title: sheep3-RAD.HiC

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

data_processing:
Contacts matrix were generated by using Juicer pipeline.
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
TADs were identified using  Insulation Score.
Compartment A/B were defined by A-B index.
Assembly: Susscrofa11.1
Supplementary files format and content: Binned raw and normalized 2D contact matrices text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Genes expression level (TPM) and counts text file
Supplementary files format and content: TAD files
Supplementary files format and content: ABindex files

organism: Ovis aries

source_name: retroperitoneal adipose

extract_protocol:
Briefly, 1 g of adipose tissue were cross-linked with a final concentration of 4% freshly prepared formaldehyde (Sigma Aldrich, Louis, MO, USA) for 30 mins at room temperature, followed by quenching with glycine (Amresco, Solon, OH, USA) at a final concentration of 0.25 mol/L. After centrifuging the mixture at 1500 × g for 10 mins at room temperature, the upper layer containing adipocytes were added to 1 mL lysis buffer (9.1 μL 1 M NaCl, 9.1 μL 1 M Tris-HCl [pH 8.0] [Invitrogen, Carlsbad, CA, USA], 18.2 μL 10% CA-630 [Sigma Aldrich, Louis, MO, USA], 50 μL protease inhibitors [Sigma Aldrich, Louis, MO, USA], and 913.6 μL nuclease-free water [Ambion, Carlsbad, CA, USA]) and homogenized with a Dunce homogenizer. After centrifuging the homogenate at 5000×g, cell nuclei were collected. The pellet was washed twice with 500 μL 1× NEBuffer 2 (NEB, Ipswich, MA, USA), followed by centrifugation at 5000 rpm for 5 mins. Next, the pellet was resuspended in 100 µL 1× NEBuffer 2, and we added SDS (Amresco, Solon, OH, USA) to a final concentration of 0.1%. After incubation at 65 °C for 10 mins, we added Triton X-100 (Sigma Aldrich, Louis, MO, USA) to a final concentration of 1%, and incubated for 15 mins at 37 °C. Nuclei were permeabilized, and DNA was digested with 200 units of MboI enzyme (NEB, Ipswich, MA, USA) at 37 °C for 1 h, 65 °C for 20 mins and 25 °C for 5 mins. We then added biotin-14-dATP, dCTP, dGTP, dTTP and Klenow fragment (NEB, Ipswich, MA, USA), and incubated the mixture at 37 °C for 45 mins. The DNA fragments were then ligated by T4 DNA ligase (Enzymatics, Beverly, MA, USA), incubated at 20 °C for 30 mins. After centrifugation at 5000 rpm for 5 mins, the pellet was resuspended in 20 µL 10X T4 DNA ligase buffer, 90 µL nuclease-free water, and 20 µL SDS and 50 µL Proteinase K (20 mg/ml) (Tiangen, Beijing, China) were added. After incubation at 55 °C for 30 min to digest proteins, the DNA were extracted and dissolved in 20 µL of 5 M NaCl, and the mixture was incubated sequentially at 65 °C for 90 mins and at 25 °C for 5 mins. The DNA were then purified by AMPure XP Beads (Beckman Coulter, Brea, CA, USA). Then, T4 DNA polymerase (Enzymatics, Beverly, MA, USA) was used to remove nonligated biotinylated DNA for 2 h at 12 °C. The DNA was then sonicated into 300-500 bp fragments using a Covaris S220 sonicator. The DNA fragments with biotin were pulldown by M280 beads (Invitrogen, Carlsbad, CA, USA).
Next, we performed end repair, A-tailing, adapter ligation, postligation cleanup and PCR amplification (8-10 cycles) using the KAPA Hyper Prep Kit (Roche, Pleasanton, CA, USA). DNAs between 300 and 800 bp in size were then isolated using AMPure XP Beads, and the libraries were sequenced using Illumina NovaSeq 6000 (paired-end sequencing with 150 bp read length).

tag: breed

value: Small-tail Han sheep

tag: developmental stage

value: Adult

value: retroperitoneal adipose


title: 11J_M_655

status: Public on Apr 25 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 11J_M_654


title: 12B_M_1551

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2


title: sheep3-MAD.HiC

source_name: mesenteric adipose

tag: tissue

value: mesenteric adipose


title: sheep3-GOM.HiC

source_name: greater omentum fat

value: greater omentum fat


title: 33_PFC_H24 [P-34]

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description:
deseq2_PFC_cpm.csv
CountsMatrix.csv
DEGlists.xlsx

library_source: transcriptomic

data_processing:
Quality control on raw reads was performed using FastQC.Sequencing reads underwent adapter trimming and were mapped to mm10 using HISAT2. Duplicates were removed using samtools rmdup. Counts of reads mapping to genes were obtained using htseq-count against Ensembl v90 annotation.
Assembly: mm10
Supplementary files format and content: CountsMatrix: A comma delimited text file containing the raw read counts for all genes. Columns represent samples and rows represent the genes.  AnnotationFile: A comma delimited text file containing the basic metadata for all samples. CPM files: A comma delimited text file containing the normalized gene expression in counts per million(cpm). Individual files are provided for the different brain regions. DEGlist: An excel file containing  the differential expression result tables for several comparisons.

molecule: total RNA

source_name: Brain

extract_protocol:
RNA extracted using Qiagen RNEasy Micro
Illumina TruSeq Gold, strand-specific RNA-seq with rRNA depletion
2x150 bp sequencing, single index

value: Brain

value: PFC

tag: mouse id

tag: genotype

value: Wild-type

tag: group


title: 12B_M_1550


title: sheep2-RAD.HiC


title: sheep2-MAD.HiC


title: sheep2-GOM.HiC


title: 11J_M_653


title: 38_PFC_H24 [P-39]


title: sheep1-RAD.HiC


title: 12B_M_1549


title: 42_PFC_H24 [P-43]


title: sheep1-GOM.HiC


title: sheep1-MAD.HiC


title: 11J_M_652


title: 12B_M_1548


title: 47_PFC_H24 [P-48]


title: 40_PFC_H24 [P-41]


title: 11J_M_651


title: 11J_M_650


title: start_nls_4

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

organism: Saccharomyces cerevisiae

source_name: budding yeast culture at OD=4

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(start_nls)-Mnase (kanMX)


title: wt_1

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(wt)-Mnase (kanMX)


title: Rep10x3_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(Rep10x3)-Mnase (kanMX)


title: Rep7x3_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(Rep7x3)-Mnase (kanMX)


title: Rep7x3_2


title: wt_2


title: 47_NAc_H24 [N-100]

description:
deseq2_NAc_cpm.csv
CountsMatrix.csv
DEGlists.xlsx

value: NAc


title: Rep7x3_1


title: 12B_M_1547


title: 48_PFC_H24 [P-49]


title: Rep10x3_1


title: MotAx3_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(MotAx3)-Mnase (kanMX)


title: MotAx3_2


title: 45_NAc_H24 [N-98]


title: 11J_M_649


title: MotAx3_4


title: 12B_M_1546


title: MotAx3_1


title: LIV_to_N_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIV_to_N)-Mnase (kanMX)


title: LIV_to_N_2


title: LIV_to_N_3


title: 42_NAc_H24 [N-95]


title: 12B_M_1545


title: 38_NAc_H24 [N-91]


title: 11J_M_648


title: LIV_to_N_1


title: LIV_to_L_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIV_to_L)-Mnase (kanMX)


title: 39_NAc_H24 [N-92]


title: LIV_to_L_2


title: 12B_M_1544


title: LIV_to_L_3


title: 11J_M_647


title: 43_NAc_H24 [N-96]


title: LIV_to_L_1


title: 51_PFC_H24 [P-52]


title: LIV_to_I_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIV_to_I)-Mnase (kanMX)


title: LIV_to_I_4


title: 51_NAc_H24 [N-104]


title: 40_NAc_H24 [N-93]


title: LIV_to_I_1


title: 12B_M_1543


title: 11J_M_646


title: LIV_to_D_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIV_to_D)-Mnase (kanMX)


title: LIV_to_D_3


title: 11J_M_645


title: LIVFWY_to_Y_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_Y)-Mnase (kanMX)


title: LIVFWY_to_Y_3


title: 12B_M_1542


title: LIVFWY_to_Y_1


title: 33_NAc_H24 [N-86]


title: 38_dStri_H24 [S-143]

description:
deseq2_dStri_cpm.csv
CountsMatrix.csv
DEGlists.xlsx

value: dStri


title: LIVFWY_to_V_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_V)-Mnase (kanMX)


title: LIVFWY_to_V_2


title: 48_dStri_H24 [S-153]


title: 11J_M_644


title: LIV_to_I_3


title: 12B_M_1541


title: 45_dStri_H24 [S-150]


title: LIVFWY_to_I_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_I)-Mnase (kanMX)


title: LIVFWY_to_Q_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_Q)-Mnase (kanMX)


title: LIVFWY_to_I_3


title: 12B_M_1540


title: 48_NAc_H24 [N-101]

value: Brain


title: 43_dStri_H24 [S-148]

value: Wild-type


title: LIVFWY_to_I_1


title: 12B_M_1539


title: 42_dStri_H24 [S-147]


title: LIVFWY_to_I_2


title: LIVFWY_to_F_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_F)-Mnase (kanMX)


title: LIVFWY_to_F_1


title: LIVFWY_to_D_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_D)-Mnase (kanMX)


title: 47_dStri_H24 [S-152]


title: 36_NAc_H24 [N-89]


title: 11J_M_642


title: 36_dStri_H24 [S-141]


title: LIVFWY_to_A_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_to_A)-Mnase (kanMX)


title: 12B_M_1538


title: LIVFWY_to_A_3


title: 33_dStri_H24 [S-138]


title: 11J_M_641


title: LIVFWY_deletion_to91_1

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to91)-Mnase (kanMX)


title: LIVFWY_deletion_to91_2


title: 12B_M_1537


title: 40_dStri_H24 [S-145]


