title: SC041_T4_BB_AMDH_R3

description: mRNA-seq


title: SC040_T4_BB_AMDH_R2

status: Public on Dec 31 2020

type: SRA

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

country: USA

institute: Northwestern University

description: mRNA-seq

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.33) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (with mm10 assembly) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw htseq count

molecule: total RNA

organism: Mus musculus

source_name: Lung CD45.1+SiglecFhigh persisting MoAM at day 81 after second bleomycin injury

growth_protocol: Male and female C57BL/6NJ mice received bone marrow chimeras and myeloablative agent busulfan. Bone marrow chimeras with thoracic shielding were used to assess the origin of pulmonary macrophages (TRAMs vs. Mo-AMs)

extract_protocol:
All groups were euthanized for isolation of AM cells by magnetic bead pre-enrichment and fluorescence-activated cell sorting. The RNeasy Plus Mini Kit (Qiagen) was used to isolate RNA and remove genomic DNA.
RNA-seq libraries were prepared from 100ng of total RNA using the NEB Next RNA Ultra Kit (Qiagen) with poly(A) enrichment. Libraries were quantified and assessed using the Qubit Fluorimeter (Invitrogen) and 4200 TapeStation.

treatment_protocol: 0.025IU bleo + 0.025IU bleo

tag: strain

tag: age

tag: exposure

value: bleomycin and bleomycin


title: SC044_T4_BB_AMDL_R6

description: mRNA-seq

source_name: Lung CD45.1+SiglecFlow MoAM at day 81 after second bleomycin injury


title: SC043_T4_BB_AMDL_R5

description: mRNA-seq


title: SC039_T4_BB_AMDH_R1

description: mRNA-seq


title: SC041_T4_BB_AMDL_R3

description: mRNA-seq


title: SC039_T4_BB_AMDL_R1

description: mRNA-seq


title: SC041_T4_BB_AMR_R3

description: mRNA-seq

source_name: Lung CD45.2+SiglecFhigh TRAM at day 81 after second bleomycin injury


title: SC044_T4_BB_AMR_R6

description: mRNA-seq


title: SC037_T3_B_AMD_R4

description: mRNA-seq

source_name: Lung CD45.1+SiglecFhigh persisting MoAM at day 60 after first bleomycin injury

treatment_protocol: 0.025IU bleo

value: bleomycin


title: SC040_T4_BB_AMR_R2

description: mRNA-seq


title: SC042_T4_BB_AMDL_R4

description: mRNA-seq


title: SC042_T4_BB_AMR_R4

description: mRNA-seq


title: SC040_T4_BB_AMDL_R2

description: mRNA-seq


title: SC038_T3_B_AMD_R5

description: mRNA-seq


title: SC036_T3_B_AMD_R3

description: mRNA-seq


title: SC043_T4_BB_AMR_R5

description: mRNA-seq


title: SC039_T4_BB_AMR_R1

description: mRNA-seq


title: SC035_T3_B_AMD_R2

description: mRNA-seq


title: SC034_T3_B_AMD_R1

description: mRNA-seq


title: SC037_T3_B_AMR_R4

description: mRNA-seq

source_name: Lung CD45.2+SiglecFhigh TRAM at day 60 after first bleomycin injury


title: SC035_T3_B_AMR_R2

description: mRNA-seq


title: SC038_T3_B_AMR_R5

description: mRNA-seq


title: SC036_T3_B_AMR_R3

description: mRNA-seq


title: SC034_T3_B_AMR_R1

description: mRNA-seq


title: SC033_T2_B_AMD_R5

description: mRNA-seq

source_name: Lung CD45.1+SiglecFlow MoAM at day 21 after first bleomycin injury


title: SC032_T2_B_AMD_R4

description: mRNA-seq


title: SC030_T2_B_AMD_R2

description: mRNA-seq


title: SC031_T2_B_AMD_R3

description: mRNA-seq


title: SC033_T2_B_AMR_R5

description: mRNA-seq

source_name: Lung CD45.2+SiglecFhigh TRAM at day 21 after first bleomycin injury


title: SC032_T2_B_AMR_R4

description: mRNA-seq


title: SC029_T2_B_AMD_R1

description: mRNA-seq


title: SC031_T2_B_AMR_R3

description: mRNA-seq


title: SC030_T2_B_AMR_R2

description: mRNA-seq


title: SC028_T1_N_AMR_R5

description: mRNA-seq

source_name: Lung CD45.2+SiglecFhigh TRAM at day0

treatment_protocol: untreated at day0

value: untreated at day0


title: SC025_T1_N_AMR_R2

description: mRNA-seq


title: SC024_T1_N_AMR_R1

description: mRNA-seq


title: CD45_1_R4

description: mRNA-seq

source_name: Lung AM cells from CD45.1 background strain

growth_protocol: Male and female C57BL/6NJ with CD45.1+ and CD45.2+ strains

treatment_protocol: untreated

value: naïve


title: CD45_1_R1

description: mRNA-seq


title: CD45_1_R3

description: mRNA-seq


title: CD45_1_R2

description: mRNA-seq


title: SC027_T1_N_AMR_R4

description: mRNA-seq


title: CD45_2_R4

description: mRNA-seq

source_name: Lung AM cells from CD45.2 background strain


title: CD45_2_R3

description: mRNA-seq


title: SC026_T1_N_AMR_R3

description: mRNA-seq


title: CD45_2_R1

description: mRNA-seq


title: SC029_T2_B_AMR_R1

description: mRNA-seq


title: AT2_O_M_R3

description: mRNA-seq

growth_protocol: Male and female C57BL/6NJ at 4 month and 18 month were treated with metformin in drinking water for 60 days

treatment_protocol: metformin for 60 days

value: 18 month

value: metformin for 60 days


title: AT2_O_M_R5

description: mRNA-seq


title: AM_O_M_R5

description: mRNA-seq


title: AT2_O_M_R1

description: mRNA-seq


title: AM_O_M_R3

description: mRNA-seq


title: CD45_2_R5

description: mRNA-seq


title: CD45_2_R2

description: mRNA-seq


title: AM_O_M_R1

description: mRNA-seq


title: AT2_O_N_R4

description: mRNA-seq

treatment_protocol: untreated with metformin

value: untreated with metformin


title: AM_O_N_R4

description: mRNA-seq


title: AT2_O_N_R3

description: mRNA-seq


title: AM_O_N_R2

description: mRNA-seq


title: AM_O_N_R3

description: mRNA-seq


title: AT2_O_N_R2

description: mRNA-seq


title: AM_O_N_R1

description: mRNA-seq


title: AT2_O_N_R1

description: mRNA-seq


title: AM_Y_M_R5

description: mRNA-seq

value: 4 month


title: AT2_Y_M_R4

description: mRNA-seq


title: AM_Y_M_R3

description: mRNA-seq


title: AT2_Y_M_R2

description: mRNA-seq


title: AM_Y_M_R4

description: mRNA-seq


title: AT2_Y_M_R5

description: mRNA-seq


title: AT2_Y_M_R1

description: mRNA-seq


title: AM_Y_M_R1

description: mRNA-seq


title: AT2_Y_M_R3

description: mRNA-seq


title: AM_Y_M_R2

description: mRNA-seq


title: AM_Y_N_R3

description: mRNA-seq

treatment_protocol: untreated with metformin (control)


title: AT2_Y_N_R4

description: mRNA-seq


title: AT2_Y_N_R2

description: mRNA-seq


title: AT2_Y_N_R3

description: mRNA-seq


title: AT2_3_8

description: mRNA-seq

growth_protocol: Parabionts were generated among young male and female C57BL/6NJ as young-young pair (6 month), young-old pair (6month and 18 month), old-old pair (18 month)

value: parabiosis


title: AT2_Y_N_R1

description: mRNA-seq


title: AT2_3_7

description: mRNA-seq


title: AM_Y_N_R2

description: mRNA-seq


title: AM_Y_N_R4

description: mRNA-seq


title: AT2_3_6

description: mRNA-seq

value: 6 month


title: AT2_3_5

description: mRNA-seq


title: AT2_3_2

description: mRNA-seq


title: AT2_3_4

description: mRNA-seq


title: AT2_2_8

description: mRNA-seq


title: AT2_2_9

description: mRNA-seq


title: AT2_3_1

description: mRNA-seq


title: AT2_2_5

description: mRNA-seq


title: AT2_2_7

description: mRNA-seq


title: AT2_2_6

description: mRNA-seq


title: AT2_2_4

description: mRNA-seq


title: AT2_2_10

description: mRNA-seq


title: AM_Y_N_R1

description: mRNA-seq


title: AT2_2_3

description: mRNA-seq


title: AT2_1_7

description: mRNA-seq


title: AT2_1_6

description: mRNA-seq


title: AT2_1_4

description: mRNA-seq


title: AT2_1_1

description: mRNA-seq


title: AM_3_8

description: mRNA-seq


title: AM_3_6

description: mRNA-seq


title: AM_3_7

description: mRNA-seq


title: AT2_3_10

description: mRNA-seq


title: AM_3_5

description: mRNA-seq


title: AM_3_4

description: mRNA-seq


title: AM_3_2

description: mRNA-seq


title: AM_3_1

description: mRNA-seq


title: AT2_1_8

description: mRNA-seq


title: AM_2_8

description: mRNA-seq


title: AM_2_7

description: mRNA-seq


title: AM_3_10

description: mRNA-seq


title: AT2_1_2

description: mRNA-seq


title: AT2_1_3

description: mRNA-seq


title: AM_2_3

description: mRNA-seq


title: AT2_1_5

description: mRNA-seq


title: AM_2_4

description: mRNA-seq


title: AM_3_9

description: mRNA-seq


title: AM_2_10

description: mRNA-seq


title: AM_1_8

description: mRNA-seq


title: AM_1_6

description: mRNA-seq


title: AM_1_7

description: mRNA-seq


title: AM_1_1

description: mRNA-seq


title: AM_3_3

description: mRNA-seq


title: AT16_AT2RO_F0_D0_R4

description: mRNA-seq

source_name: AT2 cells after adoptive transfer of young macrophages into old mice

growth_protocol: Male and female C57BL/6NJ (4 month) receive lung AM cells from male and female C57BL/6NJ (18 month)

value: adoptively transferred


title: AT14_AT2RO_F0_D0_R2

description: mRNA-seq


title: AM_2_6

description: mRNA-seq


title: AT2_3_3

description: mRNA-seq


title: AM_2_9

description: mRNA-seq


title: AT13_AT2RO_F0_D0_R1

description: mRNA-seq


title: AM_2_5

description: mRNA-seq


title: AT08_AT2RY_F0_D0_R4

description: mRNA-seq

source_name: AT2 cells after adoptive transfer of old macrophages into young mice


