title: Patient 249 [I_140]

status: Public on Nov 09 2022

city: Philadelphia

last: Guvakova

state: PA

address: 380S University Avenue

department: Surgery

institute: University of Pennsylvania

description:
I.txt
Affymetrix QuantiGene Plex 2.0 assay, custom-commercial

hyb_protocol: An appropriate volume of working bead mix was prepared and scaled for 96-well plate format. 60 uL of reagents per one well were mixed in the following order: 18.5 uL nuclease-free water, 33.3 uL lysis mixture, 2 uL blocking reagent, 0.2 uL proteinase K, 1 uL capture beads (vortex 30 sec before adding) and 5 uL probe set (heat amount to be used to 95C for 5 min before adding). The working bead mix was vortexed for 10 sec and 60 uL of it was dispensed into each well of the hybridization plate followed by addition of 40 uL of tissue homogenate to each well. For background reading, 40 uL of the homogenizing solution was added. For internal control, 40 uL containing 300 ng of RNA extracted from human cell lines was added. The plate was sealed using a pressure seal and placed on an inverted plate lid on the Labnet VorTemp 56 shaking incubator and incubated for 18-22 hr at 54°C at 600 rpm. Post-incubation, the contents of the hybridization plate were transferred to a magnetic separation plate after centrifugation at 240X g for 5 min at room temperature and mixing the contents a few times with a pipette. The magnetic separation plate was inserted into the hand-held magnetic plate washer and washed the plate three times using 100 uL of wash buffer per well. Then 100 uL of pre-amplifier working reagent (36 uL of 2.0 pre-amplifier in 12 mL of amplifier diluent) was dispensed into each well of the magnetic separation plate, sealed with the foil plate seal, and incubated at 50°C for 1 hr while shaking at 600 rpm.  After incubation, the plate was washed as above and 100 uL of amplifier working reagent per well and again incubated at 50°C for 1 hr at 600 rpm. Then the plate was washed again and 100 uL of label probe working reagent was added to each well and the sealed plate was placed into the Labnet VorTemp 56 and incubated at 50°C for 1 hr at 600 rpm. After 60 min, the washing procedure was repeated as above, 100 uL of streptavidin phycoerythrin (SAPE) working reagent (18ul of SAPE in 6.0mL of SAPE diluent) was pipetted into each well. The plate was foiled, removed from plate washer and placed on a shaking platform at room temperature with shaking at 800 rpm for 60 sec followed by shaking at 600 rpm. at 50°C for 30 min. The plate was washed three times by adding 100 uL of of SAPE wash buffer per well. Finally, 130 uL of SAPE wash buffer was added in each assay well, the plate was sealed, removed from plate washer, wrapped in aluminum foil and allowed to shake at 800 rpm for 3 min at room temperature.

scan_protocol: The plate was read immediately on FlexMAP 3D (Luminex/Merck Millipore) instrument set for specified bead regions with the following parameters: 100 uL sample volume, 5,000–25,000 DD gate, 60 sec sample time out and 100 bead events per bead region.

data_processing: The median fluorescence intensity values were recorded as raw data. After subtracting background values from each measurement, the relative target gene activity in a sample was calculated as a ratio: [(target gene expression - background)/ (PPIB gene expression - background)]x100.

label: streptavidin phycoerythrin (SAPE)

source_name: surgical exccision

growth_protocol: De-Identified residual formalin-fixed paraffin-embedded (FFPE) breast tissues from surgical excisions and diagnostic core needle biopsies were used. Studies were conducted in accordance with recognized ethical guidelines.

extract_protocol: The tissue and cell line RNA-containing lysates were obtained from five tissue curls of 10-micron each and 5 million cells grown in tissue culture plates, respectively. 10-micron tissue curls were cut from sample FFPE blocks into RNase/Dnase-free tubes by the anatomic pathology lab service. Lysates were prepared based on the QuantiGene 2.0 assay kit method.

treatment_protocol: Standard-of-care in surgery

tag: gender

value: female

value: invasive carcinoma


title: Patient 250 [I_141]

type: RNA

first: Marina

country: USA

molecule: total RNA

organism: Homo sapiens

label_protocol: 100 uL of streptavidin phycoerythrin (SAPE) working reagent (18ul of SAPE in 6.0mL of SAPE diluent) was pipetted into each well.

tag: tissue


title: Patient 248 [I_139]


title: Patient 251 [I_142]


title: Patient 247 [I_138]


title: Kasumi-1 _SAP30 (CUT-TAG)

status: Public on Nov 10 2022

type: SRA

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description: Endogenous

library_source: genomic

data_processing:
Library strategy: CUT&TAG
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.(ChIP-seq)
Clean sequenced reads were alignmented to hg38  by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to hg19 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: FPKM were calculated by R script on its defination.  BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.

molecule: genomic DNA

source_name: Cell line

growth_protocol: Kasumi-1 and THP-1 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Fluorescence activated Cell Sorting
(For ChIP-seq): Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).  (For RNA-seq): Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  (For Bisulfite-Seq): A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR.

treatment_protocol: Kasumi-1 and THP-1 cells were transduced with UHRF1 shRNA and then AML cells were selected by puromycine for 48h,finally these AML cells were subjected to RNA-seq analysis and WGBS. Kasumi-1 and THP-1 cells were treated with UHRF1 inhibitor UF146 for 24h and these cells were subjected to RNA-seq analysis.

value: Blood cell

tag: cell type

value: AML patient cell

tag: cell line

tag: chip antibody


title: Patient 245 [I_136]


title: Patient 246 [I_137]


title: Patient 244 [I_135]


title: Patient 241 [I_132]


title: Patient 240 [I_131]


title: Patient 243 [I_134]


title: Patient 242 [I_133]


title: H226_48h

city: Chongqing

first: sun

middle: yi

last: yun

address: 1YiXue Yuan,Yuzhong District

institute: Chongqing Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing fragments are randomly interrupted by mRNA. Use the HISAT2.0.5 software to quickly and accurately compare the Clean Reads after quality control with the reference genome to obtain the location information of the Reads on the reference genome.
Filter the original data: remove reads with adapters; remove reads containing N (N means base information cannot be determined); remove low-quality reads (the number of bases with Qphred<=20 accounts for 50% of the entire read length The above reads).
According to the position information of the gene alignment on the reference genome, the number of reads covered by each gene (including the new predicted gene) from the start to the end is counted. Filter out reads with a comparison quality value lower than 10, reads on unpaired comparisons, and reads that are aligned to multiple regions of the genome. This part of the analysis uses the featureCounts tool in the subread software.
FPKM(expected number of Fragments Per Kilobase of transcript sequence Per Millions base sequenced Fragments) is a set of Fragments from a gene of 1000 bases Per million Fragments.Sequencing depth and gene length were corrected by FPKM to represent gene expression values of RNA-seq.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
The total RNA was extracted from cells using TRIzolTM Reagent. After quantitative analysis and quality inspection, the RNA samples were sent to Novogene for RNA sequencing. Briefly, NEBNext® UltraTM RNA Library Prep Kit for Illumina®  was used to construct sequencing libraries. Each sample was subject to DNA sequencing with the Illumina NovaSeq6000 Sequencing System. The raw data was then preprocessed and normalized.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H226 cells were treated with either 30µM GANT-61 or DMSO control for 48h.

value: Lung squamous cell carcinomas

tag: treatment

value: 30um GANT61 for 48h


title: Patient 237 [I_128]


title: Patient 236 [I_127]


title: Patient 238 [I_129]


title: Patient 234 [I_125]


title: Patient 233 [I_124]


title: Patient 232 [I_123]


title: Patient 226 [I_117]


title: Patient 227 [I_118]


title: Patient 230 [I_121]


title: Patient 231 [I_122]


title: Patient 228 [I_119]


title: Patient 229 [I_120]


title: Patient 225 [I_116]


title: Patient 224 [I_115]


title: Patient 222 [I_113]


title: Patient 221 [I_112]


title: Patient 223 [I_114]


title: Patient 220 [I_111]


title: Patient 235 [I_126]


title: Patient 239 [I_130]


title: Patient 219 [I_110]


title: Patient 218 [I_109]


title: Patient 217 [I_108]


title: Patient 215 [I_106]


title: Patient 216 [I_107]


title: Patient 212 [I_103]


title: Patient 213 [I_104]


title: Patient 210 [I_101]


title: Patient 211 [I_102]


title: Patient 209 [I_100]


title: Patient 206 [I_097]


title: Patient 208 [I_099]


title: Patient 205 [I_096]


title: Patient 204 [I_095]


title: Patient 203 [I_094]


title: Patient 199 [I_090]


title: Patient 198 [I_089]


title: Patient 202 [I_093]


title: Patient 197 [I_088]


title: Patient 201 [I_092]


title: Patient 200 [I_091]


title: Patient 196 [I_087]


title: Patient 194 [I_085]


title: Patient 195 [I_086]


title: Patient 193 [I_084]


title: Patient 191 [I_082]


title: Patient 190 [I_081]


title: Patient 207 [I_098]


title: Patient 192 [I_083]


title: Patient 188 [I_079]


title: Patient 187 [I_078]


title: Patient 214 [I_105]


title: Patient 186 [I_077]


title: Patient 185 [I_076]


title: Patient 189 [I_080]


title: Patient 180 [I_071]


title: Patient 182 [I_073]


title: Patient 183 [I_074]


title: Patient 181 [I_072]


title: Patient 184 [I_075]


title: Patient 179 [I_070]


title: Patient 177 [I_068]


title: Patient 174 [I_065]


title: Patient 173 [I_064]


title: Patient 171 [I_062]


title: Patient 170 [I_061]


title: Patient 172 [I_063]


title: Patient 169 [I_060]


title: Patient 168 [I_059]


title: Patient 167 [I_058]


title: Patient 166 [I_057]


title: Patient 161 [I_052]


title: Patient 164 [I_055]


title: Patient 165 [I_056]


title: Patient 163 [I_054]


title: Patient 162 [I_053]


title: Patient 178 [I_069]


title: Patient 176 [I_067]


title: Patient 160 [I_051]


title: Patient 158 [I_049]


title: Patient 152 [I_043]


title: Patient 156 [I_047]


title: Patient 159 [I_050]


title: Patient 153 [I_044]


title: Patient 157 [I_048]


title: Patient 154 [I_045]


title: Patient 149 [I_040]


title: Patient 150 [I_041]


title: Patient 151 [I_042]


title: Patient 175 [I_066]


title: Patient 148 [I_039]


title: Patient 145 [I_036]


title: Patient 147 [I_038]


title: Patient 146 [I_037]


title: Patient 144 [I_035]


title: Patient 143 [I_034]


title: Patient 142 [I_033]


title: Patient 155 [I_046]


title: Patient 135 [I_026]


title: Patient 139 [I_030]


title: Patient 136 [I_027]


title: Patient 137 [I_028]


title: Patient 140 [I_031]


title: Patient 138 [I_029]


title: Patient 141 [I_032]


title: Patient 134 [I_025]


title: Patient 133 [I_024]


title: Patient 132 [I_023]


