraction was perforemd using TRIZOL following the manufacturer's recommendations.

tag: disease

value: disease:prostate cancer

tag: gleason

value: gleason:Gleason 3+4


title: mTEChi, WT, rep2

description:
Aire_14
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: MHCII-high epitherial cells

value: WT

value: male


title: mTEClo, WT, rep5

description:
Aire_5
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: female


title: Eltrombopag 15uM hMSCs, biological rep3


title: LvshGATM2

first: Jinshou

last: Yang

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng Distri

department: General Surgery

institute: Peking Union Medical College Hospital

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other style.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq was used for differential gene expression analysis between two samples with non-biological replicates.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: total_count.txt: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: fpkm.txt: Matrix table with FPKM values for every gene and every sample.

source_name: pancreatic cancer cell line

extract_protocol:
RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L) was used with 3 ug of total RNA for sequencing library construction.
RNA sequencing was performed by Illumina NovaSeq platform with PE150 strategy.

value: GATM knock-down


title: Thrombopoietin hMSCs, biological rep2


title: Eltrombopag 15uM hMSCs, biological rep2

value: Eltrombopag 15uM


title: S2

city: Changsha

first: fang

last: zhou

address: 283 Tongzipo Road, Yuelu District,

institute: hunan cancer hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: SKOV3 cells

extract_protocol:
Tumor tissue were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We experimentally stressed animals with a physical restraint system that Anil K Sood [PMID:16862152] designed firstly. Empty mouse restraint system is consist of 50ml  centrifuge tubes and had approximately 5 holes (u = 4 mm) at the bottom to ensure adequate ventilation. Sterilization of the experimental equipment was conducted daily. Briefly, after 1 week of habituation to the vivarium setting, animals received restraint stress for 2-4 h daily, and 12 h/12 h light / dark, respectively. We injected untreated SKOV3 ovarian cancer cells into nude mice peritoneal cavity after 2 weeks stressed, and  the periodic immobilization stress continued for 8 weeks. All mice were euthanized. The tumor was removed for further study.

value: Ovarian adenocarcinoma

tag: xenograft host

value: non-stressed nude mice


title: S1


title: mTEClo, WT, rep4

description:
Aire_4
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

extract_protocol:
Mouse thymus was enzymatically  digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria directly into tubes containing TCL buffer (QIAGEN)
RNA-seq libraries were prepared by applying a RamDA-seq method for single-cell RNA-seq (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018) with some modifications. Specifically, RNA was isolated using RNAClean XP beads (x2.2 vol., Beckman Coulter) directly from the lysis buffer, and was eluted into 10 uL of water containing RNase inhibitor (4u/uL RNasinPlus RNase Inhibitor, Promega). The RNA was denatured by incubating at 65C for 5min, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 15min. Then cDNA was synthesized in 30uL of 1xRT Buffer containing RT Enzyme Mix (1.5uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (3.3uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 5uL of 10x NEB buffer2 (NEB), 1.25uL of dNTP mix (10mM each nt, NEB), 1.5uL of Klenow Fragment (3'→5' exo-, NEB), 5uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 7.25uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (x2 vol., Beckman Coulter) and quantified using Qubit (Qubit dsDNA HS Assay Kit, Invitrogen). Then ds-cDNA less than 1ng was applied for Tn5 tagmentation in a 25uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). DNA was purified using AMPure XP beads (x1.7 vol.) and amplified by 10~15 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.2 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: MHCII-low epitherial cells


title: Control hMSCs (no drug), biological rep3

value: bone marrow

value: human Mesenchymal Stem/Stromal Cells (hMSCs)

value: Control


title: mTEClo, WT, rep3

description:
Aire_3
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz


title: Peri-gastrulation_precursors_4i_rep2

value: hESC-derived

value: hPGCLC precursor

value: Wild type


title: S3


title: S6

treatment_protocol: We experimentally stressed animals with a physical restraint system that Anil K Sood [PMID:16862152] designed firstly. Empty mouse restraint system is consist of 50ml  centrifuge tubes and had approximately 5 holes (u = 4 mm) at the bottom to ensure adequate ventilation. Sterilization of the experimental equipment was conducted daily. Briefly, after 1 week of habituation to the vivarium setting, animals received restraint stress for 2-4 h daily, and 12 h/12 h light / dark, respectively. We injected untreated SKOV3 ovarian cancer cells into nude mice peritoneal cavity after 2 weeks stressed, and  the periodic immobilization stress continued for 8 weeks. All mice were euthanized. The tumor was

value: stressed nude mice


title: mTEClo, WT, rep2

description:
Aire_2
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: thymus


title: Eltrombopag 50uM hMSCs, biological rep2

value: Eltrombopag 50uM


title: S5


title: Thrombopoietin hMSCs, biological rep1

value: Thrombopoietin


title: Control hMSCs (no drug), biological rep2


title: Lvcon3

value: normal control


title: LvshGATM3


title: LvshGATM1


title: Lvcon2


title: Eltrombopag 50uM hMSCs, biological rep1


title: mTEClo, WT, rep1

description:
Aire_1
AireKO.raw.cnt.csv.gz
AireKO.normalized.csv.gz

value: WT

value: male


title: Lvcon1


title: S4


title: Young Blood 2

status: Public on Jan 06 2023

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

description: 10x chromium 3' gene expression

data_processing:
The Cell Ranger Single Cell Software Suite 2.1.0 was used to perform single cells demultiplexing and UMI counting (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). The transcriptome reference used was mm10. Subsequently, the duplicates from young and old mice, respectively, were aggregated using Cellranger aggr. Cells that have more than 500 genes detected and less than 10% of mitochondrial reads were included in the downstream analysis using Seurat 2.3.0 . Young and old UMI counts were merged using the MergeSeurat function. Default parameters of Seurat was used in the analysis, unless otherwise stated. 1080 highly variable genes were used as an input for PCA. T-SNE projection and clustering analysis (dims=1:30 and resolution=0.4) were performed using Seurat. Markers genes for each cluster were found using the FindConservedMarkers function and the changes with age within each cell type were identified using the FindMarkers function.
Genome_build: mm10
Supplementary_files_format_and_content: Blood_UMI.txt contains UMI counts from 10x dataset and Blood_metadata.txt contains the metadata for the UMI counts

source_name: peripheral blood

growth_protocol: C57BL/6 female 4 month and 24 month mice were obtained from the National Institute of Aging (NIA). They were fed ad libitum and kept in standard housing conditions.