title: AT09_AT2O_F0_D0_R1

description: mRNA-seq

source_name: AT2 cells from old naïve mice

value: no adoptively transferred


title: AM_1_5

description: mRNA-seq


title: AT06_AT2RY_F0_D0_R2

description: mRNA-seq


title: AT12_AT2O_F0_D0_R4

description: mRNA-seq


title: AM_1_4

description: mRNA-seq


title: AT07_AT2RY_F0_D0_R3

description: mRNA-seq


title: AT05_AT2RY_F0_D0_R1

description: mRNA-seq


title: AM_1_3

description: mRNA-seq


title: AT01_AT2Y_F0_D0_R1

description: mRNA-seq

source_name: AT2 cells from young naïve mice


title: AT11_AMO_F0_D0_R3

description: mRNA-seq

source_name: TRAM from naïve old mice


title: AT12_AMO_F0_D0_R4

description: mRNA-seq


title: AT03_AT2Y_F0_D0_R3

description: mRNA-seq


title: AT10_AMO_F0_D0_R2

description: mRNA-seq


title: AT15_AT2RO_F0_D0_R3

description: mRNA-seq


title: AT04_AT2Y_F0_D0_R4

description: mRNA-seq


title: AT16_AMRO_F0_D0_R4

description: mRNA-seq

source_name: TRAM from old recipient mice


title: AT10_AT2O_F0_D0_R2

description: mRNA-seq


title: AT16_AMDY_F0_D0_R4

description: mRNA-seq

source_name: young (4 month) alveolar macrophages adoptively transferred into old mice (18 month)


title: AT11_AT2O_F0_D0_R3

description: mRNA-seq


title: AT14_AMDY_F0_D0_R2

description: mRNA-seq


title: AT07_AMDO_F0_D0_R3

description: mRNA-seq

source_name: old (18 month) alveolar macrophages adoptively transferred into young (4 month) mice


title: AT15_AMDY_F0_D0_R3

description: mRNA-seq


title: AT06_AMDO_F0_D0_R2

description: mRNA-seq


title: AT02_AT2Y_F0_D0_R2

description: mRNA-seq


title: AT05_AMDO_F0_D0_R1

description: mRNA-seq


title: AT04_AMY_F0_D0_R4

description: mRNA-seq

source_name: TRAM from young naïve mice


title: AT07_AMRY_F0_D0_R3

description: mRNA-seq

source_name: TRAM in young recipient mice


title: AT05_AMRY_F0_D0_R1

description: mRNA-seq


title: AT02_AMY_F0_D0_R2

description: mRNA-seq


title: AT14_AMRO_F0_D0_R2

description: mRNA-seq


title: AT08_AMRY_F0_D0_R4

description: mRNA-seq


title: SC19_T24_N_AMD_R4

description: mRNA-seq

source_name: CD45.1+ lung AM cells from 24 month old mouse

value: 24 month

value: shield chimera


title: AT01_AMY_F0_D0_R1

description: mRNA-seq


title: SC18_T24_N_AMD_R3

description: mRNA-seq


title: SC19_T24_N_AMR_R4

description: mRNA-seq

source_name: CD45.2+ lung AM cells from 24 month old mouse


title: AT13_AMRO_F0_D0_R1

description: mRNA-seq


title: SC17_T24_N_AMD_R2

description: mRNA-seq


title: AT03_AMY_F0_D0_R3

description: mRNA-seq


title: SC17_T24_N_AMR_R2

description: mRNA-seq


title: SC16_T24_N_AMR_R1

description: mRNA-seq


title: SC16_T24_N_AMD_R1

description: mRNA-seq


title: SC15_T18_N_AMR_R5

description: mRNA-seq

source_name: CD45.2+ lung AM cells from 18 month old mouse


title: SC15_T18_N_AMD_R5

description: mRNA-seq

source_name: CD45.1+ lung AM cells from 18 month old mouse


title: SC14_T18_N_AMR_R4

description: mRNA-seq


title: SC13_T18_N_AMR_R3

description: mRNA-seq


title: SC14_T18_N_AMD_R4

description: mRNA-seq


title: SC12_T18_N_AMD_R2

description: mRNA-seq


title: SC11_T18_N_AMR_R1

description: mRNA-seq


title: SC11_T18_N_AMD_R1

description: mRNA-seq


title: SC12_T18_N_AMR_R2

description: mRNA-seq


title: SC10_T6_N_AMR_R5

description: mRNA-seq

source_name: CD45.2+ lung AM cells from 6 month old mouse


title: SC10_T6_N_AMD_R5

description: mRNA-seq

source_name: CD45.1+ lung AM cells from 6 month old mouse


title: AM_1_2

description: mRNA-seq


title: SC18_T24_N_AMR_R3

description: mRNA-seq


title: SC08_T6_N_AMR_R3

description: mRNA-seq


title: SC08_T6_N_AMD_R3

description: mRNA-seq


title: SC09_T6_N_AMR_R4

description: mRNA-seq


title: SC07_T6_N_AMR_R2

description: mRNA-seq


title: SC04_T3_N_AMR_R4

description: mRNA-seq

source_name: CD45.2+ lung AM cells from 3 month old mouse

value: 3 month


title: SC03_T3_N_AMR_R3

description: mRNA-seq


title: SC04_T3_N_AMD_R4

description: mRNA-seq

source_name: CD45.1+ lung AM cells from 3 month old mouse


title: SC06_T6_N_AMR_R1

description: mRNA-seq


title: SC07_T6_N_AMD_R2

description: mRNA-seq


title: SC06_T6_N_AMD_R1

description: mRNA-seq


title: SC02_T3_N_AMR_R2

description: mRNA-seq


title: SC02_T3_N_AMD_R2

description: mRNA-seq


title: SC01_T3_N_AMR_R1

description: mRNA-seq


title: SC13_T18_N_AMD_R3

description: mRNA-seq


title: SC09_T6_N_AMD_R4

description: mRNA-seq


title: SC01_T3_N_AMD_R1

description: mRNA-seq


title: AT2_old_naive_4

description: mRNA-seq

source_name: lung AT2 cells from 18 month old mouse

growth_protocol: Male and female C57BL/6NJ mice were treated in naïve environment


title: AT2_old_naive_1

description: mRNA-seq


title: AT08_AMDO_F0_D0_R4

description: mRNA-seq


title: AM_old_naive_4

description: mRNA-seq

source_name: lung AM cells from 18 month old mouse


title: AT2_old_naive_2

description: mRNA-seq


title: AM_old_naive_3

description: mRNA-seq


title: AM_old_naive_2

description: mRNA-seq


title: AM_old_naive_1

description: mRNA-seq


title: SC03_T3_N_AMD_R3

description: mRNA-seq


title: AT2_young_naive_4

description: mRNA-seq

source_name: lung AT2 cells from 4 month old mouse


title: AM_young_naive_4

description: mRNA-seq

source_name: lung AM cells from 4 month old mouse


title: AM_young_naive_1

description: mRNA-seq


title: AM_young_naive_2

description: mRNA-seq


title: AT2_young_naive_3

description: mRNA-seq


title: AM_young_naive_3

description: mRNA-seq


title: ChIPseq-kEpi-Jun_rep1

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description:
ChIPseq-kEpi-Jun-peaks.bed
ChIPseq-kEpi-Jun-merge.bw

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ChIIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using MACS14, using input as control
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

molecule: genomic DNA

source_name: Epiblast stem cells

growth_protocol: EpiSCs were maintained in serum coated well. FN medium which comprised F12 (Ham’s F12, Gibco )/ Neurobasal ( Gibco ) (1:1) with N2 (200×, Gibco), B27 (100×, Gibco), NEAA (100×,Gibco), GlutaMAX(100×, Gibco), BSA (1mg/ml, Gibco), 100 mM 2-mercaptoethanol, 20 ng/ml ActivinA and 20 ng/ml bFGF was used for feeder-free EpiSC culture.

extract_protocol:
ChIP was performed as described previously(Liu et al., 2015), Briefly, cells were fixed in 18 ml DMEM (Hyclone) containing 1% formaldehyde for 15 min at room temperature with rotation, the reaction was quenched by the addition of 2 ml of 0.125 M glycine. And then the cells were washed with PBS 3 times. Cells were lysed in ChIP buffer A (50mM HEPES-KOH, 140 mM NaCl, 1mM EDTA (pH 8.0), 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 50 mM Tris-HCl (pH 8.0), and protease inhibitor cocktail) for 10 min at 4°C. Pellets were lysed in ChIP buffer B (1% SDS, 50 nM Tris-HCl (pH 8.0), 10mM EDTA and protease inhibitor cocktail) for 5 min at 4°C. The DNA was fragmented to 100-500 bp by sonication, and then centrifuged at 12,000g for 2 min. The supernatant was diluted with ChIP IP buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 50mM Tris-HCl (pH 8.0), 150 mM NaCl and protease inhibitor cocktail). Immunoprecipitation was performed using 2μg of H3K27ac antibody added to protein A/G Dynabeads, and incubated overnight at 4°C. Beads were washed, eluted and reverse crosslinked. DNA was purified by using the MinElute Reaction Clean up Kit (QIAGEN).
The ChIP DNA library for NextSeq 500 sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to manufacturer’s instructions. AMPure XP beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech). Libraries were sequenced on an Illumina NextSeq 500 v2 using 50bp paired-end reads.

tag: cell type

value: Epiblast stem cells

tag: chip antibody

value: c-Jun


title: ChIPseq-WT-Epi-input_rep2

value: input


title: ChIPseq-WT-Epi-input_rep1

description: ChIPseq-WT-Epi-input-merge.bw


title: ChIPseq-kEpi-Jun_rep2


title: ChIPseq-WT-Epi-Jun_rep2

value: CBA/CaJ X C57BL/6J


title: ChIPseq-kEpi-input_rep2


title: wtkiEpiSC-iCD1-D3-rp2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: bed file were generated with genomeCoverageBed and bedGraphToBigbed. Scores represent the number of fragments overlapping each genomic position.