title: 11J_M_643


title: 51_dStri_H24 [S-156]


title: LIVFWY_deletion_to71_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to71)-Mnase (kanMX)


title: LIVFWY_deletion_to71_3


title: LIVFWY_to_Q_3


title: 39_dStri_H24 [S-144]


title: 11J_M_640


title: 12B_M_1536


title: LIVFWY_deletion_to71_2


title: 38_BLA_H24 [3-7]

description:
deseq2_BLA_cpm.csv
CountsMatrix.csv
DEGlists.xlsx

value: BLA


title: LIVFWY_deletion_to51_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to51)-Mnase (kanMX)


title: 11J_M_639


title: LIVFWY_deletion_to71_1


title: LIVFWY_deletion_to51_2


title: 36_BLA_H24 [3-5]


title: LIVFWY_deletion_to51_1


title: 12B_M_1535


title: LIVFWY_deletion_to31_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to31)-Mnase (kanMX)


title: 51_BLA_H24 [3-24]


title: 11J_M_638


title: LIVFWY_to_D_1


title: LIVFWY_deletion_to31_3


title: LIVFWY_deletion_to31_2


title: 39_BLA_H24 [3-9]


title: LIVFWY_to_A_1


title: 40_BLA_H24 [3-10]


title: 12B_M_1534


title: LIVFWY_deletion_to11_1

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to11)-Mnase (kanMX)


title: LIVFWY_deletion_to31_1


title: 47_BLA_H24 [3-19]


title: LIVFWY_deletion_to111_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_to111)-Mnase (kanMX)


title: 11J_M_637


title: LIVFWY_deletion_to111_1


title: LIVFWY_deletion_to11_2


title: LIVFWY_deletion_from81_1

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_from81)-Mnase (kanMX)


title: LIVFWY_deletion_to51_4


title: 11J_M_636


title: LIVFWY_deletion_from61_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_from61)-Mnase (kanMX)


title: 45_BLA_H24 [3-17]


title: LIVFWY_deletion_from61_1


title: 33_BLA_H24 [3-2]


title: 48_BLA_H24 [3-20]


title: 12B_M_1532


title: LIVFWY_deletion_from41_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_from41)-Mnase (kanMX)


title: LIVFWY_deletion_from21_1

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_from21)-Mnase (kanMX)


title: 42_BLA_H24 [3-14]


title: 12B_M_1531


title: LIVFWY_deletion_from101_2

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion_from101)-Mnase (kanMX)


title: LIVFWY_deletion_from101_1


title: LIVFWY_deletion_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(LIVFWY_deletion)-Mnase (kanMX)


title: 11J_M_634


title: LIVFWY_deletion_1


title: LIVFWY_deletion_2


title: RNA-seq_WT_Th17_72h

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013) and quantified by cufflinks.   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. Raw reads of Hi-TrAC data were processed by tracPre2.py in cLoops2 package  into unique nonredundant interacting PETs.
Assembly: mm10
Supplementary files format and content: BEDPE files for Hi-TrAC and ChIP-seq were provided containg processed high-quality and non-redundant paired-end tags.  TXT file for gene expression quantified in FPKM is also provided.

growth_protocol: Naïve CD4 T cells were purified from lymph nodes of wildtype or MLL4 knock-out mice. Cells were then activated and cultured in Th17 cells differentiation condition.

extract_protocol:
For Hi-TrAC, genomic DNA was purified by Phenol-Chloroform extraction. For RNA-seq, RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
For Hi-TrAC, repair gaps of purified genomic DNA with T4 DNA polymerase. Remove free bridging linker using AMPure XP beads. Then, digest purified DNA with MluCI and NlaIII restriction enzymes. Enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, amplify the library by PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) at the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers.

treatment_protocol: Fix cells for Hi-TrAC with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells twice with ice-cold PBS, then resuspend  with 100 µL reaction buffer (50mM Tris-acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Incubate at 37 ℃ for 4 hours. To extract RNA for RNA-seq, add 700 µL QIAzol to 5,000 cells. Cells for ChIP-seq were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice. Then perform sonication to break chromatins. Sheared chromatin was immunoprecipitated with anti-H3K27ac, anti-H3K4me1and anti-H3K4me3 antibodies. After washing, perform Portease K digestion and reverse cross-linking at 65 ℃ overnight.

value: mixed C57BL/6 and 129

tag: cell type

value: CD4+ T cells stimulated for 72 h (horizontal axis) under Th17 condition

value: Cell Culture

value: WT DAPI-


title: 12B_M_1533


title: FWY_to_V_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(FWY_to_V)-Mnase (kanMX)


title: RNA-seq_MLL4KO_Th17_72h

value: MLL4 KO DAPI-


title: LIVFWY_deletion_3


title: 11J_M_633


title: FWY_to_V_3


title: FWY_to_V_2


title: Hi-TrAC_WT_Th17_72h_rep3

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013) and quantified by cufflinks.   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. Raw reads of Hi-TrAC data were processed by tracPre2.py in cLoops2 package  into unique nonredundant interacting PETs.
Assembly: mm10
Supplementary files format and content: BEDPE files for Hi-TrAC and ChIP-seq were provided containg processed high-quality and non-redundant paired-end tags.  TXT file for gene expression quantified in FPKM is also provided.
Library strategy: Hi-TrAC


title: LIVFWY_deletion_from81_2


title: FWY_to_N_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(FWY_to_N)-Mnase (kanMX)


title: 12B_M_1530


title: 12B_M_1529


title: 11J_M_632


title: FWY_to_N_3


title: FWY_to_N_2


title: Hi-TrAC_WT_Th17_72h_rep2


title: Hi-TrAC_WT_Th17_72h_rep1


title: LIVFWY_deletion_from41_3


title: FWY_to_N_1


title: 11J_M_635


title: Hi-TrAC_MLL4KO_Th17_72h_rep2


title: 12B_M_1528


title: FWY_to_L_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(FWY_to_L)-Mnase (kanMX)


title: FWY_to_L_3


title: 11J_M_631


title: 43_BLA_H24 [3-15]

value: Brain

value: BLA

value: Wild-type


title: 12B_M_1527


title: FWY_to_I_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(FWY_to_I)-Mnase (kanMX)


title: FWY_to_I_2


title: FWY_to_I_4


title: ChIP-seq_WT_Th17_72h_H3K4me3_rep2

tag: antibody


title: 11J_M_630


title: FWY_to_D_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(FWY_to_D)-Mnase (kanMX)


title: ChIP-seq_WT_Th17_72h_H3K4me3_rep1


title: 12B_M_1526


title: FWY_to_D_2


title: FWY_to_D_1


title: 11J_M_629


title: DE_to_Q_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(DE_to_Q)-Mnase (kanMX)


title: ChIP-seq_WT_Th17_72h_H3K4me1_rep2


title: FWY_to_D_3


title: ChIP-seq_WT_Th17_72h_H3K4me1_rep1


title: 12B_M_1525


title: DE_to_Q_3


title: ChIP-seq_WT_Th17_72h_H3K27ac_rep2


title: DE_to_N_3

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(DE_to_N)-Mnase (kanMX)


title: 11J_M_628


title: ChIP-seq_WT_Th17_72h_H3K27ac_rep1


title: DE_to_N_2


title: 12B_M_1524


title: DE_spread_5

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(DE_spread)-Mnase (kanMX)


title: ChIP-seq_MLL4KO_Th17_72h_H3K4me3_rep2


title: FWY_to_L_2


title: DE_spread_4


title: 11J_M_627


title: 12B_M_1523


title: FWY_to_L_1


title: DE_spread_2


title: DE_spread_3


title: Hi-TrAC_MLL4KO_Th17_72h_rep1


title: ChIP-seq_MLL4KO_Th17_72h_H3K4me1_rep2


title: DEKR_to_Q_4

value: MATa his3delta0 leu2delta0 met15delta0 ura3delta0 Msn2 ::Msn2(DEKR_to_Q)-Mnase (kanMX)


title: DE_spread_1


title: ChIP-seq_MLL4KO_Th17_72h_H3K4me1_rep1

value: mixed C57BL/6 and 129


title: DEKR_to_Q_5


title: 11J_M_626


title: ChIP-seq_MLL4KO_Th17_72h_H3K27ac_rep2

value: CD4+ T cells stimulated for 72 h (horizontal axis) under Th17 condition


title: TSC1 WT Ethanol 1

city: Kansas City

first: Hongmin

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

institute: The University of Kansas Medical Center

data_processing:
Adaptors and low-quality reads were trimmed by Trimmomatic v0.36
The trimmed high-quality reads were mapped to the mouse genome NCBI GRCm38 using HISAT2 v2.1.0
HTSeq-counts v0.6.0 was used to quantify the gene counts under the union model with NCBI GRCm38 genome annotations.
Assembly: NCBI GRCm38
Supplementary files format and content: raw mapped gene counts

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared for sequencing using the NEBNext Stranded mRNA library kit with polyA selection of the mRNA
NextSeq 550 High Output Single Read 75 bp Sequencing

value: Liver

value: wild type

tag: treatment

value: Gao-binge alcohol feeding

tag: time

value: 10 days


title: TSC1 WT Ethanol 3


title: TSC1 WT control 3

value: control diet


title: TSC1 WT control 4


title: TSC1 WT Ethanol 2


title: TSC1 WT Ethanol 4


title: 11J_M_625


title: TSC1 WT control 2


title: DE_to_N_4


title: ChIP-seq_MLL4KO_Th17_72h_H3K27ac_rep1

value: Cell Culture

value: MLL4 KO DAPI-


title: 11J_M_623


title: TSC1 WT control 1


title: fetal adrenal, FZ3

type: genomic

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Minfi (Aryee et al., 2014) was used to read .idat files and calculate beta values for each probe using functional normalization.

