title: DLPFC, control,4

city: BALTIMORE

first: Jiyun

last: Zhou

state: MD

address: 855 N Wolfe St Suite 300

institute: The Lieber Institute for Brain Development

description: Library name: Br1378

data_processing:
We implemented a versatile mapping pipeline (http://cemba-data.readthedocs.io/) for all the methylome based technologies developed by our group.4,16 The main steps of this pipeline include: 1) Demultiplexing FASTQ files into single-cell; 2) Reads level QC; 3) Mapping; 4) BAM file processing and QC; 5) final molecular profile generation. Sequencing reads were first trimmed to remove sequencing adaptors using Cutadapt 1.11 with the following parameters in paired-end mode: -f fastq -q 20 -m 62 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. For singleplex samples, -m parameter was set to 40. For multiplexed samples, 16 bp were further trimmed from both 5’- and 3’- ends of R1 and R2 reads to remove random primer index. sequence and C/T tail introduced by Adaptase, with the following parameters: -f fastq -u 16 -u 16 -m 30. Trimmed reads for mouse and human single nuclei were mapped to mm10 and hg19 reference genomes, respectively. R1 and R2 reads were mapped separately as single-end reads using Bismark v0.15.0 with parameter --bowtie2. --pbat option was activated for mapping R1 reads. Resulting bam files were sorted using SAMtools 1.3 sort, followed by removal of duplicate reads using Picard 1.141 MarkDuplicates with the option REMOVE_DUPLICATES=true (https://broadinstitute.github.io/picard/). Non-clonal reads were further filtered for minimal mapping quality (MAPQ ≥ 30) using samtools view with option -q30.To prevent regional mCH level estimation from being skewed by rare reads that failed to be bisulfite converted, reads with read-level mCH level greater than 0.7 were excluded.The calling of unmethylated and methylated base calls was performed by call_methylated_sites of Methylpy ( https://github.com/yupenghe/methylpy/ ).
Assembly: hg19
Supplementary files format and content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines). contact files are tab delimited files of contacts, columns in these files are: 1 - chromosome of first sequence, 2 - position of first sequence, 3 - chromosome of second sequence, 4 - position of second sequence, 5 strand of the first sequence , 6 strand of the second sequence

source_name: DLPFC

extract_protocol:
Nuclei isolation from cultured cells for snmCT-seq: Cell pellets containing 1 million cells were resuspended in 600 µl NIBT [250 mM Sucrose, 10 mM Tris-Cl pH=8, 25 mM KCl, 5mM MgCl2, 0.1% Triton X-100, 1mM DTT, 1:100 Proteinase inhibitor (Sigma-Aldrich P8340), 1:1000 SUPERaseIn RNase Inhibitor (ThermoFisher Scientific AM2694), 1:1000 RNaseOUT RNase Inhibitor (ThermoFisher Scientific 10777019)]. The lysate was transferred to a pre-chilled 2 ml dounce homogenizer (Sigma-Aldrich D8938) and dounced using loose and tight pestles for 20 times each. The lysate was then mixed with 400 µl of 50% Iodixanol (Sigma-Aldrich D1556) and gently pipetted on top of 500 µl 25% Iodixanol cushion. Nuclei were pelleted by centrifugation at 10,000 x g at 4°C for 20 min using a swing rotor. The pellet was resuspended in 2 ml of DPBS supplemented with 1:1000 SUPERaseIn RNase Inhibitor and 1:1000 RNaseOUT RNase Inhibitor. Hoechst 33342 was added to the sample to a final concentration of 1.25 nM and incubated on ice for 5 min for nuclei staining. Nuclei were pelleted by 1,000 x g at 4°C for 10 min and resuspended in 1 ml of DPBS supplemented with RNase inhibitors. Nuclei isolation from human brain tissues and GpC methyltransferase treatment Brain tissue samples were ground in liquid nitrogen with cold mortar and pestle, and then aliquoted and store at -80°C. Approximately 100mg of ground tissue was resuspended in 3 ml NIBT (250 mM Sucrose, 10 mM Tris-Cl pH=8, 25 mM KCl, 5mM MgCl2, 0.2% IGEPAL CA-630, 1mM DTT, 1:100 Proteinase inhibitor (Sigma-Aldrich P8340), 1:1000 SUPERaseIn RNase Inhibitor (ThermoFisher Scientific AM2694), 1:1000 RNaseOUT RNase Inhibitor (ThermoFisher Scientific 10777019)). The lysate was transferred to a pre-chilled 7 ml dounce homogenizer (Sigma-Aldrich D9063) and dounced using loose and tight pestles for 40 times each. The lysate was then mixed with 2 ml of 50% Iodixanol (Sigma-Aldrich D1556) to generate a nuclei suspension with 20% Iodixanol. Gently pipet 1 ml of the nuclei suspension on top of 500 µl 25% Iodixanol cushion in each of the 5 freshly prepared 2ml microcentrifuge tubes. Nuclei were pelleted by centrifugation at 10,000 x g at 4°C for 20 min using a swing rotor. The pellet was resuspended in 1ml of DPBS supplemented with 1:1000 SUPERaseIn RNase Inhibitor and 1:1000 RNaseOUT RNase Inhibitor. A 10 µl aliquot of the suspension was taken for nuclei counting using a Biorad TC20 Automated Cell Counter. One million nuclei aliquots were pelleted by 1,000 x g at 4°C for 10 min and resuspended in 200 µl of GpC methyltransferase M.CviPI (NEB M0227L) reaction containing 1X GC Reaction Buffer, 0.32 nM S-Adenoslylmethionime, 80U 4U/µl M.CviPI, 1:100 SUPERaseIn RNase Inhibitor and 1:100 RNaseOUT RNase Inhibitor and incubated at 37°C for 8 min. The reaction was stopped by adding 800 µl of ice-cold DPBS with 1:1000 RNase inhibitors and mixing. Hoechst 33342 was added to the sample to a final concentration of 1.25 nM and incubated on ice for 5 min for nuclei staining. Nuclei were pelleted by 1,000 x g at 4°C for 10 min, resuspended in 900 µl of DPBS supplemented with 1:1000 RNase inhibitors and 100 µl of 50mg/ml UltrapureTM BSA (Ambion AM2618) and incubated on ice for 5 min for blocking. Neuronal nuclei were labeled by adding 1 µl of AlexaFluor488-conjugated anti-NeuN antibody (clone A60, MilliporeSigma MAB377XMI) for 20 min. For snATAC-seq, nuclei were isolated from frozen mouse brain sections and permeabilized. Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR. Reverse transcription for snmC2T-seq Single cells or single nuclei were sorted into 384-well PCR plates (ThermoFisher 4483285) containing 1 µl mCT-seq reverse transcription reaction per well. The mCT-seq reverse transcription reaction contained 1X Superscript II First-Strand Buffer, 5mM DTT, 0.1% Triton X-100, 2.5 mM MgCl2, 500 µM each of 5’-methyl-dCTP (NEB N0356S), dATP, dTTP and dGTP, 1.2 µM dT30VN_4 oligo-dT primer (5’-AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3’ was used the cultured cell experiments; 5’-/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3’ was used for human brain experiments), 2.4 µM TSO_3 template switching oligo (/5SpC3/AAGCAGUGGUAUCAACGCAGAGUGAAUrGrG+G), 1U RNaseOUT RNase inhibitor, 0.5 U SUPERaseIn RNase inhibitor, 10U Superscript II Reverse Transcriptase (ThermoFisher 18064-071). For snmC2T-seq, the reaction further included 2 µM N6_2 random primer (/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACNNNNNN). After sorting, the PCR plates were vortexed and centrifuged at 2000 x g. The plates were placed in a thermocycler and incubated using the following program: 25°C for 5 min, 42°C for 90min, 70°C 15min followed by 4°C. cDNA amplification for snmC2T-seq 3 µl of mCT-seq cDNA amplification mix was added into each mCT-seq reverse transcription reaction. mCT-seq cDNA amplification reaction contains 1X KAPA 2G Buffer A, 600 nM ISPCR23_2 PCR primer (/5SpC3/AAGCAGUGGUAUCAACGCAGAGU), 0.08U KAPA2G Robust HotStart DNA Polymerase (5 U/μL, Roche KK5517). PCR reactions were performed using a thermocycler with the following conditions: 95°C 3min -> [95°C 15 sec -> 60°C 30 sec -> 72°C 2min] -> 72°C 5min -> 4°C. The cycling steps were repeated for 12 cycles for scmCT-seq using H1 or HEK293 cells, 15 cycles for snmCT-seq using H1 or HEK293 cells and 14 cycles for snmC2T-seq using human brain tissues. Digestion of unincorporated DNA oligos for snmCT-seq For scmCT-seq and snmCT-seq using H1 and HEK293 cells, 1 µl uracil cleavage mix was added to into cDNA amplification reaction. Each 1 µl uracil cleavage mix contains 0.25 µl Uracil DNA Glycosylase (Enzymatics G5010) and 0.25 µl Endonuclease VIII (Enzymatics Y9080) and 0.5 µl Elution Buffer (Qiagen 19086). Unincorporated DNA oligos were digested at 37°C for 30 min using a thermocycler. We have found that Endonuclease VIII is dispensable for the digestion of unincorporated DNA oligos since the alkaline condition during the desulfonation step of bisulfite conversion can effective cleave abasic sites created by Uracil DNA Glycosylase (Greenberg, 2014). Therefore for snmC2T-seq using human brain tissues, each cDNA amplification reaction was treated with 1µl uracil cleavage mix containing 0.5 µl Uracil DNA Glycosylase (Enzymatics G5010-1140) and 0.5 µl Elution Buffer (Qiagen 19086). For snATAC-seq, nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode (T5 and T7). After pooling, 20 nuclei were sorted into 768 wells and a second barcode (i5 and i7) was introduced by PCR. Libraries were sequenced on a HiSeq2500 (Illumina) with following read lengths: 50 + 14 + 14 + 50 (Read1 + Index1 + Index2 + Read2).
Single cells or single nuclei were sorted into 384-well PCR plates (ThermoFisher 4483285) containing 1 μl snmCAT-seq reverse transcription reaction per well. The snmCAT-seq reverse transcription reaction contained 1X Superscript II First-Strand Buffer, 5mM DTT, 0.1% Triton X-100, 2.5 mM MgCl2, 500 μM each of 5′-methyl-dCTP (NEB N0356S), dATP, dTTP and dGTP, 1.2 μM dT30VN_4 oligo-dT primer (5′-AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3′ was used the cultured cell snmCAT-seq experiments; 5′-/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACUTTTTTUTTTTTUTTTTTUTTTTTUTTTTTVN-3′ was used for human brain snmCAT-seq experiments), 2.4 μM TSO_3 template switching oligo (5′-/5SpC3/AAGCAGUGGUAUCAACGCAGAGUGAAUrGrG+G-3′), 1U RNaseOUT RNase inhibitor, 0.5 U SUPERaseIn RNase inhibitor, 10U Superscript II Reverse Transcriptase (ThermoFisher 18064-071). For snmCAT-seq performed with nuclei samples, the reaction further included 2 μM N6_2 random primer (5′-/5SpC3/AAGCAGUGGUAUCAACGCAGAGUACNNNNNN-3′). After sorting, the PCR plates were vortexed and centrifuged at 2000 x g. The plates were placed in a thermocycler and incubated using the following program: 25°C for 5 min, 42°C for 90min, 70°C 15min followed by 4°C. 3 μl of cDNA amplification mix was added into each snmCAT-seq reverse transcription reaction. Each cDNA amplification reaction containing 1X KAPA 2G Buffer A, 600 nM ISPCR23_2 PCR primer (5′-/5SpC3/AAGCAGUGGUAUCAACGCAGAGU-3′), 0.08U KAPA2G Robust HotStart DNA Polymerase (5 U/μL, Roche KK5517). PCR reactions were performed using a thermocycler with the following conditions: 95°C 3min -> [95°C 15 s -> 60°C 30 s -> 72°C 2min] -> 72°C 5min -> 4°C. The cycling steps were repeated for 12 cycles for snmCAT-seq using H1 or HEK293 whole cells, 15 cycles for snmCAT-seq using H1 or HEK293 nuclei and 14 cycles for snmCAT-seq using human brain tissue nuclei. Following the digestion of unused DNA oligos, 25 μl instead of 15 μl of CT conversion reagent was added to each well of a 384-well plate. 90 μl instead of 80 μl M-binding buffer was added to each well of 384-well DNA binding plates. snmCAT-seq libraries performed using whole H1 or HEK293 cells were generated using the snmC-seq method as described in Luo et al., 2017.4 The rest of the snmCAT-seq libraries were generated using the snmC-seq2 method as described in Luo et al., 2018.16 The snmCAT-seq libraries generated from H1 and HEK293 cells were sequenced using an Illumina HiSeq 4000 instrument with 150 bp paired-end reads. The snmCAT-seq libraries generated from human brain specimens were sequenced using an Illumina Novaseq 6000 instrument with S4 flowcells and 150 bp paired-end mode.