source_name: reprogramming cells

extract_protocol:
A total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

value: reprogramming cells

tag: day of reprogramming


title: wtkiEpiSC-iCD1-D3-rp1


title: ChIPseq-WT-Epi-Jun_rep1

description:
ChIPseq-WT-Epi-Jun-peaks.bed
ChIPseq-WT-Epi-Jun-merge.bw


title: wtkiEpiSC-JNKi-D3-rp2


title: kiPSC-rp2

source_name: iPSCs

value: iPSCs


title: wtkiEpiSC-JNKi-D3-rp1


title: kiPSC-rp1


title: kiPSC-iCD1-JNKi-D2-rp2


title: kiPSC-iCD1-JNKi-D3-rp1


title: ChIPseq-kEpi-input_rep1

description: ChIPseq-kEpi-input-merge.bw


title: kiPSC-iCD1-JNKi-D2-rp1


title: kiPSC-iCD1-JNKi-D3-rp2


title: kiPSC-iCD1-JNKi-D1-rp2


title: kiPSC-iCD1-JNKi-D1-rp1


title: kiPSC-iCD1-D2-rp1


title: kiPSC-iCD1-D3-rp1


title: kiPSC-iCD1-D1-rp2


title: kiPSC-iCD1-D3-rp20


title: kiPSC-iCD1-D1-rp1


title: kEpiSC-rp2


title: kiPSC-iCD1-D2-rp2


title: JunKO-kiEpiSC-JNKi-D3-rp1


title: Episc-rp1


title: JunKO-kiEpiSC-iCD1-D3-rp1


title: EpiSC-rp4


title: kEpiSC-rp1


title: Episc-rp2


title: JunKO-kiEpiSC-iCD1-D3-rp2


title: JunKO-kiEpiSC-JNKi-D3-rp2


title: EpiSC-rp3


title: 121_KMS_rep2

city: Shanghai

first: Hanyu

last: Rao

address: No.1954, hua shan Rd. Shanghai

institute: Shanghai Jiao Tong University

description:
caseVScontrol_all.xls
R-121

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <50 bp) and low quality reads using Cutadapt (v1.9.1)(Anthony M et al., Bioinformatics 2014) and Trimmomatic (v0.35) (Martin M et al., EMBnet.J 2011).
Then FastQC (Andrews S et. al., FastQC 2010) is used to ensure high reads quality.
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 (Kim, D et al., Nat. Methods 2015) software.
Peak detection was performed using the MACS (v2.1.1) (Zhang et al., Genome Biol 2008) peak finding algorithm with 0.01 set as the p-value cutoff.
Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie. Ballgown, a R package, were used to measure differential gene expression.The false discovery rate (FDR) control method was used to calculate the adjusted P-values in multiple testing in order to evaluate the significance of the differences. Here, only gene with an adjusted P-value <0.05 were used for subsequent analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Counts

source_name: renal primary tubular epithelial cells

growth_protocol: renal primary tubular epithelial cells were isolated from mice kidney cortex segment

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination.
Isolation of mRNA was performed using the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

tag: tissue

value: kidney

value: renal primary tubular epithelial cells

tag: genotype

value: SETD2fl/fl MYCfl/fl KspCre/+

value: 8 weeks


title: H3K36me3_ChIPSeq_SETD2_KO

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <50 bp) and low quality reads using Cutadapt (v1.9.1)(Anthony M et al., Bioinformatics 2014) and Trimmomatic (v0.35) (Martin M et al., EMBnet.J 2011).
Then FastQC (Andrews S et. al., FastQC 2010) is used to ensure high reads quality.
The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 (v2.2.6) (Langmead B et. al., Nature Methods 2012) software.
Peak detection was performed using the MACS (v2.1.1) (Zhang et al., Genome Biol 2008) peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package (Guangchuang Yu et al., Journal of the Royal Statistical Society Series 1995).
Genome_build: mm10
Supplementary_files_format_and_content: peaks.loc.xls files

extract_protocol:
cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-H3K36me3  antibodies.
ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.

value: SETD2fl/fl KspCre/+

value: H3K36me3 (abcam, ab9050)


title: 120_KMS_rep1

description:
caseVScontrol_all.xls
R-120


title: 93_KM_rep2

description:
caseVScontrol_all.xls
M93

value: MYCfl/fl KspCre/+


title: 104_KM_rep1

description:
caseVScontrol_all.xls
F104


title: H3K36me3_ChIPSeq_WT


title: H3K36me3_ChIPSeq_SETD2_KO_INPUT


title: 2pct-oxygen_MCT4-KO_3

city: Boston

first: Li

last: Jiang

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
alignment with Hisat2
quantification with RSEM
Genome_build: mm10 (gencode-vM17-primary-assembly)
Supplementary_files_format_and_content: read counts for genes within each sample as csv file

source_name: murine AML

growth_protocol: MLL-AF9 AML cell ine was cultured in RPMI supplemented with FBS, IL-3 and SCF

extract_protocol:
total RNA extracted by RNeasy Plus Mini Kit. mRNA was isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module
NEBNext®UltraTMII DNA Library Prep Kit for Illumina®

treatment_protocol: Cas9 was induced by 4-OHT

tag: mouse model

value: MLL-AF9 AML

tag: genotype/variation

tag: treatment

value: 2% oxygen


title: 2pct-oxygen_MCT4-KO_2


title: 2pct-oxygen_Control_4

value: control


title: 2pct-oxygen_MCT4-KO_1


title: 2pct-oxygen_Control_3


title: 2pct-oxygen_Control_2


title: 2pct-oxygen_Control_1


title: 20pct-oxygen_MCT4-KO_2

value: 20% oxygen


title: 20pct-oxygen_MCT4-KO_3


title: 20pct-oxygen_Control_3


title: 20pct-oxygen_Control_1


title: 20pct-oxygen_MCT4-KO_1


title: H3K36me3_ChIPSeq_WT_INPUT


title: 20pct-oxygen_Control_2


title: 20pct-oxygen_Control_4


title: 2pct-oxygen_MCT4-KO_4


title: 109_T_M

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: pooled RNA from in vitro meristem culture plantlets

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of repeats

organism: Vitis vinifera

source_name: whole in vitro plantlets

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar

value: Trilla 3

value: in vitro meristem culture plantlets


title: 20pct-oxygen_MCT4-KO_4


title: 106_MO14_SZ

description: pooled RNA from in vitro somatic embryogenesis plantlets

value: Muscat Ottonel H-14-1


title: 105_MO7_SZ

value: Muscat Ottonel H-7-3

value: in vitro somatic embryogenesis plantlets


title: 103_T_A

description: pooled RNA from leaf, shoot tip, flower, tendril

source_name: leaf, shoot tip, flower, tendril samples

value: mother plant,  leaf, shoot tip, flower, tendril


title: 102_MO14_A


title: 101_MO7_A


title: 107_T_SZ


title: SC1: Shine-muscat control

city: Nanjing

first: Tariq

last: Pervaiz

state: Jaingsu

address: wei Gang

department: Horticulture

institute: Nanjing Agricultural University

data_processing:
The primary raw reads obtained by Illumina HiSeqTM2000 were filtered to remove low quality reads which were low complexity or containing adaptor sequence
The cleaned reads were aligned to the reference genome of Vitis using HISAT software.
GO functional enrichment analysis and KEGG pathway analysis was continued with Blast2Go. KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates
DEGseq2 was used for gene expression analysis.

source_name: control fruit

growth_protocol: All plants were cultivated  under standard cultivation condition

extract_protocol:
Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: berries were treated with chitosan 1.5K

value: Shine-muscat

value: maturation stage

value: fruit


title: SC3: Shine-muscat control


title: ST2: Shine-muscat Botrytis cinerea treatment

source_name: fruit treated with Botrytis cinerea spores


title: SC2: Shine-muscat control


title: ST3: Shine-muscat Botrytis cinerea treatment


title: KT3: Kyoho Botrytis cinerea treatment

value: kyoho


title: KT2: Kyoho Botrytis cinerea treatment


title: ST1: Shine-muscat Botrytis cinerea treatment


title: KC3: Kyoho control

value: Kyoho


title: KC2: Kyoho control


title: KC1: Kyoho control


title: KT1: Kyoho Botrytis cinerea treatment


title: iPSCs, S22

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

data_processing:
The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality. TopHat2 (v2.0.9) aligned the reads to the mouse reference genome (Mus musculus UCSC mm10) and to the Ensembl human reference genome (GRCh38.p13) using default parameters. Alignments were then converted to expression count data using HTseq (v0.6.1) with default union mode.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

extract_protocol: Human iPSCs were homogenized and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively. Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500.

treatment_protocol: 72 hours of bath application with valproate, ACY-957, or vehicle (water)

tag: condition

value: bipolar disorder (Lithium Non-Responsive)

tag: subject id

tag: clone

value: lithium non-responsive clone 3

value: clone differentiated into neurons

value: VPA


title: iPSCs, S17


title: iPSCs, S21


title: iPSCs, S23


title: iPSCs, S18


title: iPSCs, S19


title: iPSCs, S24


title: iPSCs, S16

value: ACY


title: iPSCs, S15


title: iPSCs, S14


title: iPSCs, S20


title: iPSCs, S12


title: iPSCs, S9


title: iPSCs, S11


title: iPSCs, S10


title: iPSCs, S7


title: iPSCs, S6

value: lithium non-responsive clone 1


title: iPSCs, S8


title: iPSCs, S13


title: iPSCs, S3


title: iPSCs, S2


title: iPSCs, S5


title: iPSCs, S4


title: iPSCs, S1


title: NAc, Caudate, and Putamen_pair211_822P

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment with HISAT2
Read counts using HTSeq
Genome_build: Ensembl GRh38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: NAc, Caudate, and Putamen_pair211

extract_protocol:
Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepped for RNA-sequencing using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). 75bp paired-end dual-indexed sequencing was performed using the NextSeq 500 platform (Illumina, San Diego, CA).

