title: APP_Microglia, IL33, 8hours, rep2 [scRNAseq_IL33_8h_2]

description: Ilumina NextSeq 500/NovaSeq 6000


title: Skin T cells at Day 14 (after transplantation) [RNA-seq_Skin_14_742]

status: Public on Sep 14 2023

type: SRA

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
For ATAC-seq low quality peaks such as blacklisted peaks were eliminated.
Assembly: hg38
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Supplementary files format and content: ATAC-seq peaks were identified by using the HOMER tool

molecule: total RNA

organism: Homo sapiens

source_name: T cells

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from heparinized blood using ficoll gradient and from skin biopsies using collagenase IV + mesh filtering
Illumina

tag: tissue

value: Skin

tag: cell type

value: T cells

tag: time

value: Day 14 (after transplantation)


title: APP_Microglia, IL33, 3hours, rep3 [scRNAseq_IL33_3h_3]

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

country: China

description: Ilumina NextSeq 500/NovaSeq 6000

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files (from Novogene) were aligned to mm10 mouse reference genome by Cell Ranger (v7.0.0) with the default settings. Then, we performed downstream quality control (QC) and analyses using Seurat. We further removed microglia with ≤500 genes, ≥15,000 unique molecular identifiers and ≥5% mitochondrial genes as second round of QC. After the QC, 72,519 microglia (from 86,288 CD11b+ cells) were retained for the downstream analysis.
Supplementary files format and content: mm10
Supplementary files format and content: filtered count matrix from Seurat

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
In brief, we deeply anesthetized adult mice using isoflurane and then perfused them with ice-cold PBS. We minced the forebrain tissue into small pieces and mechanically dissociated them with a Dounce homogenizer on ice. We used a Percoll gradient (30%; Sigma-Aldrich) to remove myelin. We blocked the resultant mononuclear cell suspensions with an FcR blocker on ice for 10 min and then incubated them with antibody (all 1:100 dilution) in the dark on ice for 30 min. Next, we performed flow cytometry analysis and cell sorting with a BD Influx Cell Sorter. We used unstained controls to identify cell populations and visualized clear subpopulations of living microglia on scatter plots; the purity of microglial isolation was routinely >90% according to reanalysis of the sorted cells.
We generated scRNA-seq libraries using a Chromium Next GEM Single Cell 3′ Library Kit (v3.1 Chemistry; 10x Genomics) according to the manufacturer’s instructions. In brief, we counted sorted living CD11b+ cells on a hemocytometer. We mixed single-cell suspensions (400 cells µl−1) with reverse transcription reagent mix and loaded them into the chip for single-cell encapsulation. We immediately incubated the encapsulated cells in a thermocycler for reverse transcription. We obtained barcoded cDNA and used it for library construction according to the manufacturer’s instructions. We quantified the concentrations of the final libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). We performed paired-end sequencing of the libraries on a NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: brain

value: Microglia

tag: genotype

tag: treatment


title: APP_Microglia, IL33, 24hours, rep3 [scRNAseq_IL33_24h_3]

institute: Hong Kong University of Science and Technology

description: Ilumina NextSeq 500/NovaSeq 6000


title: control iPSCs clone 52521_9 was generated from de-identified normal skin tissues

city: Columbia

first: Wenbin

last: Tan

state: SC

address: 6311 Garners Ferry Road

department: Cell Biology and Anatomy

country: USA

institute: University of South Carolina School of Medicine

description:
Control_iPSC_52521_9
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls

data_processing:
The STAR (spliced transcripts alignment to a reference; https://github.com/alexdobin/STAR) RNA-seq aligner was used for raw reads’ alignment
The bam files generated by STAR were used as inputs to FeatureCounts (http://bioconductor.org/packages/Rsubread) for further validation and gene counts of RNA transcripts
Biostatistical analysis for differentially expressed genes (DEGs) among groups were carried out using edgeR (https://bioconductor.org/packages/edgeR/)
A set of scaling factors (effective library sizes) were used for downstream analyses after normalization of the original library sizes. Differential expressions were determined using either quasi-likelihood (QL) F-test or likelihood ratio test by glm functions in edgeR. A false discovery rate (FDR) < 0.05 was considered significant
Assembly: Human genome fasta and gtf annotation files from ensemble (Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz; Homo_sapiens.GRCh38.105.chr.gtf.gz) were retrieved for building the STAR genome index files
Supplementary files format and content: xls file includes raw counts for each sample
Supplementary files format and content: xls file includes pseudo counts for each sample

source_name: skin

growth_protocol: The iPSCs were grown in Essential 8 medium

extract_protocol:
Qiagen RNA isolation kit
Qiagen Standard RNA Library kit

treatment_protocol: The iPSCs were induced to MSCs, then differentiated into ECs

value: skin

tag: group

value: control

value: IPSC


title: NB37

city: Edmonton

first: Najmeh

last: Bozorgmehr

state: Alberta

address: 11361 87th Ave NW, 7020L Katz Group Centre

department: Dentistry

country: Canada

institute: University of Alberta

description:
Responder1, Cycle2
Female, Anal

data_processing:
Raw data alligned to human genome cDNA database (GRCh38) using Kallisto software version 0.46.2. 100 permutations selected during allignment
Differential Expression analyses extracted from the count data using the DESeq2 R package version 4.2.0 (2022-04-22
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab delimited text file including transcript count values for each sample

source_name: Blood

extract_protocol:
TRIzol reagent, Direct-Zol RNA kit, Samples with RNA Integrity Numbers (RIN) more than 6.5 were selected
TruSeq RNA library Prep Kit v2 (Illumina), Poly A selection with oligo dTs conjugated to paramagnetic beads. Then first and second strands cDNA libraries were constructed from 100 ng of extracted RNA using the TruSeq RNA Library Prep kit v2 (Illumina) as per kit’s instruction. T-A ligation was added to the blunted and A-tailed cDNA, before doing 12 cycles of PCR to incorporate illumine adapters containing multiplexing barcodes.

value: Blood

value: Peripheral blood mononuclear cells

value: Valproic acid + Avelumab


title: APP_Microglia, IL33, 24hours, rep2 [scRNAseq_IL33_24h_2]

description: Ilumina NextSeq 500/NovaSeq 6000


title: Skin T cells at Day 0 (day of transplantation) [RNA-seq_Skin_Tx_742]

value: Day 0 (day of transplantation)


title: Skin T cells at Day 14 (after transplantation) [RNA-seq_Skin_14_741]


title: APP_Microglia, IL33, 3hours, rep2 [scRNAseq_IL33_3h_2]

description: Ilumina NextSeq 500/NovaSeq 6000


title: Skin T cells at Day 14 (after transplantation) [RNA-seq_Skin_14_736]


title: MB288, G3b, Hi-C

city: La Jolla

first: Lukas

last: Chavez

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: genomic

data_processing:
Hi-C reads were trimmed using Trimmomatic 0.39.
Reads were aligned to the hg38 human genome reference using the HiC-Pro toolkit v2.11.3-beta using default parameters.
Visualization and contact normalization was performed with JuiceBox v1.11.08 and the Knight-Ruiz algorithm.
Assembly: GRCh38
Supplementary files format and content: allValidPairs (HiC-Pro)
Supplementary files format and content: hic (juicebox)

molecule: genomic DNA

source_name: medulloblastoma

extract_protocol:
Frozen tissues were pulverized using a mortar and pestle kept cold on a bed of dry ice into a fine powder. The tissue powder was then transferred to a 15mL conical tube containing 5mLs of DPBS and fixed with 2% formaldehyde for 10 minutes. The fixation was quenched by addition of 0.2M Glycine. The fixed tissue was pelleted by centrifugation, washed 1x with DPBS, and then flash frozen until ready for further processing. For Hi-C experiments, the fixed frozen tissue pellets were first resuspended in 3mLs of lysis buffer (10mM Tris-HCl pH 8.0, 5mM CaCl2, 3mM MgAc, 2mM EDTA, 0.2mM EGTA, 1mM DTT, 0.1mM PMSF, 1X Complete Protease Inhibitors). The sample was transferred to an M-tube and dissociated using a GentleMACS Tissue dissociator (Miltenyi) using the “Protein M-tube” setting. The sample was removed from the M-tube into a 50mL conical. The M-tube was washed with 3mLs of lysis buffer with 0.4% Triton X-100 added, and this wash was combined with the original 3mLs of sample for a total volume of 6mLs with final concentration of 0.2% Triton X-100. The sample was then passed through a 40µM cell strainer. The strainer was washed with an additional 2mLs of lysis buffer with 0.2% Triton X-100. The sample was then centrifuged and washed with 1mL of lysis buffer with 0.2% Triton X-100. After centrifugation, the sample was resuspended in 0.5% SDS and processed using the MboI enzyme.
Libraries were prepared using the Illumina TruSeq LT sequencing adaptors. Initial QC sequencing was first performed on a MiSeq to assess library quality, and if sufficient, was subject to production scale sequencing on the NovaSeq platform, respectively.

value: medulloblastoma


title: D458, G3, Hi-C

tag: cell line


title: RCMB56-pdx, SHH, Hi-C


title: NB32

description:
Responder3, Cycle2
Male, Tonsil


title: Skin T cells at Day 0 (day of transplantation) [RNA-seq_Skin_Tx_741]


title: NB33

description:
Responder3, Endpoint
Male, Tonsil


title: APP_Microglia, PBS, 24hours, rep2 [scRNAseq_DPBS_24h_2]

description: Ilumina NextSeq 500/NovaSeq 6000


title: NB36

description:
Responder1, Cycle1
Female, Anal

value: Valproic acid


title: MB277, G3b, Hi-C


title: 24-OB-K27Ac_S24

city: Trondheim

first: Stefan

last: Blankvoort

address: Olav Kyrresgt 9

department: Kavli Institute for systems Neuroscience

country: Norway

institute: NTNU

data_processing:
Aligning
Peak calling
Diffbind (details in methods)
Assembly:  mm10
Supplementary files format and content: Count table output from DiffBind in Rdata format.