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

growth_protocol: NCI-H295R were cultured in DMEM/F12 supplemented with 10% Nu serum, 1% ITS-X, and 1% penicillin/streptomycin in a humidified tissue culture incubator with 5% CO2 at 37°C. Alternatively, adrenal cortex tissue was microdissected.

extract_protocol: Extracted gDNA from patient samples was subject to 850k array profiling performed by the University of Michigan Advanced Genomics Core. Extracted gDNA from EZH2i-/vehicle-treated NCI-H295R in biological triplicate was submitted to Diagenode Epigenomic Services, Denville, NJ, USA for Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000). DNA was deaminated using EZ-96 DNA Methylation Kit (Zymo Research) following Illumina recommendations. Bisulfite conversion was controlled by qPCR as follows: one assay targeting a methylated region of DNAJC15 and two assays targeting GNAS (one assay for the unmethylated allele and one assay for the methylated allele) were used for quality control. Deaminated DNA derived from blood were amplified in parallel, and a sample passed quality control when the measured Ct for the two GNAS loci or DNAJC15 is within 5 Ct of the positive control.

treatment_protocol: NCI-H295R were plated in 6 well plates and treated for 96 hours with EZH2i at the IC-50 dose (62 μM EPZ-6438), or the vehicle (equivalent volume of DMSO, these are "baseline") in 3 biological replicates. Genomic DNA was extracted at endpoint for methylation array profiling.  Alternatively, human adrenal glands were microdissected for zona fasciculata, zona reticularis, or fetal zone. After microdissection, DNA was extracted and submitted for methylation profiling by Illumina EPIC array.

value: fetal adrenal (fetal zone)

tag: cell line

value: human adrenal fetal zone


title: TSC1 KO Ethanol 4

value: hepatic TSC1 KO


title: TSC1 KO Ethanol 1


title: fetal adrenal, FZ2


title: 11J_M_621


title: TSC1 KO Ethanol 2


title: 11J_M_622


title: ChIP-seq_MLL4KO_Th17_72h_H3K4me3_rep1


title: fetal adrenal, FZ1


title: adrenal cortex, ZR5

value: adrenal cortex (zona reticularis)

value: human adrenal cortex


title: 11J_M_620


title: TSC1 KO control 3


title: 12B_M_1522


title: TSC1 KO control 2


title: TSC1 KO control 1


title: TSC1 KO Ethanol 3


title: 11J_M_618


title: 11J_M_619


title: 11J_M_624


title: adrenal cortex, ZR3


title: adrenal cortex, ZR1


title: adrenal cortex, ZR4


title: adrenal cortex, ZF5

value: adrenal cortex (zona fasciculata)


title: adrenal cortex ZF4


title: 11J_M_616


title: 11J_M_615


title: adrenal cortex, ZF3


title: 11J_M_614


title: NCI-H295R, EZH2i 3

value: human adrenocortical carcinoma


title: adrenal cortex, ZF1


title: 11J_M_613


title: 11J_M_611


title: 11J_M_612


title: TSC1 KO control 4


title: NCI-H295R, EZH2i 1


title: NCI-H295R, baseline 2

value: DMSO


title: 11J_M_610


title: 11J_M_607


title: 11J_M_608


title: 11J_M_606


title: muscle, polymyositis patient 3

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Standard preprocessing for V(D)J repertoires was carried out using pRESTO v0.5.4 (http://presto.readthedocs.io).
V(D)J germline genes were then assigned with IgBLAST v1.7.0 (23) using the March 30, 2017 version of the IMGT gene database
Mutations and selection strength of FWR and CDR regions was quantified using the implementation of BASELINe in SHazaM v0.1.8 in R v3.4.2
Alakazam v0.2.7 in R was used for analysis of CDR3 physiochemical properties and diversity analysis (27).
For the single cell libraries, the cellranger mkfastq function from 10X Genomics v2.2.0 was used to convert base calls to fastq sequences and perform demultiplexing; sequences were then aligned to the GCRhg38 genome supplied by 10X Genomics. Sparse count matrices, barcode assignments and feature calls were made using the cellranger count function and Seurat v.2.3.4 was used for visualization and cluster assignment.
Assembly: GCRhg38
Supplementary files format and content: BCR repertoire sequences in Change-O format.
Library strategy: BCR-seq

source_name: muscle

extract_protocol:
The IIM biopsy tissue was prepared for sequencing by first isolating RNA from frozen sections using the Qiagen RNA Mini kit according to the manufacturer’s instructions. B cells were isolated from frozen PBMCs using a human Pan B immunomagnetic negative selection kit (StemCell).
IBM RNA libraries were made using reagents supplied by New England BioLabs as part of the NEBNext Immune Sequencing Kit. B cells were loaded directly into the Chromium Controller (10x Genomics) and prepared using the Chromium Single Cell 5′ Reagent Kit (10x Genomics) for version 3 chemistry per the manufacturer’s protocol.

tag: isolate

value: polymyositis patient 3

tag: Sex

value: Female

value: muscle

tag: disease

value: polymyositis

tag: sample type

value: frozen section

tag: anatomic site

value: right quadriceps

tag: biomaterial provider

value: UConn Health


title: NCI-H295R, baseline 1


title: 11J_M_609

tag: brain region

tag: age


title: 11J_M_617

tag: strain


title: PD-L1 KO sEVs-treated Meso-CAR T cells-3

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

data_processing:
platforms, according to effective library concentration and data amount.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.
Reference genome and gene model annotation files were downloaded from genome website  directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean2  reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the  mapping tool for that Hisat2 can generate a database of splice junctions based on the gene  model annotation file and thus a better mapping result than other non-splice mapping tool
Quantification of gene expression level  featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth and  gene length for the reads count at the same time, and is currently the most commonly used  method for estimating gene expression levels
Differential expression analysis  (For DESeq2 with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (1.20.0). DESeq2 provide statistical routines for determining differential  expression in digital gene expression data using a model based on the negative binomial  distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05  found by DESeq2 were assigned as differentially expressed.  (For edgeR without biological replicates) Prior to differential gene expression analysis, for  each sequenced library, the read counts were adjusted by edgeR program package through  one scaling normalized factor. Differential expression analysis of two conditions was  performed using the edgeR R package (3.22.5). The P values were adjusted using the  Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2  were set as the threshold for significantly differential expression
Assembly: mm10
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene.
Supplementary files format and content: FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth and  gene length for the reads count at the same time, and is currently the most commonly used  method for estimating gene expression levels.

source_name: Meso-CAR T cells

growth_protocol: Mouse Meso-CAR was constructed by fusing anti-mesothelin scFv to a mouse CD3-ζ signaling domain and a mouse 4-1BB co-stimulatory domain along with a EGFP tag. The CAR was subcloned into the MSGV vector and packaged in the Phoenix packaging cells (Allele; Phoenix Eco Cells Line ABP-RVC-10002; purchased from and authenticated by ATCC, CRL-3214, RRID: CVCL_H717) to obtain the retrovirus. T cells were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin sulfate, 1 mM pyruvate and 50 μM β-mercaptoethanol. Primary mouse T cells were isolated as suggested by the manufacturer (Miltenyi Biotec) from the spleens of mice and incubated in 12-well plates (2 × 106 cells per well), and Dynabeads Mouse T-Activator CD3/CD28 (Gibco, Cat#: 11453D) at a 1:1 ratio

extract_protocol:
cells were collected and total RNA was extracted using an invitrogen PureLink RNA Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers,  followed by the second strand cDNA synthesis using either dUTP for directional library or  dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size  selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size  selection, USER enzyme digestion, amplification, and purification.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for
size distribution detection. Quantified libraries will be pooled and sequenced on Illumina

value: Meso-CAR T cells

value: mouse T cells

value: WT

value: PD-L3 KO sEVs

value: 48 hrs


title: 11J_M_604


title: muscle, polymyositis patient 1

value: polymyositis patient 1

tag: tissue

value: left thigh


title: 11J_M_603


title: muscle, inclusion body myositis  patient 4

value: inclusion body myositis patient 4

value: inclusion body myositis

value: right biceps


title: NCI-H295R, EZH2i 2

value: human adrenocortical carcinoma


title: sEVs-treated Meso-CAR T cells-3

tag: genotype

value: PD-L2 KO sEVs


title: Control-3

value: PD-L1 KO sEVs


title: NCI-H295R, baseline 3

value: DMSO


title: muscle, inclusion body myositis  patient 3

value: inclusion body myositis patient 3

value: Female

value: muscle

value: frozen section

value: left biceps


title: 11J_M_605


title: 11J_M_601


title: muscle, polymyositis patient 2

value: polymyositis patient 2

value: polymyositis

value: UConn Health


title: muscle, inclusion body myositis  patient 2

value: inclusion body myositis patient 2

value: right quadriceps


title: sEVs-treated Meso-CAR T cells-2

value: Meso-CAR T cells

value: mouse T cells

value: WT

value: sEVs

value: 48 hrs


title: Human non-obese OSA rep  3

type: RNA

city: Zhanjiang

first: Junfen

last: Chen

address: NO.12,Minyou Road

institute: The Second Affiliated Hospital of Guangdong Medical University

description:
crr_NS
Expression profile of ceRNA in non-obese OSA group

hyb_protocol: cRNA targets that were biotinylated were then hybridized with the slides.

scan_protocol: The Agilent Microarray Scanner was used to scan the slides after hybridization (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm,R package “limma”

source_name: Peripheral Blood, non-obese OSA, replicate 3

label_protocol: The RNA from each group was then used to generate biotinylated cRNA targets for the Sino Human ceRNA array V3.0.

extract_protocol: Total RNA was isolated using RNeasy Total RNA Isolation Kit (Qiagen, GmBH, Germany)/ TRIzol reagent (Life technologies, Carlsbad, CA, US) per the manufacturer's instructions, purified using an RNeasy Mini Kit (Qiagen, GmBH, Germany), and quantified using Nanodrop.Using the Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US), the fragment distribution of total RNA was analyzed.