tag: gender

value: Male

value: Putamen

tag: race

value: Black

tag: hu

tag: pmi


title: NAc, Caudate, and Putamen_pair219_871P

source_name: NAc, Caudate, and Putamen_pair219

tag: age

value: White


title: NAc, Caudate, and Putamen_pair201_700P

source_name: NAc, Caudate, and Putamen_pair201


title: NAc, Caudate, and Putamen_pair205_736P

source_name: NAc, Caudate, and Putamen_pair205


title: NAc, Caudate, and Putamen_pair217_857P

source_name: NAc, Caudate, and Putamen_pair217


title: NAc, Caudate, and Putamen_pair207_739P

source_name: NAc, Caudate, and Putamen_pair207


title: NAc, Caudate, and Putamen_pair183_604P

source_name: NAc, Caudate, and Putamen_pair183


title: NAc, Caudate, and Putamen_pair167_1719P

source_name: NAc, Caudate, and Putamen_pair167


title: NAc, Caudate, and Putamen_pair173_1789P

source_name: NAc, Caudate, and Putamen_pair173

value: Female


title: NAc, Caudate, and Putamen_pair213_838P

source_name: NAc, Caudate, and Putamen_pair213


title: NAc, Caudate, and Putamen_pair195_688P

source_name: NAc, Caudate, and Putamen_pair195


title: NAc, Caudate, and Putamen_pair157_1637P

source_name: NAc, Caudate, and Putamen_pair157


title: NAc, Caudate, and Putamen_pair197_694P

source_name: NAc, Caudate, and Putamen_pair197


title: NAc, Caudate, and Putamen_pair187_634P

source_name: NAc, Caudate, and Putamen_pair187


title: NAc, Caudate, and Putamen_pair159_1653P

source_name: NAc, Caudate, and Putamen_pair159


title: NAc, Caudate, and Putamen_pair177_1834P

source_name: NAc, Caudate, and Putamen_pair177


title: NAc, Caudate, and Putamen_pair171_1770P

source_name: NAc, Caudate, and Putamen_pair171


title: NAc, Caudate, and Putamen_pair193_681P

source_name: NAc, Caudate, and Putamen_pair193


title: NAc, Caudate, and Putamen_pair163_1687P

source_name: NAc, Caudate, and Putamen_pair163


title: NAc, Caudate, and Putamen_pair153_1605P

source_name: NAc, Caudate, and Putamen_pair153


title: NAc, Caudate, and Putamen_pair139_1574P

source_name: NAc, Caudate, and Putamen_pair139


title: NAc, Caudate, and Putamen_pair145_1583P

source_name: NAc, Caudate, and Putamen_pair145


title: NAc, Caudate, and Putamen_pair133_1543P

source_name: NAc, Caudate, and Putamen_pair133


title: NAc, Caudate, and Putamen_pair149_1598P

source_name: NAc, Caudate, and Putamen_pair149


title: NAc, Caudate, and Putamen_pair129_1518P

source_name: NAc, Caudate, and Putamen_pair129


title: NAc, Caudate, and Putamen_pair99_1326P

source_name: NAc, Caudate, and Putamen_pair99


title: NAc, Caudate, and Putamen_pair103_1371P

source_name: NAc, Caudate, and Putamen_pair103


title: AT2_young_naive_1

description: mRNA-seq

source_name: lung AT2 cells from 4 month old mouse

tag: strain

value: 4 month

tag: exposure

value: naïve


title: NAc, Caudate, and Putamen_pair89_13149P

source_name: NAc, Caudate, and Putamen_pair89


title: NAc, Caudate, and Putamen_pair107_1374P

source_name: NAc, Caudate, and Putamen_pair107


title: NAc, Caudate, and Putamen_pair95_1318P

source_name: NAc, Caudate, and Putamen_pair95


title: NAc, Caudate, and Putamen_pair105_1372P

source_name: NAc, Caudate, and Putamen_pair105


title: NAc, Caudate, and Putamen_pair69_1284P

source_name: NAc, Caudate, and Putamen_pair69


title: NAc, Caudate, and Putamen_pair73_1298P

source_name: NAc, Caudate, and Putamen_pair73


title: NAc, Caudate, and Putamen_pair53_1196P

source_name: NAc, Caudate, and Putamen_pair53


title: NAc, Caudate, and Putamen_pair67_1268P

source_name: NAc, Caudate, and Putamen_pair67


title: NAc, Caudate, and Putamen_pair109_1391P

source_name: NAc, Caudate, and Putamen_pair109


title: AT2_young_naive_2

description: mRNA-seq


title: NAc, Caudate, and Putamen_pair115_1441P

source_name: NAc, Caudate, and Putamen_pair115


title: NAc, Caudate, and Putamen_pair59_1214P

source_name: NAc, Caudate, and Putamen_pair59


title: NAc, Caudate, and Putamen_pair81_13068P

source_name: NAc, Caudate, and Putamen_pair81


title: NAc, Caudate, and Putamen_pair117_1444P

source_name: NAc, Caudate, and Putamen_pair117


title: NAc, Caudate, and Putamen_pair119_1447P

source_name: NAc, Caudate, and Putamen_pair119


title: NAc, Caudate, and Putamen_pair111_1394P

source_name: NAc, Caudate, and Putamen_pair111


title: AT2_old_naive_3

description: mRNA-seq

source_name: lung AT2 cells from 18 month old mouse

value: 18 month


title: NAc, Caudate, and Putamen_pair87_13112P

source_name: NAc, Caudate, and Putamen_pair87


title: NAc, Caudate, and Putamen_pair63_1247P

source_name: NAc, Caudate, and Putamen_pair63


title: NAc, Caudate, and Putamen_pair41_1159P

source_name: NAc, Caudate, and Putamen_pair41


title: NAc, Caudate, and Putamen_pair83_13069P

source_name: NAc, Caudate, and Putamen_pair83


title: NAc, Caudate, and Putamen_pair77_13032P

source_name: NAc, Caudate, and Putamen_pair77


title: NAc, Caudate, and Putamen_pair39_1129P

source_name: NAc, Caudate, and Putamen_pair39


title: NAc, Caudate, and Putamen_pair65_1255P

source_name: NAc, Caudate, and Putamen_pair65


title: NAc, Caudate, and Putamen_pair43_1171P

source_name: NAc, Caudate, and Putamen_pair43


title: NAc, Caudate, and Putamen_pair37_1122P

source_name: NAc, Caudate, and Putamen_pair37


title: NAc, Caudate, and Putamen_pair15_1067P

source_name: NAc, Caudate, and Putamen_pair15


title: NAc, Caudate, and Putamen_pair11_1034P

source_name: NAc, Caudate, and Putamen_pair11


title: NAc, Caudate, and Putamen_pair1_10003P

source_name: NAc, Caudate, and Putamen_pair1


title: NAc, Caudate, and Putamen_pair21_1086P

source_name: NAc, Caudate, and Putamen_pair21


title: NAc, Caudate, and Putamen_pair213_838C

source_name: NAc, Caudate, and Putamen_pair213

value: Caudate


title: NAc, Caudate, and Putamen_pair211_822C

source_name: NAc, Caudate, and Putamen_pair211


title: NAc, Caudate, and Putamen_pair219_871C

source_name: NAc, Caudate, and Putamen_pair219


title: NAc, Caudate, and Putamen_pair197_694C

source_name: NAc, Caudate, and Putamen_pair197


title: NAc, Caudate, and Putamen_pair207_739C

source_name: NAc, Caudate, and Putamen_pair207


title: NAc, Caudate, and Putamen_pair205_736C

source_name: NAc, Caudate, and Putamen_pair205


title: NAc, Caudate, and Putamen_pair195_688C

source_name: NAc, Caudate, and Putamen_pair195


title: NAc, Caudate, and Putamen_pair193_681C

source_name: NAc, Caudate, and Putamen_pair193


title: NAc, Caudate, and Putamen_pair177_1834C

source_name: NAc, Caudate, and Putamen_pair177


title: NAc, Caudate, and Putamen_pair183_604C

source_name: NAc, Caudate, and Putamen_pair183


title: NAc, Caudate, and Putamen_pair187_634C

source_name: NAc, Caudate, and Putamen_pair187


title: NAc, Caudate, and Putamen_pair159_1653C

source_name: NAc, Caudate, and Putamen_pair159


title: NAc, Caudate, and Putamen_pair201_700C

source_name: NAc, Caudate, and Putamen_pair201


title: NAc, Caudate, and Putamen_pair173_1789C

source_name: NAc, Caudate, and Putamen_pair173


title: NAc, Caudate, and Putamen_pair171_1770C

source_name: NAc, Caudate, and Putamen_pair171


title: NAc, Caudate, and Putamen_pair29_1099P

source_name: NAc, Caudate, and Putamen_pair29


title: NAc, Caudate, and Putamen_pair25_1092P

source_name: NAc, Caudate, and Putamen_pair25


title: NAc, Caudate, and Putamen_pair157_1637C

source_name: NAc, Caudate, and Putamen_pair157


title: NAc, Caudate, and Putamen_pair153_1605C

source_name: NAc, Caudate, and Putamen_pair153


title: NAc, Caudate, and Putamen_pair149_1598C

source_name: NAc, Caudate, and Putamen_pair149


title: NAc, Caudate, and Putamen_pair145_1583C

source_name: NAc, Caudate, and Putamen_pair145


title: NAc, Caudate, and Putamen_pair27_1093P

source_name: NAc, Caudate, and Putamen_pair27


title: NAc, Caudate, and Putamen_pair217_857C

source_name: NAc, Caudate, and Putamen_pair217


title: NAc, Caudate, and Putamen_pair133_1543C

source_name: NAc, Caudate, and Putamen_pair133


title: NAc, Caudate, and Putamen_pair139_1574C

source_name: NAc, Caudate, and Putamen_pair139


title: NAc, Caudate, and Putamen_pair19_1083P

source_name: NAc, Caudate, and Putamen_pair19


title: NAc, Caudate, and Putamen_pair119_1447C

source_name: NAc, Caudate, and Putamen_pair119


title: NAc, Caudate, and Putamen_pair167_1719C

source_name: NAc, Caudate, and Putamen_pair167


title: NAc, Caudate, and Putamen_pair163_1687C

source_name: NAc, Caudate, and Putamen_pair163


title: NAc, Caudate, and Putamen_pair111_1394C

source_name: NAc, Caudate, and Putamen_pair111


title: NAc, Caudate, and Putamen_pair107_1374C

source_name: NAc, Caudate, and Putamen_pair107


title: NAc, Caudate, and Putamen_pair105_1372C

source_name: NAc, Caudate, and Putamen_pair105


title: NAc, Caudate, and Putamen_pair129_1518C

source_name: NAc, Caudate, and Putamen_pair129


title: NAc, Caudate, and Putamen_pair89_13149C

source_name: NAc, Caudate, and Putamen_pair89


title: NAc, Caudate, and Putamen_pair95_1318C

source_name: NAc, Caudate, and Putamen_pair95


title: NAc, Caudate, and Putamen_pair83_13069C