source_name: OB

growth_protocol: No culturing

extract_protocol:
Tissue was fixed with 1% formaldehyde for 10 minutes, quenched with 150mM Glycine, sonicated on a Qsonica Q800 for 30 minutes on a 10sec on-off schedule at 15-20W per tube
We used the Rubicon genomics Thruplex DNA-seq kit for library preparation
Three pools, 48 barcodeseach

value: OB

value: WT

tag: chip antibody

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196)


title: NB30

description:
Responder3, Baseline
Male, Tonsil


title: MB275, SHHa, Hi-C


title: NB31

description:
Responder3, Cycle1
Male, Tonsil


title: 22-MedSep-K27Ac_S22

source_name: MedSep

value: MedSep


title: 22-OB-K27Ac_S22


title: MB268, SHHa, Hi-C


title: Skin T cells at Baseline [RNA-seq_Skin_B_742]

value: Skin

value: T cells

value: Baseline


title: 22-MEC-Input_S22

source_name: MEC

value: MEC


title: MB274, SHHa, Hi-C


title: NB29

description:
Non-responder3, Cycle2
Male, Tonsil


title: Skin T cells at Day 0 (day of transplantation) [RNA-seq_Skin_Tx_736]


title: NB35

description:
Responder1, Baseline
Female, Anal


title: NB28

description:
Non-responder3, Cycle1
Male, Tonsil


title: APP_Microglia, PBS, 24hours, rep1 [scRNAseq_DPBS_24h_1]

description: Ilumina NextSeq 500/NovaSeq 6000

value: brain

value: Microglia


title: 21-SomCtx-Input_S21

source_name: SomCtx

value: SomCtx


title: MB248, G3a, Hi-C


title: Skin T cells at Baseline [RNA-seq_Skin_B_738]


title: 21-Ctx-K27Ac_S21

source_name: Ctx

value: Ctx


title: NB27

description:
Non-respnder3, Baseline
Male, Tonsil

value: Blood

value: Peripheral blood mononuclear cells


title: Skin T cells at Baseline [RNA-seq_Skin_B_736]


title: Skin T cells at Day 0 (day of transplantation) [RNA-seq_Skin_Tx_738]

value: Day 0 (day of transplantation)


title: MB234, SHHa, Hi-C

value: medulloblastoma


title: 21-MedSep-K27Ac_S21


title: NB25

description:
Non-responder2, Cycle2
Male, oropharynx

value: Valproic acid + Avelumab


title: 18-MEC-K27AC_S18


title: Blood T cells at Day 100 (after transplantation) [RNA-seq_Blood_100_742]

value: Day 100 (after transplantation)


title: NB24

description:
Non-responder2, Cycle1
Male, oropharynx

value: Valproic acid


title: Blood T cells at Day 100 (after transplantation) [RNA-seq_Blood_100_741]


title: MB227, G4, Hi-C


title: 17-SomCtx-K27AC_S17

value: WT

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196)


title: MB264, G4, Hi-C


title: NB23

description:
Non-responder2, Baseline
Male, oropharynx


title: MB199, G4, Hi-C


title: Blood T cells at Day 100 (after transplantation) [RNA-seq_Blood_100_740]


title: Blood T cells at Day 100 (after transplantation) [RNA-seq_Blood_100_738]


title: 14-OB-Input_S14

value: OB


title: MB174, G4, Hi-C


title: NB21

description:
Responder4, Endpoint
Female, Cervix


title: MB164, G3b, Hi-C


title: 16-OB-Input_S16


title: NB26

description:
Non-responder2, Endpoint
Male, oropharynx


title: Skin T cells at Baseline [RNA-seq_Skin_B_741]

value: Skin

value: T cells


title: NB20

description:
Responder4, Cycle2
Female, Cervix


title: Blood T cells at Day 100 (after transplantation) [RNA-seq_Blood_100_736]


title: MB244, SHHa, Hi-C


title: MB106, G3a, Hi-C


title: NB19

description:
Responder4, Cycle1
Female, Cervix


title: Blood T cells at Day 14 (after transplantation) [RNA-seq_Blood_14_742]

value: Day 14 (after transplantation)


title: NB18

description:
Responder4, Baseline
Female, Cervix


title: 13-MedSep-Input_S13

value: MedSep


title: Blood T cells at Day 14 (after transplantation) [RNA-seq_Blood_14_741]


title: MB102, SHHa, Hi-C


title: 13-Ctx-Input_S13


title: T cells, NY-ESO-1 TCR + library knockin, after 5th stim, donor 2

city: San Francisco

first: Franziska

last: Blaeschke

address: 1650 Owens Street

institute: Gladstone Institutes

description:
s6a/s6b
ModPoKI_ModPoKI-Seq_6

data_processing:
Fastq files were mapped to the human transcriptome (10x Genomics Cell Ranger, v5.0.0) and a custom knockin barcode reference and analyzed using Seurat (v4.1.1).
Assembly: 10x Genomics Cell Ranger, v5.0.0
Supplementary files format and content: Rds file generated after data processing including all samples

extract_protocol:
Chromium Single Cell 5’ Reagent Kit, v1 chemistry (10x Genomics) was used according to the manufacturer’s protocol.
After GEM (Gel Bead-In Emulsions) recovery, the mRNA library was converted to cDNA, amplified for 11 cycles, and quantified with Agilent Bioanalyzer High Sensitivity. 75% of the amplified cDNA material was carried through for transcriptome library preparation according to the manufacturer’s protocol. The remaining 25% of amplified cDNA was used for amplicon sequencing of the knockin barcodes. The cDNA was enriched for knockin barcodes using a nested PCR strategy with Kapa HiFi HotStart Ready Mix (Roche) for 8 cycles per round. For the first PCR, 0.5µM each of ModPoKI_Seq_1_forw primer and ModPoKI_Seq_1_rev primer was used. Amplified products were purified with 0.8x SPRIselect Reagent Kit (Beckman Coulter) and eluted in 10µL nuclease-free water. The libraries were further enriched with a second PCR using 0.5µM each of ModPoKI_Seq_2_forw primer and ModPoKI_Seq_2_rev primer. Amplified products were purified with 0.8x SPRIselect Reagent Kit (Beckman Coulter) and eluted in 15µL nuclease-free water. Lastly, index PCR was performed with Kapa HiFi HotStart Ready Mix (Roche) for 8 cycles with 2.5µL each Nextera Chromium i7 Sample Indices N Set A (PN 3000262) and 0.5µM ModPoKI_Seq_index primer. Amplified products were purified with 0.8x SPRIselect Reagent Kit (Beckman Coulter) and eluted in 45µL nuclease-free water. Samples were pooled and sequenced on a NovaSeq S4 flow cell with 20% PhiX using read parameters 30x8x98.
ModPoKI-Seq

tag: individual

value: donor 2

value: Primary cells

value: NY-ESO-1 TCR + TF library

value: Five stimulations with target cells


title: Blood T cells at Day 14 (after transplantation) [RNA-seq_Blood_14_740]

value: Blood


title: T cells, NY-ESO-1 TCR + library knockin, after 5th stim, donor 1

description:
s5a/s5b
ModPoKI_ModPoKI-Seq_5

value: donor 1


title: Blood T cells at Day 14 (after transplantation) [RNA-seq_Blood_14_738]


title: NB7

description:
Non-responder4, Cycle2
Female, Vulva

value: Peripheral blood mononuclear cells


title: 12-Sub-K27Ac_S12

source_name: Sub

value: Sub


title: T cells, NY-ESO-1 TCR + library knockin, after 1st stim, donor 2

description:
s4a/s4b
ModPoKI_ModPoKI-Seq_4

value: One stimulation with target cells


title: NB6

description:
Non-responder4, Cycle1
Female, Vulva

value: Valproic acid


title: 11-mPFC1-Input_S11

value: WT


title: Blood T cells at Day 14 (after transplantation) [RNA-seq_Blood_14_736]


title: T cells, NY-ESO-1 TCR + library knockin, after 1st stim, donor 1

description:
s3a/s3b
ModPoKI_ModPoKI-Seq_3


title: 11-DS-K27Ac_S11

source_name: DS

value: DS

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196)


title: NB5

description:
Non-responder4, Baseline
Female, Vulva


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_754]

value: Day 0 (day of transplantation)


title: T cells, NY-ESO-1 TCR + library knockin, input, donor 2

description:
s2a/s2b
ModPoKI_ModPoKI-Seq_2

value: T cells


title: NB3

description:
Responder2, Endpoint
Female, Unknown origin

value: Valproic acid + Avelumab


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_742]


title: T cells, NY-ESO-1 TCR + library knockin, input, donor 1

description:
s1a/s1b
ModPoKI_ModPoKI-Seq_1


title: 14-MedSep-Input_S14

value: MedSep


title: NB2

description:
Responder2, Cycle2
Female, Unknown origin


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_741]


title: 10-HDB2-Input_S10


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_740]


title: 9-VS-K27Ac_S9

source_name: VS

value: VS


title: T cells (unstim), TFAP4 knockin, donor 3

data_processing:
The sequencing data was processed using version 3.9 of the nf-core RNA-seq pipeline (https://nf-co.re/rnaseq). Fastq quality control was performed using FastQC, and filtered reads were trimmed with Trim Galore software.
The resulting trimmed fastq files were aligned to the hg38 human genome using STAR, and Salmon was used to generate a gene-by-sample count matrix for downstream analysis.
Assembly: hg38 reference genome
Supplementary files format and content: Rds file generated after data processing including all samples

extract_protocol:
RNA was isolated from 2e5 sorted CAR T cells by standard, TRIzol-based RNA precipitation method as follows. Cells were resuspended in 1 ml TRIzol (Ambion). Chloroform was added (200 µL) to this lysate and extensively vortexed to achieve a homogenous mixture; then, it was incubated for 3 minutes at room temperature before centrifugation at 14,000g at 4C for 15 min. Aqueous layer was collected from the top and transferred into a new tube (~550 µL), 1 µL GylcoBlue (Ambion) was added, and the RNA was precipitated with equal volume of 2-propanol for 20 min at room temperature. RNA precipitates were centrifuged at 16,000g for 15 min at 4C and supernatant was carefully discarded without disturbing the GlycoBlue-stained blue RNA pellet. RNA pellet was washed with 1 ml 75% EtOH and after the wash, dissolved in 30 µL nuclease-free water. RNA concentration was determined by nanodrop, and RNA quality was determined by Agilent Bioanalyzer.
Approximately 50 ng RNA was reverse-transcribed to complementary DNA (cDNA) and second strand was synthesized by the Ovation RNA-seq System V2 (Tecan) according to the manufacturer’s recommendations. Double-stranded DNA was subjected to isothermal amplification and was purified with Ampure XP beads. DNA was quantified by Qubit and 80 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 8 PCR cycles according to the manufacturer’s recommendations.

value: donor 3

value: Primary cells

value: TFAP4 knockin


title: NB1

description:
Responder2, Baseline
Female, Unknown origin

value: Blood


title: NB8

description:
Non-responder4, Endpoint
Female, Vulva


title: 12-mPFC2-Input_S12


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_738]


title: 9-HDB1-Input_S9


title: Blood T cells at Day 0 (day of transplantation) [RNA-seq_Blood_Tx_736]


title: T cells (unstim), BATF-TFAP4 knockin, donor 3

value: BATF-TFAP4 knockin


title: 8-mPFC2-K27AC_S8


title: 10-VS-K27Ac_S10


title: EHMT1-K450RK451R, Veh-rep 2

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Assembly: hg19
Supplementary files format and content: txt file for raw counts of sequence reads

source_name: LNCaP cell

growth_protocol: In RPMI 1640 medium with 10% FBS

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries of both LNCaP-tet-EHMT1 and LNCaP cells were performed by using TruSeq® Strnd Total RNA LT (Illumina).