title: Patient 131 [I_022]


title: Patient 128 [I_019]


title: Patient 124 [I_015]


title: Patient 121 [I_012]


title: Patient 129 [I_020]


title: Patient 125 [I_016]


title: Patient 122 [I_013]


title: Patient 130 [I_021]


title: Patient 119 [I_010]


title: Patient 123 [I_014]


title: Patient 127 [I_018]


title: Patient 126 [I_017]


title: Patient 120 [I_011]


title: Patient 114 [I_005]


title: Patient 118 [I_009]


title: Patient 116 [I_007]


title: Patient 115 [I_006]


title: Patient 113 [I_004]


title: Patient 111 [I_002]


title: Patient 112 [I_003]


title: Patient 107 [D_073]

description:
D.txt
Affymetrix QuantiGene Plex 2.0 assay, custom-commercial

source_name: core needle biopsy

value: carcinoma in situ


title: Patient 104 [D_070]


title: Patient 106 [D_072]


title: Patient 108 [D_074]


title: Patient 109 [D_075]


title: Patient 105 [D_071]


title: Patient 101 [D_067]


title: Patient 103 [D_069]


title: Patient 102 [D_068]


title: Patient 110 [I_001]


title: Patient 99 [D_065]


title: Patient 95 [D_061]


title: Patient 100 [D_066]


title: Patient 98 [D_064]


title: Patient 94 [D_060]


title: Patient 93 [D_059]


title: Patient 117 [I_008]


title: Patient 92 [D_058]


title: Patient 91 [D_057]


title: Patient 89 [D_055]


title: Patient 90 [D_056]


title: Patient 87 [D_053]


title: Patient 88 [D_054]


title: Patient 84 [D_050]


title: Patient 85 [D_051]


title: Patient 83 [D_049]


title: Patient 81 [D_047]


title: Patient 82 [D_048]


title: Patient 97 [D_063]


title: Patient 80 [D_046]


title: Patient 78 [D_044]


title: Patient 79 [D_045]


title: Patient 75 [D_041]


title: Patient 76 [D_042]


title: Patient 74 [D_040]


title: Patient 73 [D_039]


title: Patient 72 [D_038]


title: Patient 77 [D_043]


title: Patient 70 [D_036]


title: Patient 69 [D_035]


title: Patient 65 [D_031]


title: Patient 64 [D_030]


title: Patient 67 [D_033]


title: Patient 66 [D_032]


title: Patient 63 [D_029]


title: Patient 62 [D_028]


title: Patient 61 [D_027]


title: Patient 86 [D_052]


title: Patient 96 [D_062]


title: Patient 60 [D_026]


title: Patient 59 [D_025]


title: Patient 58 [D_024]


title: Patient 56 [D_022]


title: Patient 71 [D_037]


title: Patient 68 [D_034]


title: Patient 55 [D_021]


title: Patient 54 [D_020]


title: Patient 53 [D_019]


title: Patient 52 [D_018]


title: Patient 51 [D_017]


title: Patient 49 [D_015]


title: Patient 47 [D_013]


title: Patient 48 [D_014]


title: Patient 46 [D_012]


title: Patient 45 [D_011]


title: Patient 44 [D_010]


title: Patient 57 [D_023]


title: Patient 40 [D_006]


title: Patient 43 [D_009]


title: Patient 36 [D_002]


title: Patient 39 [D_005]


title: Patient 35 [D_001]


title: Patient 37 [D_003]


title: Patient 38 [D_004]


title: Patient 41 [D_007]


title: Patient 42 [D_008]


title: Patient 31 [M_031]

description:
M.txt
Affymetrix QuantiGene Plex 2.0 assay, custom-commercial

source_name: breast reduction

value: noncancerous


title: Patient 34 [M_034]


title: Patient 30 [M_030]


title: Patient 32 [M_032]


title: Patient 50 [D_016]


title: Patient 33 [M_033]


title: Patient 29 [M_029]


title: Patient 28 [M_028]


title: Patient 26 [M_026]


title: Patient 25 [M_025]


title: Patient 27 [M_027]


title: Patient 24 [M_024]


title: Patient 23 [M_023]


title: Patient 22 [M_022]


title: Patient 21 [M_021]


title: Patient 20 [M_020]


title: Patient 19 [M_019]


title: Patient 18 [M_018]


title: Patient 16 [M_016]


title: Patient 15 [M_015]


title: Patient 13 [M_013]


title: Patient 12 [M_012]


title: Patient 11 [M_011]


title: Patient 10 [M_010]


title: Patient 2 [M_002]


title: Patient 6 [M_006]


title: Patient 4 [M_004]


title: Patient 1  [M_001]


title: Patient 7 [M_007]


title: Patient 3 [M_003]


title: AC84P48MB7

type: genomic

city: Madison

first: Ayken

last: Askapuli

state: WI

address: 250 North Mills Street

department: Integrative Biology

institute: University of Wisconsin-Madison

data_processing:
Data processing was performed by the Gene By Gene, Ltd., Houston, TX, USA.
*neo.mt.txt files contain rsID, chromosome, position and genotype
The matrix table includes genotype of the positions that are different from rCRS along the mitochondrial DNA and the haplogroup affiliation of mtDNA.

source_name: Blood

extract_protocol: Genomic DNA was extracted from blood with a salt extraction method (Lahiri et al. 1991) with modification, or a commercial DNA extraction kit (e.g., Qiagen).

tag: Sex

value: Male

tag: population

value: Kazak


title: AC7695C76V

hyb_protocol: performed by the Gene By Gene, Ltd., Houston, TX, USA.


title: AC3753UD5Q

label_protocol: performed by the Gene By Gene, Ltd., Houston, TX, USA.


title: ACYSY65L69


title: ACCD65UB4S


title: ACT9AYC95Q


title: AC33N4G45Y


title: ACP9948G49


title: ACCX99YQ63


title: ACG6LL9484


title: Patient 17 [M_017]


title: AC393S4U7D


title: Patient 14 [M_014]


title: ACT77863TU


title: Patient 9 [M_009]


title: AC7R79M573


title: Patient 8 [M_008]


title: Patient 5 [M_005]


title: AC9S5Q7X4K


title: AC8KK7V93L


title: AC6FQ6EDFC


title: AC8HQ9UNJD


title: ACV37V4899


title: ACR4C53DR7


title: AC6RTPC4F4


title: AC4Q353M8N


title: ACN8L49CHL


title: AC65QYEYA7


title: ACP3559994


title: AC7L6H5PP8


title: ACL4L6GJ3U


title: AC7J46MB5V


title: ACVJQS6VKB


title: ACEM4PT5C6


title: AC6S57SC84


title: AC4B9LD365


title: ACC536767Y


title: ACH85J7F97


title: AC5BP3V484


title: AC576PBMM4


title: ACFM647LE3


title: AC4YV8XF77


title: AC75895384


title: ACL7KM8E8X


title: ACF3PTV46M


title: AC674J93EG


title: ACUD5A88MU


title: ACV4CQSXUE


title: ACC7DE8485


title: AC356344H5


title: AC43SJ6K84


title: AC63C3SED5


title: ACFM6K3559


title: ACDCP7A9LR


title: AC76FQ44X9


title: ACN76KN5KC


title: AC794G3645


title: AC5C8BP6XH


title: ACBRB9VV69


title: AC3J9U9684


title: AC4946775G


title: AC6MP4YPEC


title: ACT6MD53UK


title: ACBVK4358T


title: AC6843CYU5


title: AC6DH8597X


title: ACG96S8N4B


title: AC57PY4999


title: ACLEFVQV85


title: AC53B47545


title: ACQ55T8YRH


title: AC4EBNDJ37


title: AC5R4K5N5M


title: ACFJANVJD6


title: ACXM8H97QN


title: AC954693RM


title: ACPPFSTXHN


title: ACD3LL4PN3


title: ACU5Q94L44


title: AC37JTJ3CT


title: ACK5Y36DVN


title: ACF3J38894


title: AC66L6K363


title: C1-022-C96_S94

city: New Delhi

first: Sarita

last: Poonia

state: Delhi

address: IIITD

department: Computational Biology

country: India

institute: IIITD

description: Blood cells

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie2
Genomic mappings(GM) performed with RSEM/bowtie2
Quantified gene expression levels in counts and TPM using RSEM-1.3.1
Assembly: hg19
Supplementary files format and content: Count and TPM values for each sample

molecule: polyA RNA

source_name: Peripheral Blood of Healthy Person

extract_protocol:
CD45 live cells were captured using C1 single cell system (Fluidigm) and processed for whole transcriptome library preparation.  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
Amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina)
RNA-Seq, paired-end NextSeq 74bp sequencing

tag: sample type

value: Healthy Blood


title: C1-022-C93_S88

description: Blood cells


title: ACG5DVUT47


title: h- 972 cells, wild type, minimal medium, bio rep 2 [wt_MM_2]

city: Salamanca

first: Sergio

last: Moreno

email: smo@usal.es, ibfg_smp@usal.es

state: Salamanca

address: Zacarias Gonzalez 2

department: IBFG

country: Spain

institute: Institute of Functional Biology and Genomics (IBFG) (CSIC)

data_processing:
Sequencing quality was check with FastQC (v 0.11.8, Babraham Bioinformatics).
Adaptors were trimmed using Trimmomatic (v 0.38) (Bolger et al. 2014) .
Alignment was performed with HISAT2 v 2.1.0 (CCB in John Hopkins University) (Kim et al. 2015)
Read counts were obtained with featureCounts (Subread package v 1.6.3, Walter+Eliza Hall Bioinformatics) (Liao et al.2014) .
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Schizosaccharomyces pombe

growth_protocol: Wild type and cells overexpressing ppk18 + from the nmt1 + promoter were grown to mid-exponential phase in supplemented yeast extract medium (YES) and minimal medium with thiamine.

extract_protocol:
Cells were washed with cold DEPC-H2O and snap freeze. RNA extraction was carried out by disrupting the cells with cells with glass beads in TRIzol® Reagent  (Invitrogen) and following the manufacturer’s instructions.
Library preparation using the Illumina TruSeq Stranded Total RNA and subsequent NGS sequencing was performed by Macrogen.

treatment_protocol: Cells were centrifuged and washed three times in MM without thiamine, and cultured in this medium for 20 hours at 25ºC. Then 2x10 8 cells were harvested.

tag: genotype

value: WT

value: Minimal medium

tag: time

value: 0 hours


title: h- 972 cells, wild type, minimal medium, bio rep 1 [wt_MM_1]


title: C1-022-C92_S89

description: Blood cells


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 4 hours, bio rep 3

data_processing:
Sequencing quality was check with FastQC (v 0.11.8, Babraham Bioinformatics).
Adaptors were trimmed using Trimmomatic (v 0.38) (Bolger et al. 2014) .
Alignment was performed with HISAT2 v 2.1.0 (CCB in John Hopkins University) (Kim et al. 2015)
Read counts were obtained with featureCounts (Subread package v 1.6.3, Walter+Eliza Hall Bioinformatics) (Liao et al.2014) .
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text files include normalized counts after Deseq2 analysisis

source_name: h- ppk18::KanMX6 cek1::natMX6

growth_protocol: Wild type, igo1∆ and ppk18∆ cek1∆ cells were grown to mid-exponential phase in supplemented yeast extract medium (YES) and minimal medium (MM).