value: DLPFC

tag: disease state

value: Controls

tag: age of_death

tag: Sex

value: Male

tag: race

value: Caucasian


title: KI_2m_H3K27me3_rep3

status: Public on Jan 08 2025

type: SRA

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: Bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: Striatum

extract_protocol:
NeuN+ and NeuN- sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K27ac (ab4729, Abcam), H3K27me3 (C15410195, diagenode) and IgG control (C15410206, Diagenode), using 50000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.

tag: tissue

value: Striatum

tag: genotype

tag: chip antibody

value: H3K27me3:C15410195, Diagenode


title: WT_H2AK119ub.rep1

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bigwig

extract_protocol:
P2959
ChIPseq was performed with striatal tissues from R6/1 and WT mice as described by Alcala-Vida et al. (2021) using antibody targeting H2AK119ub (8240, cell signaling). Briefly, pooled tissues were cut into small fragments, fixed in 1% formaldehyde and incubated for 15 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then mechanically homogenized in sonication buffer (50mM HEPES pH7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC, 0.1% SDS, 1x PIC) and sonicated to obtain DNA fragments < 500 bp using Covaris E220Ultrasonicator (Covaris). The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (16-157, Sigma-Aldrich) for 45 min at 4 °C. Subsequently, samples were incubated overnight at 4 °C with corresponding primary antibodies. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3h at 4 °C in a shaker. Agarose beads were washed, protein–DNA complexes were eluted from the beads and de-crosslinked overnight with RNAse A at 65 °C. Proteins were eliminated by 2 h incubation at 45 °C with Proteinase K, and DNA recovered using Qiagen MiniElute PCR Purification Kit.
P3013 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 3 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 2 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.
P2959 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: WT

value: H2AK119ub (8240, cell signaling)


title: WT_6m_H3K27me3_rep3


title: 35S:WOX5-GR root Replicate 2

type: genomic

city: Freiburg im Breisgau

first: Thomas

last: Laux

address: Schänzlestr. 1

department: Institut für Biologie III

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

description: Agilent array was hybridized with both 35S:WOX5-GR ChIP (Cy3) and input control (Cy5) samples differentially labeled with Cy3 and Cy5 dye, respectively.

hyb_protocol: DNA was hybridized using SureHyb hybridization chambers according to the Agilent hybridization protocol (Agilent Mammalian ChIP-on-chip protocol, Version 10.2, 2011).

scan_protocol: Images were obtained using an Agilent microarray scanner (Model G2505C).

data_processing: Signal extraction and initial data processing were done using the Agilent's Feature Extraction Software. Additional data processing was done used Ringo software (Toedling, J. et al., 2007).

organism: Arabidopsis thaliana

source_name: Chromatin fragments precipitated with anti-WOX5 antibody

label_protocol: DNA was labeled using SureHyb hybridization chambers according to the Agilent labeling protocol (Agilent Mammalian ChIP-on-chip protocol, Version 10.2, 2011).

growth_protocol: Seeds were surface sterilized, placed at 4°C for 3 days, and grown on 0.5x MS media, 1% agar without sucrose. Plates were placed vertically in a growth chamber with 16 hours of light and 8 hours of darkness at 23 °C.

extract_protocol: The ChIP was performed as described before (Pi, L. et al., 2015) with minor modifications. Precipitated DNA was eluted with 3x 100 µL elution buffer (0.1 M glycine, 0.5 M NaCl, 0.05 % Tween-20, pH 2.8) and neutralized by adding 50 µL 1 M Tris (pH 9.0) for each elution step. Proteinase K (Roche) was added to a final concentration of 0.5 mg/mL to elute DNA and input DNA which were then incubated at 65 °C overnight. After that, equal amounts of proteinase K were added and incubated at 65 °C for 4 hours. DNA was precipitated by adding 2.5x volume of 100% ethanol, 10% sodium acetate (3M, pH 5.4), and 1 µL glycogen at -20 °C overnight and collected by centrifugation at 13000 g for 30 minutes at 4 °C. ChIP-DNA and input DNA were amplified using the WGA2 amplification kit (Sigma-Aldrich). Amplified DNA was purified with the PCR purification kit (Qiagen).

treatment_protocol: 5 days old seedlings of 35S:WOX5-GR and wox5-1 were treated with 10 μM DEX for 4 hrs. 5 mm root tips were harvested and cross-linked with 1% formaldehyde.

tag: ecotype

value: Root tips of 5-day old seedlings

source_name: Control (input) non-immunoprecipitated chromatin fragments


title: Control wox5-1 root Replicate 1

description: Agilent array was hybridized with both wox5-1 (Cy5) and input control (Cy3) samples differentially labeled with Cy5 and Cy3 dye, respectively.

value: Control wox5-1


title: Input_WT_2m

value: No antibody


title: DLPFC, control,2

country: USA

description: Library name: Br1092

organism: Homo sapiens


title: KI_2m_H3K27me3_rep2


title: DLPFC, patient, 1

description: Library name: Br1416

value: Schizophrenia


title: DLPFC, patient, 2

description: Library name: Br1682


title: Input_KI_6m


title: 35S:WOX5-GR root Replicate 1


title: WT_2m_H3K27me3_rep1


title: KI_10m_H3K27me3_rep2


title: DLPFC, control,3

description: Library name: Br2288


title: KI_10m_H3K27ac_rep3

value: H3K27ac: ab4729, Abcam


title: WT_2m_H3K27me3_rep3


title: DLD1 cell, HERV-R KO

city: Busan

first: Min-Hye

last: Kim

address: 262, Gamcheon-ro, Seo-gu

country: South Korea

institute: Kosin University College of Medicine

description: Library name: DLD1R

library_source: transcriptomic

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

molecule: total RNA

growth_protocol: DLD1 colorectal adenocarcinoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: Transfect cells with cas9 vector and sgRNA vector using lipofectamine 3000 (invitrogen) reagent, and after 24 h, treat with hygromycin to select cell colonies.

tag: cell line

tag: cell type

value: colorectal adenocarcinoma cell line

value: HERV-R Knockout

tag: treatment

value: cell transfection


title: WT_2m_H3K27me3_rep2


title: KI_10m_H3K27ac_rep1


title: DLPFC, patient, 3

description: Library name: Br1425


title: DLPFC, control,1

description: Library name: Br1446


title: DLD1 cell, control

description: Library name: DLD1


title: Input_WT.rep1


title: WT_10m_H3K27ac_rep2


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/+ rep2

city: San Francisco

first: Benoit

middle: G.