value: prostate cancer cell

value: untreated


title: T cells (unstim), BATF-RFP knockin, donor 3

value: BATF-RFP knockin


title: T cells (unstim), RFP-TFAP4 knockin, donor 3

value: RFP-TFAP4 knockin


title: 7-mPFC1-K27AC_S7

value: WT


title: Blood T cells at Baseline [RNA-seq_Blood_B_742]

value: Baseline


title: EHMT1-K450RK451R, Veh-rep 1


title: Blood T cells at Baseline [RNA-seq_Blood_B_741]


title: T cells (unstim), tNGFR knockin, donor 3

value: tNGFR knockin


title: T cells (unstim), RFP-tNGFR knockin, donor 3

value: RFP-tNGFR knockin


title: EHMT1-K451R, Dox-rep 2

value: 0.25μg/ml doxycycline for 2 days


title: Blood T cells at Baseline [RNA-seq_Blood_B_740]

value: T cells


title: 6-HDB2-K27AC_S6

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196)


title: 5-HDB1-K27AC_S5


title: EHMT1-K450RK451R, Dox-rep 2


title: T cells (unstim), tNGFR knockin, donor 2

value: donor 2


title: EHMT1-K451R, Dox-rep 1


title: 4-Sub-Input_S4

value: Sub


title: 3-DS-Input_S3

value: DS


title: EHMT1-K451R, Veh-rep 2


title: Blood T cells at Baseline [RNA-seq_Blood_B_738]


title: T cells (unstim), TFAP4 knockin, donor 2

value: Primary cells

value: TFAP4 knockin


title: EHMT1-K450RK451R, Dox-rep 1


title: T cells (unstim), BATF-TFAP4 knockin, donor 2

value: Blood

value: BATF-TFAP4 knockin


title: EHMT1-K451R, Veh-rep 1

value: prostate cancer cell

value: untreated


title: 1-VS-Input_S1

value: VS


title: EHMT1-K450R, Dox-rep 2


title: T cells (unstim), RFP-TFAP4 knockin, donor 2

value: RFP-TFAP4 knockin


title: Ets2-SE-NC-rep4

city: shanghai

first: bowen

last: zhang

state: shanghai

address: dongan road

institute: Fudan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-wise chromatin interactions for 3C-HTGTS data processing. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained through spliting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exactly alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph file using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph file using CPM (Counts Per Million in cis) normalization method, and visualized on IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6). The analysis of the correlation for experimental repetition used the R package corrplot(v.0.92).
For snRNA-seq data analysis, the cleaned data were generated by Cell Ranger (v3.0.2) (https://github.com/10XGenomics/cellranger) and filtered for the low-quality reads. The data were aligned to mouse mm10 reference genome. 10× Genomics‐derived data were collected. The downstream analysis using the Seurat (v4.0.5) (https://satijalab.org/seurat) program screened out Cells with gene numbers greater than 200, and mitochondrial gene ratios less than 25% and 2000 genes with highly variable expression in 3 or more cells. Principal component analysis was then runned using significantly variable genes, and Uniform Manifold Approximation and Projection (UMAP) was performed to visualize data. Cells were represented in a two-dimensional UMAP plane, and clusters were identified and annotated according to the previously published cardiac cell markers. The significance of differential expression was calculated using the bimod test. Functional enrichment of differentially expressed genes was then processed by Gene Ontology (GO) (http://www.geneontology.org/) analysis. The pseudotime trajectory was determined with the Monocle2 package with the default settings. Specifically, the DDRTree method was used for dimension reduction with max_components set at 2, and the cells were ordered using the orderCells function.
Bulk RNA-sequencing (RNA-seq) of mouse embryo hearts and HL-1 cells was carried on by the LC-Bio Technology, Hangzhou, China. The detailed operations were as follows: total RNA was isolated and purified using TRIzol reagent (Invitrogen, CA, USA). The RNA samples which passed quality control were fragmented into small pieces at 94℃ for 5-7min and reverse-transcribed to create the cDNA. The average insert size for the final cDNA library was 300±50 bp. The FASTQ data of sequencing reads were trimmed using paired-end sequencing. Consecutively, the trimmed reads were mapped to the mouse genome reference (mm10) by HISAT2 software (https://ccb.jhu.edu/software/hisat2). The mRNA expression abundance was analyzed using StringTie software and represented by FPKM. The differentially expressed mRNAs were selected with FC >1.5 and a parametric F-test comparing nested linear models (p value < 0.05) by the R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). Gene set enrichment analysis was run on all expressed genes which were ranked by log2FC value. Functional enrichment of differentially expressed genes was then processed by GO (http://www.geneontology.org/) analysis.
For ChIP-seq, ChIP products were end repaired, dA-tailing and linker ligation were performed, and barcoding and Illumina adapter addition were performed by PCR amplification. Libraries were purified using QiaQuick PCR purification reagents (Qiagen, Hilden, Germany) and size selected by 0.7×and 0.2×Ampure XP beads (Beckman, California, USA).
Assembly: mm10
Supplementary files format and content: bedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample. we used the custom script to get bedpe files for interaction loops identified by using raw contact frequencies.  The custom utility was used to convert the raw contact frequencies into sparse .matrix format, and  these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions.

source_name: Muscle

growth_protocol: All mouse procedures were approved and monitored by the Research Ethics Committee of the School of Basic Medical Sciences, Fudan University, China. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol: For 3C-HTGTS, mouse thymus and liver were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer. And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp or 250 bp paired-end reads. For SnRNA-seq, the E12.5 mouse embryos were microdissected in PBS solution using a Leica M205C microscope, and the heart tissues were extracted. The whole heart samples from different embryos, including six Smc3fl/fl, seven Smc3fl/+; Nkx2.5-Cre, and seven Smc3fl/fl; Nkx2.5-Cre, subjected to mechanical trituration, were made into the cell suspension. Cell counts and viability were determined for the resulting suspension, and the cell concentration was adjusted to the ideal 300-600 cells / μL. The prepared single-cell suspension was combined with a mixture of gel beads containing barcode information and enzymes and then encapsulated by oil droplets to form Gel Bead-In-EMulsions (GEMs). After the reverse transcription reaction, the GEMs were fragmented to complete the amplification of nuclear cDNA, and the quality-checked amplification products were constructed as sequencing libraries. Briefly, the cDNA was broken into fragments of 200-300 bp, end-repaired, ligated into the P7 Adapter, and finally amplified by PCR for introduction into the indexes of samples.

tag: strain

value: Cardiac muscle tissue

value: WT


title: EHMT1-K450R, Dox-rep 1


title: T cells (unstim), RFP-tNGFR knockin, donor 2

value: RFP-tNGFR knockin


title: Ets2-SE-NC-rep2


title: CD69negDP_WT_H3_ChIPseq, biol rep 1

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: ChIP-seq

data_processing:
Basecalls performed using CASAVA-1.82 or CASAVA-1.84
Hi-C Sequenced data (100 bp paired-end for primary thymus Hi-C, 35 bp paired-end for VL3 Hi-C and capture Hi-C) were mapped using the bowtie 2 (version 2.3.2) and then processed by the HiC-Pro (version 2.7.8) with default settings. After converting using the script, HiC-Pro hicpro2juicebox.sh, valid chromatin contacts were normalized and .hic files were created by the Juicer Pre (Juicer tools version 0.7.5).
ChIP-seq raw reads (50 bp single-end) were mapped using the bowtie (version 1.0.0). After alignment and duplicates removal, peaks were identified using MACS2 (version 2.1.0).
Assembly: mm9
Supplementary files format and content: .hic files were created by the Juicer Pre (Juicer tools version 0.7.5)
Supplementary files format and content: Peak files were generated using MACS2 (version 2.1.0)

source_name: thymus

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature and then the reaction was quenched with 125 mM glycine at room temperature for 5 minutes. [Hi-C] Chromatin was digested with 100 units of MboI overnight at 37 °C while shaking at 900 rpm. After overnight incubation, 100 units of MboI were added for the second-round digestion for 2-4 hours. The DNA polymerase I, large (Klenow) fragment, was used to fill in MboI-digested fragment overhangs in the presence of biotin-labelled dATP. Fragment ends were then ligated with 4000 units of T4 DNA ligase by incubating at room temperature for 4-6 h with rotation at 12 rpm. After ligation, cell nuclei were collected by centrifugation, and chromatin was reverse crosslinked overnight at 65 °C. RNase A was used to remove RNA after decrosslinking. Genomic DNA was isolated and precipitated by sodium acetate-ethanol precipitation, and then purified DNA was sheared for 8 min using a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. DNA fragments in the range of 300–500 bp were then selected using the AMPure XP beads (Beckmann Coulter). [ChIP-seq] Cell nuclei were isolated using a RIPA lysis buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors). Following isolation of cell nuclei, genomic DNA was sonicated in a high-salt RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1% SDS, 0.8M NaCl, 1X Roche protease inhibitors) for 30 minutes on a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. Immunoprecipitation was performed in a RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors), and then antibody-antigen complex was precipitated using Dynabead Protein G (Thermo Fisher). Protein was digested using Proteinase K, and then DNA-protein complex was reverse crosslinked overnight at 65 °C. RNase A was added to remove RNA after decrosslinking.
[Hi-C] After biotin-labelled DNA fragments were captured on Dynabeads MyOne Streptavidin T1 (Thermo Fisher), fragment ends were repaired in a mixture of enzymes containing T4 polynucleotide kinase, T4 DNA polymerase I and DNA polymerase I, large (Klenow) fragment, and then NEBNext adaptors for Illumina sequencing were ligated to the dA-tailed fragment ends. After the USER enzyme digestion, NEBNext oligos for Illumina sequencing were used for PCR for library preparation. A PCR titration was firstly carried out to determine the lowest number of PCR cycles (8-10 cycles in this work). Final Hi-C sequencing libraries were quantified and checked for size distribution using Bioanalyzer (Agilent Technologies), and then sequenced on an HiSeq 2500 sequencer (Illumina). [Capture Hi-C] Capture Hi-C library preparation was performed according to the published protocol (Sanborn et al., 2015, PNAS). [ChIP-seq] ChIP-seq library preparation was carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) according to the manufacturer’s protocol.