extract_protocol:
Cell were washed with cold DEPC-H2O and snap freeze. RNA extraction was carried out by disrupting the cells with glass beads using RNAeasy Mini kit (Qiagen) and following manufacturer’s instructions.
Library preparation, using the Illumina Ribo Zero and TruSeq Stranded, and subsequent NGS sequencing was performed by Macrogen.

treatment_protocol: Cells were centrifuged and washed three times in MM-N, and cultured in MM-N at 25ºC. 2x10 8 cells were harvested at times 0,1 and 4 hours,

value: h- ppk18::KanMX6 cek1::natMX6

value: ppk18 knockdown and cek1 knockdown

value: Minimal medium without nitrogen

value: 4 hours


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 4 hours, bio rep 2


title: h- P3-nmt-GFP-ppk18 cells, ppk18 overexpression, minimla medium, bio rep 1 [ppk_1_ON_MM_1]

source_name: h- P3-nmt1-GFP-ppk18

value: h- P3-nmt1-GFP-ppk18

value: ppk18 overexpression


title: h- P3-nmt-GFP-ppk18 cells, ppk18 overexpression, minimla medium, bio rep 2 [ppk_1_ON_MM_2]


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 4 hours, bio rep 1


title: C1-022-C91_S90

description: Blood cells


title: C1-022-C89_S83

description: Blood cells


title: AC7638Q9L3


title: C1-022-C90_S82

description: Blood cells


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 1 hour, bio rep 3

value: 1 hour


title: C1-022-C87_S76

description: Blood cells


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 1 hour, bio rep 2


title: C1-022-C88_S84

description: Blood cells


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium without nitrogen 1 hour, bio rep 1


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium, bio rep 3


title: C1-022-C86_S77

description: Blood cells


title: C1-022-C85_S78

description: Blood cells


title: C1-022-C84_S70

description: Blood cells


title: C1-022-C95_S95

description: Blood cells


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium, bio rep 2


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 2

source_name: h- igo1::kanMX6

value: h- igo1::kanMX6

value: igo1 knockdown


title: h- ppk18::KanMX6 cek1::natMX6 cells, cek1ppk18 mutant, minimal medium, bio rep 1


title: C1-022-C94_S96

description: Blood cells


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 3


title: C1-022-C83_S71

description: Blood cells


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 1


title: C1-022-C81_S64

description: Blood cells


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium, bio rep 3


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 1 hour, bio rep 1


title: C1-022-C79_S66

description: Blood cells


title: C1-022-C80_S65

description: Blood cells


title: C1-022-C82_S72

description: Blood cells


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 1 hour, bio rep 2


title: C1-022-C78_S58

description: Blood cells


title: C1-022-C77_S59

description: Blood cells


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium, bio rep 2


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium, bio rep 1


title: C1-022-C76_S60

description: Blood cells


title: C1-022-C75_S52

description: Blood cells


title: E. coli, 20 min infected with T4 phage, R1 [t20_R1]

city: Marburg

first: Katharina

last: Höfer

address: Karl-von-Frisch-Str. 14

country: Germany

institute: Max-Planck-Institute for terrestrial Microbiology

description: total RNA with depletion of rRNA

data_processing:
The quality of reads obtained from Illumina RNA-Seq was assessed pre- and post-adapter trimming using FastQC (version 0.11.9). Fastq files were processed using the cutadapt tool (version 1.18) in order to remove reads containing Illumina TruSeq adapter sequences. Reads were aligned to the genome of E. coli (U00096.3) and bacteriophage T4 (NC_000866.4) using the hisat2 aligner (version 2.2.1) at default settings. Thereby, 88.71 to 96.51 % of reads were successfully aligned to the reference genomes. Samtools (version 1.7) was applied to select for primary alignments. Bam files were manually inspected as genomic maps using the Integrative Genomics Viewer (version 2.4.9). The reads mapped to individual features (annotated in gff3 files for U00096.3 and NC_000866.4 as gene) were quantified using featureCounts (Subread package version 2.0.1) with default settings while excluding reads overlapping multiple features. Using R (R version 4.1.2), genes annotated as rRNA (22 genes) from E. coli, which account for up to 0.6 % of reads per sample (Supplementary Fig. 2), were manually removed from the counts table prior to further analysis because they have been depleted from the total RNA before sequencing. The count data was normalized to transcripts per million (TPM) which allows to compare expression levels of genes between samples. Sample clustering was assessed by PCA with the prcomp package. The fractions of TPM normalized reads per sample and entity (T4 phage or E. coli) were calculated accordingly. Genes with low read counts (average read count below 1.5 across all samples) were removed from the TPM normalized count data including 338 E. coli and 17 T4 phage genes. These genes would otherwise confuse the analysis due to low and variable read counts. Further analyses in R focussed on data visualization using the pheatmap (1.0.12) and ggplot2 (3.3.6) package. Differential gene expression analysis during the early infection phase was assessed with DESeq2 applying a Wald-test at a log2fold change greater or smaller than 0 with a Benjamini-Hochberg-corrected p-value threshold of 0.05. Other infection phases were not assessed by DESeq2 as dramatic changes in the host and phage transcriptome have already been recorded 4 minutes post infection. Assignment of differentially expressed genes to Clusters of Orthologous Groups (COGs) was conducted in R using the COG database from the National Center for Biotechnology Information.
Assembly: E. coli (U00096.3) and bacteriophage T4 (NC_000866.4)
Supplementary files format and content: one table is provided which contains TPM normalized count data for all samples substracted by rRNAs

organism: Escherichia coli B

source_name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (DSM 613, ATCC 11303)

growth_protocol: A culture of E. coli strain B (DSMZ, Braunschweig, Germany, DSM 613) was grown at 37 °C in LB (Luria/Miller) medium supplemented with 1 mM CaCl2 and 1 mM MgCl2 to an OD600 of 0.5.

extract_protocol:
Lysis and RNA extraction were performed with the hot lysis method. Therefore, 5 ml of sampled culture were incubated with 1 volume of lysis solution (1 % SDS, 4 mM EDTA) at 95 °C for 2 min each. 1 volume of water-saturated phenol (Roti-aqua phenol, Carl-Roth, Karlsruhe, Germany) was added to each sample and incubated at 67 °C for 10 min. Samples were centrifuged at 10,000 x g for 10 min, and the upper phase was added to 1 volume of phenol/chloroform/isoamyl alcohol (Carl-Roth, Karlsruhe, Germany). Samples were centrifuged again (10,000 x g, 10 min). The upper phase was precipitated by centrifugation (14,000 x g, 90 min, 4 °C) in the presence of 0.3 M sodium acetate and 1 volume isopropanol. The RNA pellet was resuspended in RNase-free water, and residual DNA was digested with 2 µl DNase I (Roche, Basel, Schweiz) in 1 x DNase buffer at 37 °C for 30 min. The RNA was extracted with 1 volume phenol/chloroform/isoamylalcohol (Carl-Roth, Karlsruhe, Germany) twice and residual phenol was removed by diethyl ether (Fisher Scientific, Schwerte, Germany) extraction. RNA was again precipitated in the presence of 0.3 M sodium acetate and 1 volume isopropanol by centrifugation (14,000 g, 4 °C, 90 min). The RNA pellet was resuspended in 50 µl RNase-free water each. The RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, US) and a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, MA, US). RNA integrity was evaluated on a Bioanalyzer (Agilent, Santa Clara, CA, US) using the RNA 6000 Nano Kit according to the manufacturer’s instructions.
1 μg total RNA was subjected to ribosomal RNA depletion (rRNA) by Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Illumina, San Diego, CA, US). rRNA-depleted RNA was randomly sheared in 10 μL dH2O, at 94 °C 10 min. Fragmented RNA was processed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, US) for Illumina. cDNA was barcoded by PCR amplification using Illumina TruSeq adapters for Illumina. Further cDNA size selection in the range of 300 to 500 bp was performed, employing the Agencourt RNAClean XP kit (Beckman Coulter, Brea, CA, US). Primer-depleted cDNA was examined by Bioanalyzer and the concentration was measured by Qubit(Thermo Fisher Scientific, Waltham, MA, US). Multiplexed libraries were sequenced on a NextSeq 500 platform.

treatment_protocol: Escherichia phage T4 (T4 phage) (DSMZ, Braunschweig, Germany, DSM 4505) suspension was added to a multiplicity of infection (MOI) of 3.1 to E. coli strain B in exponential growth phase and subsequently grown at 30 °C.  5 ml of culture were taken at 0 min (before infection), 1 min, 4 min, 7 min and 20 min post-infection and immediately lysed using the hot lysis method.

tag: medium

value: LB

tag: growth stage

value: exponential

value: infected with T4 phage

value: 20 min

tag: phage moi

tag: strain

tag: bacteriophage

value: Escherichia phage T4 (DSMZ, Braunschweig, Germany, DSM 4505)


title: E. coli, 20 min infected with T4 phage, R3 [t20_R3]

description: total RNA with depletion of rRNA

value: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (DSM 613, ATCC 11303)


title: h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 3

value: WT


title: E. coli, 20 min infected with T4 phage, R2 [t20_R2]

description: total RNA with depletion of rRNA


title: C1-022-C73_S54

description: Blood cells

value: Healthy Blood


title: h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 1


title: C1-022-C74_S53

description: Blood cells


title: E. coli, 7 min infected with T4 phage, R1 [t7_R1]

description: total RNA with depletion of rRNA

value: 7 min


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 1 hour, bio rep 3


title: E. coli, 4 min infected with T4 phage, R3 [t4_R3]

description: total RNA with depletion of rRNA

value: 4 min


title: E. coli, 4 min infected with T4 phage, R2 [t4_R2]

description: total RNA with depletion of rRNA


title: E. coli, 7 min infected with T4 phage, R3 [t7_R3]

description: total RNA with depletion of rRNA


title: C1-022-C71_S47

description: Blood cells


title: C1-022-C72_S48

description: Blood cells


title: E. coli, 7 min infected with T4 phage, R2 [t7_R2]

description: total RNA with depletion of rRNA


title: h- 972 cells, wild type, minimal medium without nitrogen 1 hour, bio rep 3

value: Minimal medium without nitrogen


title: h- 972 cells, wild type, minimal medium without nitrogen 1 hour, bio rep 1


title: E. coli, 1 min infected with T4 phage, R2 [t1_R2]

description: total RNA with depletion of rRNA

value: 1 min


title: E. coli, 4 min infected with T4 phage, R1 [t4_R1]

description: total RNA with depletion of rRNA


title: C1-022-C69_S42

description: Blood cells


title: h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 2

value: 4 hours


title: h- 972 cells, wild type, minimal medium, bio rep 3

value: Minimal medium

value: 0 hours


title: E. coli, uninfected, R2 [t0_R2]

description: total RNA with depletion of rRNA

value: uninfected

value: 0 min

value: no phage added


title: E. coli, uninfected, R3 [t0_R3]

description: total RNA with depletion of rRNA

value: LB

value: exponential


title: E. coli, 1 min infected with T4 phage, R3 [t1_R3]

description: total RNA with depletion of rRNA

value: infected with T4 phage


title: E. coli, uninfected, R1 [t0_R1]

description: total RNA with depletion of rRNA


title: E. coli, 1 min infected with T4 phage, R1 [t1_R1]

description: total RNA with depletion of rRNA

value: Escherichia phage T4 (DSMZ, Braunschweig, Germany, DSM 4505)


title: h- 972 cells, wild type, minimal medium, bio rep 2


title: C1-022-C66_S36

description: Blood cells


title: C1-022-C70_S46

description: Blood cells


title: C1-022-C67_S40

description: Blood cells


title: C1-022-C68_S41

description: Blood cells


title: C1-022-C64_S34

description: Blood cells


title: Mig_KO_D28_3

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

hyb_protocol: 100ng total RNA was hybridised to fluorescent barcode labelled probes from the nCounter Myeloid Innate Immunity v2 panel, as per manufacturer's instructions

scan_protocol: All samples were read on nCounter Analysis System (NanoString Technologies).