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description: Library name: snm-3C-wtc11_TBX5het_d20_r2

data_processing:
Raw sequence FASTQ files were mapped using YAP (Yet Another Pipeline) software (cemba-data v1.6.9), as previously described (Zemke 2023). Briefly, FASTQ files were demultiplexed by cell barcodes and read quality assessment (cutadapt, v.2.10). Two-pass mapping was performed with bismark (v0.20, with bowtie2 v2.3) for alignment to hg38 reference genome assembly. BAM file processing and QC was performed using samtools (v1.9) and Picard (v3.0.0). Chromatin contacts were called and methylome profiles were generated using Allcools software (v1.0.23).
Assembly: hg38
Supplementary files format and content: .mcds of aggregated methylation levels of genomic intervals, .csv of mapping summary metrics, and pairwise contacts

growth_protocol: Cells were grown in one well of 6-well dish per biological replicate.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 300 x g for 5 min at room temperature. Pellets were washed once in 1 ml DPBS and counted using Countess II Automated Cell Counter with optimized setting.  2 million cells were aliquoted into a 1.5 ml tube and centrifuged at 300 x g for 5 min at room temperature. Cell pellets were resuspended in 1 ml DBPS and 16% methanol-free formaldehyde (ThermoFisher Scientific #28908) was added to final concentration of 2% and incubated on nutator at room temperature for 5 mins. Samples were quenched with 2.5 M glycine to a final concentration of 0.2 M and incubated on nutator at room temperature for 5 min, followed by centrifugation at 1000 x g for 5 min at 4˚C. Samples were washed once in ice cold DPBS and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.    Two replicates per time point were processed for snm3C-seq and library preparation. Cells were subjected to in situ 3C procedure following the steps in the Arima-3C BETA Kit (Arima Genomics), with some modifications. Cells were lysed for 15 min on ice in 20 µl of Lysis Buffer. 24 µl of Conditioning Solution was added, and cells were transferred to a 0.2 mL PCR tube, and mixed gently by pipetting. Tubes were incubated at 62°C for 30 min in a thermal cycler, with the lid temperature set to 85°C. 20 µl of Stop Solution 2 was added, and mixed gently by pipetting. Tubes were incubated at 37°C for 15 min in a thermal cycler with a lid temperature set to 85°C.  28 µl of the restriction enzyme digestion mix (9.8 µl water, 9.2 µl Buffer H, 4.5 µl Enzyme H1, 4.5 µl Enzyme H2) was added and gently pipette mixed. Tubes were incubated in a thermal cycler for 37°C for 60 min, 65°C for 20 min, then 25°C for 10 min. 82 µl of ligation mix was added (70 µl Buffer C, 12 µl Enzyme C) and gently mixed by pipetting, then incubated at 25°C for 15 min. Nuclei were transferred to a tube containing 850 µl 1% BSA in DPBS on ice and filtered through a 30um Celltrics strainer to a new tube on ice. Nuclei were centrifuged at 1000 x g for 10 min at 4°C (in bucket rotor). Supernatant was removed and pellets were resuspended each sample in 800 µl of 1% BSA in DPBS. Nuclei were stained with DRAQ7 at 1:200 and mixed gently with a pipette and incubated on ice for 5 min. One tube of Proteinase K (Zymo #D3001-2-D) was dissolved in 1 mL of Proteinase K Resuspension Buffer (Zymo #D3001-2-B) then added to a mix of 15 mL M-Digestion Buffer 2x (Zymo #D5021-9) and 14 mL water to make pK Digestion Buffer. 2 µl of pK Digestion Buffer were added to each well of an Eppendorf twin.tec® PCR Plate 384 LoBind®, skirted, 45 µl, PCR clean (Eppendorf  #0030129547). Single DRAQ7 positive nuclei were sorted into individual wells of the 384-well plate using a Sony SH800 cell sorter. One 384-well plate was used per biological replicate. Plates were sealed then incubated in a thermal cycler at 50°C for 20 min with a heated lid at 85°C for nuclei digestion.
The snm3C-seq bisulfite conversion procedure and library preparation protocol was carried out as previously described (Liu 2021; Zemke 2023). This procedure was automated using the Beckman Coulter Biomek i7 liquid handlers for all reactions in 384 and 96-well plates.

value: cardiomyocyte

value: atrial cardiomyocyte differentation


title: KI_6m_H3K27ac_rep3


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep1

description: Library name: snm-3C-wtc11_TBX5hom_d20_r1


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/del rep2

description: Library name: snm-3C-wtc11_TBX5hom_d20_r2


title: DLPFC, patient, 4

description: Library name: Br1245

value: DLPFC


title: KI_6m_H3K27ac_rep1


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/+ rep1

description: Library name: snm-3C-wtc11_TBX5het_d20_r1


title: WT_6m_H3K27ac_rep3


title: Zea mays 7 days old shoot, replicate 2

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description: CAM-seq on maize polyA enriched RNA

data_processing:
Sequencing adapters were trimmed from the 3′ ends of read 1 and read 2 using the Cutadapt tool. Low-quality and short reads were filtered out by applying ‘-q 20 –max-n 0 -m 20’ arguments. 10nt of a random sequence in the 5’ end of read 1were extracted as a unique molecular barcode for each sequence. Processed reads were mapped to Zea Mays  genomes (Zm-B73-REFERENCE-NAM-5.0) accordingly using hisat2-3n tool.
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: TSV
Library strategy: CAM-seq

molecule: polyA RNA

organism: Zea mays

source_name: shoot

growth_protocol: Maize inbred line B73 seeds were germinated at 28 °C with 14 h of light per 24 h. The shoots of maize of 7-day old plants were harvested.

extract_protocol:
Cellular or plant total RNA was extracted from cells or plant tissue using TRIzol reagent (Ambion by Life Technologies) and Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer’s protocol. After RNA extraction, two rounds of Poly(A) enrichment were conducted using DynaBeads mRNA Direct Purification kit (Thermo Fisher Scientific) following the manufacturer’s protocol with some modifications.
Following the CAM-seq treatment, RNA samples were purified and sequencing libraries were prepared using the cDNA ligation method. Briefly, the RNA was end-repaired and ligated with a 3' adapter, then reverse transcribed into cDNA under various enzymatic and RT conditions. Subsequently, the cDNA was ligated with a cDNA adapter. The sequencing libraries were then amplified using a dual-index primer for Illumina sequencing.

value: shoot


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep2

description: Library name: snm-3C-wtc11_TBX5unmod_d20_r2


title: WT_6m_H3K27ac_rep1


title: Zea mays 7 days old shoot, replicate 1

description: CAM-seq on maize polyA enriched RNA


title: WT_6m_H3K27ac_rep2


title: KI_2m_H3K27ac_rep3


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep1

description: Library name: snm-3C-wtc11_TBX5unmod_d20_r1


title: Arabidopsis seedling replicate 3

description: CAM-seq on Arabidopsis polyA enriched RNA

data_processing:
Sequencing adapters were trimmed from the 3′ ends of read 1 and read 2 using the Cutadapt tool. Low-quality and short reads were filtered out by applying ‘-q 20 –max-n 0 -m 20’ arguments. 10nt of a random sequence in the 5’ end of read 1were extracted as a unique molecular barcode for each sequence. Processed reads were mapped to Arabidopsis  genomes (TAIR10) accordingly using hisat2-3n tool.
Assembly: TAIR10
Supplementary files format and content: TSV
Library strategy: CAM-seq

source_name: seedling

growth_protocol: Arabidopsis plants were grown at 22 °C with 16 h of light per 24 h. Arabidopsis seedlings were harvested after growing on 1/2 Murashige and Skoog medium (MS) plates for 7 d.

value: seedling


title: KI_2m_H3K27ac_rep1

value: Striatum


title: snm3c-seq of homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D23 rep2

description: Library name: snm-3C-wtc11_vCM_d23_r2


title: Arabidopsis seedling replicate 2


title: WT_2m_H3K27ac_rep3


title: WT_10m_H3K27ac_rep3


title: KI_6m_H3K27ac_rep2


title: snm3c-seq of homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D23 rep1

description: Library name: snm-3C-wtc11_vCM_d23_r1


title: WT_2m_H3K27ac_rep1


title: Zea mays 7 days old shoot, replicate 3

description: CAM-seq on maize polyA enriched RNA


title: WT_2m_H3K27ac_rep2


title: KI_2m_H3K27me3_rep1

value: H3K27me3:C15410195, Diagenode


title: Arabidopsis seedling replicate 1


title: snm3c-seq of homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D6 rep2

description: Library name: snm-3C-wtc11_vCM_d6_r2

value: cardiac precursor

value: WT


title: KK_2

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

country: China

institute: University of Science and Technology of China

description: Library name: KK-P2

data_processing:
The raw sequencing data are called raw reads. We obtained clean reads using the SOAPnuke(Chen et al., 2018b) (version 1.5.0) with the parameter ‘-p 0.7 -z 18’. The filtering rules were as follows: removed low quality reads (The number of bases with base quality less than 10 is ≥4 or the number of bases with base quality less than 13 is ≥6; removed reads with 5’ primer contaminants; remove reads without 3’ primer; removed reads without insertion; removed reads with poly A; removed reads shorter than 18 nt. The small RNA analysis was performed using SPORTS1.1(Shi et al., 2018).  Briefly, after filtering, clean reads were mapped to the reference genome and others sRNA database using Bowtie with the parameter ‘--mm10_genome, miRBase_21-mmu, rRNAdb/mouse_rRNA, GtRNAdb/mm10/mm10-tRNAs, piRBase/piR_mouse, Mus_musculus. GRCm38.ncrna and Rfam-12.3-mouse’, allowing for one base mismatch. For piRNA mapping, clipped reads were filtered by length (24–32 nt) and aligned to the following sets of sequences: piRNA clusters, repeats, coding RNAs, non-coding RNAs and intron. Reads not mapping to the above five sets of sequences were classified as ‘other’. Alignments were performed with Bowtie (one base mismatch allowed). The classes (DNA, LINE, LTR, SINE, Satellite and rRNA) of reads mapped to repeats as defined by RepeatMasker. The ping-pong signature analysis and nucleotide base distribution analyses were performed by piPipes(Han et al., 2015).
Assembly: mm10
Supplementary files format and content: txt files contained genes and trancripts expression information

source_name: Testis

extract_protocol:
The total RNA was isolated from testicular enriched fractions of pachytene spermatocytes using Trizol (Invitrogen) following manufacturers’ protocol.1 ug of total RNA was used for the construction of RNA sequencing libraries.25 ng CB RNA was used for the construction of sequencing librarie.200 ng total RNA was used for the construction of small RNA sequencing libraries.
RNA libraries for RNA-seq were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina®  in accordance with the manufacturer's recommendations.

treatment_protocol: Isolation  pachytene spermatocytes from mouse using our published protocol (Cao et al., 2022).Briefly, testes were decapsulated and digested Leydig cells using Collagenase buffer. Then used trypsin buffer to digestion for germ cells. Germ cells suspension was centrifugal elution in JE5.0 elutriator system. Round spermatids and pachytene spermatocytes are obtained according to different parameters settings. Collected and washed the cells for follow-up experiment. The purity of fractions verified with DAPI staining.

value: Testis

value: Germ cells

value: pachytene spermatocytes

value: DDX4 homozygous knock-in

value: The cells from the testes used two-step digestion method.


title: Input_WT_NeuN-

extract_protocol:
NeuN+ and NeuN- sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K9ac (Ab4441, Abcam), H3K18ac (C15410139, Diagenode) and IgG control (C15410206, Diagenode) with 50000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.

value: No antibody


title: snm3c-seq of homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D6 rep1

description: Library name: snm-3C-wtc11_vCM_d6_r1


title: Input_R61_NeuN-


title: Input_WT_NeuN+


title: KK_1

description: Library name: KK-P1


title: R61_H3K18ac_NeuN+_Rep2

value: H3K18ac (C15410139, Diagenode)