treatment_protocol: All participants provided two blood samples at 8:00 a.m., following a full night of Watch-PAT sleep monitoring and overnight fasting. Then, we collected the blood into EDTA purple anticoagulant tubes; one was sent for blood glucose and blood lipid detection, while the other was used for ceRNA chip detection. Within 60 min of blood collection, the blood was centrifuged for 10 min at 3000 g to separate plasma. The supernatant was transferred to an RNase-free Eppendorf tube and stored at -80 °C until RNA extraction.

value: blood plasma

tag: gender

value: male

tag: subject status

value: non-obese OSA


title: muscle, inclusion body myositis  patient 1

value: inclusion body myositis patient 1

value: Male

value: inclusion body myositis


title: PD-L1 KO sEVs-treated Meso-CAR T cells-2

tag: cell type


title: 11J_M_600


title: Human non-obese OSA rep  1

description:
cm_NS
Expression profile of ceRNA in non-obese OSA group

source_name: Peripheral Blood, non-obese OSA, replicate 1


title: 11J_M_599


title: Human non-obese OSA rep  2

description:
shb_NS
Expression profile of ceRNA in non-obese OSA group

source_name: Peripheral Blood, non-obese OSA, replicate 2


title: Human obesity OSA rep  1

description:
lj_NS
Expression profile of ceRNA in obese OSA group

source_name: Peripheral Blood, obesity OSA, replicate 1

value: obesity OSA


title: Human obesity OSA rep  3

description:
lyy_NS
Expression profile of ceRNA in obese OSA group

source_name: Peripheral Blood, obesity OSA, replicate 3


title: Control-2

tag: treatment


title: muscle, dermatomyositis patient 3

value: dermatomyositis patient 3

value: Female

value: muscle

value: dermatomyositis

value: frozen section

value: not available


title: Human obesity OSA rep  2

description:
tyj_NS
Expression profile of ceRNA in obese OSA group

source_name: Peripheral Blood, obesity OSA, replicate 2


title: PD-L1 KO sEVs-treated Meso-CAR T cells-1

value: Meso-CAR T cells

value: mouse T cells

value: PBS

tag: time


title: 11J_M_598


title: muscle, dermatomyositis patient 2

value: dermatomyositis patient 2

value: left thigh

value: UConn Health


title: 11J_M_602


title: Human normal rep  3

description:
mtf_NS
Expression profile of ceRNA in normal group

source_name: Peripheral Blood, normal, replicate 3

value: blood plasma

value: male

value: normal


title: BNYVV biol rep 3, CNDV biol rep 2

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description:
3' RACE-seq
Processeddata_polyA_allvirus_B1B2.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Two processed data file is given. They includes the processed data for the analyzed 21 virus, the poladenylated RNA virus  (Processeddata_polyA_allvirus_B1B2.txt), and the non polyadenylated virus (Processeddata_nonpolyA_allvirus_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

organism:
Spinacia oleracea
Nicotiana benthamiana

source_name: Infected leaves of S. oleracea, or  N. benthamiana

growth_protocol: Leaves from virus infected plants

extract_protocol:
Total RNA from infected leaves of C. quinoa, N. benthamiana and grapevine were extracted using the RNeasy plant Mini Kit (Qiagen). Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: WT

value: BNYVV, CNDV


title: BNYVV biol rep 2, CNDV biol rep 1

value: Infected leaves of S. oleracea, or  N. benthamiana


title: 11J_M_597


title: sEVs-treated Meso-CAR T cells-1

tag: cell line

value: 48 hrs


title: muscle, dermatomyositis patient 1

tag: isolate

value: dermatomyositis patient 1

value: Female

value: muscle

value: right thigh


title: 11J_M_596


title: BNYVV biol rep 1

organism: Spinacia oleracea

source_name: Infected leaves of S. oleracea

value: Infected leaves of S. oleracea

value: BNYVV


title: Control-1

value: Meso-CAR T cells

value: mouse T cells

value: PBS


title: Human normal rep  2

description:
tw_NS
Expression profile of ceRNA in normal group

source_name: Peripheral Blood, normal, replicate 2


title: Human normal rep 1

description:
lym_NS
Expression profile of ceRNA in normal group

source_name: Peripheral Blood, normal, replicate 1


title: GRGV biol rep 3, TuMV biol rep 2

organism:
Arabidopsis thaliana
Vitis vinifera

source_name: Infected leaves of V. vinifera, or A. thaliana

value: GRGV, TuMV


title: CD44-CD62L+ DN1 T cells in LN from mouse 3

city: Chicago

first: Chyung-Ru

last: Wang

state: IL

address: 320 E Superior Street

department: Microbiology and Immunology

institute: Northwestern University

data_processing:
Trimmomatic 0.33 was used to trim reads (TRAILING:30 MINLEN:20)
STAR 2.5.2 was used to align reads to mm10 genome
Reads were counted using htseq-count
DESeq2 was used to analyze data for differential expression
Assembly: mm10
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 normalized gene expression and associated differential expression analysis results.

source_name: Lymph nodes

extract_protocol:
RNA was extracted with RNAeasy® mini kit (Qiagen).
Libraries were generated by using the Illumina Truseq preparation kit

treatment_protocol: mixed BM chimeric mice were intratracheally vaccinated with either 2.5 micrograms of MA in MA-BCN or equivalent volume of PBS. CD44+CD62L+ and CD44-CD62L+ DN1 T cells were sorted from LNs of DN1-hCD1Tg BM chimera mice vaccinated with MA-BCN at 6 weeks post vaccination

value: Lymph nodes

value: mixed human CD1 Tg/DN1Tg bone marrow chimeric mice

value: vaccination with 2.5 micrograms of mycolic acid encapsulated in (MA) bicontinuous nanospheres (BCN)


title: 11J_M_595

source_name: C57BL/6J Male P56 Mouse Brain


title: CD44-CD62L+ DN1 T cells in LN from mouse 1


title: CD44-CD62L+ DN1 T cells in LN from mouse 2


title: 11J_M_593


title: 11J_M_592


title: 11J_M_594


title: GRSPaV biol rep 3, BNYVV biol rep 1

organism:
Spinacia oleracea
Vitis vinifera

source_name: Infected leaves of V. vinifera or S. oleracea

value: WT

value: GRSPaV, BNYVV


title: NPC_NesKO_rep3

city: Hong Kong

first: Andrew

middle: M.

last: Chan

address: Room 407, 4/F, Lo Kwee-Seong Integrated Biomedical Sciences Building,, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Science

country: Hong Kong

institute: The Chinese University of Hong Kong

description: NPC.ct.vs.ko.csv

data_processing:
Mapped by HISAT2
Quantified by featureCounts
Differential analysis by DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: csv, matrix of all samples in the comparison with normalized counts, p-value and adjusted p-value

source_name: Neuroprogenitor cells

extract_protocol:
TRIzol
NEB

value: Neuroprogenitor cells

value: Nes-KO


title: CD44+CD62L+ DN1 T cells in LN from mouse 3


title: CD44+CD62L+ DN1 T cells in LN from mouse 2


title: 11J_M_591


title: 11J_M_589


title: 11J_M_590


title: CD44+CD62L+ DN1 T cells in LN from mouse 1


title: NPC_NesKO_rep2

description: NPC.ct.vs.ko.csv


title: 11J_M_588


title: 11J_M_587


title: NPC_NesKO_rep1

description: NPC.ct.vs.ko.csv


title: 11J_M_586


title: NPC_CTRL_rep3

description: NPC.ct.vs.ko.csv

value: CONTROL


title: RNA-seq_CTCF-AID_Ctrl_rep2

data_processing:
Mouse sequencing data were processed to the reference genome mm10, and human data were processed to hg38. Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013) and quantified by cufflinks.   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. Raw reads of Hi-TrAC data were processed by tracPre2.py in cLoops2 package  into unique nonredundant interacting PETs.
Assembly: hg38, mm10
Supplementary files format and content: BEDPE files for Hi-TrAC and ChIP-seq were provided containg processed high-quality and non-redundant paired-end tags.  TXT file for gene expression quantified in FPKM is also provided.

growth_protocol: Mouse naïve CD4 T cells were purified from lymph nodes of wildtype or MLL4 knock-out mice. Cells were then activated and cultured in Th17 cells differentiation condition. CTCF-AID and active sub-TAD boundary deletion K562 cells were generated using the CRISPR/Cas9 system. The targeting sequences were cloned into the pSpCas9(BB)-2A-Puro (PX459) V2.0 vector (Addgene, #62988). For CTCF-AID cells, K562 cells were co-transfected with CRISPR and donor plasmids, which contain Hygromycin selection marker. After 24 hours, cells were treated with 2 g/mL Puromycin and 200 g/mL Hygromycin for 48 hours to remove non-transfected cells. Surviving cells were selected further by treating with 200 g/mL Hygromycin for two weeks. The survived cells were sorted into 96-well plate with one cell per well and cultured for two to three weeks, then genotyped by PCR, western blotting, and sequencing. For generating active sub-TAD boundary deletion cells, K562 cells were transfected with CRISPR plasmids. After 24 hours, cells were treated with 2 g/mL Puromycin for 48 hours to remove non-transfected cells. Survived cells were sorted into 96-well plate with one cell per well, and further cultured for two to three weeks. Cell clones were genotyped by PCR and sequencing.

value: CTCF-AID control


title: Hi-TrAC_CTCF-AID_Tir1_bio2_tech3

data_processing:
Mouse sequencing data were processed to the reference genome mm10, and human data were processed to hg38. Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013) and quantified by cufflinks.   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. Raw reads of Hi-TrAC data were processed by tracPre2.py in cLoops2 package  into unique nonredundant interacting PETs.
Assembly: hg38, mm10
Supplementary files format and content: BEDPE files for Hi-TrAC and ChIP-seq were provided containg processed high-quality and non-redundant paired-end tags.  TXT file for gene expression quantified in FPKM is also provided.
Library strategy: Hi-TrAC

value: CTCF-AID auxin IAA treatment for rapid depeletion of CTCF


title: BAT from 8 week-old mouse, replicate 2

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

country: Japan

institute: AIST

hyb_protocol: Hybridization was done by using Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instruction.