data_processing: Normalization was performed using the ROSALIND platform and calculated using criteria provided by Nanostring, following the nCounter Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString

organism: Mus musculus

source_name: Microglia

label_protocol: manufacturer's protocol

extract_protocol: RNA was prepared by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and Direct-zol RNA mini prep (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: SCs from PBS-perfused WT and Trem2-/- mice were finely minced with a razor blade. Minced tissues were enzymatically digested using papain-based Neural Tissue Dissociation Kit (P) according to the manufacture’s instruction (Miltenyi Biotec). After digestion, SC-derived cells were isolated using percoll gradients as described above, and then stained with CD45, CD11b and Ly6G for 30 min on ice. SC-derived microglia (CD45intCD11b+) and BMDM (CD45hiCD11b+Ly6G-) were purified using a FACSAria cell sorter (BD Biosciences). Microglia from naïve mice and circulating monocytes were used as controls of microglia and SC-infiltrated BMDM after infection, respectively.

tag: cluster name

value: Trem2 KO

tag: time course


title: Mig_KO_D0_2


title: h- 972 cells, wild type, minimal medium, bio rep 1

value: WT


title: Mig_WT_D0_2


title: Mig_KO_D0_1


title: Mig_KO_D28_4


title: alveolar macrophage, NC-3, LncRNA-seq

city: 扬州

first: 靳

last: 健

state: 江苏

address: 扬州大学荷花池校区

institute: 扬州大学

data_processing:
Data quality control was performed on ATAC-seq raw reads obtained from the sequencer before information analysis, and low-quality reads containing adapter reads, reads containing more than 10% unknown nucleotides (N), and low-quality reads containing more than 50% low quality (Q-value≤20) bases were removed to obtain high quality clean reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using Bowtie2 v2.2.8 with reads aligned to mitochondrial genome discarded, and reads that are uniquely aligned were used for subsequent analysis. The distribution map of insert fragments of each sample was drawn by ATACseqQC. DeepTools was used to visualize the read distribution flanking transcription start sites (TSSs). Peak calling was performed using MACS v2.1.2 with a threshold of q-value < 0.05. Only the common peaks among replicates (with overlap more than 50%) were retained for analysis. Peak annotation was performed using ChIPseeker v1.16.1.
We used fastp v0.18.0for quality control and data filtering of raw reads from rRNA-depleted library, to remove reads containing adapters, with a N-containing proportion greater than 10%, with all A bases, or with bases with Q-value≤20 accounting for more than 50% of the whole reads. The processed reads were aligned to the pig reference genome (release Sscrofa11.1) using HISAT2 v2.1.0. To examine the relationship among different samples, Principal component analysis (PCA) was performed using R package gmodels (http://www.rproject.org/). Differentially expressed genes were identified by DESeq2, with cut-off: FDR<0.05 and foldChange≥2. The raw data of small RNA library was filtered to remove low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N) in the data, to filter out reads without 3 'adapters, to filter out reads containing 5' adapters, and to filter out reads containing poly A. All clean tags were searched to identify known porcine miRNAs (exist miRNAs) using the miRbase database (release 22).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Peak calling was performed using MACS v2.1.2. Peak annotation was performed using ChIPseeker v1.16.1
Supplementary_files_format_and_content: LncRNA_CodeGenesExpression_fpkm.csv
Supplementary_files_format_and_content: all_mirna_tpm.xlsx

organism: Sus scrofa

growth_protocol: Porcine alveolar macrophages (3D4/21) were cultured in RPMI-1640 (Gibco) medium containing 10% fetal bovine serum (Gibco) and 1% antibiotics (penicillin (100 U/mL), streptomycin (0.1 mg/mL) (Beijing Solarbio Science & Technology Co., Ltd.) at 37℃ in a saturated humidity constant temperature incubator continuously supplied with 5% CO2.

extract_protocol:
Total RNA was extracted from the experimental samples using the Trizol (Invitrogen, USA) kit according to the instructions, RNA purity and concentration were preliminarily detected using a NanoDrop2000 spectrophotometer (Thermo Scientific, MA, USA), and RNA integrity was accurately quantified using an Agilent 2100 (Agilent Technologies, CA, USA) bioanalyzer.
We remove the rRNAs from the total RNA of the sample, retain mRNAs and ncRNAs, reverse transcribe the obtained RNA, purify the cDNA fragment using QiaQuick PCR kit (Qiagen, Venlo, Holland), repair the end, add PolyA, add sequencing linker, degrade the product by UNG (Uracil-N-Glycosylase) enzyme and amplify the product by PCR, and sequence the library by Illumina HiSeqTM4000.

treatment_protocol: The cell viability of porcine alveolar macrophages (3D4/21) cells treated with different concentrations (0, 10, 20, 30, 40, 50, and 60μg/mL) of FB1 at different culture time points (24, 48, and 72 h) was measured on a Tecan Infinit 200 microplate reader (Tecan) platform using the Cell CountingKit-8 (CCK-8) kit (Dojindo), and finally 50μg/mL FB1 was induced for 24 h as the optimal treatment concentration and action time to investigate the cytotoxicity of FB1 on 3D4/21 cells. Porcine alveolar macrophages were seeded in 6-well plates at a density of 5 × 105 cells/mL and cultured in a 5% CO2 incubator at 37℃ for 24 h. FB1 at a final concentration of 50 µg/mL was added to the culture medium of the experimental wells, and the same amount of enzyme-free water was added to the culture medium of the control wells.

value: alveolar macrophage

value: control


title: C1-022-C62_S29

description: Blood cells

value: Healthy Blood


title: Mig_WT_D0_1


title: h- 972 cells, wild type, minimal medium without nitrogen 1 hour, bio rep 2

value: Minimal medium without nitrogen

value: 1 hour


title: C1-022-C65_S35

description: Blood cells


title: C1-022-C61_S28

description: Blood cells


title: alveolar macrophage, NC-2, LncRNA-seq


title: alveolar macrophage, FB1-2, LncRNA-seq

value: Fumonisin B1 (FB1)


title: alveolar macrophage, NC-1, LncRNA-seq


title: Mig_KO_D12_2


title: C1-022-C63_S30

description: Blood cells


title: Mig_WT_D28_3


title: Mig_KO_D12_1


title: alveolar macrophage, NC-3, ATAC-seq

extract_protocol:
The cell samples were collected and the nuclei were extracted, and the transposable mixture containing Tn5 transposase was added to the nuclear suspension for transposable reaction.
Tn5 transposase entered the nucleus and preferentially cleaved exposed DNA in the open region of chromatin, while ligating specific sequencing adaptor. The DNA fragments ligated with adaptors were amplified by PCR, and the amplified PCR products were purified with the Qiagen MinElute kit and sequenced by Gene Denovo Biotechnology Company (Guangzhou, China).


title: alveolar macrophage, FB1-3, LncRNA-seq


title: Mig_WT_D28_2


title: Mac_KO_D0_1

source_name: Macrophage Blood


title: Mac_WT_D0_2


title: Mac_WT_D0_1


title: Mig_WT_D28_1


title: C1-022-C58_S22

description: Blood cells


title: C1-022-C56_S17

description: Blood cells


title: alveolar macrophage, FB1-3, ATAC-seq


title: Mig_WT_D12_2


title: Mac_WT_D28_2

source_name: Macrophage


title: Mig_WT_D12_1


title: alveolar macrophage, FB1-2, ATAC-seq


title: Mac_KO_D0_2


title: alveolar macrophage, FB1-1, ATAC-seq


title: Mac_KO_D12_2


title: alveolar macrophage, FB1-1, LncRNA-seq


title: Mac_WT_D12_4


title: Mac_KO_D12_1


title: C1-022-C59_S23

description: Blood cells


title: C1-022-C60_S24

description: Blood cells


title: Mac_WT_D12_1


title: alveolar macrophage, NC-2, ATAC-seq


title: alveolar macrophage, NC-1, ATAC-seq


title: C1-022-C57_S18

description: Blood cells


title: Mac_KO_D28_2


title: Mac_WT_D28_3


title: THRLBCL_926

city: MILAN

first: Maria Rosaria

last: Sapienza

state: Italy

address: Via Ripamonti, 435

department: Division of Haematopathology

country: Italy

institute: IEO, European Institute of Oncology IRCCS

hyb_protocol: Probes were hybridized to 300 ng of total RNA for 20 hours at 65°C and applied to the nCounter preparation station for automated removal of excess probe and immobilization of probe-transcript complexes on a streptavidin-coated cartridge.

scan_protocol: Data were collected with the nCounter digital analyzer by counting the individual barcodes.

data_processing: The quality control and normalization of NanoString nCounter data were performed using R package NanoStringNorm. The raw NanoString counts for each gene were subjected to a technical normalization considering positive and negative probes. A normalization factor was calculated by obtaining the geometric mean of the positive controls used for each sample and applied to the raw counts of the nCounter output data to eliminate variability that was unrelated to the samples. The resulting data were normalized again with the geometric mean of the housekeeping genes. Normalized data were log2-transformed for further analyses.

source_name: THRLBCL

label_protocol: We assessed the expression of 770 genes by using the nCounter PanCancer Immune Profiling Panel of the NanoString technology (NanoString Technologies, Seattle WA, U.S.A). Each biotinylated capture probe in the panel was manufactured with specificity to a 100-base region of the target mRNA. A complementary reporter probe tagged with a specific fluorescent barcode was also included, thus resulting in two sequence-specific probes for each target transcript.

extract_protocol: On average, 5 sections 10 um-thick were prepared for the extraction of total RNA from FFPE tumor samples, using the RNAstorm™ FFPE extraction kit (Cell Data Sciences, CA, USA). All the samples passed the quality control step with a 260/280 and 260/230 ratios ≥ 1.8 and RNA concentration ≥ 60 ng/ul.