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep2

description: Library name: snm-3C-wtc11_aCM_d45_r2


title: WT_H3K18ac_NeuN+_Rep2


title: WT_H3K9ac_NeuN+_Rep2

value: H3K9ac (Ab4441, Abcam)


title: KI_2m_H3K27ac_rep2

value: H3K27ac: ab4729, Abcam


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep1

description: Library name: snm-3C-wtc11_aCM_d45_r1

value: cardiomyocyte

value: atrial cardiomyocyte differentation


title: R61_H3K18ac_NeuN-_Rep1


title: R61_H3K9ac_NeuN-_Rep1


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep2

description: Library name: snm-3C-wtc11_aCM_d6_r2


title: R61_H3K9ac_NeuN+_Rep1


title: γδ T cells, KO3

city: zhuhai

first: xianghong

last: wang

state: Please Select

address: 79 Kangning Road, Xiangzhou District

institute: Zhuhai People’s Hospital

description: Library name: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: spleen

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: spleen


title: snm3c-seq of homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep1

description: Library name: snm-3C-wtc11_aCM_d6_r1


title: WT_H3K9ac_NeuN-_Rep1


title: γδ T cells, KO2

description: Library name: Sample 5


title: Input_R61_NeuN+


title: WT_H3K18ac_NeuN-_Rep1


title: WT_1

description: Library name: WT-P1


title: γδ T cells, KO1

description: Library name: Sample 4


title: WT_H3K18ac_NeuN+_Rep1


title: snm3c-seq of homo sapiens: WTC11 rep1

description: Library name: snm-3C-wtc11_wt_d0_r1

value: iPSC


title: Landrace Post-challenge MDM at 48 hours post infection (LI4-2)

city: Bareilly

first: AMIT

last: KUMAR

state: Uttar Pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

data_processing:
Reads with phred score < 30 and adapter sequences were filtered using Trim_galore
Filtered reads were aligned to the Sus scrofa 11.1 transcriptome using Kallisto 0.46.1 and TPM abundances were generated
The TPM abundances generated by kallisto were converted to raw gene counts using tximport R package
Differential expression analysis was carried out through DEseq2
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: Text file containing gene expression counts for each sample

organism: Sus scrofa

source_name: Monocyte-derived macrophages

growth_protocol: Blood samples were collected from experimental unvaccinated animals after ensuing seronegativity for maternal derived antibodies against CSF. PBMCs were isolated from blood samples  via density gradient centrifugation method using Histopaque-1077. The cell viability of PBMCs was assessed using the Trypan-blue dye method. Cell seeding was done by adding around 12-14 mL of RPMI-1640 containing antibiotic-antimycotic blend and 15% fetal calf serum.

extract_protocol:
At 48 hpi, the MDMs were harvested from the culture plates. RNA isolation from MDMs was performed using TRIzol method. The quantification of viral load in MDMs of two groups (Ghurrah and Landrace) was undertaken via absolute quantification with qPCR using primers that were specific to 5’UTR.
Library preparation was done through Illumina Truseq RNA sample preparation kit V2 (PolyA capture).

treatment_protocol: The virulent IVRI strain of CSF virus cultured in PK-15 (Porcine kidney) cell line at passage level 7 (P-7) was used as challenge virus for infection of macrophages. The virus infectivity was achieved at 1x10^6.5 TCID50. The MDMs were infected on day 14 of culture by replacing 500 µL of media in the wells with the same volume of viral suspension. The viral infectivity was confirmed at 48 hours post infection by Immunofluorescence antibody test (IFAT). The presence of virus in MDMs was confirmed by using anti-CSFV monoclonal Antibody conjugated with FITC. Viral infectivity of MDMs was also confirmed by detecting viral RNA in macrophages using qPCR.

tag: breed

value: Landrace

tag: infection

value: Classical Swine fever virulent virus strain

value: Monocyte-derived macrophages


title: WT_H3K9ac_NeuN+_Rep1

value: Striatum

value: WT


title: γδ T cells, WT3

description: Library name: Sample 3


title: Landrace Post-challenge MDM at 48 hours post infection (LI2-3)


title: Hi-C of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D23 rep1

description: Library name: Ventricular_D23_rep1

data_processing:
Hi-C 3.0 data were processed using 4D Nucleome (4DN) Hi-C data Processing Pipeline (v0.2.7) (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline), which generated .mcool file with iterative correction and eigenvector decomposition (ICE) normalization.
Reads were mapped to GRCh38 using bwa.
Valid HiC alignments were filtered using pairtools.
Biological replicates were merged using https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.s
The pairs files were converted to cool files using cooler.
Assembly: hg38
Supplementary files format and content: .mcool file of interaction contact frequencies at different resolutions

growth_protocol: WTc11 iPSCs and WTc11 iPSCs with genome-edited mutations for TBX5 (TBX5in/+ and TBX5in/del) were previously generated and characterized in both ventricular (Kathiriya 2021) and atrial cardiomyocyte (CM) differentiations (Kathiriya biorxiv). WTc11 iPSCs used for atrial and ventricular time course Hi-C 3.0 experiments were grown on hESC-qualified Matrigel (Corning #354277). Human iPSCs for all other experiments were grown on growth factor-reduced basement membrane Matrigel (Corning #356231) in mTeSR-1 (StemCell Technologies #85850) or mTeSR+ medium (StemCell Technologies #100-0276). iPSCs were routinely passaged using ReLesR (StemCell Technologies #100-0483). For CM differentiations, iPSCs were dissociated using Accutase (StemCell Technologies #07920) and seeded into 6-well or 12-well plates. Cells were grown for three day until 70-90% confluency and induced using Stemdiff Cardiomyocyte Ventricular (StemCell Technologies #05010) or Atrial (StemCell Technologies #100-0215) kits, according to manufacturer’s instructions.

extract_protocol:
CMs were grown in 3 wells of a 6-well dish per replicate, with all 3 wells pooled together after dissociation for the crosslinking step (approximately 10 million cells). CMs were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. CMs were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 5 ml HBSS before resuspending entire cell pellet in exactly 10 ml HBSS. 16% methanol-free formaldehyde was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, then 15 min at 4˚C and followed by centrifugation at 1000 x g for 5 min at room temperature. Samples were washed once in DPBS. Pellets were resuspended in 1 ml of 3 mM DSG in PBS, transferred to 1.5 ml tubes and incubated on nutator for 40 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min. Samples were centrifuged at 2000 x g for 5 min at RT. Cell pellets were resuspended in 5 mg/ml BSA in DPBS, to prevent cells sticking to tube after DSG crosslinking, and centrifuged at 2000 x g for 5 min at 4˚C. Supernatant was carefully removed and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.
Samples were processed for Hi-C using Arima-HiC+ kit (Arima Genomics). >1 µg per sample was used as determined by Arima’s Estimating Input Amount Protocol using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854) Samples were processed by following manufacturer’s user guide for mammalian cell lines with one exception: DNA was digested using 50 U DpnII (New England Biolabs #R0543M) and 50 U DdeI (New England Biolabs #R0175L) restriction enzymes in 1x NEB Buffer 3.1 for 60 min at 37˚C. All samples passed Arima-QC1 Quality Control. Sequencing libraries were prepared by following Arima’s user guide for Library Prep Using KAPA Hyper Prep Kit (Roche #7962347001). Between 1.5-4 µg of DNA was fragmented in 130 µl microtube (Covaris #520045) using a Covaris S2 sonicator for 55s at 10% duty cycle, intensity 4, 200 cycles per burst in a water bath maintained at 4˚C. An average fragment size of 400 bp was verified using Agilent 2100 Bioanalyzer. Between 400-1000 ng of size-selected DNA was used for biotin enrichment, end repair, dA-tailing and adapter ligation. The number of PCR cycles was determined following Arima-QC2 Quality Control using KAPA Library Quantification Kit (Roche KK4824) and libraries were amplified to at least 10 nM. All samples passed Arima-QC2 Quality Control. DNA cleanup steps were done using Ampure XP beads (Beckman Coulter #A63881). Final libraries were quantified using Qubit Fluorometer and dsDNA HS Assay Kit and assessed on Agilent BioAnalyzer. Pooled, equimolar libraries were sequenced using NovaSeq technology (Illumina).


title: Landrace Post-challenge MDM at 48 hours post infection (LI1-5)


title: γδ T cells, WT2

description: Library name: Sample 2


title: WT_2

description: Library name: WT-P2

value: Testis

value: Germ cells


title: Landrace Pre-challenge MDM  (LC4-2)

value: control


title: Hi-C of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D11 rep1

description: Library name: Ventricular_D11_rep1


title: γδ T cells, WT1

description: Library name: Sample 1


title: Landrace Pre-challenge MDM  (LC2-3)


title: Hi-C of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D6 rep1

description: Library name: Ventricular_D6_rep1

value: cardiac precursor


title: Landrace Pre-challenge MDM  (LC1-5)


title: R61_H3K18ac_NeuN+_Rep1


title: Ghurrah Post-challenge MDM at 48 hours post infection (DI4-2)

value: Ghurrah


title: Ghurrah Post-challenge MDM at 48 hours post infection (DI2-3)


title: Hi-C of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D4 rep1

description: Library name: Ventricular_D4_rep1

value: cardiac mesoderm


title: snm3c-seq of homo sapiens: WTC11 rep2

description: Library name: snm-3C-wtc11_wt_d0_r2


title: Mouse brain cortex, dscHi-C, 3 month-old

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: b3-month-BC-dscHiC

data_processing:
dscHiCtools (https://github.com/MaoxuWang/dscHiCtools) firstly identify the true cell barcodes from index reads against whitelist (cellranger-atac-2.1.0/lib/python/atac/barcodes/737K-cratac-v1.txt.gz) barcodes that allows one mismatch. Barcodes with no or multiple hits will be discarded. Called cell barcodes are added to read name. Reads then were mapped to reference genome by bwa-mem in "5SP" mode. Hickit were used to extract and dedup contacts from sam file. Notably, we did minor modifications to Hickit (https://github.com/MaoxuWang/hickit) to adapt the single-cell features. Briefly, we extracted the cell barcode to each contact information and cell barcode was also considered in contacts duplication rather than distance (set parameters --dup-dist=100”) alone. Cells with too few contacts were considered as technique noise and were filtered.
Assembly: mm10 / hg38
Supplementary files format and content: .contacts.pairs.gz includes unique valid contact pairs for each single cell in 4DN format
Supplementary files format and content: .metadata.txt includes basic statistics for each single cell

source_name: Brain cortex

growth_protocol: K562 (ATCC, CCL-243) were cultured in Iscove’s Modified Dulbecco’s medium, BJ (ATCC, CRL-2522) were grown in ATCC-formulated Eagle's Minimum Essential Medium, eHAP (Cellosaurus), engineered haploid chronic myeloid leukemia cell line, were grown in Iscove’s Modified Dulbecco’s Medium, GM12878 (Coriell Institute), B lymphoblastoid cells, were grown in Roswell Park Memorial Institute 1640 Medium. These media were supplemented with 10% FBS and 1% Penicillin/Streptomycin, except for GM12878 supplemented with 15% FBS. mESC were grown in knockout DMEM medium containing 15% FBS, 1% Pen/Strep, 2 mM L-glutamine, 1 mM non-essential amino acids, 1 x nucleosides, 3 μM CHIR99021, 1 μM PD0325901, 0.1 mM 2-mercaptoethanol and 1000 U/mL LIF. The plate was pretreated with 1% gelatin. All cells were maintained at 37°C with 5% CO2 at recommended density.