scan_protocol: Scanning was performed by Agilent Microarray Scanner with 3 micro meter Scan Resolution and 20 bit TIFF dynamic range.

data_processing: Spot intensities were measured by using Agilent Feature Extraction 11.0.1.1.

source_name: BAT

label_protocol: Laballing was performed by using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instruction.

extract_protocol: Total RNA was extracted by using ISOGEN (Nippongene)

value: BAT

value: 8 weeks


title: RNA-seq_CTCF-AID_Ctrl_rep1


title: BAT from 8 week-old mouse, replicate 3


title: RNA-seq_CTCF-AID_Tir1_rep1


title: BAT from 4 week-old mouse, replicate 2

value: 4 weeks


title: NPC_CTRL_rep2

description: NPC.ct.vs.ko.csv


title: Exceptionally rare IDH1-mutant adult medulloblastoma with concurrent GNAS mutation

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: normalized signal intensities computed with lumi

label: Cy3 and Cy5

source_name: IDH1- and GNAS-mutant adult FFPE medulloblastoma tissue

extract_protocol: genomic DNA was extracted and purified from tumor sample using QIAamp DNA FFPE tissue (Qiagen)

treatment_protocol: tumor tissue was formalin-fixed and paraffin embedded

value: Medulloblastoma sample

value: 26 years old

value: male


title: BAT from 8 week-old mouse, replicate 1


title: BAT from 4 week-old mouse, replicate 3


title: RNA-seq_CTCF-AID_Tir1_rep2


title: BAT from day 10 pup, replicate 3


title: BAT from 4 week-old mouse, replicate 1


title: 11J_M_585

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: BAT from day 10 pup, replicate 2


title: NPC_CTRL_rep1

description: NPC.ct.vs.ko.csv


title: Hi-TrAC_CTCF-AID_Tir1_bio2_tech1


title: BAT from day 10 pup, replicate 1


title: Hi-TrAC_CTCF-AID_Tir1_bio2_tech2


title: 11J_M_583


title: PCN_HET_rep3

description:
Harvest at DIV14
PCN.wt.vs.ht.csv

source_name: Cortical neurons

value: Cortical neurons

value: Pten+/-


title: BAT from day 4 pup, replicate 4


title: 11J_M_582


title: Hi-TrAC_CTCF-AID_Tir1_bio1_tech3


title: BAT from day 4 pup, replicate 3


title: Hi-TrAC_CTCF-AID_Tir1_bio1_tech2


title: PCN_HET_rep2

description:
Harvest at DIV14
PCN.wt.vs.ht.csv


title: 11J_M_581


title: 11J_M_580


title: PCN_WT_rep3

description:
Harvest at DIV14
PCN.wt.vs.ht.csv

value: wild type


title: Hi-TrAC_CTCF-AID_Tir1_bio1_tech1


title: PCN_HET_rep1

description:
Harvest at DIV14
PCN.wt.vs.ht.csv


title: Hi-TrAC_CTCF-AID_Ctrl_bio2_tech3


title: PCN_WT_rep2

description:
Harvest at DIV14
PCN.wt.vs.ht.csv


title: 11J_M_579


title: 11J_M_578


title: PCN_WT_rep1

description:
Harvest at DIV14
PCN.wt.vs.ht.csv


title: 11J_M_584


title: Hi-TrAC_CTCF-AID_Ctrl_bio2_tech2


title: DM_plusDox_3_biol rep 3

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided

molecule: polyA RNA

source_name: EBV negative Akata

growth_protocol: EBV-negative Akata cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (#74106, Qiagen) as per manufacturer's protocol. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 1ug total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7765, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: EBV-negative Akata cells were transduced with lentivirus expressing doxycycline-inducible vector bearing respective LMP1 (wildtype, TES1mutant, TES2mutant and TES double mutant) transgenes. Transduced cells were subjected to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 5 days post transduction before confirming dox-induced LMP1 expression in respective stable cell lines. Stable cell lines then underwent 24 hours of untraeted or treatment with Doxycycline (Sigma #D9891) treatment at 250ng/ml

value: EBV negative Akata

value: Burkitt Lymphoma

value: Double Mutant LMP1

value: Doxycycline

value: 24 hours


title: PCA_HET_rep3

description: AST.wt.vs.ht.csv

source_name: Cortical astrocytes

value: Cortical astrocytes


title: Hi-TrAC_CTCF-AID_Ctrl_bio2_tech1

value: CTCF-AID control


title: DM_plusDox_2_biol rep 2


title: 11J_M_577


title: 11J_M_576


title: PCA_HET_rep2

description: AST.wt.vs.ht.csv


title: BAT from E18 embryo, replicate 3


title: BAT from day 4 pup, replicate 1


title: BAT from E18 embryo, replicate 2


title: BAT from E18 embryo, replicate 1


title: 11J_M_511


title: Hi-TrAC_CTCF-AID_Ctrl_bio1_tech2


title: DM_plusDox_1_biol rep 1


title: PCA_HET_rep1

description: AST.wt.vs.ht.csv


title: Hi-TrAC_CTCF-AID_Ctrl_bio1_tech1


title: DM_-Dox_3_biol rep 3

value: no Doxycycline


title: PCA_WT_rep3

description: AST.wt.vs.ht.csv


title: 11J_M_510


title: BAT from day 4 pup, replicate 2

value: BAT


title: 11J_M_509


title: PCA_WT_rep2

description: AST.wt.vs.ht.csv


title: 11J_M_508


title: DM_-Dox_1_biol rep 1


title: RNA-seq_cas9_LMO2-right_rep1

value: LMO2 active sub-TAD right boundary deletion


title: PCA_WT_rep1

description: AST.wt.vs.ht.csv


title: 11J_M_507


title: RNA-seq_cas9_GATA1-left_rep2

value: GATA1 active sub-TAD left boundary deletion


title: Hi-TrAC_CTCF-AID_Ctrl_bio1_tech3


title: Mouse large intestinal cells-Cdx2, ATAC-seq Wt replicate 2

city: Ottawa

first: Sanzida

last: Jahan

state: ON

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
[ATAC-seq] Mapped paired-end reads to the mm10 genome assembly using bwa mem
[ATAC-seq] Filtered BAM files to retain only properly paired reads with a MAPQ >30, remove fragments mapped to ENCODE blacklist regions (mm10_v2), and to remove fragments arising from duplicate read pairs
[ATAC-seq] Called ATAC-seq peaks using MACS2 separately for each replicate.
[ChIP-seq] Mapped reads to the GRCm38/mm10 genome assembly using bowtie2. Filtered the resulting bamfiles to remove reads mapping to ENCODE blacklist regions (mm10_v2)
[ChIP-seq] Called ChIP-seq peaks using MACS2
[RNA-seq] Processed raw sequences with fastp to perform automatic adapter trimming, and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls)
Quantified transcripts from GENCODE vM25 with salmon v1.3.0 using --gcBias flag and genomic decoys in index
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object using the model ~condition (treatment)
Calculated fold changes with the lfcShrink() function using the apeglm method.
Genome_build: GRCm38
Supplementary_files_format_and_content: MACS and ATAC-seq peaks in narrowPeak format
Supplementary_files_format_and_content: Transcript quantification as salmon quant.sf files
Supplementary_files_format_and_content: Fold change results as tab-delimited text of DESeq2 results output

source_name: Large intestinal cells

growth_protocol: Colon epithelial cells were enriched by incubating fresh colon tissue in 5 mM EDTA in phosphate-buffered saline (PBS; pH 8) for 10 min at 4°C with 3-4 repeated washes. Each aliquot was collected and cells were run through a 70-µm strainer and cells were isolated for RNA-seq or ATAC-seq, or fixed for ChIP-seq.

extract_protocol:
[RNA-seq] Total RNA was isolated using a Qiagen RNeasy mini kit according to the manufacturer's protocol and RNA quality assessed by Bioanalyzer.  [ChIP-seq] Cells were crosslinked with 1% formaldehyde, resuspended in RIPA lysis buffer and sonicated to obtain 200- to 500-bp chromatin fragments using a Branson sonicator. Lysates were incubated overnight at 4°C with primary antibodies or with isotype-specific IgG control. Lysates were clarified from sonicated nuclei and Cdx2-bound DNA were isolated with antibody. [ATAC-seq] Transposed samples were PCR-amplified for the optimal number of cycles using NEBNext High-Fidelity master mix, a common forward primer, and uniquely barcoded reverse primers for each sample. The reaction was purified using MinElute PCR purification kits (Qiagen), and primer dimers were removed using Ampure XP beads (Beckman Coulter).
[RNA-seq] Single end libraries were prepared by Genome Qubec and sequenced as per illumina Hi-seq protocol. [ChIP-seq] Single end library was prepared by Genome Qubec as per illumina Hi-seq protocol. [ATAC-seq] Library construction and sequencing were performed using and Illumina Hi-seq 4000 system (paired-end) by Genome Quebec.
RNA-seq (4 samples), ChIP-seq (1 sample), ATAC-seq (4 samples)

treatment_protocol: Mice were treated with Tamoxifen for 6 days.