extract_protocol:
Blood samples were drawn from four young and four old mice. Samples from two mice within each age group were pooled, resulting in two pooled young and two pooled old samples. Subsequently, the pooled samples were diluted 1:1 with PBS+2% FBS and loaded into SepMate-15™ tubes with 4.5 mL of LymphoprepTM with a density of 1.077g/mL (StemCell Technologies). Cells were centrifuged at 1200x g for 20min at 4℃. The top layer was collected and centrifuged at 300xg for 8 min. Supernatant was removed and cells were resuspended in PBS + 2% FBS and this step was repeated. Subsequently, red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi Biotec) following the manufacturer’s protocol that includes the washing step.
Single-cell RNA-seq was performed using 10x Genomics 3' expression protocol

value: young

value: peripheral blood

tag: gender

value: female


title: Old Blood 2

description: 10x chromium 3' gene expression

value: old


title: Young Blood 1

description: 10x chromium 3' gene expression


title: Eltrombopag 15uM hMSCs, biological rep1

value: bone marrow

value: Eltrombopag 15uM


title: Control hMSCs (no drug), biological rep1

value: human Mesenchymal Stem/Stromal Cells (hMSCs)

value: Control


title: LCL65AW

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

description: total RNA extracted using Trizol.  mutant sample coming from Lymphoblastoid Cell Lines (LCL). RNA is in water, frost and conserved at -80 degree Celsius

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
For small RNA data analysis, adapters were trimmed from total reads using FASTX_Toolkit. Only trimmed reads with a length between 15 and 40 nucleotides were kept for further analysis.
Data analysis was performed according to published pipeline ncPRO-seq [https://www.ncbi.nlm.nih.gov/pubmed/23044543]. Briefly, reads were mapped onto the human genome assembly hg19 with Bowtie v1.0.0. The annotations for miRNAs were done with miRBase v21.
The normalization and comparisons of interest were performed using the test for differential expression, proposed by Love, M.I et al. and implemented in the Bioconductor package DESeq2 v1.22.2
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text files include raw expression values, normalized expression values, DESeq2 result for comparison mutant vs WT

source_name: Lymphoblastoid cell line (LCL)

growth_protocol: The cells were cultured in RPMI-1640 medium with L-glutamine and sodium bicarbonate (ref. R8758-500ML, SIGMA) supplemented with 10% FBS (Gibco) and 1% penicillin–streptomycin (ref. P0781, SIGMA) at 37 °C with 5%CO2.

extract_protocol:
Cells were split at ½ dilution approximately 24h before being collected for RNA extraction with TRI-Reagent (Sigma Aldrich) following the manufacturer’s instructions.
Small RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer’s instructions. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3’ RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5’ RNA adapter. Small RNA ligated with 3’ and 5’ adapters were reverse transcribed and PCR amplified (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 15 sec at 72°C] x 13 cycles; 10 min at 72°C) to create cDNA constructs. Amplified cDNA constructs of 20 to 40 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis and sequenced on the Illumina HiSeq 4000 at the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) GenomEast sequencing platform.

treatment_protocol: no treatment

value: LCL

value: FTSJ1 -/-


title: LCL22


title: LCL18

description: total RNA extracted using Trizol.  control (WT) sample coming from Lymphoblastoid Cell Lines (LCL). RNA is in water, frost and conserved at -80 degree Celsius

value: Wild Type


title: LCL16


title: LCL65JW


title: LCL54


title: LCL11


title: II8_C

city: Chengdu

first: Wei

last: Li

state: Sichuan

address: Department of Liver Surgery and Liver Transplantation Centre, West China Hospital, Sichuan University

description: C:tumor; F: adjacent liver; I: samples of the first surgery; II: samples from the recurrent surgery

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hepatocellular carcinoma

growth_protocol: Clinical sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Clinical sample

tag: tumor type

value: Recurrent

tag: sample type

value: tumor

tag: first or second surgery

value: second


title: II6_C

institute: Department of Liver Surgery and Liver Transplantation Centre, West China Hospital, Sichuan University


title: II7_C


title: Old Blood 1

description: 10x chromium 3' gene expression

tag: strain


title: II5_C


title: II4_F

value: adjacent liver


title: II9_C


title: II4_C


title: II3_F


title: II2_C


title: II3_C


title: II2_F


title: LCLMM


title: II17_C


title: II1_F


title: II16_C


title: II1_C


title: II18_C


title: II15_F


title: II15_C


title: II14_C


title: LCL25


title: II11_C


title: II12_F


title: II11_F


title: II10_C


title: II10_F


title: II12_C


title: I8_C

value: primary

value: first


title: I9_C


title: II13_C


title: I5_C


title: I7_C


title: I3_C


title: I2_C


title: I18_F


title: I1_C


title: I18_C


title: I6_C


title: I15_C


title: I16_C


title: I17_F


title: I17_C