extract_protocol:
Cultured cell line or isolated nuclei from primary brain cortex were processed with Hi-C 3.0 protocol. Cells were firstly double-crosslinked with PFA followed by DSG, then treated with SDS and Triton X-100 to open chromatin. Then the chromatin was digested by resuspending the nuclei in digestion mix containing DdeI and DpnII without detergent, and incubated at 37°C for 2 hours, followed by inactivating the REs. The DNA ends was filled by biotin labeled dATP, followed by proximity ligation using T4 ligase by incubating at room temperature for 2 hours. For sample prepared for dscHi-C multiome experiment, all reaction mix was supplemented 0.5 U/μL Protector RNase inhibitor.
Nuclei processed through Hi-C 3.0 procedure were bulk tagmented with Tn5 transposome, then loaded to 10x Chromium platform according to either ATAC kit or multiome kit. For dscHi-C, the DNA were barcoded by linear amplification in droplet, followed pooling droplets, further amplification and sample index were incorporated. For dscHi-C-multiome, the DNA and RNA from the same cell were barcoded in droplet, the then droplets were pooled and nuclei were decrosslinked. Genomic DNA were pull down using streptavidin beads, and cDNA were further proceeded with second time reverse transcription. Then the genomic DNA were direct subjected to library preparation. The cDNA were further fragmented and amplified for library construction.

value: Brain cortex


title: Ghurrah Pre-challenge MDM  (DC4-2)


title: Ghurrah Post-challenge MDM at 48 hours post infection (DI1-5)


title: Mouse brain cortex, dscHi-C, 23 month-old

description: Library name: b23-month-BC-dscHiC


title: Hi-C of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D2 rep1

description: Library name: Ventricular_D2_rep1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep2

description: Library name: Atrial_D45_rep2


title: Ghurrah Pre-challenge MDM  (DC2-3)


title: NCCIT RNA-Seq Biological Replicate 3

city: New York

first: Lubbertus

last: Mulder

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: NCCIT_biol_rep3

data_processing:
RNAseq data in fastq format were aligned to the human reference genome (build hg38) using HISAT2 (v2.2.1) with options --score-min L,0,-0.14 -k 100 for a maximum of 100 alignments reported.
Aligned sam files were sorted by location and input into Telescope (v1.0.3) to assign ambiguosuly mapped fragments to a single genomic source locus and quantify fragments at each HERV locus, including only reads that could be mapped with >90% confidence.
Assembly: hg38
Supplementary files format and content: a single comma-separated values file containing raw counts for each sample and each genomic locus, with chromosome, start location, end location, and strand specified (hg38 assembly coordinates)

source_name: non-seminomatous germ cell tumor

growth_protocol: NCCIT cell line (46,48), was purchased from the ATCC (CRL-2073), cultured at 37C 5%CO2 in RPMI 20% FCS (GemCell), 100 IU/ml penicillin-streptomycin, and 2mM L-glutamine, and regularly tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen/Thermo Fisher) following manufacturer's instructions. DNA contamination was eliminated by DNase I treatment using the DNA-free kit (Ambion) according the manufacturer’s instructions.
Total RNA was examined for quantity and quality using the TapeStation (Agilent) and Quant-It RNA (ThermoFisher) systems. RNA samples with sufficient material (>50 ng) were passed to whole-transcriptome library preparation using the Stranded mRNA kit, (Illumina) following the manufacturer’s instructions. Completed libraries were quantified using Quant-iT reagents and equimolar pools were generated and sequenced on the NextSeq 550 using NextSeq 500/550 Mid Output kit v2.5 (300 CYS) flow cells with 150bp paired-end reads.

value: non-seminomatous germ cell tumor

value: NCCIT

value: embryonal carcinoma

tag: batch


title: Ghurrah Pre-challenge MDM (DC1-5)


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D45 rep1

description: Library name: Atrial_D45_rep1

value: cardiomyocyte

value: atrial cardiomyocyte differentation


title: NCCIT RNA-Seq Biological Replicate 1

description: Library name: NCCIT_biol_rep1


title: NCCIT RNA-Seq Biological Replicate 2

description: Library name: NCCIT_biol_rep2


title: mESC, dscHi-C-multiome, cultured, no biotin enrichment, RNA

description: Library name: mESC_dscHi-C_Multiome_no_biotin_RNA

library_source: other

molecule: other

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep2

description: Library name: Atrial_D20_rep2


title: TO Patient6(2) Control rep3

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
Illumina bcl2fastq2 v2.20 software was used for basecalling.
The adapters were trimmed with fastp 0.21.1 (Chen et al., 2018).
Reads were mapped with STAR 2.7.7a (Dobin et al., 2013).
Count matrix was generated with featureCount tool from ssubread-2.0.1 aligner (Liao et al., 2013, 2014).
Assembly: GENCODE release 37 GRCh38.primary assembly.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Metastatic colorectal tumor organoids

growth_protocol: Cell suspension was mixed with Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning, USA). Then 50 μl drops of the resulting suspension in the extracellular matrix were transferred into the wells of a 24-well culture plate (TPP, Switzerland) and placed into cell culture incubator (37 °C, 5% CO2) for 20 minutes for solidification of the gel. Then, 750 μl of complete cell culture medium (van de Wetering et al., 2015) was added to each well, and the plate was incubated in cell culture incubator. Cell culture medium was replaced every 48 hours. Cells were inspected visually by an inverted Primo Vert microscope (Carl Zeiss, Germany). Organoids were subcultured every two weeks with the help of TrypLE Express (Thermo Fisher Scientific, USA).

extract_protocol:
Cells were lysed with the QIAzol Lysis Reagent (Qiagen, Germany). RNA isolation was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol. Nanodrop ND-1000 (Thermo Fisher Scientific, USA) was used to assess quantity and purity of the extracted RNA. Total RNA samples were also QC-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using Illumina Stranded mRNA Library Prep Kit (Illumina, USA).

treatment_protocol: No treatment.

value: Metastatic colorectal tumor organoids

value: No treatment


title: TO Patient6(2) Control rep2


title: TO Patient6(2) Control rep1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D20 rep1

description: Library name: Atrial_D20_rep1


title: mESC, dscHi-C-multiome, cultured, no biotin enrichment, HiC

description: Library name: mESC_dscHi-C_multiome_no_biotin


title: mESC, dscHi-C-multiome, cultured, biotin enrichment, second RT, RNA

description: Library name: mESC_dscHi-C_Multiome_biotin_second_RT_RNA


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep2

description: Library name: Atrial_D11_rep2


title: TO Patient6(1) Control rep1


title: TO Patient5 Control rep3


title: mESC, dscHi-C-multiome, cultured, biotin enrichment, second RT,HiC

description: Library name: mESC_dscHi-C_multiome_biotin


title: TO Patient5 Control rep2


title: Mouse brain cortex, dscHi-C, 12 month-old

description: Library name: b12-month-BC-dscHiC


title: TO Patient4 Control rep3


title: TO Patient5 Control rep1


title: TO Patient4 Control rep2


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep1

description: Library name: Atrial_D11_rep1


title: TO Patient4 Control rep1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep2

description: Library name: Atrial_D6_rep2


title: mESC, dscHi-C, cultured, subsample

description: Library name: mESC_dscHi-C_sub


title: mESC, dscHi-C, cultured, rep2

description: Library name: mESC_dscHi-C_2


title: TO Patient3 Control rep2


title: mESC, dscHi-C, cultured, rep1

description: Library name: mESC_dscHi-C_1


title: TO Patient6(1) Control rep2


title: TO Patient2 Control rep3


title: TO Patient3 Control rep1


title: TO Patient6(1) Control rep3


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D4 rep1

description: Library name: Atrial_D4_rep1


title: TO Patient3 Control rep3


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D4 rep2

description: Library name: Atrial_D4_rep2


title: TO Patient2 Control rep2


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D2 rep2

description: Library name: Atrial_D2_rep2


title: TO Patient2 Control rep1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D2 rep1

description: Library name: Atrial_D2_rep1


first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_37_tFL-P6_cellLine_tazemetostat_H3K27me3CnR_repl3

data_processing:
H3K27me3 CUT&RUN sequencing results were aligned to a concatenated mm10 and dm6 genome using BWA-MEM and normalized to dm6 spike-in reads using CompChIPseq algorithm.  Peaks were called using SICER2 algorithm.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed according to EpiCypher CUTANA CUT&RUN protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645L). Pooled libraries were sequenced using Novaseq 6000 with a target of 10 million paired end reads per sample.

value: B lymphoma cells

value: tri-methyl-histone H3 (Lys27) (C36B11) rabbit mAb (Cell Signaling #9733)

value: Treated with 5 µM tazemetostat for 14 days


title: TO Patient1 Control rep2


description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_36_tFL-P6_cellLine_tazemetostat_H3K27me3CnR_repl2


title: TO Patient1 Control rep3


description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_35_tFL-P6_cellLine_tazemetostat_H3K27me3CnR_repl1


title: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D6 rep1

description: Library name: Atrial_D6_rep1

value: WT


title: TO Patient1 Control rep1


title: Hi-C of Homo sapiens: WTC11 rep1

description: Library name: D0_rep1

value: iPSC


title: tFL-P6_cellLine_DMSO_H3K27me3CnR_repl3

description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_34_tFL-P6_cellLine_DMSO_H3K27me3CnR_repl3

value: Treated with DMSO for 14 days


title: A549 cells, essentiality screen, pool #6, day 0

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: Lewis-Sigler Institute for Integrative Genomics, Princeton University

institute: Princeton University

description: Library name: Sample 42

data_processing:
fastq files from amplicon seq experiements were aligned to the specific locus and edited reads were called by CRISPRESSO2.  fastq files from CRISPR screen was analyzed using MAGeCK.
Assembly: mm10 for mouse, hg19 for human.
Supplementary files format and content: processed data is in XLSX format and contains results for the F1 cross (C57BL/6 and 129S1/SVlmJ) and essentiality (A549) screens.
Library strategy: CRISPR Screen

source_name: cell line

extract_protocol:
phenol chloroform
For random/selected sgRNA sequencing (Samples 1-31), PCR encompassing ~250bp surrounding the edit site was performed using loci-specific primers, and standard P7/P5 adapters were added to the PCR amplicon by Genewiz/Azenta for subsequent NGS.  For CRISPR sequencing (Samples 32-43), a 2 step PCR approach was used to first amplify the region of sgRNA region after genomic DNA extraction, then standard P7/P5 adapters and unique barcodes were added in a second PCR reaction.