tag: diagnosis

value: THRLBCL

tag: tissue

value: Tumor lymph node

tag: age

value: Male

value: non GCB

value: ABC

value: Untreated


title: Mac_KO_D12_4


title: Mac_KO_D28_1


title: Mac_KO_D12_3


title: ThTC1

city: Boston

first: Kok Siong

last: Chen

state: Massachusetts

address: 60 Fenwood Road

department: Neurosurgery

institute: Brigham and Women's Hospital

data_processing:
BGI Dr.Tom
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Soapnuke from BGI
Clean reads were aligned to GCF_000001635.26_GRCm38.p6 using HISAT
Read count extraction and normalization were performed using Dr.Tom
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared and sequencing were performed by BGI Genomics using DNBseq platform at a total of 4.47Gb bases per sample.

tag: cell line

tag: cell type

value: Murine GBM

value: ThTC

value: Day 5 post resection


title: THRLBCL_9

tag: Sex

value: GCB

tag: treatment


title: C1-022-C55_S16

description: Blood cells

tag: sample type


title: C1-022-C54_S12

description: Blood cells


title: Mac_WT_D28_1

value: WT


title: ThTC3


title: Mac_WT_D12_3


title: C1-022-C50_S5

description: Blood cells


title: C1-022-C53_S11

description: Blood cells


title: Mac_WT_D12_2


title: ThTC2


title: GFP_TC1

value: GFP-TC


title: C1-022-C52_S10

description: Blood cells


title: sECM_only3

value: sECM only


title: C1-022-C51_S6

description: Blood cells

value: Healthy Blood


title: THRLBCL_7601

value: Female


title: C1-022-C46_S91

description: Blood cells


title: THRLBCL_6908


title: GFP_TC2


title: THRLBCL_2504


title: THRLBCL_254


title: DLBCL_43

source_name: DLBCL

value: DLBCL


title: THRLBCL_116


title: THRLBCL_1310


title: C1-022-C45_S87

description: Blood cells


title: C1-022-C49_S4

description: Blood cells


title: mammary epithelial cells,peak lactation,P3

city: 泰安

first: 君

middle: 舒

last: 王

state: 山东省

address: 泰前街道

department: 动物科技学院

institute: 山东农业大学

data_processing:
fastp (version 0.18.0)
reads containing adaptors were removed;
reads containing more than 10% unknown nucleotides (N) were removed;
reads containing more than 50% of low-quality bases (q value ≤ 20) were removed

organism: Capra hircus

source_name: mammary gland

extract_protocol:
Total RNA was extracted using a TRIzol kit (Invitrogen, USA).
Eukaryotic mRNA from the extracted total RNA was enriched using Oligo (dT) beads, and a Ribo-ZeroTM Magnetic Kit (Epicentre, USA) was used to remove rRNA and enrich prokaryotic mRNA. Then, the enriched mRNA fragments were divided into short fragments using fragment buffer, and the RNA was divided into 2 samples, 1 of which was used as the input control. The transcriptome sequencing library was constructed to eliminate noise during the capture of methylated fragments, another  RNA sample was enriched with an m6A-specific antibody.

value: mammary gland

value: mammary epithelial cells

tag: breed

value: Laoshan


title: C1-022-C48_S93

description: Blood cells


title: THRLBCL_218

value: THRLBCL

value: Tumor lymph node

value: Unclassified


title: THRLBCL_2501

value: Male

value: non GCB

value: Untreated


title: THRLBCL_2006


title: THRLBCL_196


title: DLBCL_2402


title: C1-022-C47_S92

description: Blood cells


title: GFP_TC3

value: Murine GBM

tag: time

value: Day 5 post resection


title: C1-022-C43_S85

description: Blood cells


title: sECM_only2


title: sECM_only1


title: DLBCL_87


title: DLBCL_154

value: GCB


title: DLBCL_2516


title: mammary epithelial cells,Early lactation,E3


title: mammary epithelial cells,peak lactation,P2


title: DLBCL_1211

value: ABC


title: DLBCL_108


title: mammary epithelial cells,peak lactation,P1


title: C1-022-C42_S81

description: Blood cells


title: C1-022-C44_S86

description: Blood cells


title: C1-022-C39_S75

description: Blood cells


title: DLBCL_2010


title: C1-022-C40_S79

description: Blood cells


title: DLBCL_137


title: OPM-2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: cancer cell line

hyb_protocol: The labelled RNA samples were hybridized at 65°C for at least 16 hours but not more than 48 hours in a thermal cycler.

scan_protocol: Each individual lane were scanned 194 Fields of View (FOV).The system images these FOVs separately, and sums the barcode counts of all FOVs from a single lane to form the final raw data count for each unique barcode target. Finally, the system reports the number of FOVs successfully imaged as FOV Counted.

data_processing: The raw data were processed using NanoString nSolver. The raw data were normalized using postive control and housekeeping genes control.

label: biotin

source_name: cancer cell lines

label_protocol: 100ng of unamplifed total RNA were labelled with nanoString Reporter CodeSet and Capture ProbeSet, procedure as per  MAN-10023-11_nCounter_XT_Assay_User_Manual.

extract_protocol: RNA from the cell lines were extracted using QIAGEN RNeasy FFPE Kit (Cat No./ID: 73504).

value: blood

tag: disease

value: myeloma

tag: cel line


title: MiaPaCa2

description: cancer cell line

value: pancreas

value: pancreatic cancer


title: HeLa-MaTu-ADR

description: cancer cell line

value: cervix

value: cervical cancer

value: HeLa-MaTu-ADR


title: HeLa-MaTu

description: cancer cell line

value: HeLa-MaTu


title: DLBCL_22

value: DLBCL

value: Tumor lymph node

value: Female


title: mammay epithelial cells,peak lactation IP,P2

data_processing:
fastp (version 0.18.0)
reads containing adaptors were removed;
reads containing more than 10% unknown nucleotides (N) were removed;
reads containing more than 50% of low-quality bases (q value ≤ 20) were removed
Library strategy: MeRIP-Seq

value: mammary gland

value: mammary epithelial cells

value: Laoshan


title: mammary epithelial cells,Early lactation,E2


title: C1-022-C37_S73

description: Blood cells

value: Healthy Blood


title: mammary epithelial cells,Early lactation,E1


title: mammay epithelial cells,peak lactation IP,P1


title: mammay epithelial cells,peak lactation IP,P3


title: C1-022-C38_S74

description: Blood cells


title: PC3

description: cancer cell line

value: prostate

value: prostate cancer


title: TMD-8

description: cancer cell line

value: blood

value: Diffuse large B-cell lymphoma, ABC


title: C1-022-C41_S80

description: Blood cells


title: mammay epithelial cells,Ealy lactation IP,E3


title: NCI-H82

description: cancer cell line

value: lung

value: small cell lung cancer


title: C1-022-C35_S68

description: Blood cells


title: HBL-1

description: cancer cell line


title: IGR-OV-1

description: cancer cell line

value: ovary

value: ovarian cancer


title: mammay epithelial cells,Ealy lactation IP,E2


title: SU-DHL-6

description: cancer cell line

value: Diffuse large B-cell lymphoma, GCB


title: HT-29

description: cancer cell line

value: colorectal cancer


title: HT-144

description: cancer cell line

value: skin

value: Melanoma


title: C1-022-C36_S69

description: Blood cells


title: MFM223

description: cancer cell line

value: breast

value: breast cancer, triple-negative


title: C1-022-C34_S67

description: Blood cells


title: C1-022-C31_S61

description: Blood cells


title: 22Rv1

description: cancer cell line


title: LapC4 (internal)

description: cancer cell line

value: LapC4 (internal)


title: SK-OV-3

description: cancer cell line


title: Lovo

description: cancer cell line

value: Lovo


title: C1-022-C32_S62

description: Blood cells

value: Healthy Blood


title: C1-022-C30_S57

description: Blood cells


title: C1-022-C33_S63

description: Blood cells


title: spontaneously hypertensive rats, treated with angiotensin receptor-neprilysin inhibitor (ARNI) [ARNI_A_3]

first: du

last: jianlin

address: 74 Linjiang Road

department: Cardiology

institute: The Second Affiliated Hospital of Chongqing Medical University

data_processing:
SOAPnuke (v1.5.2)
Sequenced reads were trimmed for adaptor sequence by SOAPnuke (v1.5.2), afterwards clean reads were obtained and stored in FASTQ format.
Clean reads were mapped to GCF_000001895.5_rnor_6.0 using HISAT2(v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to GCF_000001895.5_rnor_6.0
Sequenced Fragments Per Kilobase of exon per Million fragments mapped to Rattus_norvegicus genome (FPKM) were calculated using RESEM(v1.2.12).
Assembly: Rattus_norvegicus NCBI GCF_000001895.5_rnor_6.0
Supplementary files format and content: tab-delimited text file include FPKM values for each sample.

organism: Rattus norvegicus

source_name: left atrium

growth_protocol: Spontaneously hypertensive/Wistar-Kyoto rats were housed in groups of 3-4 rats/cage in a controlled environment (22 ± 2°C, 12-h/12-h light/dark cycle with lights on at 7:00 am) and ad libitum access to water and standard rat chow.

extract_protocol:
Total RNA was extracted from the rat tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.1.3 ug of total RNA was used for the construction of sequencing libraries.
The final library was generated by heated denaturing and circularizing the above double stranded PCR products using the splint oligo sequence, then followed by formatting the single strand circle DNA (ssCir DNA). DNA nanoballs (DNBs) were generated by library amplification and loaded into the patterned nanoarray and single end 50 bases reads on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: Wistar-Kyoto rats were treated with saline vehicle control daily for 4 weeks. Spontaneous hypertension rats were treated with valsartan at the dose of 30mg/kg/d or sacubitril/valsartan at the dose of 60mg/kg/d or saline vehicle control daily for 4 weeks.

value: left atrium

value: Wistar-Kyoto

tag: phenotype

value: spontaneously hypertensive rat

value: sacubitril/valsartan (60mg/kg/d)


title: JVM-2

description: cancer cell line

value: blood

value: mantle cell lymphoma


title: HCT-116

description: cancer cell line


title: A2780

description: cancer cell line

value: ovary


title: spontaneously hypertensive rats, treated with angiotensin receptor blocker (ARB) [ARB_A_3]

tag: strain

value: valsartan (30mg/kg/d)


title: GRANTA-519

description: cancer cell line


title: Jeko-1

description: cancer cell line


title: mammay epithelial cells,Ealy lactation IP,E1

value: mammary gland

value: mammary epithelial cells

value: Laoshan


title: spontaneously hypertensive rats, treated with angiotensin receptor blocker (ARB) [ARB_A_2]


title: WT_wo_myelin C_K5_18_2_S61882

city: Vienna

first: Jure

last: Fabjan

address: Spitalgasse 4

department: Department of Pathobiology of the Nervous System

country: Austria

institute: Medical University of Vienna

data_processing:
STAR
Mapping was done using STAR to hg38 genome.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using poly-A selection.