value: Large intestinal cells

value: Cdx1-/-Cdx2f/f vill (-)

value: Tamoxifen treated


title: ID_plusDox_2_biol rep 2

value: TES2mutant LMP1


title: RNA-seq_cas9_GATA1-left_rep1


title: 11J_M_505


title: ID_plusDox_1_biol rep 1


title: RNA-seq_cas9_BHLHE40-left_rep1

value: BHLHE40 active sub-TAD left boundary deletion


title: Mouse large intestinal cells-Cdx2, ATAC-seq DKO replicate 2

value: Cdx1-/-Cdx2f/f vill (+)


title: 11J_M_506


title: DM_-Dox_2_biol rep 2

value: EBV negative Akata


title: RNA-seq_cas9_contrl_rep2

value: CRISPR/Cas9 control


title: ID_-Dox_3_biol rep 3

value: Burkitt Lymphoma


title: Mouse large intestinal cells-Cdx2, ATAC-seq DKO replicate 1


title: 11J_M_504


title: ID_-Dox_2_biol rep 2


title: Mouse large intestinal cells-Cdx2, ChIP-seq Wt

value: untreated


title: 11J_M_502


title: RNA-seq_cas9_contrl_rep1


title: ID_-Dox_1_biol rep 1

value: 24 hours


title: ID_plusDox_3_biol rep 3

value: Doxycycline


title: Hi-TrAC_cas9_LMO2-right_rep2


title: PQ_plusDox_3_biol rep 3

value: TES1mutant LMP1


title: 11J_M_501


title: Mouse large intestinal cells-Cdx2, RNA-seq Wt replicate 2


title: PQ_plusDox_2_biol rep 2


title: Mouse large intestinal cells-Cdx2, RNA-seq Wt replicate 1


title: Hi-TrAC_cas9_LMO2-right_rep1


title: 11J_M_500


title: Hi-TrAC_cas9_GATA1-left_rep2


title: Mouse large intestinal cells-Cdx2, RNA-seq DKO replicate 2


title: Mouse large intestinal cells-Cdx2, ATAC-seq Wt replicate 1


title: RNA-seq_cas9_BHLHE40-left_rep2


title: 11J_M_499


title: RNA-seq_cas9_LMO2-right_rep2


title: PQ_plusDox_1_biol rep 1


title: Mouse large intestinal cells-Cdx2, RNA-seq DKO replicate 1


title: PQ_-Dox_3_biol rep 3

value: no Doxycycline


title: 11J_M_503


title: 11J_M_497


title: 11J_M_498


title: Purified virions GFLV B844

description:
3' RACE-seq
Processed_Data_CAPSID_B1B2.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: One processed data file is given. They includes the processed data for total RNA and RNA from purified virion of the K30 and B844 isolates. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, Information about isolate et purification (Sample Description), biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

organism: Arabidopsis thaliana

source_name: Infected leaves of A. thaliana

growth_protocol: Leaves from GFLV infected plants

extract_protocol:
Viral particles of GFLV K30 and B844 isolates were purified from C. quinoa by sucrose gradient. RNA was extracted from purified virions using phenol-chloroform.
3'RACE-seq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: Infected leaves of A. thaliana

value: WT

value: GFLV


title: Hi-TrAC_cas9_GATA1-left_rep1

value: GATA1 active sub-TAD left boundary deletion


title: Purified virions GFLV K30


title: Hi-TrAC_cas9_BHLHE40-left_rep1


title: Total RNAs GFLV B844


title: PQ_-Dox_1_biol rep 1


title: Hi-TrAC_cas9_control_rep4


title: WT_plusDox_3_biol rep 3

value: Wildtype LMP1


title: Total RNAs GFLV K30


title: 11J_M_496

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: WT_plusDox_2_biol rep 2


title: 5'RACE minus plant3

description:
3' RACE-seq
Processed_data_RACE_MINUS_5.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Three processed data files are given. They includes the processed data for the 3' end of the minus strand  (Processed_data_RACE_MINUS_3.txt), for the 5 end of the minus strand (Processed_data_RACE_MINUS_5.txt) and for the 5 end of the plus strand (Processed_data_RACE_PLUS_5.txt) for each genotype and biological replicate.  Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) or poly(U) tail sequence (polyX), poly(A) or poly(U) tail length (polyX.size), non-A or non U extension sequence (modification), length of the non-A or non-U extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N or 8N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

extract_protocol:
Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3' RACE-seq and 5' RACE-seq


title: Hi-TrAC_cas9_control_rep3


title: Hi-TrAC_cas9_control_rep2


title: 11J_M_495


title: 5'RACE plus plant5

description:
3' RACE-seq
Processed_data_RACE_PLUS_5.txt


title: 11J_M_494


title: 11J_M_493


title: WT_plusDox_1_biol rep 1


title: Hi-TrAC_cas9_control_rep1


title: WT_-Dox_3_biol rep 3


title: 10X307_3

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

data_processing:
Single-cell sequencing data were processed using the CellRanger pipeline (version 3.0.2; 10X Genomics). Reads were mapped against the human genome (ENSEMBL genome assembly, release 93) and annotated with GENCODE gene annotations for the GRCh38-3.0.0 genome assembly (GENCODE release 32).
Using the BAM files from CellRanger, molecules were mapped into spliced and unspliced transcripts using velocyto (0.17.17) into which loom files were generated for each sample.
The single-cell count matrix was first enriched for protein-coding RNA and lincRNA gene types. Cells with fewer than 500 genes and genes expressed in fewer than 15 cells were excluded from the analysis. Cells with over 25% mitochondrial gene expression were also discarded.
Normalization, dimensionality reduction, and clustering of scRNA-seq data were performed using the Seurat package (Seurat v4.0.1) (25), and top 6000 genes with high dispersion were selected using the FindVariableGenes function. Cell cycle activity (26), number of genes, and mitochondrial content across the data were regressed out using the ScaleData function. Principal component analysis (PCA) was performed on the 50 most significant components as determined by the PCElbowPlot function, showing the standard deviation of the principal components. Clusters were identified using the FindClusters function by using Louvain resolution 1.2 for scRNA-seq.
Assembly: GENCODE gene annotations for the GRCh38-3.0.0 genome assembly (GENCODE release 32)
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample
Supplementary files format and content: Annotated cell metadata
Supplementary files format and content: Cell embeddings in PCA (raw), Harmony (batch-corrected) and UMAP space.

extract_protocol:
The W5-W7 spinal cord tissues were used as one piece while W8-12 spinal cords were divided into three pieces (cervical, thoracic, and lumbar regions) before dissociation. Each piece tissue was minced into smaller pieces using sterile blades and scissors. Artificial cerebrospinal (aCSF) was prepared as previously described (24), with modification for Ca2Cl2 (1 mM) and MgCl2 (2 mM). The aCSF was oxygenated with 95 % O2:5 % CO2 for 20 min at 4 °C. The samples were then digested at 37°C in aCSF (Zeisel et al., 2018).  Papain solution (Worthington Biochemical; cat. no. LK003178; 20 U/ml in CSF) and DNase I (Worthington Biochemical; cat. no. LK003172; 1mg/ml) were added to the aCSF as dissociation buffer. Enzymatic incubation time was adjusted based on developmental stage, ranging from 15-25 minutes. The spinal cord tissues were subsequently dissociated manually with fire polished glass pipettes. When tissues were mostly dissociated into single cells, the solution was filtered using a 30-µm cell strainer (CellTrics, Sysmex, 04-0042-2316) and collected in a 15-ml falcon tube. The digestion solution was diluted with 7.5 ml of aCSF and centrifuged at 300g for 5 min at 4°C. The pellets were resuspended in aCSF and transferred to Eppendorf tubes pre-coated with 30% BSA (Sigma-Aldrich, 9048-46-8). After cell counting, the single cell solution was diluted to a centration with 800-1200 cells/ul and kept on ice for immediate chip loading.
Droplet-based single-cell RNA sequencing was performed using the 10x Genomics Chromium Single Cell Kit v3. Single-cell suspensions concentrated at 800-1200 cells/ml were mixed with master mix and nuclease free water according to the Chromium manual, targeting 5000 cells per reaction. The library preparation and sequencing were prepared according to the Chromium v3 standard protocol. Sequencing was performed using the Illumina NovaSeq 6000 with an average 152,486 reads/cell.

tag: donor

tag: location

value: thoracic

tag: pcw


title: 5'RACE minus plant2


title: 11J_M_492

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: PQ_-Dox_2_biol rep 2


title: 10X307_2

value: lumbar


title: Hi-TrAC_cas9_BHLHE40-left_rep2

extract_protocol:
For Hi-TrAC, genomic DNA was purified by Phenol-Chloroform extraction. For RNA-seq, RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit.
For Hi-TrAC, repair gaps of purified genomic DNA with T4 DNA polymerase. Remove free bridging linker using AMPure XP beads. Then, digest purified DNA with MluCI and NlaIII restriction enzymes. Enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, amplify the library by PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) at the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers.

value: BHLHE40 active sub-TAD left boundary deletion


title: WT_-Dox_2_biol rep 2


title: 11J_M_491


title: 5'RACE minus plant1


title: 3'RACE minus plant4

description:
3' RACE-seq
Processed_data_RACE_MINUS_3.txt


title: 10X307_1

value: cervical


title: 3'RACE minus plant3


title: 10X294_3


title: 11J_M_489


title: 11J_M_488


title: 3'RACE minus plant2


title: 10X294_2


title: pos_CD40L_2_biol rep 2

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided.

source_name: EBV negative BL41

growth_protocol: EBV-negative BL41 cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

treatment_protocol: To make the LMP1 expressing stable cell lines, EBV-negative BL41 cells were transduced with lentivirus expressing doxycycline-inducible vector bearing respective LMP1 (wildtype, TES1mutant, TES2mutant and TES double mutant) transgenes. Transduced cells were subjected to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 5 days post transduction before confirming dox-induced LMP1 expression in respective stable cell lines. Stable cell lines then underwent 24 hours of untreated or treatment with Doxycycline (Sigma #D9891) treatment at 250ng/ml. Wildtype EBv-negative BL41 (wihtout LMP1 transgene) were either left untreated or treated with CD40L (Mega CD40Ligand, soluble (human) recombinant, Enzo  Life Sciences #ALX-522-110-C010) at 50ng/ml

value: EBV negative BL41

value: Wildtype


title: pos_CD40L_3_biol rep 3

value: Burkitt Lymphoma


title: 10X294_1


title: TCV_heso1_3urt1_1_Plant3

description:
3' RACE-seq
Processed_data_TCV_A.txt

data_processing:
Fastq files were analyzed by a homemade pipeline adapted from Scheer et al. 2021 composed of scripts using python (v2.7), biopython (v1.63) and regex (v2.4) libraries.
Python and bash source code are available in github (https://github.com/hzuber67/RACEseq_virus)
Assembly: cf the associated publication
Supplementary files format and content: Three processed data files are given. They includes the processed data for the analyzed GFLV  (Processed_data_GFLV_B1B2.txt), TuMV (Processed_data_TuMV_B1B2.txt) and TCV (Processed_data_TCV_A.txt) for each genotype and biological replicate. Each line corresponds to one individual reads.
Supplementary files format and content: For each read, we indicate read ID (read.ID), Virus RNA name (Target), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension),  tail size (extension.size), a tag (classification) indicating the category of the tail, the 15N random sequence used for deduplication (random), barcode, biological replicate (Plant), Virus RNA (RNA), infected plant (Host) and Virus name (Virus).