value: cell line

value: lung epithelial cells


title: A549 cells, essentiality screen, pool #6, day 18

description: Library name: Sample 43


title: GM12878_dscHi-C, dscHi-C, cultured

description: Library name: GM12878_dscHi-C

source_name: B lymphoblastoid

value: B lymphoblastoid


title: A549 cells, essentiality screen, pool #5, day 0

description: Library name: Sample 40


title: tFL-P6_cellLine_DMSO_H3K27me3CnR_repl2

description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_33_tFL-P6_cellLine_DMSO_H3K27me3CnR_repl2


title: Human cell line mixture, dscHi-C, cultured

description: Library name: Cell-line_dscHi-C

source_name: mixture

value: mixture


title: A549 cells, essentiality screen, pool #4, day 18

description: Library name: Sample 39


title: A549 cells, essentiality screen, pool #4, day 0

description: Library name: Sample 38


title: A549 cells, essentiality screen, pool #3, day 18

description: Library name: Sample 37


title: A549 cells, essentiality screen, pool #2, day 18

description: Library name: Sample 35


title: CCN2-FLOX, scRNAseq

city: Atlanta

first: Qian

state: GA

address: 101 Woodruff Circle

institute: Emory University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The initial filtered data resulting from Cell Ranger 7.02 were then utilized for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

extract_protocol:
Following euthanasia, mice were immediately subjected to perfusion with PBS. The aortic root and ascending aorta were subsequently excised, stopping at the commencement of the descending artery. The excised tissue was rinsed thoroughly three times with PBS, then transferred into an enzymatic dissociation cocktail that contains 2U/mL of Liberase TM (Sigma-Aldrich) and 2U/mL of elastase (LS002279, Worthington) in Hank’s Balanced Salt Solution (HBSS), and finely minced. After an incubation period at 37 °C for 1 hour, the resulting cell suspension underwent straining and was subsequently pelletized through centrifugation at 300g for 5 minutes. The enzyme solution was then discarded, and the cells were resuspended in fresh HBSS. For each single-cell RNA capture, a total of 3 pairs of mice were utilized, distinguishing between control and SMC-CCN2-KO groups. The aortic cells were subsequently captured using separate but parallel runs of the identical scRNA-seq workflow, with the datasets later merged for all subsequent analyses.
The Emory Integrated Genomics Core (EIGC) was responsible for conducting all single-cell capture and library preparation procedures. To initiate the process, single cells were suspended in a solution of 2% BSA in PBS, subsequently quantified, and promptly subjected to processing using a 10x Genomics Chromium device. This device facilitated the encapsulation of individual cells, barcoding, and RNA preparation for single-cell analysis. The scRNA-seq libraries were generated using the NextGEM Single Cell 3' Kit from 10x Genomics, following the manufacturer's established protocol.  For sequencing, the libraries from various individual samples were combined and multiplexed into a single lane. Sequencing was carried out on an Illumina platform utilizing a NovaSeq SP Flow Cell with 100 cycle kits, aligning with the specifications provided by the manufacturer. In terms of data analysis, the raw sequencing data was mapped to the mouse reference genome mm10 using Cell Ranger v3.0.2. The quantification of Unique Molecular Identifiers (UMIs) for each cellular barcode enabled the assessment of the number of cells that were successfully captured and sequenced.

value: Aorta

value: Vascular cells


title: A549 cells, essentiality screen, pool #2, day 0

description: Library name: Sample 34


title: tFL-P6_cellLine_DMSO_H3K27me3CnR_repl1

description:
Rosa26LSL.BCL2.IRES.GFP;Ezh2Y641F;Cγ1-cre
B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro
SICER2 peaks
Sample_32_tFL-P6_cellLine_DMSO_H3K27me3CnR_repl1


title: A549 cells, essentiality screen, pool #3, day 0

description: Library name: Sample 36


title: CCN2-FLOX-SMC,scRNAseq

description: 10x Genomics

value: CCN2flox/flox, Myh11-Cre-ERT2


title: A549 cells, essentiality screen, pool #1, day 18

description: Library name: Sample 33


title: Multiome, #1144, CAR-VST, hTCR

city: Houston

first: Helen

last: Heslop

address: 1102 Bates Ave

institute: Baylor College of Medicine

description:
Library name: 5v3_1144_VST_hTCR
10x Genomics

data_processing:
Reads from the gene expression library were aligned to the chimeric reference with those from the 10x Genomics V(D)J TCR enriched library, following the 10x Genomics standard, using Cell Ranger multi (v8.0.0). Cells with UMI > 0 matching the GD2CAR sequence were identified as CAR+ cells.
Before cell clustering, the raw feature barcode matrices were filtered by removing cells with fewer than 100 genes, cells with less than 10,000 genes and cells with more than 15% of the feature set being comprised of mitochondrial genes. Quality controls were then conducted by removing the residual cells with more or less than the 95th and 5th percentile of features per cell and the upper 95th percentile of mitochondrial gene counts per cell.
Clonotypes were defined as cells that shared a common CDR3 beta sequence and when possible, each single cell was annotated by the corresponding CDR3 beta sequence. UMI counts were normalized using the Seurat4.3 function scTransform. The most 2,000 variable genes were identified and genes associated with the TCR were removed, leaving 1898 variable marker genes for integration and clustering with a k-nearest neighbor graph. Cells from CAR-ATC and CAR-VST products were integrated across all three patient samples using the Seurat functions.
When clustering, we performed principal component analysis (PCA) on the scaled data and clustered the cells using the function FindClusters. The Louvain clustering algorithm with default parameters and a resolution of 0.4. A total of 11 clusters were identified from the integrated 3 pre-infusion product samples manufactured from ATCs and the 3 pre-infusion product samples manufactured from VSTs. Cells in each cluster were projected onto a two-dimensional UMAP with a spread of 0.25 to illustrate the differences in gene expression in the cells between the two manufacturing methods. For cluster proportion analysis, cells were down sampled to the lowest number of cells detected from the ATC and VST infusion products and a 2-tailed p-value was then calculated with the hypergeometric distribution by sampling from the average proportion over the patient samples per cluster for the ATCs and the VSTs separately and comparing this with the total cell number from the down sampled data. Dot plot visualization was performed using the Seurat DotPlot function.
Shannon entropy was calculated with minus the sum of the clonotype frequency multiplied by the natural logarithm of the clonotype frequency.
Link to accompanying Rscript: https://doi.org/10.5281/zenodo.14544634
Assembly: The GD2CAR sequence was indexed together with the human reference genome (version: GRCh38.p14) to generate a chimeric reference before read alignment.
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: 10x genomics Cell Ranger multi feature barcode matrices for the reads from the gene expression libraries and corresponding contig_annotations.csv files for each sample. RDS files containing processed data from ATCs and VSTs combined for each patient sample and the RDS file of the integrated data are also provided.
Library strategy: TCR-Seq

source_name: Peripheral blood

extract_protocol:
Frozen CAR-T products stored in the GMP laboratory were thawed and resuspended in PBS. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 5' ver.3 GEM Library and Gel Bead kit.
The TCR library was amplified using Chromium single-cell V(D)J enrichment kit (human T cell) (10x Genomics). KAPA Library Quantification kit (Roche) was used to quantify libraries.

tag: library type

value: TCR

value: Peripheral blood

value: EBV virus-specific T cells

value: T cells

value: GD2 1st gen CAR

value: CAR-T products

value: Patient #1144


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep2

description: Library name: TBX5_null_rep2

data_processing:
Fastq files were aligned to the hg38 reference genome using bowtie2. Reads were filtered to include of those with a mapq score of 30 or greater and removing duplicate reads using SAMtools. Blacklisted regions were removed using BEDtools. Chip-seq peaks were called on each individual replicate relative to input using macs2 and the narrowpeaks parameter. CTCF ChIP bigwig files for visualization were generated using deepTools2 bamCoverage.
Assembly: hg38
Supplementary files format and content: .narrowPeak of peaks and .bw of signal profiles