value: thymus

value: Primary T cell

value: wild type

tag: antibody

value: Histone H3 (Abcam, #ab1791)

tag: developmental stage


title: Ets2-SE-NC-rep3


title: CD69posCD4SP_WT_H3_ChIPseq, biol rep 2

description: ChIP-seq


title: EHMT1-K450R, Veh-rep 2


title: CD69negDP_WT_H3_ChIPseq, biol rep 2

description: ChIP-seq


title: Blood T cells at Baseline [RNA-seq_Blood_B_736]

value: T cells

value: Baseline


title: Ets2-SE-NC-rep1


title: T cells (unstim), BATF-RFP knockin, donor 2

value: donor 2

value: Primary cells

value: BATF-RFP knockin


title: T cells (unstim), tNGFR knockin, donor 1

value: donor 1

value: Blood

value: tNGFR knockin


title: CD69posCD4SP_WT_H3_ChIPseq, biol rep 1

description: ChIP-seq


title: Ets2-SE-KO-rep4


title: EHMT1-WT, Dox-rep 2

value: prostate cancer cell

value: 0.25μg/ml doxycycline for 2 days


title: Ets2-SE-KO-rep3

value: Cardiac muscle tissue


title: EHMT1-K450R, Veh-rep 1

value: untreated


title: EHMT1-WT, Dox-rep 1


title: Ets2-SE-KO-rep2


title: T cells (unstim), BATF-TFAP4 knockin, donor 1

value: BATF-TFAP4 knockin


title: T cells (unstim), TFAP4 knockin, donor 1

value: TFAP4 knockin


title: CD69posCD4SP_WT_H3K27ac_ChIPseq, biol rep 2

description: ChIP-seq

value: thymus

value: Primary T cell

value: H3K27ac (Active Motif, #39133)


title: EHMT1-WT, Veh-rep 2


title: T cells (unstim), RFP-TFAP4 knockin, donor 1

value: T cells

value: RFP-TFAP4 knockin


title: CD69posCD4SP_WT_H3K27ac_ChIPseq, biol rep 1

description: ChIP-seq

value: wild type


title: CD69posCD4SP_WT_Input_ChIPseq, biol rep 2

description: ChIP-seq


title: Ets2-SE-KO-rep1


title: T cells (unstim), BATF-RFP knockin, donor 1

value: Primary cells


title: EHMT1-WT, Veh-rep 1


title: HL-1-SMC3-NC-rep3

value: Cardiac muscle cells HL-1

value: Atrial tissue


title: CD69posCD4SP_WT_Input_ChIPseq, biol rep 1

description: ChIP-seq


title: siEHMT1-rep 2

value: LNCaP

value: Treated with 20nM siEHMT1


title: T cells, tNGFR knockin, day 7, donor 4

description:
YC34_S133_L002_R1_001
RNA-2_day7.rds

data_processing:
Kallisto was used to map the reads to the human reference transcriptome and genes with zero counts in more than 80% of samples were removed from the analysis.
DESeq2 R package was used for differential gene expression, fgsea package for gene set enrichment analysis (GSEA) with MSigDB v7.2 hallmark gene sets as reference gene lists.
Assembly: Pseudo-alignment (Kallisto)
Supplementary files format and content: Rds file generated after data processing including all samples

extract_protocol:
RNA was isolated using Direct-zol RNA kits (Zymo Research).
RNA was prepared for sequencing as previously described (Cortez et al., Nature, 2020) by the Functional Genomics Laboratory at UC Berkeley and sequenced by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.

value: donor 4

value: Blood

value: tNGFR knockin

value: day 7


title: T cells (unstim), RFP-tNGFR knockin, donor 1

value: donor 1

value: RFP-tNGFR knockin


title: VL3_HIC_Enh_Insertion

description: Capture Hi-C

value: T cell line, VL3-3M2

value: CMV Enh+/+


title: siEHMT1-rep 1

value: prostate cancer cell


title: HL-1-SMC3-NC-rep2


title: T cells, tNGFR knockin, day 7, donor 3

description:
YC32_S131_L002_R1_001
RNA-2_day7.rds

value: donor 3

value: T cells


title: VL3_HIC_CTR

description: Capture Hi-C

value: wild type


title: siNTC-rep 1

value: Treated with 20nM siNTC


title: siNTC-rep 2


title: VL3_WT_HIC, biol rep 3

description:
in situ Hi-C
VL3WTR1R2R3.hic


title: ChIP, EHMT1, LNCaP-rep 2

description:
ChIP_EHMT1_LNCaP.bw
ChIP_EHMT1_LNCaP_peaks.narrowPeak.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Assembly: hg19
Supplementary files format and content: bw, narrowPeak

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

value: untreated

value: anti-EHMT1 (Abcam)


title: T cells, TFAP4 knockin, day 7, donor 4

description:
YC33_S132_L002_R1_001
RNA-2_day7.rds

value: Primary cells

value: TFAP4 knockin


title: VL3_WT_HIC, biol rep 2

description:
in situ Hi-C
VL3WTR1R2R3.hic


title: ChIP, EHMT1, LNCaP-rep 1

value: LNCaP


title: VL3_WT_HIC, biol rep 1

description:
in situ Hi-C
VL3WTR1R2R3.hic


title: HL-1-SMC3-NC-rep1

value: Cardiac muscle cells HL-1

value: Atrial tissue


title: HL-1-SMC3-KD-rep2


title: CD69posCD4SP_DKO_HIC, biol rep 2

description:
in situ Hi-C
CD69posCD4SPDKOR1R2.hic

value: thymus

value: Primary T cell


title: HL-1-SMC3-NC-ChIP

value: Input


title: HL-1-SMC3-KD-rep3


title: T cells, RFP-tNGFR knockin, day 15, donor 2

description:
YC29_S128_L002_R1_001
RNA-2_day15.rds

value: donor 2

value: Blood

value: RFP-tNGFR knockin

value: Stimulated with target cells

value: day 15


title: ChIP, H3K9me2, LNCaP, EHMT1-K450RK451R, Dox-rep 2

description:
ChIP_H3K9me2_LNCaP_EHMT1_K450RK451R_Dox.bw
ChIP_H3K9me2_LNCaP_EHMT1_K450RK451R_Dox_peaks.narrowPeak.gz

value: prostate cancer cell

value: 0.5μg/ml doxycycline for 2 days

value: anti-H3K9me2 (Abcam)


title: HL-1-SMC3-KD-rep1


title: T cells, RFP-JUN knockin, day 15, donor 2

description:
YC30_S129_L002_R1_001
RNA-2_day15.rds

value: T cells

value: RFP-JUN knockin


title: CD69posCD4SP_DKO_HIC, biol rep 1

description:
in situ Hi-C
CD69posCD4SPDKOR1R2.hic


title: T cells, RFP-TFAP4 knockin, day 15, donor 2

description:
YC28_S127_L002_R1_001
RNA-2_day15.rds

value: Primary cells

value: RFP-TFAP4 knockin


title: HL-1-SMC3-KD-ChIP

value: Cardiac muscle cells HL-1


title: ChIP, H3K9me2, LNCaP, EHMT1-K450RK451R, Dox-rep 1


title: HL-1-SMC3-NC-ChIP-rep3 H3K4me3

value: Atrial tissue


title: ChIP, H3K9me2, LNCaP, EHMT1-K451R, Dox-rep 2

description:
ChIP_H3K9me2_LNCaP_EHMT1_K451R_Dox.bw
ChIP_H3K9me2_LNCaP_EHMT1_K451R_Dox_peaks.narrowPeak.gz


title: HL-1-SMC3-NC-ChIP-rep2 H3K4me3


title: CD69posCD4SP_WT_HIC, biol rep 2

description:
in situ Hi-C
CD69posCD4SPWTR1R2.hic

value: thymus

value: wild type


title: T cells, TFAP4 knockin, day 7, donor 3

description:
YC31_S130_L002_R1_001
RNA-2_day7.rds

value: donor 3

value: TFAP4 knockin

value: day 7


title: CD69posCD4SP_WT_HIC, biol rep 1

description:
in situ Hi-C
CD69posCD4SPWTR1R2.hic

value: Primary T cell


title: T cells, BATF-TFAP4 knockin, day 15, donor 2

description:
YC26_S125_L002_R1_001
RNA-2_day15.rds

value: donor 2

value: Blood

value: BATF-TFAP4 knockin

value: Stimulated with target cells


title: 20% sample ATAC

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

library_source: genomic single cell

data_processing:
GEX + ATAC: base calling and quality scoring were performed using Illumina Real-Time Analysis on board software (version 2.11.3).
Raw base call files were demultiplexed into FASTQ files using the mkfastq pipeline in Cellranger ARC (version 2.0.0).
Reads were aligned to the human reference genome, filtering, barcode counting, peak calling were performed, and gene counts were generated using the count pipeline in CellRanger ARC (version 2.0.0).
Long reads: MinKNOW PromethION Release (version 20.06.9), base calling with Guppy (version 5.0.12).
Cell barcode matching and counting was performed with FLAMES (version 0.1.0, https://github.com/LuyiTian/FLAMES).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files with cell-associated barcodes, features, and matrix outputs from CellRanger.
Supplementary files format and content: scM2_20_FLAMES_stats.txt: comma-delimited file with cell IDs and counts

source_name: Lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The cell lines were mixed to achieve 16,000 nuclei captured, 9,700 nuclei in total, following the 10X Genomics nuclei preparation protocol.
GEX + ATAC:  10X Genomics Chromium nextgeM Single Cell Multiome ATAC +  Gene Expression kit,  Illumina NextSeq 500 sequencing chemistry v2.5. Long reads: Full length cDNA was obtained using 10X Multiome protocol to step 6. Elongation time was changed to 6 minutes. The ligation sequencing kit (SQK-LSK110) was used with the supplied ONT protocol. Libraries were loaded on 1 PromethION R9.4 flow cell and sequenced with ONT PromethION.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Lung adenocarcinoma

value: mixture of cell lines:H2228, H1975, A549, H838, HCC827


title: HL-1-SMC3-KD-ChIP-rep3 H3K4me3


title: T cells, RFP-JUN knockin, day 15, donor 1

description:
YC25_S124_L002_R1_001
RNA-2_day15.rds

value: donor 1

value: T cells

value: RFP-JUN knockin

value: day 15


title: 80% sample ATAC


title: ChIP, H3K9me2, LNCaP, EHMT1-K451R, Dox-rep 1

value: prostate cancer cell

value: 0.5μg/ml doxycycline for 2 days

value: anti-H3K9me2 (Abcam)


title: T cells, RFP-tNGFR knockin, day 15, donor 1

description:
YC24_S123_L002_R1_001
RNA-2_day15.rds

value: Primary cells

value: RFP-tNGFR knockin


title: ChIP, H3K9me2, LNCaP, EHMT1-K450R, Dox-rep 1

description:
ChIP_H3K9me2_LNCaP_EHMT1_K450R_Dox.bw
ChIP_H3K9me2_LNCaP_EHMT1_K450R_Dox_peaks.narrowPeak.gz


title: HL-1-SMC3-KD-ChIP-rep2 H3K4me3

value: Cardiac muscle cells HL-1

value: Atrial tissue


title: ChIP, H3K9me2, LNCaP, EHMT1-WT, Dox-rep 2

description:
ChIP_H3K9me2_LNCaP_EHMT1_WT_Dox.bw
ChIP_H3K9me2_LNCaP_EHMT1_WT_Dox_peaks.narrowPeak.gz


title: 80% sample RNA


title: HL-1-SMC3-KD-ChIP-rep1 H3K4me3


title: T cells, RFP-TFAP4 knockin, day 15, donor 1

description:
YC23_S122_L002_R1_001
RNA-2_day15.rds

value: RFP-TFAP4 knockin


title: T cells, BATF-RFP knockin, day 15, donor 1

description:
YC22_S121_L002_R1_001
RNA-2_day15.rds

value: Blood

value: BATF-RFP knockin


title: ChIP, H3K9me2, LNCaP, EHMT1-WT, Dox-rep 1


title: 20% sample RNA


title: T cells, BATF-TFAP4 knockin, day 15, donor 1

description:
YC21_S120_L002_R1_001
RNA-2_day15.rds

value: BATF-TFAP4 knockin

value: Stimulated with target cells


title: ChIP, V5, LNCaP, EHMT1-K450RK451R, Dox-rep 2

description:
ChIP_V5_LNCaP_EHMT1_K450RK451R_Dox.bw
ChIP_V5_LNCaP_EHMT1_K450RK451R_Dox_peaks.narrowPeak.gz

value: anti-V5 (Invitrogen)


title: HL-1-SMC3-NC-ChIP-rep2 H3K27ac


title: MDA-MB-231 cells, MLL1-KO2, rep2

city: Dallas

first: Lei

last: Bao

state: TX

address: 5323 Harry Hines Blvd, NB6.126

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
The Fastq files were subjected to quality check using fastqc (version 0.11.2) and fastq_screen (version 0.4.4), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806).
Trimmed fastq files were mapped to hg19 using Tophat.
Read counts were generated using featureCounts.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include RPKM values for all samples