source_name: Infected leaves

growth_protocol: Leaves from GFLV, TuMV and TCV infected Arabidpsis plants (genotype WT, urt1-1, heso1-3 and heso1-3 urt1-1)

extract_protocol:
Total RNA of Arabidopsis infected leaves was extracted using Tri-Reagent (Molecular Research Center).
3'RACEseq
3'RACEseq protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

value: Infected leaves

value: heso1-3 urt1-1

value: TCV


title: neg_CD40L_3_biol rep 3

value: Untreated_no CD40L

value: 24 hours


title: 10X292_3


title: 11J_M_487


title: 10X292_2


title: neg_CD40L_2_biol rep 2


title: WT_-Dox_1_biol rep 1

value: EBV negative Akata

value: no Doxycycline


title: TCV_heso1_3urt1_1_Plant2

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 11J_M_485


title: TCV_heso1_3urt1_1_Plant1

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 11J_M_490


title: 11J_M_484


title: neg_CD40L_1_biol rep 1


title: 10X292_1


title: 11J_M_483


title: 10X287_3

value: whole


title: DM_pos_Dox_3_biol rep 3

value: Double Mutant LMP1

value: Doxycycline


title: TCV_heso1_3_Plant3

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 11J_M_482


title: DM_pos_Dox_2_biol rep 2


title: 10X287_2


title: DM_pos_Dox_1_biol rep 1


title: pos_CD40L_1_biol rep 1


title: 3'RACE minus plant1

value: Infected leaves of A. thaliana

value: WT

value: GFLV


title: 11J_M_481


title: TCV_heso1_3_Plant1

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: ID_pos_Dox_3_biol rep 3

value: TES2mutant LMP1


title: 11J_M_486


title: 11J_M_480


title: TCV_urt1_1_Plant3

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 10X284_3

value: thoracic


title: ID_pos_Dox_2_biol rep 2

value: EBV negative BL41


title: 11J_M_479


title: 10X284_2

value: lumbar


title: ID_pos_Dox_1_biol rep 1

value: Burkitt Lymphoma


title: 10X284_1

value: cervical


title: TCV_urt1_1_Plant2

description:
3' RACE-seq
Processed_data_TCV_A.txt

value: Infected leaves

value: TCV


title: TCV_urt1_1_Plant1

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: PQ_pos_Dox_3_biol rep 3

value: TES1mutant LMP1

value: 24 hours


title: 11J_M_478


title: 11J_M_477


title: TCV_WT_Plant3

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: PQ_pos_Dox_2_biol rep 2


title: 10X273_2


title: 11J_M_476


title: TCV_heso1_3_Plant2

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: PQ_pos_Dox_1_biol rep 1


title: TCV_WT_Plant2

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 10X273_1


title: TCV_WT_Plant1

description:
3' RACE-seq
Processed_data_TCV_A.txt


title: 10X271_4


title: WT_pos_Dox_2_biol rep 2

value: Wildtype LMP1


title: TuMV_heso1_3urt1_1_Plant6

description:
3' RACE-seq
Processed_data_TuMV_B1B2.txt

value: heso1-3 urt1-1

value: TuMV


title: 10X287_1

value: whole


title: 11J_M_475


title: 11J_M_474


title: WT_pos_Dox_3_biol rep 3

value: Doxycycline


title: 11J_M_473


title: 10X271_3


title: 10X271_2


title: TuMV_heso1_3urt1_1_Plant4


title: WT_neg_Dox_3_biol rep 3

value: Untreated_no Doxycycline


title: 10X271_1


title: TuMV_heso1_3urt1_1_Plant3


title: 11J_M_472


title: 10X273_3


title: 11J_M_471


title: WT_neg_Dox_2_biol rep 2


title: TuMV_heso1_3urt1_1_Plant2


title: 11J_M_470


title: 11J_M_469


title: 10X226_2


title: 10X207_4


title: TuMV_heso1_3urt1_1_Plant1


title: 10X201_2


title: TuMV_heso1_3_Plant6


title: 10X201_1


title: TuMV_heso1_3_Plant5


title: FGSC_T_3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq data were trimmed and aligned to mouse genome (mm9), then Hisat2 was used to mapping the reads with default parameters.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of p value < 0.05 and log2 fold change > 1.
Assembly: mm9
Supplementary files format and content: bigwig file

source_name: treated female germline stem cells

growth_protocol: FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries was prepared using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems, Wilmington, MA, USA), following the manufacturer's protocol

treatment_protocol: Treated with 1μM metformin (Sigma-Aldrich) for 24h

value: female germline stem cell (FGSCs)

tag: passages

value: 1μM metformin for 24h


title: 11J_M_468


title: TuMV_heso1_3urt1_1_Plant5


title: 11J_M_467


title: FGSC_T_2


title: TuMV_heso1_3_Plant4


title: 11J_M_466


title: 10X183_2


title: TuMV_urt1_1_Plant6


title: FGSC_T_1


title: TuMV_urt1_1_Plant5


title: WT_pos_Dox_1_biol rep 1


title: 10X183_3

value: thoracic


title: WT_neg_Dox_1_biol rep 1

value: EBV negative BL41


title: TuMV_urt1_1_Plant4


title: FGSC_C_3

source_name: female germline stem cells

value: none; control


title: 11J_M_464


title: 10X162_3


title: 10X162_2

value: lumbar


title: 11J_M_462


title: 11J_M_465


title: TuMV_WT_Plant6

value: WT


title: NCI-H295R input

data_processing:
We used bowtie2 (Langmead and Salzberg, 2012) to align the reads to the hg38 and dm10 version of the human and fly genomes, respectively. Reads overlapping with blacklisted regions (defined by ENCODE), and reads with a mapping score < 20 were filtered.
BAM files were down-sampled to account for Drosophila spike-in control, enabling quantitative comparison of epitopes accounting for net chromatin recruitment across treatment conditions.
To perform ChIP-seq peak calling, we used SPAN and the JBR browser (Shpynov et al., 2021). These tools allow for empirical parameter adjustment after visual inspection of the peaks to obtain the best possible signal-to-noise ratio (FRIP).
BigWigs files were generated using deepTools 2.0 (Ramírez et al., 2016) with RPGC normalization.
Assembly: hg38/dm10
Supplementary files format and content: BigWig
Supplementary files format and content: broadPeaks - called peaks

growth_protocol: NCI-H295R were cultured in DMEM/F12 supplemented with 10% Nu serum, 1% ITS-X, and 1% penicillin/streptomycin in a humidified tissue culture incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were harvested for ChIP-seq with Drosophila melanogaster histone spike-in for all epitopes according to Active Motif's Epigenetic Services ChIP Cell Fixation protocol. Briefly, media was supplemented with 1/10 media volume of freshly prepared Formaldehyde Solution (11% formaldehyde, 0.1 M NaCl, 0.5 M EDTA pH 8.0, 1 M HEPES pH 7.9 in nuclease-free water), and plate was agitated for 15 minutes at room temperature. Fixation was stopped with addition of 1/20 volume of Glycine Solution (2.5 M Glycine, MW 75 in nuclease-free water) and incubating at room temperature for 5 minutes. Cells were then scraped, collected into a conical tube, and pelleted at 800xg at 4°C for 10 minutes. Supernatant was aspirated and each tube of cells was re-suspended in 10 mL chilled PBS-Igepal (0.5% Igepal CA-630 in PBS). Cell were pelleted again, supernatant aspirated, and cells resuspended in 10 mL chilled PBS-Igepal supplemented with 100 μL of 100 mM PMSF in ethanol. Cells were pelleted again, supernatant aspirated, snap frozen on dry ice, stored at -80°C, and shipped on dry ice to Active Motif Services (Carlsbad, CA) for chromatin preparation and ChIP-seq. Chromatin was isolated by addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin (pooled from all submitted samples) with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were immunoprecipitated using the following antibodies: EZH2 (Active Motif, Cat. No. 39901; concentration 8 μL Ab/30 μg chromatin), H3K27me3 (ActiveMotif, Cat. No. 39155; concentration 4 μg Ab/30 μg chromatin), H3K27ac (ActiveMotif, Cat. No. 39133; concentration 4 μg Ab/30 μg chromatin), SF1 (EMD Millipore, Cat. No. 07-618; concentration 5 μg Ab/30 μg chromatin) and β-catenin (Invitrogen, Cat. No. 71-2700; concentration 4 μg Ab/30 μg chromatin). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

treatment_protocol: NCI-H295R were plated in standard culture medium in 10 cm dishes at a density of 2.4 million cells per plate. To best account for biological variability, experiment was performed using 24 plates of cells total, where 16 plates were reserved for EZH2i administration at the IC-50 dose (62 μM EPZ-6438) and 8 plates were reserved for vehicle administration (equivalent volume of DMSO, these are considered "baseline" NCI-H295R). 24 hours after plating and daily thereafter, media was changed for media containing IC-50 EZH2i or vehicle. After approximately 96 hours of drug administration (120 hours post-plating), cells were harvested for ChIP-seq.