growth_protocol: Cells were grown in one 6-well plate per replicate, with all 6 wells pooled together after dissociation for the crosslinking step (approximately 20 million cells). Each plate was one biological replicate. To generate TBX5-bio cell line, a codon-optimized BioTAP (Alekseyenko 2014) tag was inserted immediately after the start methionine codon in the N-terminus of the endogenous TBX5 locus using ribonucleoprotein (RNP) complexes of sgRNA (GCCCTCGTCTGCGTCGGCCA, ordered from Synthego) and SpCas9-NLS ‘HiFi’ protein (QB3 MacroLab, University of California Berkeley). This tag can be biotinylated by endogenous biotin ligases. The BioTAP tag was codon optimized for integration using HDR Alt-R gene blocks donor template (IDT). RNPs were prepared by mixing 1 µl of 40 µM Cas9 with 1.2 µl of 100 µM sgRNA and made to a total volume of 10 µl with Lonza P3 transfection buffer (Lonza #197179) and incubated at room temperature for 10 min. 250000 WTc11 iPSCs were resuspended in 12.2 µl Lonza P3 transfection buffer and nucleofected with 1 µg codon-optimized BioTAP donor template and 10 µl RNPs using Lonza Nucleofector 4D system in 96-well format using DS-138 settings. After nucleofection, mTeSR1 supplemented with CloneR (StemCell Technologies #05888) was added to cells and incubated for 10 min at 37˚C, before transferring cells into a single well of a matrigel-coated 48-well plate. The following day, media was replaced with fresh mTeSR1. The cells were expanded into a 12-well plate. Single cells were dissociated with Accutase and were sorted into 96-well plates for colony selection using Namocell Hana single-cell dispenser. Plates were cultured in mTeSR1 supplemented with CloneR for 3 days post sorting to ensure survival and then replaced with mTeSR1. Colonies were screened by PCR using primers pairs flanking the whole insertion site (F: 5’-TCCTCAGAGCAGAACCTTGC, R: 5’-CTTACCTGCTGGGTGAAGG), 5’ integration site (F: 5’-AAACTGCTCCCTCCTGTCAC, R: 5’-ATTTTCATGGCCTCAAGCAC) and 3’ integration site (F: 5’-CCGATGGTAAGGTCGAGAAG, R: 5’-CGAGGTCTCCTTACCTGCTG). Amplicon from whole insertion site PCR was amplified and verified by Sanger sequencing. Copy number variation was determined by droplet digital PCR (Bio-Rad QX200 Droplet Reader) and using the RPP30 assay (Bio-Rad #10031243) and comparing to custom primers (F: 5’-GCGTTTATCTCCGTCTCCATTT and R: 5’- GGACTGTCAGTAAGATCCTTGTT) and probe (5’- CAAGCACCGTTTGCCCTGCTTTAA) for the knock-in TBX5-biotin allele. The cells were determined to have a normal karyotype.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 15 ml tube and centrifuged at 800 rpm for 5 min at room temperature. Pellets were washed once in 10 ml DPBS plus 1x protease inhibitors (DBPS+PI) before resuspending entire cell pellet in exactly 10 ml DPBS+PI. 16% methanol-free formaldehyde (ThermoFisher Scientific #28908) was added to a final concentration of 1% and samples incubated on nutator at room temperature for 10 min. Samples were quenched with 2.5 M glycine to a final concentration of 0.125 M and incubated on nutator at room temperature for 5 min, followed by centrifugation at 500 x g for 5 min at 4˚C. Samples were washed once in ice cold DPBS+PI, before being transferred to 2 ml protein lo-bind rubes, centrifuged at 2500 x g at 4˚C. for 5 min and cell pellets were snap frozen in liquid nitrogen and stored at -80˚C.  TBX5-bio cross-linked cells were thawed on ice and resuspended in 1 ml of ice cold cell lysis buffer (25 mM Tris-HCl, pH 7.4, 85 mM KCl, 0.25% Triton X-100 and 1x Protease inhibitors in ddH2O) and incubated at 4˚C rotating for 30 minutes. Sample were centrifuged at 2500 x g for 5 min at 4˚C and resuspended in 1 ml nuclear lysis buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O). Samples were transferred to 1 ml millitube (Covaris #520130) and sheared using a Covaris S2 sonicator for 15 min at 5% duty cycle, intensity 5, 200 cycles per burst in a water bath maintained at 4˚C. After shearing, 5 µl of each sample was kept for reverse crosslinking and the remaining sonicated sample was transferred to a new protein lo-bind tube and snap frozen in liquid nitrogen. The 5 µl sample was made up to 100 µl and incubated for 30 min at 37˚C with 1 µl RNase A, followed addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. The following day the reverse crosslinked samples were purified using Qiagen MinElute PCR Purification kit (Qiagen #28006) and DNA quantified using Qubit Fluorometer and dsDNA HS Assay Kit (ThermoFisher Scientific #Q32854). Samples were run on an Agilent 2100 Bioanalyzer to verify that chromatin was sheared to fragments between 100-500bp in size. Based on these measurements, the amount of DNA in each lysed sample could be extrapolated and equal amounts of sheared chromatin could be used per ChIP. Sheared samples were thawed quickly at 37˚C and the equivalent of 55 µg of chromatin was transferred to a 5 ml protein lo-bind tube for ChIP and made up to 1 ml in nuclear lysis buffer. 50 µl (5%) of each sample was collected as input and stored at 4˚C until reverse crosslinking step. ChIP samples were then diluted 1:5 with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 167 mM NaCl and 1x protease inhibitors in ddH2O). 50 µl of pre-washed Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific #65601) were added to each sample and incubated overnight with rotation at 4˚C. The following day, beads were collected using a magnetic stand and transferred to 2 ml protein lo-bind tubes and washed with 1 ml twice of the following wash buffers: wash buffer 1 (2% SDS in ddH2O), wash buffer 2 (0.1% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl in ddH2O), wash buffer 3 (250 mM LiCl, 0.5% IGEPAL CA-630 [Sigma #I8896], 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and TE buffer (10 mM Tris-HCl pH 7.5 and 1 mM EDTA ddH2O).  After adding each wash buffer, beads were vortexed for 15 s, spun briefly and collected against a magnet. DNA was eluted with 150 µl elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0 in ddH2O) shaking at 1000 rpm at 65˚C overnight. The following day, beads were collected on a magnetic stand and supernatant was transferred to a new DNA lo-bind tube. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1.5 µl RNase A, followed addition of 18 µl 5 M NaCl and reverse crosslinking with 1.5 µl proteinase K at 65˚C for 6 hours. DNA was purified using Qiagen MinElute PCR Purification kit (Qiagen #28006). CTCF ChIP-seq was performed generally as above with changes detailed here. The following buffers were used: cell lysis buffer recipe (20 mM Tris-HCl pH 8.0, 85 mM KCl, 0.5% IGEPAL CA-630 and 1x protease inhibitors in ddH2O), nuclear lysis buffer recipe (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and 1x protease inhibitors in ddH2O), wash buffer 1 recipe (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O), wash buffer 2 recipe (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100 in ddH2O) and wash buffer 3 (250 mM LiCl, 1% IGEPAL CA-630 [Sigma #I8896], 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl pH 8.0 in ddH2O) and elution buffer (1% SDS, 100 mM NaHCO3 in ddH2O). 70 µg of chromatin was used per sample. After diluting in dilution buffer, each ChIP sample was incubated rotating at 4˚C overnight with 6 µg antibody (combination of both Active Motif #61311 [discontinued] and Abcam #ab128873 used in each sample) and the following day incubated with 50 µl prewashed Magna ChIP protein A/G beads (Sigma #16-663) for 4 hours at 4˚C. Bead washes were performed by resuspending beads in 1 ml buffer using P1000 pipette, spinning briefly and collecting on magnet. Following the bead washes, DNA was eluted in 50 µl shaking at 37˚C, transferring to new tube and repeating bead elution to pool eluates to a total volume of 100 µl. Both ChIP and input samples were incubated at 37˚C for 30 min at 37˚C with 1 µl RNase A, followed by addition of 12 µl 5 M NaCl and reverse crosslinking with 1 µl proteinase K at 65˚C overnight. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research #D5205).
For Illumina sequencing library preparation, the entire ChIP sample or 2 µl of each input was used. End repair was performed in a 100 µl reaction with 15 U T4 DNA polymerase (New England Biolabs #M0203L), 5 U Klenow fragment DNA polymerase (New England Biolabs, #M0210L), 50 U T4 PNK (New England Biolabs #M0201L), 400 µM dNTP (Promega #U1511) and 1x T4 DNA ligase buffer w 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 30 min at room temperature, followed by 1.6x bead:sample AmpureXP purification. Entire eluate was used for A-tailing in a 50 µl reaction with 1 mM dATP (New England Biolabs #N0440S), 15 U Klenow 3’>5’ exonuclease (New England Biolabs #M0212L) and 1x NEB buffer 2 in nuclease-free water for 30 min at 37˚C, followed by 1.6x bead:sample AMPureXP purification. Entire eluate was used for adapter ligation in a 50 µl reaction with 6000 U T4 DNA ligase (New England Biolabs #M0202L), 20 nM annealed and uniquely indexed adapters and 1x T4 DNA ligase buffer with 10 mM ATP (New England Biolabs #B0202S) in nuclease-free water for 2 hours at room temperature, followed by 1x bead:sample AMPureXP purification. Adapters were prepared by annealing following HPLC purified oligos: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T and 5’Phos-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG where * represents a phosphothiorate bond and NNNNNN is a Truseq index sequence.The entire eluate was used for PCR amplification in a 50 µl reaction with 1x NEB Next High-Fidelity 2x PCR master mix (New England Biolabs #M0541L), 10 µM primers (F: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA, R: 5’-CAAGCAGAAGACGGCATACGAGAT) in nuclease free water, using thermocycler settings 98˚C for 30 sec; 16 cycles of 98˚C for 10 sec, 58˚C for 40 sec and 72˚C for 30 sec; 72˚C for 5 min and followed by 0.8x bead:sample AMPureXP purification. DNA was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer.

value: cardiomyocyte

value: atrial cardiomyocyte differentation


title: APC_male_apc_5

city: Fayetteville

first: Nicholas

middle: P

last: Greene

state: Arkansas

address: 155 Stadium Dr. HPER Building 321

institute: University of Arkansas

data_processing:
Raw counts were obtained using Salmon 1.10.2 and imported into R 4.4.1 using the tximport package, with GRCm39 annotation from AH116909.
The RNA-seq count data was stored in a DGEList object from the edgeR package, which was then transformed using the voom function from the limma package.
CPM and calcNormFactors were used to normalize the data.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts.