source_name: NAc, Caudate, and Putamen_pair83


title: NAc, Caudate, and Putamen_pair87_13112C

source_name: NAc, Caudate, and Putamen_pair87


title: NAc, Caudate, and Putamen_pair77_13032C

source_name: NAc, Caudate, and Putamen_pair77


title: NAc, Caudate, and Putamen_pair73_1298C

source_name: NAc, Caudate, and Putamen_pair73


title: NAc, Caudate, and Putamen_pair67_1268C

source_name: NAc, Caudate, and Putamen_pair67


title: NAc, Caudate, and Putamen_pair65_1255C

source_name: NAc, Caudate, and Putamen_pair65


title: NAc, Caudate, and Putamen_pair117_1444C

source_name: NAc, Caudate, and Putamen_pair117


title: NAc, Caudate, and Putamen_pair59_1214C

source_name: NAc, Caudate, and Putamen_pair59


title: NAc, Caudate, and Putamen_pair43_1171C

source_name: NAc, Caudate, and Putamen_pair43


title: NAc, Caudate, and Putamen_pair39_1129C

source_name: NAc, Caudate, and Putamen_pair39


title: NAc, Caudate, and Putamen_pair41_1159C

source_name: NAc, Caudate, and Putamen_pair41


title: NAc, Caudate, and Putamen_pair53_1196C

source_name: NAc, Caudate, and Putamen_pair53


title: NAc, Caudate, and Putamen_pair115_1441C

source_name: NAc, Caudate, and Putamen_pair115


title: NAc, Caudate, and Putamen_pair69_1284C

source_name: NAc, Caudate, and Putamen_pair69


title: NAc, Caudate, and Putamen_pair37_1122C

source_name: NAc, Caudate, and Putamen_pair37


title: NAc, Caudate, and Putamen_pair29_1099C

source_name: NAc, Caudate, and Putamen_pair29


title: NAc, Caudate, and Putamen_pair109_1391C

source_name: NAc, Caudate, and Putamen_pair109


title: NAc, Caudate, and Putamen_pair27_1093C

source_name: NAc, Caudate, and Putamen_pair27


title: NAc, Caudate, and Putamen_pair103_1371C

source_name: NAc, Caudate, and Putamen_pair103


title: NAc, Caudate, and Putamen_pair25_1092C

source_name: NAc, Caudate, and Putamen_pair25


title: NAc, Caudate, and Putamen_pair99_1326C

source_name: NAc, Caudate, and Putamen_pair99


title: NAc, Caudate, and Putamen_pair19_1083C

source_name: NAc, Caudate, and Putamen_pair19


title: NAc, Caudate, and Putamen_pair81_13068C

source_name: NAc, Caudate, and Putamen_pair81


title: NAc, Caudate, and Putamen_pair11_1034C

source_name: NAc, Caudate, and Putamen_pair11


title: NAc, Caudate, and Putamen_pair63_1247C

source_name: NAc, Caudate, and Putamen_pair63


title: NAc, Caudate, and Putamen_pair15_1067C

source_name: NAc, Caudate, and Putamen_pair15


title: NAc, Caudate, and Putamen_pair1_10003C

source_name: NAc, Caudate, and Putamen_pair1


title: NAc, Caudate, and Putamen_pair219_871N

source_name: NAc, Caudate, and Putamen_pair219

value: Nac


title: NAc, Caudate, and Putamen_pair213_838N

source_name: NAc, Caudate, and Putamen_pair213


title: NAc, Caudate, and Putamen_pair211_822N

source_name: NAc, Caudate, and Putamen_pair211


title: NAc, Caudate, and Putamen_pair217_857N

source_name: NAc, Caudate, and Putamen_pair217


title: NAc, Caudate, and Putamen_pair201_700N

source_name: NAc, Caudate, and Putamen_pair201


title: NAc, Caudate, and Putamen_pair205_736N

source_name: NAc, Caudate, and Putamen_pair205


title: NAc, Caudate, and Putamen_pair195_688N

source_name: NAc, Caudate, and Putamen_pair195


title: NAc, Caudate, and Putamen_pair197_694N

source_name: NAc, Caudate, and Putamen_pair197


title: NAc, Caudate, and Putamen_pair193_681N

source_name: NAc, Caudate, and Putamen_pair193


title: NAc, Caudate, and Putamen_pair187_634N

source_name: NAc, Caudate, and Putamen_pair187


title: NAc, Caudate, and Putamen_pair163_1687N

source_name: NAc, Caudate, and Putamen_pair163


title: NAc, Caudate, and Putamen_pair171_1770N

source_name: NAc, Caudate, and Putamen_pair171


title: NAc, Caudate, and Putamen_pair167_1719N

source_name: NAc, Caudate, and Putamen_pair167


title: NAc, Caudate, and Putamen_pair177_1834N

source_name: NAc, Caudate, and Putamen_pair177


title: NAc, Caudate, and Putamen_pair21_1086C

source_name: NAc, Caudate, and Putamen_pair21


title: NAc, Caudate, and Putamen_pair173_1789N

source_name: NAc, Caudate, and Putamen_pair173


title: NAc, Caudate, and Putamen_pair159_1653N

source_name: NAc, Caudate, and Putamen_pair159


title: NAc, Caudate, and Putamen_pair157_1637N

source_name: NAc, Caudate, and Putamen_pair157


title: NAc, Caudate, and Putamen_pair149_1598N

source_name: NAc, Caudate, and Putamen_pair149


title: NAc, Caudate, and Putamen_pair153_1605N

source_name: NAc, Caudate, and Putamen_pair153


title: NAc, Caudate, and Putamen_pair139_1574N

source_name: NAc, Caudate, and Putamen_pair139


title: NAc, Caudate, and Putamen_pair133_1543N

source_name: NAc, Caudate, and Putamen_pair133


title: NAc, Caudate, and Putamen_pair207_739N

source_name: NAc, Caudate, and Putamen_pair207


title: NAc, Caudate, and Putamen_pair129_1518N

source_name: NAc, Caudate, and Putamen_pair129


title: NAc, Caudate, and Putamen_pair111_1394N

source_name: NAc, Caudate, and Putamen_pair111


title: NAc, Caudate, and Putamen_pair119_1447N

source_name: NAc, Caudate, and Putamen_pair119


title: NAc, Caudate, and Putamen_pair107_1374N

source_name: NAc, Caudate, and Putamen_pair107


title: NAc, Caudate, and Putamen_pair117_1444N

source_name: NAc, Caudate, and Putamen_pair117


title: NAc, Caudate, and Putamen_pair109_1391N

source_name: NAc, Caudate, and Putamen_pair109


title: NAc, Caudate, and Putamen_pair95_1318N

source_name: NAc, Caudate, and Putamen_pair95


title: NAc, Caudate, and Putamen_pair105_1372N

source_name: NAc, Caudate, and Putamen_pair105


title: NAc, Caudate, and Putamen_pair87_13112N

source_name: NAc, Caudate, and Putamen_pair87


title: NAc, Caudate, and Putamen_pair77_13032N

source_name: NAc, Caudate, and Putamen_pair77


title: NAc, Caudate, and Putamen_pair83_13069N

source_name: NAc, Caudate, and Putamen_pair83


title: NAc, Caudate, and Putamen_pair99_1326N

source_name: NAc, Caudate, and Putamen_pair99


title: NAc, Caudate, and Putamen_pair67_1268N

source_name: NAc, Caudate, and Putamen_pair67


title: NAc, Caudate, and Putamen_pair65_1255N

source_name: NAc, Caudate, and Putamen_pair65


title: NAc, Caudate, and Putamen_pair63_1247N

source_name: NAc, Caudate, and Putamen_pair63


title: NAc, Caudate, and Putamen_pair103_1371N

source_name: NAc, Caudate, and Putamen_pair103


title: NAc, Caudate, and Putamen_pair183_604N

source_name: NAc, Caudate, and Putamen_pair183


title: NAc, Caudate, and Putamen_pair59_1214N

source_name: NAc, Caudate, and Putamen_pair59


title: NAc, Caudate, and Putamen_pair145_1583N

source_name: NAc, Caudate, and Putamen_pair145


title: NAc, Caudate, and Putamen_pair81_13068N

source_name: NAc, Caudate, and Putamen_pair81


title: NAc, Caudate, and Putamen_pair89_13149N

source_name: NAc, Caudate, and Putamen_pair89


title: NAc, Caudate, and Putamen_pair73_1298N

source_name: NAc, Caudate, and Putamen_pair73


title: NAc, Caudate, and Putamen_pair69_1284N

source_name: NAc, Caudate, and Putamen_pair69


title: NAc, Caudate, and Putamen_pair41_1159N

source_name: NAc, Caudate, and Putamen_pair41


title: NAc, Caudate, and Putamen_pair39_1129N

source_name: NAc, Caudate, and Putamen_pair39


title: NAc, Caudate, and Putamen_pair37_1122N

source_name: NAc, Caudate, and Putamen_pair37


title: NAc, Caudate, and Putamen_pair27_1093N

source_name: NAc, Caudate, and Putamen_pair27


title: NAc, Caudate, and Putamen_pair19_1083N

source_name: NAc, Caudate, and Putamen_pair19


title: NAc, Caudate, and Putamen_pair43_1171N

source_name: NAc, Caudate, and Putamen_pair43


title: NAc, Caudate, and Putamen_pair11_1034N

source_name: NAc, Caudate, and Putamen_pair11


title: NAc, Caudate, and Putamen_pair115_1441N

source_name: NAc, Caudate, and Putamen_pair115


title: NAc, Caudate, and Putamen_pair29_1099N

source_name: NAc, Caudate, and Putamen_pair29


title: NAc, Caudate, and Putamen_pair21_1086N

source_name: NAc, Caudate, and Putamen_pair21


title: NAc, Caudate, and Putamen_pair15_1067N

source_name: NAc, Caudate, and Putamen_pair15


title: NAc, Caudate, and Putamen_pair53_1196N

source_name: NAc, Caudate, and Putamen_pair53


title: MM.1S dCBP-1 RNA-Seq rep2

first: Christopher

last: Ott

address: 149 13th Street

department: Cancer Center

institute: Masschusetts General Hospital

description: RNA-seq sample

data_processing:
Illumina's NextSeq 500 system used to sequence libraries
Reads were aligned to hg19 genome
Genome_build: hg19
Supplementary_files_format_and_content: Read counts .csv file derived from read alignments to the human genome

source_name: MM1.S multiple myeloma cell line

growth_protocol: MM.1S cells were grown in RPMI medium with FBS 10% and Pen/Strep1% added

extract_protocol:
Cells were lysed in Trizol with addition of ERCC synthetic spike-in controls; RNA was purified using Qiagen RNeasy columns.
Libraries were constructed using the Lexogen QuantSeq 3' mRNA-Seq FWD Library Prep Kit.

treatment_protocol: MM.1S cells were treated for 6 hours with DMSO, and the following inhibitors: A-485, GNE-781, A-485 & GNE-781 combined, dCBP-1; 100 nM of each.