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyper Prep kit following manufacturer's protocols.

value: Breast cancer cells

value: MLL1 knockout

value: No treatment


title: T cells, BATF-RFP knockin, day 15, donor 2

description:
YC27_S126_L002_R1_001
RNA-2_day15.rds

value: donor 2

value: T cells

value: day 15


title: MDA-MB-231 cells, MLL1-KO2, rep1


title: HL-1-SMC3-NC-ChIP-rep1 H3K4me3


title: ChIP, V5, LNCaP, EHMT1-K450RK451R, Dox-rep 1

value: prostate cancer cell

value: 0.5μg/ml doxycycline for 2 days


title: MDA-MB-231 cells, MLL1-KO1, rep2


title: ChIP, H3K9me2, LNCaP, EHMT1-K450R, Dox-rep 2

value: anti-H3K9me2 (Abcam)


title: ChIP, V5, LNCaP, EHMT1-K451R, Dox-rep 2

description:
ChIP_V5_LNCaP_EHMT1_K451R_Dox.bw
ChIP_V5_LNCaP_EHMT1_K451R_Dox_peaks.narrowPeak.gz


title: HL-1-SMC3-NC-ChIP-rep1 H3K27ac

value: Cardiac muscle cells HL-1


title: T cells, RFP-JUN knockin, day 14, donor 2

description:
YC20_S85_L001_R1_001
RNA-2_day14.rds

value: Primary cells

value: RFP-JUN knockin

value: day 14


title: HL-1-SMC3-KD-ChIP-rep3 H3K27ac

value: Atrial tissue


title: ChIP, V5, LNCaP, EHMT1-K451R, Dox-rep 1


title: MDA-MB-231 cells, SIN3A+SIN3B-DKO2, rep2

value: SIN3A+SIN3B knockout


title: MDA-MB-231 cells, MLL1-KO1, rep1


title: T cells, BATF-RFP knockin, day 14, donor 2

description:
YC17_S82_L001_R1_001
RNA-2_day14.rds

value: Blood

value: BATF-RFP knockin


title: HL-1-SMC3-KD-ChIP-rep2 H3K27ac


title: T cells, RFP-TFAP4 knockin, day 14, donor 2

description:
YC18_S83_L001_R1_001
RNA-2_day14.rds

value: RFP-TFAP4 knockin


title: ChIP, V5, LNCaP, EHMT1-K450R, Dox-rep 2

description:
ChIP_V5_LNCaP_EHMT1_K450R_Dox.bw
ChIP_V5_LNCaP_EHMT1_K450R_Dox_peaks.narrowPeak.gz

value: anti-V5 (Invitrogen)


title: HL-1-SMC3-KD-ChIP-rep1 H3K27ac


title: HL-1-SMC3-NC-ChIP-rep3 H3K27ac


title: T cells, BATF-TFAP4 knockin, day 14, donor 2

description:
YC16_S81_L001_R1_001
RNA-2_day14.rds

value: BATF-TFAP4 knockin


title: MDA-MB-231 cells, SIN3A+SIN3B-DKO1, rep2

value: Breast cancer cells

value: No treatment


title: ChIP, V5, LNCaP, EHMT1-K450R, Dox-rep 1


title: MDA-MB-231 cells, SIN3A+SIN3B-DKO2, rep1


title: HL-1-SMC3-NC-ETS2-3C-HTGTS-rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-wise chromatin interactions for 3C-HTGTS data processing. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained through spliting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exactly alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph file using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph file using CPM (Counts Per Million in cis) normalization method, and visualized on IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6). The analysis of the correlation for experimental repetition used the R package corrplot(v.0.92).
For snRNA-seq data analysis, the cleaned data were generated by Cell Ranger (v3.0.2) (https://github.com/10XGenomics/cellranger) and filtered for the low-quality reads. The data were aligned to mouse mm10 reference genome. 10× Genomics‐derived data were collected. The downstream analysis using the Seurat (v4.0.5) (https://satijalab.org/seurat) program screened out Cells with gene numbers greater than 200, and mitochondrial gene ratios less than 25% and 2000 genes with highly variable expression in 3 or more cells. Principal component analysis was then runned using significantly variable genes, and Uniform Manifold Approximation and Projection (UMAP) was performed to visualize data. Cells were represented in a two-dimensional UMAP plane, and clusters were identified and annotated according to the previously published cardiac cell markers. The significance of differential expression was calculated using the bimod test. Functional enrichment of differentially expressed genes was then processed by Gene Ontology (GO) (http://www.geneontology.org/) analysis. The pseudotime trajectory was determined with the Monocle2 package with the default settings. Specifically, the DDRTree method was used for dimension reduction with max_components set at 2, and the cells were ordered using the orderCells function.
Bulk RNA-sequencing (RNA-seq) of mouse embryo hearts and HL-1 cells was carried on by the LC-Bio Technology, Hangzhou, China. The detailed operations were as follows: total RNA was isolated and purified using TRIzol reagent (Invitrogen, CA, USA). The RNA samples which passed quality control were fragmented into small pieces at 94℃ for 5-7min and reverse-transcribed to create the cDNA. The average insert size for the final cDNA library was 300±50 bp. The FASTQ data of sequencing reads were trimmed using paired-end sequencing. Consecutively, the trimmed reads were mapped to the mouse genome reference (mm10) by HISAT2 software (https://ccb.jhu.edu/software/hisat2). The mRNA expression abundance was analyzed using StringTie software and represented by FPKM. The differentially expressed mRNAs were selected with FC >1.5 and a parametric F-test comparing nested linear models (p value < 0.05) by the R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). Gene set enrichment analysis was run on all expressed genes which were ranked by log2FC value. Functional enrichment of differentially expressed genes was then processed by GO (http://www.geneontology.org/) analysis.
For ChIP-seq, ChIP products were end repaired, dA-tailing and linker ligation were performed, and barcoding and Illumina adapter addition were performed by PCR amplification. Libraries were purified using QiaQuick PCR purification reagents (Qiagen, Hilden, Germany) and size selected by 0.7×and 0.2×Ampure XP beads (Beckman, California, USA).
Assembly: mm10
Supplementary files format and content: bedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample. we used the custom script to get bedpe files for interaction loops identified by using raw contact frequencies.  The custom utility was used to convert the raw contact frequencies into sparse .matrix format, and  these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions.
Library strategy: 3C-HTGTS


title: T cells, RFP-JUN knockin, day 14, donor 1

description:
YC15_S80_L001_R1_001
RNA-2_day14.rds

value: donor 1

value: T cells


title: MDA-MB-231 cells, SIN3A+SIN3B-DKO1, rep1


title: T cells, RFP-tNGFR knockin, day 14, donor 1

description:
YC14_S79_L001_R1_001
RNA-2_day14.rds

value: RFP-tNGFR knockin


title: HL-1-SMC3-NC-ETS2-3C-HTGTS-rep1


title: T cells, RFP-tNGFR knockin, day 14, donor 2

description:
YC19_S84_L001_R1_001
RNA-2_day14.rds

value: donor 2


title: HL-1-SMC3-KD-ETS2-3C-HTGTS-rep2

value: Cardiac muscle cells HL-1


title: ChIP, V5, LNCaP, EHMT1-WT, Dox-rep 2

description:
ChIP_V5_LNCaP_EHMT1_WT_Dox.bw
ChIP_V5_LNCaP_EHMT1_WT_Dox_peaks.narrowPeak.gz

value: prostate cancer cell

value: 0.5μg/ml doxycycline for 2 days


title: MDA-MB-231 cells, SAP30-KO2, rep2

value: SAP30 knockout


title: MDA-MB-231 cells, SAP30-KO2, rep1


title: T cells, BATF-RFP knockin, day 14, donor 1

description:
YC12_S77_L001_R1_001
RNA-2_day14.rds

value: Primary cells

value: day 14


title: HL-1-SMC3-KD-ETS2-3C-HTGTS-rep1

value: Atrial tissue


title: T cells, RFP-TFAP4 knockin, day 14, donor 1

description:
YC13_S78_L001_R1_001
RNA-2_day14.rds

value: Blood


title: D80

city: Guangzhou

first: xiao

last: yuhua

state: Guangdong

address: No. 7 Jinsui Road

institute: sun yat-sen university

data_processing:
Cellranger v3.1 was used for demultiplexing, aligment and quantification.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file format

source_name: retinal organoid

extract_protocol:
All retina tissues were digested at 37℃, and were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in PBS solution. Single cell suspensions were diluted at a concentration of 500-1800 cells/uL in 0.04% BSA/Ames.
10x Genomics Chromium single cell system with v2

tag: time point


title: D120


title: MDA-MB-231 cells, SAP30-KO1, rep2


title: T cells, BATF-TFAP4 knockin, day 14, donor 1

description:
YC11_S76_L001_R1_001
RNA-2_day14.rds


title: MDA-MB-231 cells, SAP30-KO1, rep1


title: SP_Nivolumab_2

city: Shanghai

first: Ruifeng

last: Ding

address: No. 415 Fengyang Road, Huangpu District

department: Department of Anesthesiology

institute: Changzheng Hospital, Second Affiliated Hospital of Naval Medical University

data_processing:
Initially, the quality of the raw reads was evaluated using FastQC(v0.11.5)
Trimmomatic was employed to remove single-end sequence adapters, and a sliding window approach was used to detect the average base quality. Bases at the trailing end were trimmed if the average quality within a window fell below 20, and reads below 50bp after quality filtering were discarded
After sequence filtering, the resulting high-quality reads were aligned to the mouse reference genome (GRCm38) using Hisat2
StringTie was used for gene expression quantification for each gene, which produced a gene expression matrix
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file include raw counts for each Sample

source_name: spinal dorsal horn

extract_protocol:
Following the instructions of the TRIzol reagent kit, total RNA was extracted from the spinal cord and colon samples of each experimental group
The cDNA libraries were prepared using the SmartScribeTM Reverse Transcriptase kit (TAKARA, Japan). Ampure XP Beads (Beckman Coulter, USA) were used to select DNA fragments with lengths of 300-450 bp from the indexed libraries. The libraries were quantified using an Agilent 2100 Bioanalyzer and then combined at a concentration of 2 nM in a 1:1 ratio