value: Blood

value: Macrophages

tag: genotype

value: Control

value: no treatment


title: C1-022-C29_S56

description: Blood cells


title: spontaneously hypertensive rats, treated with angiotensin receptor-neprilysin inhibitor (ARNI) [ARNI_A_2]


title: C1-022-C28_S55

description: Blood cells


title: spontaneously hypertensive rats, treated with angiotensin receptor-neprilysin inhibitor (ARNI) [ARNI_A_1]


title: WT_wo_myelin C_K9_18_3_S61887


title: WT_wo_myelin C_K36_18_9_S61900


title: WT_wo_myelin C_K2_18_1_S61894


title: spontaneously hypertensive rats, treated with angiotensin receptor blocker (ARB) [ARB_A_1]


title: WT_wo_myelin C_K21_18_6_S61917


title: spontaneously hypertensive rats [WKY_A_3]

value: saline


title: REC-1

description: cancer cell line


title: WT_wo_myelin C_K19_18_5_S61912


title: MDA-MB-436

description: cancer cell line

value: breast

value: breast cancer


title: spontaneously hypertensive rats [WKY_A_2]

value: left atrium

value: Wistar-Kyoto


title: ALD_wo_myelin A_K35_18_9_S61898

value: X-ALD


title: C1-022-C25_S49

description: Blood cells

value: Healthy Blood


title: C1-022-C24_S43

description: Blood cells


title: C1-022-C26_S50

description: Blood cells


title: ALD_wo_myelin A_K34_18_8_S61906


title: ALD_wo_myelin A_K23_18_7_S61903


title: Wistar-Kyoto rats [SHR_A_2]


title: C1-022-C22_S45

description: Blood cells


title: ALD_wo_myelin A_K78_17_3_S61884


title: ALD_wo_myelin A_K57_15_2_S61891


title: C1-022-C23_S44

description: Blood cells


title: spontaneously hypertensive rats [WKY_A_1]

value: spontaneously hypertensive rat


title: ALD_wo_myelin A_K20_18_6_S61911


title: ALD_wo_myelin A_K1_18_1_S61889


title: Wistar-Kyoto rats [SHR_A_1]


title: Wistar-Kyoto rats [SHR_A_3]


title: ALD_wo_myelin A_K18_18_5_S61921


title: ALD_wo_myelin A_K11_18_4_S61920


title: WT_wo_myelin C_K24_18_7_S61905


title: C1-022-C27_S51

description: Blood cells


title: C1-022-C21_S37

description: Blood cells


title: WT_wo_myelin C_K12_18_4_S61919


title: C1-022-C19_S39

description: Blood cells


title: wt_for_comparison_with_SceI48A_rep3

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

data_processing:
Read quantification was performed from fastq files using Salmon (Patro et al., 2017).
Abundances were summarized from transcript- to gene-level with the Bioconductor package Tximeta (Love et al., 2020).
Differential expression analysis was performed using the DESeq2 package (Love et al., 2014)
PCA analysis was used to select datasets from wild-type and mutant embryos of the same developmental stage.
Assembly: dm6
Supplementary files format and content: Bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).
Supplementary files format and content: Two tables (1 for the comparison between wt and Asx0 mutants and 1 for the comparison between wt and SceI48A mutants) containing differential gene expression information from DESeq2 (Love et al., 2014).

organism: Drosophila melanogaster

source_name: Stage 16 single embryo

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Single Drosophila embryos of the desired genotypes were collected and disrupted in 1 mL of Trizol (ThermoFisher Scientific) complemented bwith 8 µg of UltraPure glycogen (ThermoFisher Scientific). Purification of total RNA was performed according to instructions accompanying the Trizol reagent.
Libraries were prepared according to Illumina's instructions using a polyA enrichment step.

value: Stage 16 single embryo

value: wt


title: C1-022-C18_S31

description: Blood cells


title: C1-022-C17_S32

description: Blood cells


title: wt_for_comparison_with_Asx0_rep3


title: wt_for_comparison_with_SceI48A_rep1


title: wt_for_comparison_with_Asx0_rep2


title: C1-022-C15_S25

description: Blood cells


title: C1-022-C16_S33

description: Blood cells


title: wt_for_comparison_with_SceI48A_rep4


title: C1-022-C20_S38

description: Blood cells


title: wt_for_comparison_with_Asx0_rep1


title: RT4 R1 PD (1)

city: Leeds

first: Margaret

last: Knowles

address: Beckett Street

country: United Kingdom

institute: University of Leeds

description: bladder cancer

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 7G microarray scanner.

data_processing:
Data QC was analysed using Affymetrix Expression Console Software and samples were normalised using RMA.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

source_name: urothelial carcinoma cell line

label_protocol: Total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to manufacturer's instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45 degrees C.

growth_protocol: Standard growth media

extract_protocol: Total RNA was extracted from cultured cells using an RNeasy Mini Kit (Qiagen). The protocol for cultured cells was followed with the inclusion of a DNase digestion step at the end of the protocol. DNase treated RNA was purified with an RNeasy Mini Kit (Qiagen) using the RNA Clean-up protocol according to the manufacturer’s protocol.

treatment_protocol: FGFR inhibitor (PD173074) was added to growth media in some conditions

value: urothelial carcinoma cell line, RT4


title: C1-022-C14_S26

description: Blood cells


title: RT4 R1 PD (3)

description: bladder cancer


title: wt_for_comparison_with_SceI48A_rep2


title: SceI48A_rep4


title: RT4 parental no PD (1)

description: bladder cancer


title: RT4 parental no PD (3)

description: bladder cancer


title: RT4 R1 no PD (2)

description: bladder cancer


title: RT4 parental no PD (2)

description: bladder cancer


title: RT4 R1 no PD (1)

description: bladder cancer


title: SceI48A_rep3


title: C1-022-C13_S27

description: Blood cells


title: C1-022-C12_S19

description: Blood cells


title: RT4 R1 no PD (3)

description: bladder cancer


title: RT112 R3 no PD (2)

description: bladder cancer

value: urothelial carcinoma cell line, RT112


title: RT112 R3 PD (3)

description: bladder cancer


title: RT112 R2 PD (3)

description: bladder cancer


title: RT112 R3 PD (1)

description: bladder cancer


title: RT112 R3 PD (2)

description: bladder cancer


title: C1-022-C11_S20

description: Blood cells


title: RT4 R1 PD (2)

description: bladder cancer


title: RT112 R3 no PD (3)

description: bladder cancer


title: C1-022-C10_S21

description: Blood cells


title: Asx0_rep4


title: Asx0_rep5


title: C1-022-C09_S13

description: Blood cells


title: C1-022-C08_S14

description: Blood cells


title: SceI48A_rep2


title: SceI48A_rep1


title: RT112 R2 PD (2)

description: bladder cancer


title: Asx0_rep3


title: C1-022-C06_S7

description: Blood cells


title: Asx0_rep1


title: Asx0_rep2


title: C1-022-C07_S15

description: Blood cells


title: C1-022-C05_S8

description: Blood cells


title: RT112 R2 no PD (1)

description: bladder cancer


title: RT112 R2 no PD (2)

description: bladder cancer


title: RT112 R3 no PD (1)

description: bladder cancer


title: RT112 R1 PD (3)

description: bladder cancer


title: RT112 R2 PD (1)

description: bladder cancer


title: RT112 R1 PD (2)

description: bladder cancer


title: RT112 R2 no PD (3)

description: bladder cancer


title: RT112 R1 no PD (1)

description: bladder cancer


title: RT112 parental PD (2)

description: bladder cancer


title: RT112 parental no PD (3)

description: bladder cancer


title: RT112 R1 PD (1)

description: bladder cancer


title: RT112 parental PD (1)

description: bladder cancer


title: C1-022-C04_S9

description: Blood cells


title: shSuv4-20h2_#1_3

city: Frankfurt am Main

first: Mohammed

middle: Hossameldin

last: Mosa

state: Hessen

address: Paul-Ehrlich Str. 42-44

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#1_n3

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20. The sequencing quality was asserted using FastQC (Andrews, S. (2014).
FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sequences were aligned to the reference genome Mus musculus (GRCm38, https://www.ensembl.org/Mus_musculus/Info/Index) using the RNA-Seq alignment tool (Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.)(version 2.5) allowing for 2 mismatches within 50 bases.
Read counting was performed using featureCounts (Liao, Yang, Gordon K. Smyth, and Wei Shi. "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features." Bioinformatics 30.7 (2013): 923-930.).
Read counts were analyzed in the R/Bioconductor environment (version 3.6.3, www.bioconductor.org) using the DESeq2 (Love, Michael I., Simon Anders, and Wolfgang Huber. "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome biology 15.12 (2014): 550.) package version 1.29.4 Candidate genes were filtered using an absolute log2 fold-change >1 and FDR-corrected p-value <0.05.
Assembly: GRCm38
Supplementary files format and content: .txt
Supplementary files format and content: processed data files contain raw read counts (clone#1) and normalized read counts (clone#2)

source_name: small intestinal

growth_protocol: Organoids were grown and maintaied as reported before (Mosa et.al, 2020)

extract_protocol:
organoids were  harvested directly in lysis buffer form RNeasy Mini Kit; QIAGEN for RNA isolation according to manufacturer's instruction.
mRNA-focused RNA libraries were prepared using Illumina’s TruSeq stranded RNA library prep kit. Poly(A)-positive mRNA transcripts were isolated from total RNA by binding to magnetic oligo(d)T beads and subsequently fragmented and reverse transcribed during first and second strand synthesis to yield double-stranded cDNA. The fragmented cDNA was then end-repaired and adenylated followed by ligation of the appropriate six-nucleotide TruSeq RNA Single Index (Illumina) or eight-nucleotide NEXTFLEX DNA barcode adapter (PerkinElmer). The final ligation product was amplified via PCR. Intermediate and final library purification steps were done using AMPure XP beads (Beckman Coulter). Final library quantity and quality was assessed using the Qubit dsDNA HS AssayKit (Invitrogen) and the Agilent High Sensitivity DNA kit.

treatment_protocol: To induce the expression of the doxycycline-inducible hairpins, organoids were maintained for 4 days in the presence of 0.5 µg/ml doxycycline in the culture medium.