tag: cell type

value: Multiple myeloma


title: MM.1S A485_GNE781 RNA-Seq rep2

description: RNA-seq sample


title: MM.1S A485_GNE781 RNA-Seq rep3

description: RNA-seq sample


title: MM.1S GNE-781 RNA-Seq rep2

description: RNA-seq sample


title: MM.1S dCBP-1 RNA-Seq rep1

description: RNA-seq sample


title: MM.1S A-485 RNA-Seq rep1

description: RNA-seq sample


title: MM.1S GNE-781 RNA-Seq rep1

description: RNA-seq sample


title: MM.1S A-485 RNA-Seq rep3

description: RNA-seq sample


title: MM.1S dCBP-1 RNA-Seq rep3

description: RNA-seq sample


title: SC006_T2_F_AMD_R1

description: mRNA-seq

source_name: Lung CD45.1+SiglecFlow MoAM at day 4 after first influenza injury

treatment_protocol: 25pfu WSN

value: influenza


title: MM.1S A-485 RNA-Seq rep2

description: RNA-seq sample


title: NAc, Caudate, and Putamen_pair25_1092N

source_name: NAc, Caudate, and Putamen_pair25

tag: tissue


title: MM.1S A485-GNE781 RNA-Seq rep1

description: RNA-seq sample


title: MM.1S DMSO RNA-Seq rep3

description: RNA-seq sample

value: DMSO (control)


title: MM.1S GNE-781 RNA-Seq rep3

description: RNA-seq sample


title: SC007_T2_F_AMD_R2

description: mRNA-seq


title: MM.1S DMSO RNA-Seq rep2

description: RNA-seq sample


title: MM.1S DMSO RNA-Seq rep1

description: RNA-seq sample


title: MM.1S  A-485 input

description: input sample

data_processing:
Illumina's NextSeq 500 system used to sequence libraries.
Reads were aligned to hg19 genome using bowtie2
Mapped reads were filtered for unmapped/low quality with samtools and duplicates were removed with Picard
Peaks called and signal tracks were generated with MACS2 for the H3K27ac samples and SPP peak caller for the p300 &CBP samples
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in narrowPeak or regionPeak bigbed format with the following content: chromsosome, chrom. start, chrom. End, region name, peak darkness score, strand, pValue, qValue (FDR), point source called for a peak
Supplementary_files_format_and_content: Signal files in bigwig format which are binary files containg chromosome start and end coordinates and a probability score for each signal
Supplementary_files_format_and_content: Alignment files in bam format for input samples

extract_protocol:
Cells were crosslinked and lysed,  lysates were sonicated, nuclei were clarified, and histone-DNA complexes were isolated with antibody
Used Illumina’s Nextera DNA Library Prep Kit to perform ChIPmentation protocol for ChIP samples.

tag: chip antibody


title: MM.1S A-485/GNE-781 input

description: input sample


title: MM.1S GNE-781 input

description: input sample


title: MM.1S input

description: input sample


title: MM.1S p300

description: ChIP antibody sample


title: MM.1S DMSO input

description: input sample


title: MM.1S A-485/GNE-781 H3K27ac

description: ChIP antibody sample


title: MM.1S dCBP-1 H3K27ac

description: ChIP antibody sample


title: MM.1S CBP

description: ChIP antibody sample

value: CBP


title: MM.1S dCBP-1 input

description: input sample


title: NAc, Caudate, and Putamen_pair1_10003N

source_name: NAc, Caudate, and Putamen_pair1


title: MM.1S GNE-781 H3K27ac

description: ChIP antibody sample


title: MM.1S DMSO H3K27ac

description: ChIP antibody sample


title: MM.1S A485_GNE781 ATAC-Seq rep2

description: ATAC-seq sample

data_processing:
Illumina's NextSeq 500 system used to sequence libraries.
Reads were aligned to hg19 genome using bowtie2
Adapters were trimmed with cutadapt
Mapped reads were filtered for unmapped/low quality with samtools and duplicates were removed with Picard
Peaks called and signal tracks were generated with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in narrowPeak bigbed format with the following content: chromsosome, chrom. start, chrom. End, region name, peak darkness score, strand, pValue, qValue (FDR), point source called for a peak
Supplementary_files_format_and_content: Signal files in bigwig format which are binary files containg chromosome start and end coordinates and a probability score for each signal

extract_protocol:
Cells were lysed and then transposed, DNA was purified and amplified, and libraries were sequenced.
Used Illumina’s Nextera DNA Library Prep Kit to perform tagmentation reaction  for the ATAC-seq samples


title: MM.1S dCBP-1 ATAC-Seq rep1

description: ATAC-seq sample


title: MM.1S  A-485 H3K27ac

description: ChIP antibody sample


title: MM.1S dCBP-1 ATAC-Seq rep3

description: ATAC-seq sample


title: MM.1S A485_GNE781 ATAC-Seq rep3

description: ATAC-seq sample


title: MM.1S A485-GNE781 ATAC-Seq rep1

description: ATAC-seq sample


title: MM.1S dCBP-1 ATAC-Seq rep2

description: ATAC-seq sample


title: MM.1S GNE-781 ATAC-Seq rep1

description: ATAC-seq sample


title: MM.1S A-485 ATAC-Seq rep3

description: ATAC-seq sample


title: MM.1S GNE-781 ATAC-Seq rep3

description: ATAC-seq sample


title: MM.1S A-485 ATAC-Seq rep1

description: ATAC-seq sample


title: MM.1S A-485 ATAC-Seq rep2

description: ATAC-seq sample


title: MM.1S GNE-781 ATAC-Seq rep2

description: ATAC-seq sample


title: MM.1S DMSO ATAC-Seq rep3

description: ATAC-seq sample


title: MM.1S DMSO ATAC-Seq rep1

description: ATAC-seq sample


title: MM.1S DMSO ATAC-Seq rep2

description: ATAC-seq sample


title: Small RNA Stroke_33

city: Jerusalem

first: Katarzyna

last: Winek

state: Israel

address: The Edmond J. Safra Campus

department: ELSC

country: Israel

institute: Hebrew University of Jersusalem

description:
Stroke_33
9_30074_50_S10_R1_001

data_processing:
Fastq files were generated within BaseSpace using FASTQ Generation, Version: 1.0.0
Quality control was performed using FastQC, version 0.11.2. Flexbar (with parameters “-q TAIL -qf Sanger -qw 4 -min-read-length 16”) served for adapter trimming and quality based filtering of all raw reads. Small RNA was aligned to the miRBase version 21 using miRExpress 2.1.4 with default parameters but skipping adapter trimming for miR expression, and to the tRNA transcriptome using the MINTmap pipeline with default parameters for tRF expression (using only reads mapping exclusively to the  tRNA space).
Differential expression was determined using the R/DESeq2 package including the log2 fold change shrinkage estimation “apeglm” algorithm. Genes were considered differentially expressed at an adjusted p-value of < 0.05. The analysis was performed on the raw count tables (outliers already removed) with correction of covariates (age, batch, time2blood) in the model formula. Outliers were identified by sample clustering based on batch-corrected variance-stabilized expression, leading to exclusion of sample 4044 (stroke patient) in the small RNA sequencing experiment.
Supplementary_files_format_and_content: csv files used as input to DESeq2 analysis

source_name: whole blood

extract_protocol:
RNA was extracted from 3 ml of whole blood of 484 PREDICT patients using Tempus Spin RNA isolation kit (Invitrogen, Thermo Fisher Scientific, Waltham MA, USA). Pre-sequencing Bioanalyzer 6000 (Agilent, Santa Clara CA, USA) tests showed high RNA quality (RIN values 7.9-9.9, median 8.8).
Libraries constructed from 600 ng total RNA of 43 samples were subjected to small RNA-sequencing (NEBNext® Multiplex Small RNA library prep set for Illumina, New England Biolabs, Ipswich MA, USA). Sequencing was performed on the Illumina NextSeq 500 platform at the Hebrew University’s Center for Genomic Technologies.

value: stroke

tag: Sex

value: male

tag: batch

value: B


title: Small RNA Stroke_32

description:
Stroke_32
9_30053_mor_det_45787820_R1

value: C


title: Small RNA Stroke_31

description:
Stroke_31
8_60004_mor_det_45796771_R1


title: Small RNA Stroke_27

description:
Stroke_27
5_40026_S8_R1_001


title: Small RNA Stroke_29

description:
Stroke_29
6_40049_eve_imp_45790782_R1


title: Small RNA Stroke_28

description:
Stroke_28
6_30065_S9_R1_001


title: Small RNA Stroke_30

description:
Stroke_30
7_30040_mor_det_45785850_R1


title: Small RNA Stroke_25

description:
Stroke_25
4_90003_S7_R1_001


title: Small RNA Stroke_24

description:
Stroke_24
4_10177_eve_imp_45795771_R1


title: Small RNA Stroke_26

description:
Stroke_26
5_10171_eve_imp_45788808_R1


title: Small RNA Stroke_20

description:
Stroke_20
25_10146_D4_R1

value: A


title: Small RNA Stroke_23

description:
Stroke_23
3_10189_45_S6_R1_001


title: Small RNA Stroke_18

description:
Stroke_18
23_10116_D2_R1


title: Small RNA Control_8

description:
Control_8
22_Control_blood_17_45792776_R1

value: control


title: Small RNA Control_6

description:
Control_6
20_Control_blood_15_45793787_R1


title: Small RNA Stroke_14

description:
Stroke_14
18_10136_I3_R1


title: Small RNA Stroke_22

description:
Stroke_22
3_10166_mor_imp_45795773_R1


title: Small RNA Stroke_21

description:
Stroke_21
26_10156_D5_R1


title: Small RNA Control_5

description:
Control_5
19_Control_blood_14_45759905_R1


title: Small RNA Stroke_15

description:
Stroke_15
20_10155_I5_R1


title: Small RNA Control_4

description:
Control_4
18_Control_blood_13_45786842_R1


title: Small RNA Stroke_13

description:
Stroke_13
17_10108_I2_R1


title: Small RNA Control_7

description:
Control_7
21_Control_blood_16_45775870_R1


title: Small RNA Control_10

description:
Control_10
24_Control_blood_19_45793789_R1


title: Small RNA Control_9

description:
Control_9
23_Control_blood_18_45794783_R1


title: Small RNA Stroke_17

description:
Stroke_17
21_10181_I6_R1


title: Small RNA Stroke_10

description:
Stroke_10
14_10104_eve_det_45791770_R1


title: Small RNA Control_2

description:
Control_2
16_Control_blood_11_45796768_R1


title: Small RNA Stroke_12

description:
Stroke_12
16_10103_I1_R1


title: Small RNA Control_3

description:
Control_3
17_Control_blood_12_45792774_R1


title: Small RNA Control_1

description:
Control_1
15_Control_blood_9_45784879_R1


title: Small RNA Stroke_11

description:
Stroke_11
15_40047_S16_R1_001


title: Small RNA Stroke_1

description:
Stroke_1
10_40039_S11_R1_001


title: Small RNA Stroke_9

description:
Stroke_9
13_90006_eve_det_45796767_R1


title: Stroke_22

data_processing:
Fastq files were generated within BaseSpace using FASTQ Generation, Version: 1.0.0
Quality control was performed using FastQC, version 0.11.2. Flexbar (with parameters “-q TAIL -qf Sanger -qw 4 -min-read-length 16”) served for adapter trimming and quality based filtering of all raw reads. Long RNA was aligned to the human reference transcriptome (ENSEMBL GRCh38 release 79) using salmon with default parameters.
Differential expression was determined using the R/DESeq2 package including the log2 fold change shrinkage estimation “apeglm” algorithm. Genes were considered differentially expressed at an adjusted p-value of < 0.05. The analysis was performed on the raw count tables (outliers already removed) with correction of covariates (age, batch, time2blood) in the model formula. Outliers were identified by sample clustering based on batch-corrected variance-stabilized expression.
Genome_build: ENSEMBL GRCh38 release 79
Supplementary_files_format_and_content: csv file used as input to DESeq2 analysis