value: spinal dorsal horn

value: WT

value: Nivolumab


title: D45


title: SP_Nivolumab_3


title: T cells, RFP-tNGFR knockin, day 6, donor 2

description:
YC9_S74_L001_R1_001
RNA-2_day6.rds

value: day 6


title: SP_Cancer_3

value: Cancer


title: T cells, RFP-JUN knockin, day 6, donor 2

description:
YC10_S75_L001_R1_001
RNA-2_day6.rds

value: RFP-JUN knockin


title: SP_Nivolumab_1


title: MDA-MB-231 cells, parental, rep2

value: Breast cancer cells

value: Parental

value: No treatment


title: T cells, RFP-TFAP4 knockin, day 6, donor 2

description:
YC8_S73_L001_R1_001
RNA-2_day6.rds

value: donor 2

value: T cells

value: RFP-TFAP4 knockin


title: ChIP, V5, LNCaP, EHMT1-WT, Dox-rep 1

value: prostate cancer cell

value: 0.5μg/ml doxycycline for 2 days

value: anti-V5 (Invitrogen)


title: MDA-MB-231, SAP30-KO1, H3, CST, rep2

data_processing:
FASTQ files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4). Low-quality reads and adapter were removed using fastq-mcf (v 1.05). The reads from FASTQ files were aligned to the human genome (hg19) using bowtie2 (v2.3.3.1). Picard-tool’s (v 2.10.10) MarkDuplicates module was then used to remove duplicate alignments
The duplicate removed alignment files were used to call peaks using MACS2 (v2.1.0), with a q-value threshold of 0.05 and using DNA input as background controls (histone H3 ChIP samples were used as background controls for H3K4me3 and H3K9ac ChIP).The resulting peak summits (called peak sites with coordinate of single-nucleotide) and bed files from peak-calling were defined.
Assembly: hg19
Supplementary files format and content: bed (except for Input sample and Histone H3 ChIP samples)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator (Brandson).
ChIP-seq libraries were prepared using the ThruPLEX DNA-seq kit (Takara). 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified 13 cycles on the thermocycler. Post amplification libraries were gel-purified for size selection at 300-500bp. Libraries were validated using Tapestation (Agilent) and quantified using Qubit Fluorometer (Invitrogen).

value: SAP30 knockout

value: Histone H3 (CST, #4620)


title: MBD6-FL-RFP_rep2_batch2

city: Los Angeles

first: Lucia

last: Ichino

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

data_processing:
For ChIP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage, bin size 10bp, --normalizeUsing RPKM.
Peaks were called with MACS2 (v 2.1.0) using an FDR cutoff of 0.01. The FLAG and RFP associated hyperchippable regions, defined as peaks called in the anti-FLAG Col0 or anti-RFP Col0 controls, were subtracted from the peak sets of each sample. The peaks of individual replicates for ACD15 and ACD21 were merged with homer mergePeaks using the option -d given.
Assembly: TAIR10
Supplementary files format and content: bigWig files are Sequencing depth tracks.
Supplementary files format and content: Peaks files were generated with MACS2.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown on soil in a greenhouse under long-day conditions (16h light / 8h dark).

extract_protocol:
The experimental procedure for ChIP-seq was performed as described in PMID 20734276 with some variations. 2 or 2.5 g of inflorescences were used for each ChIP sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer containing 1% formaldehyde. Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with 3.5 µl of Anti-FLAG M2 (Sigma, F1804). 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers and eluted with elution buffer (1% SDS and 0.1 M NaHCO3). Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions, with 15 cycles of PCR.

value: inflorescence

tag: ecotype

value: wild-type

tag: transgene

value: anti-FLAG M2


title: MBD6-FL-RFP-acd15acd21_rep2_batch2

value: acd15 acd21


title: SP_Cancer_2

value: spinal dorsal horn

value: WT

value: Cancer


title: SP_Cancer_1


title: T cells, BATF-RFP knockin, day 6, donor 2

description:
YC7_S72_L001_R1_001
RNA-2_day6.rds

source_name: Blood

value: Blood

value: Primary cells

value: BATF-RFP knockin

value: day 6


title: MBD6-FL-RFP-acd15acd21_rep1_batch2


title: MDA-MB-231, SAP30-KO1, H3, CST, rep1

value: Breast cancer cells


title: T cells, BATF-TFAP4 knockin, day 6, donor 2

description:
YC6_S71_L001_R1_001
RNA-2_day6.rds

value: donor 2

value: T cells

value: BATF-TFAP4 knockin


title: MBD6-FL-RFP_rep1_batch2


title: SP_Sham_2

value: Sham


title: Col0_RFP_rep1_batch2


title: T cells, RFP-JUN knockin, day 6, donor 1

description:
YC5_S70_L001_R1_001
RNA-2_day6.rds

value: donor 1

value: RFP-JUN knockin


title: SP_Sham_3


title: MDA-MB-231, parental, H3, CST, rep2

value: Parental

value: Histone H3 (CST, #4620)


title: MDA-MB-231, parental, H3, CST, rep1


title: SP_Sham_1


title: T cells, RFP-TFAP4 knockin, day 6, donor 1

description:
YC3_S68_L001_R1_001
RNA-2_day6.rds

value: RFP-TFAP4 knockin


title: T cells, RFP-tNGFR knockin, day 6, donor 1

description:
YC4_S69_L001_R1_001
RNA-2_day6.rds

value: RFP-tNGFR knockin


title: MDA-MB-231 cells, parental, rep1

value: No treatment


title: MDA-MB-231, SAP30-KO1, H3K9Ac, Abcam, rep2

value: SAP30 knockout

value: H3K9Ac (Abcam, #ab10812)


title: Colon_Nivolumab_3

source_name: Colon

value: Colon

value: WT

value: Nivolumab


title: T cells, BATF-RFP knockin, day 6, donor 1

description:
YC2_S67_L001_R1_001
RNA-2_day6.rds

value: Blood

value: Primary cells

value: BATF-RFP knockin

value: day 6


title: MDA-MB-231, SAP30-KO1, H3K9Ac, Abcam, rep1

value: Breast cancer cells


title: ACD15rep2_flag_batch1

value: inflorescence

value: wild-type

value: anti-FLAG M2


title: ACD15rep1_flag_batch1


title: Col0_RFP_rep2_batch2


title: ACD21rep2_flag_batch1


title: MDA-MB-231, parental, H3K9Ac, Abcam, rep2

value: Parental


title: T cells, BATF-TFAP4 knockin, day 6, donor 1

description:
YC1_S66_L001_R1_001
RNA-2_day6.rds

value: donor 1

value: T cells

value: BATF-TFAP4 knockin


title: Colon_Nivolumab_1


title: ACD21rep1_flag_batch1


title: Colon_Cancer_3

value: Cancer


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 15, donor 3

value: donor 3

value: tNGFR CD19-BBz CAR knockin

value: day 15


title: Colon_Cancer_2

value: Colon

value: WT


title: RNAseq_acd15acd21sln_rep5_batch2

data_processing:
Reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Assembly: TAIR10. We used custom transcripts annotations available from Github at: https://github.com/clp90/mbd56_pollen
Supplementary files format and content: bigWig files are Sequencing depth tracks.
Supplementary files format and content: *.count.txt files include transcript counts.

source_name: Mature pollen

extract_protocol:
Mature pollen was harvested with Galbraith Buffer method. RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo) with in column DNase I digestion.
300-700 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

value: Mature pollen

value: acd15.5 acd21.4 sln


title: MDA-MB-231, SAP30-KO1, H3K4me3, CST, rep1

value: SAP30 knockout


title: Colon_Cancer_1


title: RNAseq_acd15acd21sln_rep4_batch2


title: MDA-MB-231, parental, H3K4me3, CST, rep2

value: Breast cancer cells


title: T cells, tNGFR CD19-28z CAR knockin, day 15, donor 2

value: donor 2

value: Blood

value: Primary cells

value: tNGFR CD19-28z CAR knockin


title: Colon_Nivolumab_2

value: Nivolumab


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 15, donor 2

value: T cells


title: Colon_Sham_3

value: Sham


title: Colon_Sham_2


title: MDA-MB-231, parental, H3K4me3, CST, rep1

value: Parental


title: MDA-MB-231, SAP30-KO1, Input for Pol II, rep2


title: RNAseq_acd15acd21sln_rep2_batch1


title: Colon_Sham_1


title: Col0_flag_batch1

value: inflorescence

value: wild-type

value: anti-FLAG M2


title: MDA-MB-231, SAP30-KO1, H3K4me3, CST, rep2


title: T cells, tNGFR HA GD2-28z CAR knockin, day 15, donor 2

value: tNGFR HA GD2-28z CAR knockin

value: day 15


title: MDA-MB-231, parental, H3K9Ac, Abcam, rep1

value: H3K9Ac (Abcam, #ab10812)


title: RNAseq_acd15acd21sln_rep1_batch1

value: Mature pollen

value: acd15.5 acd21.4 sln


title: T cells, tNGFR CD19-28z CAR knockin, day 15, donor 1

value: donor 1


title: MDA-MB-231, SAP30-KO1, Input for Pol II, rep1

value: Breast cancer cells

value: SAP30 knockout


title: MDA-MB-231, parental, Input for Pol II, rep2


title: T cells, tNGFR CD19-28z CAR knockin, day 15, donor 3

value: donor 3

value: Blood

value: Primary cells


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 15, donor 1

value: T cells

value: tNGFR CD19-BBz CAR knockin


title: RNAseq_acd15acd21_rep5_batch2


title: RNAseq_acd15acd21_rep4_batch2


title: MDA-MB-231, parental, Input for Pol II, rep1

value: Parental


title: T cells, tNGFR HA GD2-28z CAR knockin, day 15, donor 3


title: Spleen, replicate 2, scRNA-seq

city: Silver Spring

first: Luis

middle: V

last: Santana-Quintero

state: MD

address: 1627 Whitehall Dr

department: CBER

institute: US FDA

description: 10X genomics

data_processing:
the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software version 5.0.1
Genomic sequences for Mus musculus  and Leishmania donovani were downloaded from RefSeq and merged into one file.
The merged genome and annotation file were then processed by cellranger mkref (version 5.0.1), using the default parameters, to create the appropriate index of an artificial single genome
The base calling was performed using cellranger mkfastq (version 5.0.1) using the default parameters. Samples were processed separately using the cellranger count (version 5.0.1) against the host/parasite merged genome and the corresponding annotation file. The  hits from host and parasites were processed using an internally developed script.
The alignments produced by cellranger count were processed with samtools (version 1.3.1) to produce host and parasite specific metrics including the estimated number of cells, the median genes per cell, the total number of genes detected and median UMI counts per cell.
Reads aligned to L. donovani transcripts were  aligned against the nt database using BLAST59 to test for similarities to the host genome that would suggest false positive hits.
Assembly: Mus musculus (assembly GRCm38 with accession number GCF_000001635.27) and Leishmania donovani (assembly ASM22713v2 with accession number GCF_000227135.1)