value: small intestinal

value: APT organoids

value: tumor organoids

value: Suv4-20h2 knockdown1

value: chromatin compaction


title: shSuv4-20h2_#1_2

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#1_n2


title: shCtrl_#1_3

description: Control APT organoids with short hairpin control_n3 for clone#1


title: shSuv4-20h2_#1_1

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#1_n1


title: RT112 parental PD (3)

description: bladder cancer


title: Scm_calyC131S_13-17hr_rep1_#7

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched-regions and H3K27me3 enriched-regions.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

source_name: 13-17hr old embryos

growth_protocol: Drosophila embryos and larvae were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected imaginal disc tissues (for 3rd instar larvae). Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

value: 13-17hr old embryos

tag: antibodies

value: Scm (Gambetta et al., 2009)

tag: normalization factor


title: C1-022-C02_S2

description: Blood cells

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie2
Genomic mappings(GM) performed with RSEM/bowtie2
Quantified gene expression levels in counts and TPM using RSEM-1.3.1
Assembly: hg19
Supplementary files format and content: Count and TPM values for each sample

source_name: Peripheral Blood of Healthy Person

extract_protocol:
CD45 live cells were captured using C1 single cell system (Fluidigm) and processed for whole transcriptome library preparation.  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
Amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina)
RNA-Seq, paired-end NextSeq 74bp sequencing


title: RT112 parental no PD (2)

description: bladder cancer


title: shCtrl_#1_1

description: Control APT organoids with short hairpin control_n1 for clone#1


title: RT112 parental no PD (1)

description: bladder cancer


title: shSuv4-20h2_#2_4

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#2_n4

value: Suv4-20h2 knockdown2


title: C1-022-C01_S3

description: Blood cells


title: Scm_wt_13-17hr_rep1_#7


title: shSuv4-20h2_#2_1

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#2_n1


title: RT112 R1 no PD (3)

description: bladder cancer


title: shSuv4-20h2_#2_2

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#2_n2


title: shSuv4-20h2_#2_3

description: Suv4-20h2-depleted APT organoids with short hairpin targeting Suv4-20h2 clone#2_n3


title: Pho_wt_13-17hr_rep1_#6

value: Pho (Papp and Mueller, 2006)


title: shCtrl_#2_4

description: Control APT organoids with short hairpin control_clone#2_n4


title: shCtrl_#1_2

description: Control APT organoids with short hairpin control_n2 for clone#1


title: shCtrl_#2_2

description: Control APT organoids with short hairpin control_clone#2_n2


title: Pho_wt_0-6hr_rep1_#6

source_name: 0-6hr old embryos

value: 0-6hr old embryos


title: shCtrl_#2_3

description: Control APT organoids with short hairpin control_clone#2_n3


title: PolIIS5P_Asx0_21-24hr_rep1_#11

source_name: 21-24hr old embryos

value: 21-24hr old embryos

value: RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (Abcam (ab5131))


title: Pho_wt_21-24hr_rep1_#8


title: shCtrl_#2_1

description: Control APT organoids with short hairpin control_clone#2_n1


title: Pho_calyC131S_13-17hr_rep1_#7


title: SVF, Bmal1 KO2

city: Stockholm

first: Jieyu

last: Wu

address: Solnavagen 9

country: Sweden

institute: Karolinska institutet

description: KO, replicate 2

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: GRCm38.102
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Tumor

growth_protocol: MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tumor

value: Stromal vascular fractions (SVF)


title: SVF, Bmal1 KO3

description: KO, replicate 3


title: SVF, Bmal1 KO6

description: KO, replicate 4


title: SVF, Bmal1 KO1

description: KO, replicate 1


title: Pc_wt_21-24hr_rep1_#5

value: wt

value: Pc (Papp and Mueller, 2006)


title: SVF, Bmal1 WT4

description: WT, replicate 4


title: SVF, Bmal1 WT2

description: WT, replicate 2


title: Pc_Asx0_21-24hr_rep1_#5


title: SVF, Bmal1 WT3

description: WT, replicate 3


title: PolIIS5P_wt_21-24hr_rep1_#11


title: RT112 R1 no PD (2)

description: bladder cancer

value: urothelial carcinoma cell line, RT112


title: SVF, Bmal1 WT1

description: WT, replicate 1


title: H3K36me2_wt_21-24hr_rep1_#2

value: H3K36me2 (Abcam ab9049)


title: C1-022-C03_S1

description: Blood cells

value: Healthy Blood


title: H3K27me3_wt_13-17hr_rep1_#6

value: H3K27me3 (Cell Signaling (#9733))


title: H3K27me3_wt_0-6hr_rep2_#7


title: KHRNABCSK_0202 [25010570]

city: New York

first: Melissa

middle: Boneta

last: Davis

state: New York

institute: Weill Cornell Medicine

data_processing:
All sequencing reads were converted to industry standard FASTQ files using BCL2FASTQ (version 1.8.4).
Raw RNAseq reads were assessed with Fast QC (version 0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were aligned using HISAT2 (version 2.0.4) with the GrCh37 reference genome
Picard tools (version 2.18.3, https://broadinstitute.github.io/picard/) was used to pull alignment metrics for the samples, where a number of sequenced reads were found to have high levels of read duplication. Duplicate reads were removed using Picard, and only samples that had 10M reads post de-duplication were utilized in subsequent gene expression analyses.
Stringtie (version 1.3.3) was used to quantify gene expression from our de-duplicated aligned reads
Assembly: GrCh37
Supplementary files format and content: tab-delimited text matrix include TPM values for each Sample

source_name: breast tumor

extract_protocol:
RNA was extracted from archival FFPE tissue using a modified QIAGEN Rneasy® FFPE kit protocol. Briefly, prior to deparaffinization of the FFPE tissue, the samples are incubated with 1X acidic antigen retrieval solution at 90C for 5 minutes. Following incubation, samples are cooled to room temperature, and any excess paraffin is removed from the tube. We then proceeded through the standard kit protocol. RNA yield was quantified using the Qubit® RNA Broad Range kit and Qubit® 4.0 fluorometer.
For RNA sequencing, 100 ng of total RNA molecules were used to construct libraries using Illumina TruSeq RNA Exome Library Prep Kit, following manufacturer’s protocols. The final libraries were then quantified using Agilent D1000 Screen Tape as well as sequenced on Illumina MiSeq V2 Micro Kit to assess insert sizes and integrity before sequencing on a high-throughput sequencer. Each library was normalized to 4 nM and pooled and sequenced on Illumina NextSeq500 High Output Kit (Illumina, San Diego, CA).

value: breast tumor

value: female

tag: breast cancer_subtype

value: tnbc

tag: self-reported race

value: African/Ethiopian


title: KHRNABCSK_0010 [24013910]

tag: tissue

value: African American


title: KHRNABCSK_0204 [25067030]


title: KHRNABCSK_0207 [25067040]


title: KHRNABCSK_0018 [24015350]


title: H3K27me3_wt_13-17hr_rep2_#7

value: 13-17hr old embryos


title: H3K27me3_SceI48A_13-17hr_rep2_#7


title: Pho_wt_21-24hr_rep2_#6

value: Pho (Papp and Mueller, 2006)


title: H3K27me3_SceI48A_13-17hr_rep1_#6


title: KHRNABCSK_0101 [24013650]


title: H3K27me3_wt_0-6hr_rep1_#6

value: 0-6hr old embryos


title: KHRNABCSK_0203 [25010790]


title: KHRNABCSK_0009 [24013490]


title: KHRNABCSK_0013 [24012330]


title: KHRNABCSK_0033 [24012480]


title: H3K27me3_SceI48A_0-6hr_rep1_#6


title: H3K27me3_SceI48A_0-6hr_rep2_#7


title: KHRNABCSK_0015 [24012110]


title: KHRNABCSK_0111 [24011990]


title: KHRNABCSK_0007 [24013470]


title: H3K27me3_calyC131S_21-24hr_rep2_#7

value: 21-24hr old embryos


title: H3K27me3_calyC131S_21-24hr_rep1_#6


title: H3K27me3_calyC131S_13-17hr_rep2_#7


title: KHRNABCSK_0003 [24011560]


title: KHRNABCSK_0108 [24011700]


title: KHRNABCSK_0002 [24011210]


title: KHRNABCSK_0006 [24011830]


title: H3K27me3_calyC131S_13-17hr_rep1_#6


title: 3_SU-MB002-72H-DMSO

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

hyb_protocol: Illumina Human Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) array was performed at The Centre for Applied Genomics, The Hospital for Sick Children (Toronto) using the manufacturer’s standard protocol.

data_processing:
Raw IDAT files (annotation: ilm10b4.hg19) were processed using R (Version 4.1.2) and quality control and normalization was performed using minfi. (Ref: Aryee, M. J. et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30, 1363–1369 (2014))
Intensity and density plots were generated, and no samples were removed from the analysis as the mean detection p-values for all probed genomic positions were < 0.01 for each sample. Probes with mean detection p-values > 0.01 across all samples were excluded. Probes mapping sex chromosomes, single nucleotide polymorphisms (SNPs), and cross-hybridization probes were removed. Quantile normalization was performed, and density plots were generated before and after normalization.
Differential analysis was completed with beta values of 768467 CpGs for 8 samples comparing BAY to DMSO at 48h and 72h using limma. P-values were adjusted for False Discovery Rate (FDR) using Benjamini and Hochberg method, and a 10% FDR and logFC of >|0.1| cut-off was used. (REF: Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015))
Differentially methylated positions (DMPs) were annotated using the USCS (UCSC_RefGene_Name, UCSC_RefGene_Group and Relation_to_Island) from the Infinium MethylationEPIC Manifest. The analysis was performed focussing on DMPs within promotor islands (considering TSS1500, TSS200, 5'UTR and 1st exon as promotor regions). Enrichment analysis of unique genes (using UCSC RefGene Name) identified within DMPs at promotor islands was performed using Enrichr (ENCODE TF ChIP-seq 2015). (REF: Kuleshov, M. V et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90-7 (2016))
Table S4. Methylation analysis.xlsx (The file contains 5 different sheets with (a) Normalized beta values for all samples, (b) DMPs for BAY vs DMSO at 48h using 10% FDR and FC >|0.1|, (c) DMPs for BAY vs DMSO at 72h using 10% FDR and FC >|0.1|, (d) Unique genes identified within promotor islands (DMPs at 72h), (e) Normalized beta values across all samples for the 123 DMPs identified at 72h.

label: Cy3, Cy5

extract_protocol: gDNA was extracted using Puregene Cell and Tissue kit (Qiagen) as per manufacturer’s instructions and quantified using spectrophotometry

treatment_protocol: SU_MB002 cells were treated with DMSO or BAY (IC50) and collected at 48h and 72h (2 technical replicates per condition)

value: brain cancer

tag: cell line

value: medulloblastoma

tag: karyotype

value: XX


title: KHRNABCSK_0110 [24011040]

tag: Sex


title: 6_SU-MB002-48H-12nM-BAY

scan_protocol: Illumina Human Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) array was performed at The Centre for Applied Genomics, The Hospital for Sick Children (Toronto) using the manufacturer’s standard protocol.

tag: cell type

tag: treatment


title: KHRNABCSK_0114 [24011030]


title: 5_SU-MB002-48H-DMSO

label_protocol: Illumina Human Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) array was performed at The Centre for Applied Genomics, The Hospital for Sick Children (Toronto) using the manufacturer’s standard protocol.