extract_protocol:
RNA was extracted from 3 ml of whole blood of 484 PREDICT patients using Tempus Spin RNA isolation kit (Invitrogen, Thermo Fisher Scientific, Waltham MA, USA). Pre-sequencing Bioanalyzer 6000 (Agilent, Santa Clara CA, USA) tests showed high RNA quality (RIN values 7.9-9.9, median 8.8).
24 of the small RNA-sequenced samples served for PolyA-selected long mRNA sequencing (1000 ng total RNA per sample, TruSeq RNA library preparation kit (Illumina, San Diego CA, USA)). Sequencing was performed on the Illumina NextSeq 500 platform at the Hebrew University’s Center for Genomic Technologies.


title: Small RNA Stroke_3

description:
Stroke_3
1_10115_88_S4_R1_001


title: Stroke_19


title: Small RNA Stroke_8

description:
Stroke_8
13_10119_94_S14_R1_001


title: Small RNA Stroke_7

description:
Stroke_7
12_40035_S13_R1_001


title: Stroke_14


title: Small RNA Stroke_19

description:
Stroke_19
2_40058_mor_imp_45775868_R1


title: Small RNA Stroke_6

description:
Stroke_6
12_20042_eve_det_45788807_R1


title: Stroke_12


title: Small RNA Stroke_4

description:
Stroke_4
11_10102_mor_det_45794778_R1


title: Small RNA Stroke_5

description:
Stroke_5
11_40044_S12_R1_001


title: Stroke_11


title: Small RNA Stroke_16

description:
Stroke_16
2_10131_83_S5_R1_001


title: Stroke_24


title: Small RNA Stroke_2

description:
Stroke_2
10_90002_mor_det_45776883_R1


title: Control_10


title: Control_21


title: Stroke_23


title: Stroke_8


title: Stroke_4


title: Stroke_20


title: Stroke_6


title: Stroke_18


title: Stroke_3


title: Stroke_16


title: Stroke_17


title: Control_15


title: Stroke_13


title: Stroke_2


title: Stroke_1


title: cMYC-overexpressed NCI-H1963 cells_3 [ATAC-seq]

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ATAC-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option and filtered off an ATAC blacklist (Buenrostro et al., 2013) for mitochondrial DNA and homologous sequences.
Both fragment ends were shifted +4 nucleotides for positive strand and -5 for negative strand.
Peak were called with MACS2 with parameters --nomodel --extsize 100 --shift 50 --nolambda --keep-dup all
Peaks were filtered by MYC motif using findMotifsGenome function in Homer using four motif matrices MA0058.2 (MAX), MA0059.1 (MAX::MYC), MA0104.4 (MYCN), and MA0147.3 (MYC
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed

source_name: small cell lung cancer

growth_protocol: Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Five thousand cells were harvested and pre-treated with DNase I. Nuclei were isolated and resuspended in transposase reaction mixture carried out at 37C for 30 minutes followed by DNA purification with DNA Clean and Concentrator-25 (Zymo Research) according to manufacturer’s recommendation.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000 or Illumina NextSeq500 with paired-end 75bp reads.

tag: cell line

value: small cell lung cancer cell line

tag: overexpression vector

tag: grna vector

tag: cas9 vector


title: LacZ-overexpressed NCI-H1963 cells_1 [ATAC-seq]


title: ATAC for NCIH82 [ATAC-seq]


title: Stroke_9


title: Stroke_7


title: ATAC for NCIH2171 [ATAC-seq]


title: ATAC for NCIH524 [ATAC-seq]


title: LMyc-overexpressed with MYC gRNA 3 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgMYC3
H82_LMYCsgMYC3_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95.
Transcript abundance was estimated using kallisto (v0.45.0).
Genome_build: GRCh38.95
Supplementary_files_format_and_content: *_kallisto_abundance.txt: Tab-delimited text files include transcript abundance.

growth_protocol: NCI-H82 and NCI-H1963 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.


title: cMYC-overexpressed NCI-H1963 cells_1 [RNA-seq]

description:
NCIH1963_cMyc_rep1
H1963_cMYCrep1_RNA_S31
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: cMYC-overexpressed NCI-H1963 cells_3 [RNA-seq]

description:
NCIH1963_cMyc_rep3
H1963_cMYCrep3_RNA_S19
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LacZ-overexpressed NCI-H1963 cells_3 [RNA-seq]

description:
NCIH1963_LacZ_rep3
H1963_LacZrep3_RNA_S20
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: cMYC-overexpressed NCI-H1963 cells_2 [RNA-seq]

description:
NCIH1963_cMyc_rep2
H1963_cMYCrep2_RNA_S32
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LacZ-overexpressed NCI-H1963 cells_2 [RNA-seq]

description:
NCIH1963_LacZ_rep2
H1963_LacZrep2_RNA_S30
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 2 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgMYC2
H82_LMYCsgMYC2_RNA_S27
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: Control_5


title: LMy-overexpressed with non-target gRNA NCI-H82 cells_3 [RNA-seq]

description:
NCIH82_LMyc_sgNT2
H82_LMYCsgNT2_RNA_S25
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed with non-target gRNA NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgNT1
H82_LMYCsgNT1_RNA_S24
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_3 [RNA-seq]

description:
NCIH82_LacZ_sgNT2
H82_LacZsgNT2_RNA_S22
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: cMYC-overexpressed NCI-H1963 cells_1 [ATAC-seq]


title: LacZ-overexpressed NCI-H82 cells_1 [RNA-seq]

description:
NCIH82_LacZ
H82_LacZ_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: cMYC-overexpressed NCI-H1963 cells_2 [ATAC-seq]


title: LacZ-overexpressed NCI-H1963 cells_2 [ATAC-seq]


title: LacZ-overexpressed NCI-H1963 cells_3 [ATAC-seq]


title: Lomustine, 142_07 (miRNA-seq)

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
Basecalls performed using bcl2fastq2
Starting from raw FASTQ files, quality of reads obtained from each sample was assessed using FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapters were trimmed and reads with length <18bp or >27bp were filtered out with cutadapt (1.16).
Filtered reads were aligned to the miRBase 21 using SHRiMP2 (2.2.3) with the “mirna” option activated. Mature miRNAs were assigned to the fragments based on the mapping position on the hairpin miRNAs.
The number of unique-UMI mapped fragments were counted for each mature miRNA and the counts were normalized dividing them by the total number of sequenced fragments in a given sample and multiplying them for the mean value of sequenced fragments in all the samples.
Supplementary_files_format_and_content: Tab-delimited text file includes normalized expression values for every microRNAs and every sample.
Tab-delimited text file includes normalized expression values for each sample of microRNAs expressed in all samples

source_name: FFPE GBM tumor tissue

growth_protocol: Starting RNA was from formalin-fixed paraffin-embedded (FFPE) slices obtained from tumor tissue at first surgery

extract_protocol:
Total RNA for analysis of miRNA was extracted from formalin-free alcoholic-based fixative FineFIX® and paraffin-embedded samples by MiRNeasy FFPE minikit (Qiagen, Venlo, Netherlands). RNA was quantified with Qubit 3.0 and Qubit RNA HS Assay kits (Applied Biosystems).
350 ng of total RNA were processed with the QiAseq miRNA kit (QIAGEN) according to manufacturer instructions. miRNA-seq libraries were  assessed by capillary electrophoretic analysis with the Agilent 4200 Tape station and sequenced with 1X75bp-reads on an Illumina NextSeq500.

tag: overall survival (months)

tag: treatment

value: Lomustine

value: FFPE GBM tumor tissue


title: Regorafenib, 142_08 (miRNA-seq)

value: Regorafenib


title: Regorafenib, 142_02 (miRNA-seq)


title: Regorafenib, 142_03 (miRNA-seq)


title: Regorafenib, 142_06 (miRNA-seq)


title: Regorafenib, 140_05 (miRNA-seq)


title: ATAC for NCIH209 [ATAC-seq]


title: Lomustine, 142_01 (miRNA-seq)


title: Regorafenib, 138_01 (miRNA-seq)


title: ATAC for NCIH1963 [ATAC-seq]


title: LacZ-overexpressed NCI-H1963 cells_1 [RNA-seq]

description:
NCIH1963_LacZ_rep1
H1963_LacZrep1_RNA_S29
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 1 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_Lmyc_sgMYC1
H82_LMYCsgMYC1_RNA_S26
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: Regorafenib, 136_06 (miRNA-seq)