value: human adrenocortical carcinoma

tag: chip antibody

value: Input (pooled)


title: 10X162_1

value: cervical


title: TuMV_WT_Plant5

value: Infected leaves


title: TuMV_WT_Plant4


title: V19N18-116_C1

data_processing:
Sequenced Spatial Transcriptomics libraries were processed using the Space Ranger v1.0.0 pipeline(10X Genomics).
Reads were aligned to the human reference genome (ENSEMBL genome assembly, release 93) and annotated using GRCh38-3.0.0 to obtain expression matrixes.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample
Supplementary files format and content: Annotated cell metadata
Supplementary files format and content: Cell embeddings in PCA (raw), Harmony (batch-corrected) and UMAP space.

extract_protocol:
Human spinal cord tissues at W5, 8, 9 and 12 were embedded in Tissue-Tek (OCT) and snap-frozen using an isopentane/dry ice slurry. W8-12 samples were pre-divided into three pieces along the rostral-caudal axis. To enable spatial protein and gene expression analyses, the spinal cords were cryosectioned at 16 μm thickness and systematically placed either on Superfrost microscope glass slides (Thermo Fisher Scientific) or 10X Visium spatial gene expression slides, after which they were stored at -80°C.
Spatial Gene Expression libraries were generated using Visium Spatial Gene Expression kit from 10x Genomics (https://support.10xgenomics.com/spatial-gene-expression). Each Visium barcoded glass slide contains 4 capture areas, each with ~5000 spots, every spot containing probes consisting of a spatial barcode, a unique molecular identifier (UMI) and a poly-dT-VN sequence allowing for mRNA capture.  The diameter of each spot is 55 µm and the center-to-center distance between the adjacent spots is 100 µm. Several sections of the same post-conceptional week were placed in each capture area, depending on the size of each section. Sections were fixed for 30 min in Methanol, stained with Hematoxylin and Eosin and imaged using Metafer Slide Scanning system (Metasystem, Altlussheim, Germany). Optimal permeabilization time for spinal cord sections was determined to be 20 min using 10x Genomics Visium Tissue Optimization Kit. In total, Visium Spatial Gene Expression libraries from 76 spinal cord sections were prepared by following manufacturer’s protocol. Libraries were sequenced using Illumina platform (NovaSeq6000, NextSeq2000). The number of cycles for read 1 was 28 bp and 120 bp for read 2.

value: spinal cord


title: FGSC_T_IP_Rep2

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Assembly: mm9
Supplementary files format and content: bigwig file

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min at room temperature and quenched with 125mM glycine. Cells were then put on ice, resuspended in cold cell lysis buffer (140mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100 and 0.1% SDS and Protease Inhibitors (Roche)). Nuclei were sonicated into 200-1000 bp. The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-H2BK5bhb (PTM-1230, PTM BIO).After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

tag: antibody

value: anti-H2BK5bhb (PTM-1230, PTM BIO)


title: V19N18-116_D1


title: FGSC_T_IP_Rep1


title: 11J_M_460

tag: brain region

tag: age


title: 11J_M_459

tag: strain


title: 11J_M_458


title: V19N18-116_B1


title: 11J_M_463


title: TuMV_heso1_3_Plant3

tag: tissue

tag: genotype

value: TuMV


title: FGSC_C_2


title: FGSC_T_Input_Rep1


title: TuMV_heso1_3_Plant2


title: 11J_M_457


title: FGSC_C_1


title: FGSC_C_IP_Rep2


title: V19N18-116_A1


title: TuMV_heso1_3_Plant1


title: 11J_M_456


title: 11J_M_454


title: FGSC_C_Input_Rep2


title: 11J_M_453


title: FGSC_T_Input_Rep2


title: V10T03-302_D1


title: V10T03-302_C1


title: FGSC_C_Input_Rep1


title: TuMV_urt1_1_Plant2


title: PCN_DIV14_NesKO_rep3

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv

data_processing:
Mapped by HISAT2
Quantified by featureCounts
Differential analysis by DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: csv, matrix of all samples in the comparison with normalized counts, p-value and adjusted p-value

value: Cortical neurons

value: Nes-KO


title: TuMV_urt1_1_Plant3


title: TuMV_urt1_1_Plant1


title: TuMV_WT_Plant3


title: V10T03-302_B1


title: V10T03-302_A1


title: 11J_M_452


title: PCN_DIV14_NesKO_rep2

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv


title: 11J_M_451


title: V10T03-290_B1


title: V10T03-290_D1


title: 11J_M_450


title: V10T03-290_C1


title: 11J_M_449


title: TuMV_WT_Plant1


title: PCN_DIV14_NesKO_rep1

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv


title: FGSC_C_IP_Rep1


title: TuMV_WT_Plant2


title: GFLV_heso1_3urt1_1_Plant8

description:
3' RACE-seq
Processed_data_GFLV_B1B2.txt

value: heso1-3 urt1-1

value: GFLV


title: PCN_DIV14_CTRL_rep3

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv

value: CONTROL


title: PCN_DIV14_CTRL_rep2

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv


title: V10T03-290_A1


title: 11J_M_448


title: 11J_M_255


title: GFLV_heso1_3urt1_1_Plant7


title: PCN_DIV14_CTRL_rep1

description:
Harvest at DIV14
PCN14dKO.ct.vs.ko.csv


title: V10T03-288_D1


title: 11J_M_254


title: V10T03-288_C1


title: GFLV_heso1_3urt1_1_Plant6


title: PCA_NesKO_rep3

description: AST.ct.vs.ko.csv

value: Cortical astrocytes


title: V10T03-288_B1


title: GFLV_heso1_3urt1_1_Plant5


title: 11J_M_253


title: PCA_NesKO_rep2

description: AST.ct.vs.ko.csv


title: V10T03-288_A1


title: PCA_NesKO_rep1

description: AST.ct.vs.ko.csv


title: 11J_M_252


title: GFLV_heso1_3_Plant7


title: GFLV_heso1_3_Plant6


title: 11J_M_251


title: PCA_CTRL_rep2

description: AST.ct.vs.ko.csv


title: PCA_CTRL_rep3

description: AST.ct.vs.ko.csv


title: V10F24-107_D1


title: 11J_M_250


title: V10F24-107_B1


title: GFLV_heso1_3_Plant5


title: PCA_CTRL_rep1

description: AST.ct.vs.ko.csv


title: 11J_M_249


title: 11J_M_248


title: V10F24-107_A1


title: GFLV_urt1_1_Plant8


title: NPC_HET_rep3

description: NPC.wt.vs.ht.csv

value: Neuroprogenitor cells

value: Pten+/-


title: V10F24-106_D1


title: NPC_HET_rep2

description: NPC.wt.vs.ht.csv


title: 11J_M_247


title: GFLV_urt1_1_Plant7


title: GFLV_urt1_1_Plant6


title: GFLV_heso1_3_Plant8


title: V10F24-106_B1


title: 11J_M_245


title: V10F24-106_C1


title: NPC_HET_rep1

description: NPC.wt.vs.ht.csv


title: GFLV_urt1_1_Plant5


title: NPC_WT_rep2

description: NPC.wt.vs.ht.csv

value: wild type


title: V10F24-107_C1


title: NPC_WT_rep1

description: NPC.wt.vs.ht.csv


title: NPC_WT_rep3

description: NPC.wt.vs.ht.csv


title: 11J_M_244


title: GFLV_WT_Plant8

value: WT


title: ATH1041

city: Newark

first: Pamela

middle: J

last: Green

state: DE

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: Delaware Biotechnology Institute

description:
PARE
Leaf_PARE_Scores.bg

data_processing:
PARE libraries (Illumina HiSeq 2500); GMUCT and RNA-seq libraries (Illumina NextSeq 550)
Reads were mapped to Arabidopsis TAIR10 genome using Tophat v2.0
PARE and GMUCT libraries were analyzed as per Hurtig et al., 2021 (PNAS) using the ComPARE pipeline
Bedgraph files contain ComPARE scores from PARE and GMUCT libraries comparing normalized abundances (expressed as counts per million, CPM) at every 5'P site between Col-0, xrn4 and mfl1xrn4
Genome_build: Arabidopsis TAIR10 (Ensemble v49)
Supplementary_files_format_and_content: RNA-seq: gene_exp.diff is a cuffdiff output file; PARE and GMUCT: Genomic coordinate file (with annotations) containing RNA Degradome scores where 5'P site CPM >= 1 in xrn4 in both replicates (bedgraph files)

source_name: six-week-old rosette leaves

growth_protocol: Seedlings grown on 1X MS, 1% (w/v) sucrose, 1% (w/v) agar for two-weeks in a climate-controlled growth chamber (21C; 16h day: 8h night); Fully expanded rosette leaves were collected from adult plants grown in soil under long day growth chamber conditions at 21/22C

extract_protocol: PARE libraries were prepared as per Nagarajan et al., (2019); GMUCT libraries were prepared according to Wilmann et al., 2014 with modifications suggested in Carpentier et al., 2021; RNA-seq libraries: 50 ug polyA+ RNA (2x enriched) prepared as per NEBNext Ultra II Directional Library Preparation kit;

tag: ecotype

tag: genotype/variation

tag: rep


title: 11J_M_246


title: V10F24-106_A1


title: GFLV_WT_Plant5

tag: treatment


title: 11J_M_243


title: ATH1040

description:
PARE
Leaf_PARE_Scores.bg


title: GFLV_WT_Plant7


title: GFLV_heso1_3urt1_1_Plant4


title: MSCs, 0d

city: Barcelona

first: Winona

middle: Oliveros

last: Diez

state: Barcelona

address: C. Maria Cubi 92, 2-2

country: Spain

institute: BSC

description: OmniC data

data_processing:
4D Nucleome pipeline was used. More details on OmniC analysis are described in the paper.
Assembly: hg38
Supplementary files format and content: cool files including interaction matrix
Library strategy: OmniC

source_name: MSCs

extract_protocol:
Mapping Hi-C/OmniC protocol is described in the manuscript.
Details on library preparation are described in the manuscript.

tag: cell type

value: MSCs


title: GFLV_WT_Plant6


title: 11J_M_241


title: 11J_M_242


title: 11J_M_239