title: KHRNABCSK_0019 [24010290]


title: 8_SU-MB002-72H-BAY


title: 4_SU-MB002-72H-BAY


title: 7_SU-MB002-72H-DMSO


title: H3K27me3_calyC131S_0-6hr_rep2_#7


title: H3K27me3_calyC131S_0-6hr_rep1_#6


title: KHRNABCSK_0504 [23104770]

value: African/Ghanaian


title: KHRNABCSK_0040 [23104140]


title: KHRNABCSK_0103 [23101520]


title: H3K27me2_wt_21-24hr_rep1_#12

value: wt

value: H3K27me2 (Cell Signaling (#9728))


title: 2_SU-MB002-48H-12nM-BAY


title: KHRNABCSK_0036 [23101460]


title: KHRNABCSK_0035 [23101420]


title: H3K27me3_wt_Wing_Larva_rep2_#14

source_name: wing imaginal discs form 3rd instar larvae


title: KHRNABCSK_0039 [23104110]


title: THP1 cells, GSK-LSD1, 24h

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
Seq2science RNA-seq analysis.
Sequence reads were trimmed using default fastp.
Trimmed sequence reads were mapped to hg38 using STAR.
Assembly: hg38
Supplementary files format and content: tab-delimited value file includes raw counts for each Sample

growth_protocol: THP1 cells were maintained in RPMI 1640 (Gibco) supplemented with 10% fetal calf serum (FCS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Mini RNA Isolation II Kit (Zymo Research). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) with RNA fragmentation of approximately 300 bp fragments.

treatment_protocol: Monocytic differentiation was induced by treatment with 0.2 µM GSK-LSD1 (Signa-Aldrich) for 8 or 24 hours.

value: Acute monocytic leukemia

value: LSD1 inhibition


title: THP1 cells, GSK-LSD1, 8h


title: THP1 cells, Control, 0h

value: WT


title: H3K27me3_wt_Wing_Larva_rep1_#13

value: wing imaginal discs form 3rd instar larvae

value: H3K27me3 (Cell Signaling (#9733))


title: THP1 cells, GSK-LSD1, 8h, rep3

data_processing:
rRNA reads were filtered. Reads were mapped using BWA (MAPQ >= 20). Reads with MAPQ < 20 were mapped again using HISAT2.
Read bam files were processed to CTSS by HeliScopeCAGE read alignment.
Bigwig files were generated using convertBED2BigWig from CAGEfightR R package.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
RNA was isolated using Mini RNA Isolation II Kit (Zymo Research). 2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for CAGE-seq were prepared by DNAFOM CAGE library preparation.


title: H3K27me3_wt_HaltereLeg_Larva_rep2_#14

source_name: haltere and 3rd leg imaginal discs from 3rd instar larvae


title: 1_SU-MB002-48H-DMSO


title: H3K27me3_wt_HaltereLeg_Larva_rep1_#13

value: haltere and 3rd leg imaginal discs from 3rd instar larvae


title: THP1 cells, GSK-LSD1, 8h, rep2


title: THP1 cells, GSK-LSD1, 8h, rep1


title: THP1 cells, Control, 0h, rep3

value: control


title: H3K27me3_Asx0_21-24hr_rep2_#9


title: THP1 cells, Control, 0h, rep2


title: THP1 cells, Control, 0h, rep1


title: input_wt_Wing_Larva__#14


title: HepG2 cells, f-RCP+660 nm [B 3]

city: Suzhou

first: fang

last: jing

state: Jiangsu province

address: Renai street

institute: Suzhou university

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads the human genome (GRCh38/hg38) using HISAT2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Differential expression analysis was performed using the DESeq (2012) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: HepG2 cells were cultured in high-glucose DMEM (Hyclone Inc.) supplemented with 10% fetal bovine serum (Hyclone Inc.) and 1% penicillin streptomycin (Beyotime Inc.)

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: liver

value: liver cancer cells

value: cell apoptosis; f-RCP+660 nm


title: Genomic DNA from endometrioid endometrial cancer_F17373

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

country: Japan

institute: Keio University School of Medicine

description: Endometrioid endometrial cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Hybridization fluorescence signals were read by the iScan reader using standard recommended Illumina scanner setting.

data_processing: Genome Studio methylation software

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis. Areas showing a tumor cell content of more than 80% were dissected from FFPE tissue samples using a toothpick under a microscope, avoiding contamination with non-cancerous epithelial cells, myometrial cells and infiltrating inflammatory cells. Subsequently, the genomic DNA was extracted from the microdissected specimens using a GeneRead FFPE Kit (QIAGEN GmbH, Hilden, Germany).

tag: sample type

value: FFPE


title: input_wt_Wing_Larva__#13


title: AML, MLL-AF9, 3

data_processing:
rRNA reads were filtered. Reads were mapped using BWA (MAPQ >= 20). Reads with MAPQ < 20 were mapped again using HISAT2.
Read bam files were processed to CTSS by HeliScopeCAGE read alignment.
Bigwig files were generated using convertBED2BigWig from CAGEfightR R package.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: AML

value: AML

tag: type

value: High MECOM MLL-AF9


title: Genomic DNA from endometrioid endometrial cancer_F13384

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_F07222

description: Endometrioid endometrial cancer


title: AML, MLL-AF9, 2


title: HepG2 cells, f-RCP+660 nm [B 1]


title: input_wt_21-24hr__#7

value: 21-24hr old embryos


title: AML, MLL-AF9, 1


title: Genomic DNA from endometrioid endometrial cancer_F10683

description: Endometrioid endometrial cancer


title: HepG2 cells, f-RCP+660 nm [B 2]


title: Genomic DNA from endometrioid endometrial cancer_F05600

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_T2

description: Endometrioid endometrial cancer


title: HepG2 cells, RCP+660 nm [A 3]

value: cell apoptosis; RCP+660 nm


title: input_wt_21-24hr__#6

value: wt


title: Lnc152_Overexpression_38_S14_R1_001.fastq.gz

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: merged

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using TopHat a fast splice junction mapper for RNA-Seq reads using the ultra high-throughput short read aligner Bowtie (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

source_name: MDA-MB-231 cell line

growth_protocol: All animal experiments were performed in compliance with the Institutional Animal Care and Use Committee (IACUC) at the UT Southwestern Medical Center.  Female NOD-scid-gamma (NSG) mice at 6-8 weeks of age were used

extract_protocol:
The frozen xenograft tumor tissues were pulverized using a tissue mill and lysed in Whole Cell Lysis Buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS, 1 mM DTT, supplemented with protease and phosphatase inhibitors) for extraction of protein
Total RNA from seven xenograft tumor tissue of each group using the RNeasy Plus Kit (Qiagen, 74134) according to the manufacturer’s instructions were used to generate strand-specific RNA-seq libraries.  The RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2500 and NextSeq 500

treatment_protocol: To establish breast cancer xenografts, MDA-MB-231 cells engineered for Dox-inducible expression of GFP mRNA or lnc152 (5 x 106 in 100 uL) were injected subcutaneously into the flank of the mice in a 1:1 ratio PBS and Matrigel.  Ten days post-tumor cell injection, the mice were placed on a Dox-containing diet (625 mg/kg; Envigo)

value: xenograft tumor

tag: genotype/variation

value: Lnc152 overexpression

tag: rna-seq

value: polyA-RNA


title: Genomic DNA from endometrioid endometrial cancer_T3

description: Endometrioid endometrial cancer


title: HepG2 cells, RCP+660 nm [A 2]

value: WT


title: input_wt_13-17hr__#7

value: 13-17hr old embryos


title: Genomic DNA from endometrioid endometrial cancer_T4

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_F07936

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_F08461

description: Endometrioid endometrial cancer


title: HepG2 cells, RCP+660 nm [A 1]


title: Genomic DNA from endometrioid endometrial cancer_TY51

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_TY49

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_T1

description: Endometrioid endometrial cancer


title: MB002_T30C

description:
PACE_118
gRNA amplicon

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequences using a bespoke Perl script
Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:  -p 16 -v 3 -l 18 --chunkmbs 256 -t TKOv3 --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was then enumerated for each .sam file, and alignment statistics were recorded.  Guide IDs and counts were then written to individual count files, and subsequently merged into a full read count matrix with library annotations using R.
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPRseq

source_name: brain cancer

extract_protocol:
Genomic DNA was extracted using Puregene Cell and Tissue kit (Qiagen) as per manufacturer’s instructions and quantified using spectrophotometry
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harbouring Illumina TruSeq adaptors with i5 and i7 barcodes.  The resulting sequencign libraries were pooled and gel purified.

tag: time point

value: brain cancer

value: medulloblastoma


title: input_wt_13-17hr__#6


title: input_wt_0-6hr__#7

value: 0-6hr old embryos


title: Lnc152_Overexpression_18_S11_R1_001.fastq.gz

description: merged


title: Genomic DNA from endometrioid endometrial cancer_TY46

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_TY43

description: Endometrioid endometrial cancer


title: Lnc152_Overexpression_27_S10_R1_001.fastq.gz

description: merged


title: input_wt_21-24hr__#12


title: Lnc152_Overexpression_21_S9_R1_001.fastq.gz

description: merged


title: Genomic DNA from endometrioid endometrial cancer_F18203

description: Endometrioid endometrial cancer


title: input_wt_0-6hr__#6


title: MB002_T30A

description:
PACE_116
gRNA amplicon


title: Genomic DNA from endometrioid endometrial cancer_TY24

description: Endometrioid endometrial cancer


title: input_wt_21-24hr__#11


title: Lnc152_Overexpression_17_S8_R1_001.fastq.gz

description: merged


title: input_wt_21-24hr__#10


title: Genomic DNA from endometrioid endometrial cancer_TY33

description: Endometrioid endometrial cancer


title: GFP_Overexpression_40_S7_R1_001.fastq.gz

description: merged

value: GFP overexpression


title: MB002_T30B

description:
PACE_117
gRNA amplicon


title: CAF3-exo

city: Nanjing

first: Hongqian

last: Guo

state: Jiangsu

address: 321 Zhongshan Road

department: Department of Urology

institute: Drum Tower Hospital, Medical School of Nanjing University

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) , repeats, and sequences <18 nt or >26 nt in length. Subsequently, the unique sequences with a length of 18~26nt were mapped to miRNA sequences in miRBase 22.0 (http://www.mirbase.org/).
Assembly: hg38
Supplementary files format and content: excel including the raw counts of all expressed miRNAs for each sample

source_name: kidney

growth_protocol: CAFs and NFs were isolated from fresh RCC tissues and their paired normal kidney tissues respectively, and cultured with 10% FBS DMEM culture medium at 37℃ in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted from exosomes using TRIzol reagent (Invitrogen).
Approximately 1 µg of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (1x50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

treatment_protocol: Exosomes were isolated from the cell culture medium  using Total Exosome Isolation Kit (Invitrogen, California, United States) following the manufacturer’s instructions

value: kidney

value: primary cancer-associated fibroblasts derived from fresh RCC tissue of patient 3

value: primary cancer-associated fibroblasts

value: cancer-associated fibroblasts

value: collecting exosomes from the cell culture medium


title: CAF2-exo

value: primary cancer-associated fibroblasts derived from fresh RCC tissue of patient 2


title: Lnc152_Overexpression_22_S13_R1_001.fastq.gz

description: merged


title: Genomic DNA from endometrioid endometrial cancer_TY30

description: Endometrioid endometrial cancer

value: FFPE


title: Genomic DNA from endometrioid endometrial cancer_F20387

description: Endometrioid endometrial cancer


title: input_wt_21-24hr__#8

value: 21-24hr old embryos

value: wt


title: Genomic DNA from endometrioid endometrial cancer_TY45

description: Endometrioid endometrial cancer