source_name: Tibialis anterior

extract_protocol:
TA were snap frozen in liquid nitrogen. RNA was extracted using trizol and a commercial kit (Thermo Fisher, PureLink RNA Mini Kit, Cat. No. 12183025).
The RNA sequencing was rered to Novogene for a mRNA library preparation (poly A enrichment)

value: Tibialis anterior

value: male

tag: timepoint

value: APC+/Min


title: APC_male_apc_6


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep1

description: Library name: TBX5_null_rep1


title: Multiome, #1144, CAR-ATC, hTCR

description:
Library name: 5v3_1144_ATC_hTCR
10x Genomics

value: Activated T cells


title: A549 cells, essentiality screen, pool #5, day 18

description: Library name: Sample 41

value: cell line

value: lung epithelial cells


title: Multiome, #1290, CAR-VST, hTCR

description:
Library name: 5v3_1290_VST_hTCR
10x Genomics

value: Patient #1290


title: Multiome, #1632, CAR-VST, hTCR

description:
Library name: 5v3_1632_VST_hTCR
10x Genomics

value: Patient #1632


title: APC_male_apc_4


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/+ rep2

description: Library name: TBX5_Het_rep2


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with  TBX5in/+ rep1

description: Library name: TBX5_Het_rep1


title: APC_male_apc_3


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep1

description: Library name: TBX5_WT_rep1

value: WT


title: GM12878 and mESC cell mixture, dscHi-C, cultured

description:
Library name: mESC-GM_dscHi-C
Species mixing experiment; Reference genome is set to be hg38_mm10

source_name: B lymphoblastoid, mouse embryonic stem cell


title: ChIP-seq of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WT WTC11 rep2

description: Library name: TBX5_WT_rep2


title: Multiome, #1632, CAR-ATC, hTCR

description:
Library name: 5v3_1632_ATC_hTCR
10x Genomics

value: TCR

value: Peripheral blood


title: A549 cells, essentiality screen, pool #1, day 0

description: Library name: Sample 32


title: APC_male_apc_2


title: Multiome, #1144, CAR-VST, GEX

description:
Library name: 5v3_1144_VST_GEX
10x Genomics

data_processing:
Reads from the gene expression library were aligned to the chimeric reference with those from the 10x Genomics V(D)J TCR enriched library, following the 10x Genomics standard, using Cell Ranger multi (v8.0.0). Cells with UMI > 0 matching the GD2CAR sequence were identified as CAR+ cells.
Before cell clustering, the raw feature barcode matrices were filtered by removing cells with fewer than 100 genes, cells with less than 10,000 genes and cells with more than 15% of the feature set being comprised of mitochondrial genes. Quality controls were then conducted by removing the residual cells with more or less than the 95th and 5th percentile of features per cell and the upper 95th percentile of mitochondrial gene counts per cell.
Clonotypes were defined as cells that shared a common CDR3 beta sequence and when possible, each single cell was annotated by the corresponding CDR3 beta sequence. UMI counts were normalized using the Seurat4.3 function scTransform. The most 2,000 variable genes were identified and genes associated with the TCR were removed, leaving 1898 variable marker genes for integration and clustering with a k-nearest neighbor graph. Cells from CAR-ATC and CAR-VST products were integrated across all three patient samples using the Seurat functions.
When clustering, we performed principal component analysis (PCA) on the scaled data and clustered the cells using the function FindClusters. The Louvain clustering algorithm with default parameters and a resolution of 0.4. A total of 11 clusters were identified from the integrated 3 pre-infusion product samples manufactured from ATCs and the 3 pre-infusion product samples manufactured from VSTs. Cells in each cluster were projected onto a two-dimensional UMAP with a spread of 0.25 to illustrate the differences in gene expression in the cells between the two manufacturing methods. For cluster proportion analysis, cells were down sampled to the lowest number of cells detected from the ATC and VST infusion products and a 2-tailed p-value was then calculated with the hypergeometric distribution by sampling from the average proportion over the patient samples per cluster for the ATCs and the VSTs separately and comparing this with the total cell number from the down sampled data. Dot plot visualization was performed using the Seurat DotPlot function.
Shannon entropy was calculated with minus the sum of the clonotype frequency multiplied by the natural logarithm of the clonotype frequency.
Link to accompanying Rscript: https://doi.org/10.5281/zenodo.14544634
Assembly: The GD2CAR sequence was indexed together with the human reference genome (version: GRCh38.p14) to generate a chimeric reference before read alignment.
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: 10x genomics Cell Ranger multi feature barcode matrices for the reads from the gene expression libraries and corresponding contig_annotations.csv files for each sample. RDS files containing processed data from ATCs and VSTs combined for each patient sample and the RDS file of the integrated data are also provided.

value: mRNA

value: EBV virus-specific T cells

value: T cells


title: Tsix-stop cells, neg control, Day15

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

data_processing:
Illumina conventional base calls were performed.
A pseudo-129 genome was assembled by replacing available SNPs of 129 (Sanger Center) into the BL6 mm10 reference genome. A pseudo-cast genome was assembled by replacing available SNPs of cast (Sanger Center) into the BL6 mm10 reference genome.
RNA-seq reads were mapped using bowtie/v2.4.5 and tophat/v2.1.1 to the genome and transcriptome of both the pseudo-129 and the pseudo-cast genomes. Only those reads that mapped uniquely and with a high-quality mapping score (MAPQ ≥ 30) to either the pseudo-129 or pseudo-cast genomes were kept for further analyses.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each gene.

source_name: embryonic stem cells

growth_protocol: ES cells were maintained in the presence of 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on a inactivated MEFs, in high glucose DMEM media supplemented with 15% fetal bovine serum (FBS), 1% non-essential amino acids, 10 mg/ml APS, 0.1mM 2mercaptoethanol and 25mM L-glutamine, in a humidified incubator at 37ºC and 5% CO2. Differentiation was induced by culturing as embryoid bodies and removal of LIF

extract_protocol:
RNA was collected using Rneasy mini kit (Qiagen). 1ug of total RNA was used for the construction of RNA sequencing libraries
cDNA libraries were constructed using the Ilumina TruSeq V2 prep kit.

treatment_protocol: CRISPR/Cas9 and sgRNA constructs targeting Kdm6a were transfected at the stem cell stage (day0) followed by differentiation using lipid based methods.

value: embryonic stem cells

value: Tsix-stop

value: CRISPR control

value: nondirected differentiation


title: Tsix-stop cells, knockout, Day15, rep 2

value: Kdm6a knockout


title: Tsix-stop cells, neg control, Day0


title: APC_male_apc_1

value: Tibialis anterior

value: male

value: APC+/Min


title: APC_male_wt_8

value: wild type


title: Multiome, #1144, CAR-ATC, GEX

description:
Library name: 5v3_1144_ATC_GEX
10x Genomics

value: Activated T cells

value: GD2 1st gen CAR

value: CAR-T products

value: Patient #1144


title: Tsix-stop cells, knockout, Day15, rep 1


title: Multiome, #1290, CAR-VST, GEX

description:
Library name: 5v3_1290_VST_GEX
10x Genomics

value: Peripheral blood

value: Patient #1290


title: Tsix-stop cells, wildtype control, Day15, rep 2

value: WT


title: PBMCs, Figure_3

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Hybridized Probe-based RNA capture on 10x Barcoded Beads. Multiplexed pool with samples: BL05012_3, BL05013_3, BL05044_3, BL05045_3, BL05729_3, BL05730_3, BL05731_3, PB02183_3
BL05731_FACS.csv
BL05731_FACS_sample_filtered_feature_bc_matrix.h5

data_processing:
10x Cell Ranger Pipeline
Scrublet Doublet Detection
Assembly: GRCh38
Supplementary files format and content: H5 cell by gene matrix, csv with doublet information, fcs files represent data for the flow cytometry results shown in our figure 2

source_name: Blood

extract_protocol:
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)
PBMC enriched samples were processed according to the 10x Genomics protocol for Fixation of Cells and Nuclei (CG000478, Rev C). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A).
10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev A).
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)

value: Blood

value: mRNA


title: Multiome, #1290, CAR-ATC, hTCR

description:
Library name: 5v3_1290_ATC_hTCR
10x Genomics

value: TCR

value: T cells


title: APC_male_wt_6


title: Tsix-stop cells, wildtype control, Day0, rep 2

value: embryonic stem cells

value: Tsix-stop

value: nondirected differentiation


title: KI_10m_H3K27ac_rep2

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Striatum

extract_protocol:
NeuN+ and NeuN- sorted nuclei preparations from R6/1 and WT mice were divided to allow immunoprecipitation of the same extract with H3K27ac (ab4729, Abcam), H3K27me3 (C15410195, diagenode) and IgG control (C15410206, Diagenode), using 50000 nuclei/CUT&Tag. CUT&Tag was essentially performed as described by Kaya-Okur et al. (2020). Briefly, concanavalinA-coated beads (93569S, Cell signaling) were added to nuclei suspension at room temperature under rotation to attach nuclei. Then corresponding primary antibodies were incubated overnight at 4 °C. Beads-nuclei complex were washed and incubated 1h at RT with proteinA-Transposase5 complex (C01070001, Diagenode) to a final concentration of 1:250. Tagmentation was done by incubating samples 1h in MgCl2 at 37°C, then proteins were eliminated by 1h incubation in SDS and Proteinase K at 55°C. DNA was recovered using Qiagen MinElute PCR Purification Kit.
CUT&Tag libraries were prepared from the eluted double-strand DNA using NEBNext HiFi 2x PCR master mix (BioLabs) and Illuminas compatible indexes (20091654, Illumina Nextera) (13 cycles). Amplified libraries were purified and size-selected using SPRI select beads (B23317, Beckmann Coulter) at 1.3 time, two times consecutively.

value: Striatum

value: H3K27ac: ab4729, Abcam


title: APC_male_wt_5

value: Tibialis anterior

value: male

value: wild type


title: Tsix-stop cells, knockout, Day0, rep 1

value: Kdm6a knockout


title: Tsix-stop cells, knockout, Day0, rep 2


title: Tsix-stop cells, wildtype control, Day15, rep 1


title: Tsix-stop cells, wildtype control, Day0, rep 1


title: E8 stem cells, knockout, Day15,rep1


title: Multiome, #1632, CAR-ATC, GEX

description:
Library name: 5v3_1632_ATC_GEX
10x Genomics

value: Activated T cells

value: GD2 1st gen CAR

value: CAR-T products

value: Patient #1632


title: E8 stem cells, knockout, Day7,rep2


title: APC_male_wt_4


title: E8 stem cells, knockout, Day15,rep2


title: H1 STEM 3

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description: Library name: H1 STEM 3

data_processing:
RNA-seq reads were mapped to the GRCh38 (human) reference and genome using the STAR aligner
Counts were tabulated using ENSEMBL release 101 annotations with featureCounts.
Assembly: GRCh38, ENSEMBL release 101
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries were prepared using the SMART-Seq  v4 low input RNA kit

value: Stem cell

value: No treatment


title: E8 stem cells, knockout, Day7,rep1


title: APC_male_wt_3


title: APC_male_wt_7


title: H1 STEM 2

description: Library name: H1 STEM 2

value: Stem Cell


title: E8 stem cells, wildtype control, Day15,rep2

value: WT


title: E8 stem cells, wildtype control, Day15,rep1

value: embryonic stem cells


title: E8 stem cells, wildtype control, Day7,rep2


title: APC_male_wt_2


title: Multiome, #1290, CAR-ATC, GEX

description:
Library name: 5v3_1290_ATC_GEX
10x Genomics

value: mRNA

value: Peripheral blood

value: T cells

value: Patient #1290


title: APC_male_wt_1

value: Tibialis anterior


title: H1 STEM 1

description: Library name: H1 STEM 1


title: APC_female_apc_6

value: female

value: APC+/Min


title: E8 stem cells, wildtype control, Day7,rep1

value: nondirected differentiation


title: Multiome, #1632, CAR-VST, GEX

description:
Library name: 5v3_1632_VST_GEX
10x Genomics

value: EBV virus-specific T cells