source_name: Spleen

extract_protocol:
Spleen and bone marrow were isolated from the mice. Single cell suspensions were generated by mecanical dissagregation of the spleen agaisnt a 70 micrometers strainer and by flushing the bone marrow with 3 ml of complete RPMI medium. Cells were passed through a MACS-LS column to remove the non-targeted cells by using monocyte isolation kit.
Library was performed according to manufacturer's instructions (10x Genomics Chromium Controller and the Chromium Next GEM Single cells 3’ Library Kit v3.1 )

treatment_protocol: 9-10 weeks old female mice were infected with 10 million Leishmania donovani parasites. The tissue harvest was performed 72 days post  intection

value: Spleen

tag: disease stage

value: chronic infection

tag: age

value: 9-10 weeks

tag: Sex

value: Female


title: Spleen,replicate 1, scRNA-seq

description: 10X genomics

tag: tissue


title: RNAseq_acd15acd21_rep3_batch2


title: MDA-MB-231, SAP30-KO1, Pol II, Abcam, rep2

tag: cell type

value: Pol II (Abcam, #ab817)


title: T cells, tNGFR HA GD2-28z CAR knockin, day 15, donor 1

tag: genotype

value: tNGFR HA GD2-28z CAR knockin

tag: time

value: day 15


title: RNAseq_acd15acd21sln_rep3_batch2

value: Mature pollen

value: acd15.5 acd21.4 sln


title: BM,replicate 2,  scRNA-seq

description: 10X genomics

source_name: Bone marrow

value: Bone marrow


title: T cells, tNGFR CD19-28z CAR knockin, day 6, donor 3

value: tNGFR CD19-28z CAR knockin

tag: treatment

value: day 6


title: MDA-MB-231, SAP30-KO1, Pol II, Abcam, rep1

tag: cell line

value: Breast cancer cells

value: SAP30 knockout


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 6, donor 3

value: donor 3

value: Blood

value: Primary cells

value: T cells


title: RNAseq_acd15acd21_rep2_batch1


title: RNAseq_acd15acd21_rep1_batch1


title: BM,replicate 1,  scRNA-seq

description: 10X genomics

value: chronic infection


title: RNAseq_acd21_rep5_batch2


title: MDA-MB-231, Input for SIN3B, rep2

value: Parental

tag: chip antibody


title: MDA-MB-231, parental, Pol II, Abcam, rep1


title: T cells, tNGFR CD19-28z CAR knockin, day 6, donor 2

tag: individual

value: donor 2


title: T cells, tNGFR HA GD2-28z CAR knockin, day 6, donor 3


title: Formate anti-PD-1 1

first: Osmaan

last: Shahid

address: 77 Avenue Louis Pasteur

department: Department of Immunology

institute: Harvard Medical School

description:
10X Genomics 5'v2
F.P. 10 -GEX

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, and UMI counting were performed using the Cell Ranger analysis pipeline v5.0.0
and aligned to the mm10 reference genome.
Data pre-processing and filtering was performed using Python v3.8.5 and the Scanpy v1.5.1 package.
Normalization, integration, and clustering was performed using the R v3.6.2 package Seurat v3.2.2 with SCTransform method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Assembly: mm10
Supplementary files format and content: The .rds file contains Seurat objects with the count matrix as an RNA assay, and other metadata in the @meta.data field.
Supplementary files format and content: The .h5ad file contains a Scanpy/Adata object with the count matrix, and the associated metadata in the .obs data field.

source_name: tumor (TIL)

growth_protocol: B16-OVA cells were grown in vitro for 2 passages then implanted into C57BL/6 mice.

extract_protocol:
Tumor dissected from animals and mechanically dissociated. Incubated with Collagenase I (in PBS Mg+Cl+) in a shaking incubator. Lymphocytes separated using lymphocyte separation media (LSM) density gradient. Collected cells stained for Live Dead and CD8 then sorted using FACSAria for viable CD8+ cells. 3 mice per replicate pooled together.
Libraries were contructued according to the manufactures protocol for 10X Genomics single cell 5'v2. Isolated cells resuspended in master mix and placed in chip with gel beads and partitioning oil to create gel bed in emulsion (GEM)s. GEMs utilized for reverse transcription (RT) with addition of 10X barcode, unique molecular identifier (UMI), and R1 primer. cDNA amplified before preparation of libraries for gene expression. cDNA fragmented and size selected using SPRI beads for gene expression (GEX) library construction. Duringh library construction Illumina R2 primer, paired end constructs with P5 and P7, and sample index were added.

treatment_protocol: At day 9 post B16-OVA tumor implantation mice received either control or formate (5 mg/mL) drinking water. At day 10 post implantation mice received a 100 ug dose of either anti-PD-1 or isotype control antibody.

value: tumor (TIL)

value: CD8+ T cell

value: formate drinking water,anti-PD-1 mAb


title: Control anti-PD-1 2

description:
10X Genomics 5'v2
C.P. 8 -GEX

value: control drinking water,anti-PD-1 mAb


title: Formate anti-PD-1 3

description:
10X Genomics 5'v2
F.P. 12 -GEX


title: Formate anti-PD-1 2

description:
10X Genomics 5'v2
F.P. 11 -GEX


title: RNAseq_acd21_rep3_batch2

value: Mature pollen


title: T cells, tNGFR HA GD2-28z CAR knockin, day 6, donor 2

value: tNGFR HA GD2-28z CAR knockin


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 6, donor 2

value: tNGFR CD19-BBz CAR knockin


title: Control anti-PD-1 1

description:
10X Genomics 5'v2
C.P. 7 -GEX


title: T cells, tNGFR CD19-28z CAR knockin, day 6, donor 1

value: donor 1

value: tNGFR CD19-28z CAR knockin

value: day 6


title: RNAseq_acd21_rep1_batch1


title: MDA-MB-231, Input for SAP30 SIN3A, rep1

value: Breast cancer cells


title: T cells, tNGFR CD19-BBz CAR CAR knockin, day 6, donor 1

value: Blood


title: MDA-MB-231, SIN3B, Novus, rep2

value: SIN3B (Novus, #NBP2-20367)


title: T cells, tNGFR HA GD2-28z CAR knockin, day 6, donor 1

value: Primary cells

value: T cells


title: MDA-MB-231, parental, Pol II, Abcam, rep2

value: Parental

value: Pol II (Abcam, #ab817)


title: Formate Isotype 2

description:
10X Genomics 5'v2
F.I. 5 -GEX

value: tumor (TIL)

value: formate drinking water, isotype control mAb


title: Formate Isotype 1

description:
10X Genomics 5'v2
F.I. 4 -GEX

value: CD8+ T cell


title: RNAseq_acd15_rep4_batch2


title: RNAseq_acd21_rep4_batch2


title: MDA-MB-231, SIN3B, Novus, rep1


title: T cells, tNGFR knockin, donor 3

data_processing:
The ATAC-seq libraries were processed using the pepatac pipeline (http://pepatac.databio.org/), with default options.
The fastq files were first trimmed to remove adapter sequences, and then prealigned to the mitochondrial genome to exclude mitochondrial reads. Furthermore, multimapping reads aligning to repetitive regions of the genome were filtered out to ensure the accuracy of downstream analysis.
After these initial steps, Bowtie2 was used to align the reads to the hg38 genome.
Samtools was then employed to identify uniquely aligned reads, and Picard was used to remove the duplicate reads. The resulting deduplicated aligned BAM file was used for downstream analysis.
Assembly: hg38 reference genome
Supplementary files format and content: Rds file generated after data processing including all samples

extract_protocol:
Nuclei were isolated with ATAC Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). Nuclei were subjected to tagmentation using Nextera DNA Library Preparation Kit (Illumina). After tagmentation, DNA was purified with MinElute PCR Purification Kit (Qiagen).
Tagmented DNA was then amplified with Phusion high-fidelity PCR master mix (NEB) using 14 PCR cycles. Amplified libraries were purified again with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a Novaseq 6000 platform with 150bp paired-end sequencing.

value: donor 3

value: tNGFR knockin


title: RNAseq_acd15_rep3_batch2

value: Mature pollen


title: MDA-MB-231, SIN3A, Abcam, rep2

value: SIN3A (Abcam, #ab3479)


title: T cells, TFAP4 knockin, donor 3

value: TFAP4 knockin


title: Control Isotype 3

description:
10X Genomics 5'v2
C.I. 3 -GEX

value: control drinking water, isotype control mAb


title: MDA-MB-231, Input for SIN3B, rep1


title: MDA-MB-231, SIN3A, Abcam, rep1


title: RNAseq_acd15_rep1_batch1


title: Control Isotype 2

description:
10X Genomics 5'v2
C.I. 2 -GEX


title: RNAseq_acd15_rep2_batch1


title: RNAseq_acd21_rep2_batch1


title: T cells, BATF-TFAP4 knockin, donor 3

value: BATF-TFAP4 knockin


title: Control Isotype 1

description:
10X Genomics 5'v2
C.I. 1 -GEX


title: MDA-MB-231, Input for SAP30 SIN3A, rep2

value: Breast cancer cells


title: T cells, RFP-TFAP4 knockin, donor 3

value: Blood

value: RFP-TFAP4 knockin


title: Formate Isotype 3

description:
10X Genomics 5'v2
F.I. 6 -GEX


title: MDA-MB-231, SAP30, Bethyl, rep2

value: SAP30 (Bethyl Laboratories, #A303-551A)


title: RNAseq_sln_rep5_batch2

value: sln


title: RNAseq_acd15_rep5_batch2


title: MDA-MB-231, SAP30, Bethyl, rep1

value: Parental


title: T cells, BATF-RFP knockin, donor 3

value: Primary cells

value: T cells

value: BATF-RFP knockin


title: 50-wk-old C57BL6 ABCs-3

city: Fukuoka

first: Chisato

last: Ono

address: 3-1-1, maidashi, Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was harvested from cells using miRNeasy Micro Kit (Qiagen).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

tag: strain

value: Primary B cells


title: 50-wk-old C57BL6 ABCs-2


title: T cells, RFP-tNGFR knockin, donor 3

value: donor 3

value: RFP-tNGFR knockin


title: 50-wk-old C57BL6 ABCs-1


title: RNAseq_sln_rep3_batch2

value: Mature pollen


title: T cells, tNGFR knockin, donor 2

value: donor 2

value: tNGFR knockin


title: MDA-MB-231, SAP30-KO1, ATAC, rep3

data_processing:
FASTQ files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4). Low-quality reads and adapter were removed using Trim Galore (v 0.4.5).The reads from FASTQ files were aligned to the human genome (hg19) using bowtie2 (v2.3.3.1). Picard-tool’s (v 2.10.10) MarkDuplicates module was then used to remove duplicate alignments.
The duplicate removed alignment files were used to call peaks using MACS2 (v2.1.0), with a q-value threshold of 0.05. The resulting peak summits and bed files from peak-calling were defined. ChIPseeker was used to annotate the peak files.
Assembly: hg19
Supplementary files format and content: bed

extract_protocol:
Cells were washed with PBS and re-suspended in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Transposition reaction was applied using Nextera XT Index Kit (Illumina), followed by DNA purification using a MinElute PCR Purification Kit (QIAGEN). The transposed DNA fragments were then subjected to 5 cycles PCR for pre-amplification first, and then amplified by PCR for additional 5 cycles.The amplified libraries subjected to gel size selection to purify 200-500 bp fragments.Libraries were validated using Tapestation (Agilent) and quantified using Qubit Fluorometer (Invitrogen)

value: SAP30 knockout


title: MDA-MB-231, SAP30-KO1, ATAC, rep2


title: 50-wk-old C57BL6 FO B cells-3


title: RNAseq_sln_rep2_batch1


title: T cells, TFAP4 knockin, donor 2

value: TFAP4 knockin


title: MDA-MB-231, SAP30-KO1, ATAC, rep1

value: Breast cancer cells


title: 50-wk-old C57BL6 FO B cells-2


title: T cells, BATF-TFAP4 knockin, donor 2

value: Blood

value: BATF-TFAP4 knockin


title: 50-wk-old C57BL6 FO B cells-1


title: RNAseq_mbd56_rep5_batch2

value: mbd5 mbd6


title: MDA-MB-231, parental, ATAC, rep2


title: RNAseq_mbd56_rep4_batch2


title: T cells, RFP-TFAP4 knockin, donor 2

value: RFP-TFAP4 knockin


title: MDA-MB-231, parental, ATAC, rep1

value: Parental


title: RNAseq_sln_rep1_batch1

value: sln


title: 8-wk-old C57BL6 FO B cells-2


title: KU143t

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Assembly: hg19
Supplementary files format and content: .gct file format (tab-delimited text) including normalized gene expression levels normalized within 106 1st biopsy tissues (NAFLD.HUn106.gct) and within the 58 high-risk patients with paired biopsy tissues (NAFLD.HUn164.gct).

source_name: Liver

extract_protocol:
RNA was isolated from 10 micron-thick FFPE tissue using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.
Truseq RNA Exome kit (Illumina, CA) following manufacturer’s protocol.
Exome-enriched RNA-seq

value: Liver

value: Male

tag: recurrence

value: No


title: RNAseq_sln_rep4_batch2


title: 8-wk-old C57BL6 FO B cells-3

value: Primary B cells


title: RNAseq_mbd56_rep2_batch1


title: 8-wk-old C57BL6 FO B cells-1


title: T cells, BATF-RFP knockin, donor 2

value: Primary cells

value: T cells

value: BATF-RFP knockin


title: RNAseq_mbd56_rep1_batch1

value: Mature pollen


title: 7.5M 5xFADP522R mice; NeuN negative cells  [R3P_20]

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 with --expect-cells=5000 --nosecondary --include-introns commands.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain, Cortex

extract_protocol:
Nuclei were isolated from the fresh-frozen cortical brain region as previously described (Hahn et al., 2021). NeuN-negative nuclei were separately sorted into 1.5 ml DNA LoBind tubes with 1 ml Dijon buffer. A total of 50,000 single nuclei were sorted from each sample. Nuclei were counted, and concentrations were adjusted to ∼1 million nuclei/ml.
Reagents for the Chromium Single Cell 3ʹ Library & Gel Bead Kit v3 (10X Genomics). The nuclei/master mix solution was adjusted to target 10,000 nuclei per sample (5,000 nuclei from male mice and 5,000 nuclei from female mice) and loaded on a standard Chromium Controller (10X Genomics). Illumina sequencing of 10X snRNA-seq libraries was performed by Novogene Co. Inc.

value: NeuN negative cells

value: Brain, Cortex

value: 5xFAD; P522R


title: T cells, TFAP4 knockin, donor 1

value: donor 1

value: Blood

value: TFAP4 knockin


title: MDA-MB-231, parental, ATAC, rep3

value: Breast cancer cells


title: RNAseq_Col0_rep5_batch2

value: wild-type


title: 7.5M 5xFADM28L mice; NeuN negative cells  [R3M_18]


title: KU135t


title: RNAseq_Col0_rep4_batch2


title: T cells, BATF-TFAP4 knockin, donor 1

value: BATF-TFAP4 knockin


title: T cells, RFP-TFAP4 knockin, donor 1

value: RFP-TFAP4 knockin


title: 7.5M 5xFAD mice; NeuN negative cells [R3AD_16]


title: RNAseq_Col0_rep3_batch2


title: KU130t

value: Liver

value: Female


title: RNAseq_mbd56_rep3_batch2

value: mbd5 mbd6


title: KU128t1

value: Male

value: No


title: T cells, BATF-RFP knockin, donor 1

value: Primary cells

value: T cells

value: BATF-RFP knockin


title: 7.5M 5xFADP522R mice; NeuN negative cells  [R2P_14]

value: NeuN negative cells

value: Brain, Cortex


title: 7.5M 5xFADM28L mice; NeuN negative cells  [R2M_12]


title: RNAseq_Col0_rep2_batch1

value: Mature pollen


title: T cells, RFP-tNGFR knockin, donor 2

value: donor 2

value: Blood

value: RFP-tNGFR knockin


title: KU126t

value: Yes


title: T cells, RFP-tNGFR knockin, donor 1

value: donor 1


title: KU140t


title: RNAseq_Col0_rep1_batch1

value: wild-type


title: KU124t

value: Liver


title: T cells, tNGFR knockin, donor 1

value: tNGFR knockin


title: 7.5M 5xFAD mice; NeuN negative cells [R2AD_10]


title: KU122t

value: Female


title: KU138t

value: Male


title: 7-5M_M9-17_M28L_HOM_5xFAD_Ctx

description:
Bulk RNA-seq
RNAseq_STAR_featureCounts_matrix.tsv.gz

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM26 by STAR 2.7.2b. Reads mapped to each gene were counted using featureCounts.
Assembly: gencode.vM26
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: brain, cortex

extract_protocol:
RNA was isolated by chloroform extraction and purified using the Purelink RNA Mini Kit
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep kit following manufacturer's protocols.

value: brain, cortex

value: Transgenic mice


title: 7-5M_M7-9_M28L_HOM_5xFAD_Ctx


title: KU118t


title: 7-5M_M6-1270_WT_5xFAD_Ctx


title: KU116t2

value: No


title: 7-5M_M7-31_P522R_HOM_5xFAD_Ctx


title: KU119t


title: 7-5M_M4-27_P522R_HOM_5xFAD_Ctx


title: 7-5M_M5-1269_WT_5xFAD_Ctx


title: KU111t


title: 7-5M_M3-23_P522R_HOM_5xFAD_Ctx


title: KU113t


title: 14837T-3

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

data_processing:
Normal sequence Illumina Novaseq PE150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x  -1  -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Assembly: mm10
Supplementary files format and content: counts

source_name: PDAC

growth_protocol: cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA is used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PDAC

value: PDAC cells

value: WT


title: KU107t


title: KU109t


title: 7-5M_M2-21_P522R_HOM_5xFAD_Ctx


title: KU106t


title: 6-10B cells transfected with EBV-microRNA-BART2-5p mimics for 48 hours [microRNAseq-B2-5p-1]

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description: microRNA expression data for 6-10B cells transfected with EBV-microRNA-BART2-5p mimics

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: human genome GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each samples

source_name: a human-derived nasopharyngeal hypofractionated squamous cell carcinoma cell line

growth_protocol: The human 6-10B cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
For microRNA-Seq, enrichment of microRNAs were performed according to the manufacturer's instructions
microRNA libraries were prepared for sequencing using standard protocols.

treatment_protocol: 6-10B cells were transfected with either BART2-5p mimics or negative control (NC)  microRNA mimics for 48 hours.

tag: agent


title: LIN28B KO 15376T-3

value: LIN28B knockout


title: 7-5M_M2-1181_WT_5xFAD_Ctx


title: 14837T-2


title: 6-10B cells transfected with EBV-microRNA-BART2-5p mimics for 48 hours [microRNAseq-B2-5p-2]


title: 7-5M_M1-11_M28L_HOM_5xFAD_Ctx


title: 6-10B cells transfected with negative control (NC) microRNA mimics for 48 hours [microRNAseq-NC-2]

description: microRNA expression data for 6-10B cells transfected with negative control microRNA mimics

value: transfected with negtive control (NC) microRNA mimics


title: KU102t


title: KU100t2


title: 6-10B cells transfected with negative control (NC) microRNA mimics for 48 hours [microRNAseq-NC-1]


title: 15376T-3


title: 7-5M_M1-1177_WT_5xFAD_Ctx


title: KU099t


title: 7-5M_F9-16_M28L_HOM_5xFAD_Ctx


title: 15376T-2


title: KU097t


title: 6-10B cells transfected with EBV-microRNA-BART2-5p mimics for 48 hours [RNAseq-B2-5p-1]

description: mRNA expression data for 6-10B cells transfected with EBV-microRNA-BART2-5p mimics

extract_protocol:
For mRNA-seq, mRNA was enriched by polyA selection.
RNA libraries were prepared for sequencing using standard Solexa protocols.


title: LIN28B KO 15376T-2


title: 14837T


title: 6-10B cells transfected with EBV-microRNA-BART2-5p mimics for 48 hours [RNAseq-B2-5p-2]


title: KU095t


title: LIN28B KO 15376T


title: 7-5M_M2-15_M28L_HOM_5xFAD_Ctx


title: KU094t2


title: 7-5M_F8-14_M28L_HOM_5xFAD_Ctx


title: 6-10B cells transfected with negative control (NC) microRNA mimics for 48 hours [RNAseq-NC-1]

description: mRNA expression data for 6-10B cells transfected with negative control microRNA mimics


title: 15376T


title: 6-10B cells transfected with negative control (NC) microRNA mimics for 48 hours [RNAseq-NC-2]


title: 7-5M_F7-12_M28L_HOM_5xFAD_Ctx


title: 7-5M_F4-54_P522R_HOM_5xFAD_Ctx


title: KU091t


title: 7-5M_F4-1248_WT_5xFAD_Ctx


title: LPS+50-3

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM value for gene and transcript

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

tag: group


title: KU089t


title: LPS+50-2


title: KU088t


title: DRG2a

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

description: Visium 10X Genomics

data_processing:
Fastq.gz files were generated and demultiplexed with Spaceranger 1.3.0
Raw sequencing data was processed through the Spaceranger (v1.3.0) pipeline. Loupe browser files and filtered matrices were generated.
Assembly: gencode v39
Supplementary files format and content: filtered_feature_bc_matrix.h5 (counts matrix from space ranger)
Supplementary files format and content: web_summary.html (metrics from space ranger)
Supplementary files format and content: .cloupe (cloupe file from space ranger)
Supplementary files format and content: image.png
Library strategy: Spatial Transcriptomics

source_name: Lumbar DRG

extract_protocol:
Human DRG was harvested and flash-frozen postmortem. Samples were embedded in OCT and sectioned at 16µm onto a 10x Visium expression slide (Serial numbers V11N01-301-A1 and V11N01-301-B1) and visualized with H&E. RNA within the tissue was hybridized to barcoded probes according to manufacturer’s protocol.
Libraries were prepared with the Visium Spatial Gene Expression FF kit V1 from 10X Genomics and sequenced on an SP 28x150nt lane in a NovaSeq 6000.

value: Lumbar DRG

value: 96 years

tag: biol rep