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LacZ_sgNT1
H82_LacZsgNT1_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: ATAC for CORL88 [ATAC-seq]


title: LMyc-overexpressed NCI-H82 cells_1 [RNA-seq]

description:
NCIH82_LMyc
H82_LMYC_RNA_S23
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: Regorafenib, 136_02 (miRNA-seq)


title: Regorafenib, 136_22 (miRNA-seq)


title: Lomustine, 142_05 (miRNA-seq)


title: Regorafenib, 136_10 (miRNA-seq)


title: Lomustine, 136_01 (miRNA-seq)


title: Lomustine, 140_02 (miRNA-seq)


title: Regorafenib, 135_19 (miRNA-seq)


title: Lomustine, 135_18 (miRNA-seq)


title: Regorafenib, 135_13 (miRNA-seq)


title: Regorafenib, 140_01 (miRNA-seq)


title: Regorafenib, 135_14 (miRNA-seq)


title: Lomustine, 135_12 (miRNA-seq)


title: Regorafenib, 135_10 (miRNA-seq)


title: Regorafenib, 134_09 (miRNA-seq)


title: Regorafenib, 134_08 (miRNA-seq)


title: Lomustine, 138_02 (miRNA-seq)


title: Lomustine, 138_03 (miRNA-seq)


title: Lomustine, 142_04 (miRNA-seq)


title: Lomustine, 136_08 (miRNA-seq)


title: Regorafenib, 136_05 (miRNA-seq)


title: Lomustine, 136_03 (miRNA-seq)


title: Lomustine, 135_08 (miRNA-seq)


title: Lomustine, 136_16 (miRNA-seq)


title: Regorafenib, 136_13 (miRNA-seq)


title: Lomustine, 135_07 (miRNA-seq)


title: Lomustine, 135_21 (miRNA-seq)


title: Regorafenib, 135_03 (miRNA-seq)


title: Regorafenib, 134_10 (miRNA-seq)


title: Regorafenib, 133_09 (miRNA-seq)


title: Lomustine, 135_09 (miRNA-seq)


title: Lomustine, 133_33 (miRNA-seq)


title: Regorafenib, 135_11 (miRNA-seq)


title: Regorafenib, 133_03 (miRNA-seq)


title: Lomustine, 134_07 (miRNA-seq)


title: Regorafenib, 133_29 (miRNA-seq)


title: Regorafenib, 133_31 (miRNA-seq)


title: Lomustine, 134_05 (miRNA-seq)


title: Regorafenib, 134_06 (miRNA-seq)


title: Lomustine, 133_24 (miRNA-seq)


title: Lomustine, 134_13 (miRNA-seq)


title: Lomustine, 134_04 (miRNA-seq)


title: Lomustine, 134_12 (miRNA-seq)


title: Lomustine, 133_27 (miRNA-seq)


title: Lomustine, 133_08 (miRNA-seq)


title: Regorafenib, 133_07 (miRNA-seq)


title: Lomustine, 133_04 (miRNA-seq)


title: Lomustine, 133_15 (miRNA-seq)


title: Lomustine, 133_18 (miRNA-seq)


title: Regorafenib, 133_16 (miRNA-seq)


title: Lomustine, 133_28 (miRNA-seq)


title: Lomustine, 133_22 (miRNA-seq)


title: Regorafenib, 133_06 (miRNA-seq)


title: Lomustine, 133_13 (miRNA-seq)


title: Lomustine, 142_07 (RNA-seq)

data_processing:
Basecalls performed using bcl2fastq2
The quality of sequenced reads obtained from each sample was assessed using FastQC software. UMI sequences were extracted using UMI-Tools (v1.0.1). Raw reads were trimmed to remove low-quality ends, polyA tails, and adapters sequences using bbduk (v38.76).
Trimmed reads were aligned to the reference human genome (GRCh38) using STAR (v2.7.3a).
After mapping, PCR duplicates were removed from the BAM files based on UMI sequence using UMI-tools. The number of reads mapping to each gene was determined using HTSeq-count (v0.11.2) and considering only reads aligned to the last exon of each transcript. Genes having on average less than 3 reads counts across all samples were filtered out. Reads counts were normalized with the TMM normalization method and subsequently for reads depth as count per million (CPM) using the cpm function implemented in edgeR.
Genome_build: version 99 of human reference genome GRCh38
Supplementary_files_format_and_content: Tab-delimited text file include CPM values for every gene and every sample.
Tab-delimited text file include CPM values for each sample of genes expressed in all samples with at least 10 CPM on average across all samples.

molecule: polyA RNA

extract_protocol:
Total RNA for analysis of mRNA was extracted from formalin-free alcoholic-based fixative FineFIX® and paraffin-embedded samples by MiRNeasy FFPE minikit (Qiagen, Venlo, Netherlands). RNA was quantified with Qubit 3.0 and Qubit RNA HS Assay kits (Applied Biosystems).
RNAseq libraries were prepared from 100 ng of total RNA using the QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) according to manufacturer’s instructions including the recommendation for FFPE samples. Briefly, after synthesizing the first strand using Oligo-dT and removing the RNA template, the second strand synthesis was initiated by random primer and DNA polymerase. During this step, Unique Molecular Identifiers (UMIs) were added to the libraries between the partial P5 adapter and the random priming sequence. After a magnetic beadbased  purification step, the libraries were then amplified by 16 PCR cycles and labelled with different single indexes. Quality and size of generated libraries were assessed using High sensitivity D1000 DNA assay Screen Tape (Agilent) and quantified by Qubit HS (Thermofisher). Libraries were then pooled at equimolar concentrations and sequenced on a NextSeq 500 sequencer (Illumina), by applying standard manufacturer protocols.


title: Regorafenib, 142_08 (RNA-seq)


title: Regorafenib, 133_25 (miRNA-seq)


title: Lomustine, 133_21 (miRNA-seq)


title: Lomustine, 133_20 (miRNA-seq)


title: Lomustine, 133_14 (miRNA-seq)


title: Lomustine, 133_02 (miRNA-seq)


title: Regorafenib, 133_19 (miRNA-seq)


title: Lomustine, 136_16 (RNA-seq)


title: Regorafenib, 136_22 (RNA-seq)


title: Regorafenib, 133_17 (miRNA-seq)


title: Regorafenib, 133_12 (miRNA-seq)


title: Regorafenib, 142_06 (RNA-seq)


title: Lomustine, 142_05 (RNA-seq)


title: Regorafenib, 136_13 (RNA-seq)


title: Regorafenib, 133_30 (miRNA-seq)


title: Regorafenib, 133_01 (miRNA-seq)


title: Regorafenib, 142_02 (RNA-seq)


title: Lomustine, 142_04 (RNA-seq)


title: Regorafenib, 136_10 (RNA-seq)


title: Regorafenib, 142_03 (RNA-seq)


title: Lomustine, 134_13 (RNA-seq)


title: Regorafenib, 140_01 (RNA-seq)


title: Lomustine, 135_21 (RNA-seq)


title: Lomustine, 140_02 (RNA-seq)


title: Lomustine, 138_03 (RNA-seq)


title: Lomustine, 136_08 (RNA-seq)


title: Regorafenib, 133_31 (RNA-seq)


title: Lomustine, 133_33 (RNA-seq)


title: Lomustine, 142_01 (RNA-seq)


title: Regorafenib, 140_05 (RNA-seq)


title: Lomustine, 138_02 (RNA-seq)


title: Regorafenib, 135_19 (RNA-seq)


title: Regorafenib, 136_02 (RNA-seq)


title: Regorafenib, 136_06 (RNA-seq)


title: Lomustine, 135_18 (RNA-seq)


title: Regorafenib, 136_05 (RNA-seq)


title: Regorafenib, 135_14 (RNA-seq)


title: Regorafenib, 135_13 (RNA-seq)


title: Lomustine, 135_08 (RNA-seq)


title: Regorafenib, 135_10 (RNA-seq)


title: Regorafenib, 135_03 (RNA-seq)


title: Regorafenib, 134_10 (RNA-seq)


title: Lomustine, 134_12 (RNA-seq)


title: Lomustine, 134_07 (RNA-seq)


title: Regorafenib, 134_09 (RNA-seq)


title: Regorafenib, 134_06 (RNA-seq)


title: Regorafenib, 133_29 (RNA-seq)


title: Lomustine, 136_03 (RNA-seq)


title: Lomustine, 134_05 (RNA-seq)


title: Lomustine, 136_01 (RNA-seq)


title: Lomustine, 135_09 (RNA-seq)


title: Lomustine, 133_27 (RNA-seq)


title: Regorafenib, 133_25 (RNA-seq)


title: Lomustine, 133_28 (RNA-seq)


title: Lomustine, 133_24 (RNA-seq)


title: Lomustine, 133_22 (RNA-seq)


title: Lomustine, 135_12 (RNA-seq)


title: Lomustine, 133_21 (RNA-seq)


title: Regorafenib, 133_19 (RNA-seq)


title: Lomustine, 133_18 (RNA-seq)


title: Regorafenib, 138_01 (RNA-seq)


title: Regorafenib, 133_17 (RNA-seq)


title: Lomustine, 135_07 (RNA-seq)


title: Regorafenib, 133_16 (RNA-seq)


title: Lomustine, 133_14 (RNA-seq)


title: Lomustine, 133_13 (RNA-seq)


title: Lomustine, 133_15 (RNA-seq)


title: Regorafenib, 133_12 (RNA-seq)


title: Regorafenib, 134_08 (RNA-seq)


title: Lomustine, 133_08 (RNA-seq)


title: Regorafenib, 133_30 (RNA-seq)


title: Regorafenib, 133_07 (RNA-seq)


title: Regorafenib, 133_06 (RNA-seq)


title: Lomustine, 133_02 (RNA-seq)


title: Regorafenib, 133_03 (RNA-seq)


title: Lomustine, 133_04 (RNA-seq)


title: Regorafenib, 133_01 (RNA-seq)


title: Lomustine, 133_20 (RNA-seq)


title: Regorafenib, 135_11 (RNA-seq)


title: Neutrophils from recovered patient 30946

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

description:
30946_neutros
30946_S2_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient

data_processing:
FASTQ polyA trimming
STAR alignment (version 2.7.3a): outFilterMismatchNmax 1, alignEndsType EndToEnd
Gene counts performed using quant3p
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix counts. Each column corresponds to gene counts for each generated BAM (after merging all resequenced samples and downsampled to 10 millions of reads for each one).

source_name: Neutrophils from peripheral blood

extract_protocol:
Cells were FACSorted in Lysis Binding Buffer and mRNA was extracted through Dynabeads polyT
RNA was sample-barcodad by a RT reaction. After, cDNA was purified with SPRIselect and amplified using the T7 promotor as template. RNA molecules were fragmented and purified again. Afterwards, a ssRNA adaptor was ligated to the 3’-end of the RNA fragments and, finally, cDNA was amplified.

tag: covid status

value: Recovered

tag: gender

value: Female

tag: hospitalization

value: Yes

tag: exitus

tag: haematological tumor

value: Acute myeloid leukemia

tag: number of cells


title: Neutrophils from recovered patient 30943

description:
30943_neutros
30943_S6_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient

tag: age

value: No


title: Neutrophils from recovered patient 30917

description:
30917_neutros
30917_S10_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient

value: Male


title: Neutrophils from recovered patient 30969

description:
30969_neutros
30969_S9_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient


title: Neutrophils from recovered patient 30913

description:
30913_neutros
30913_S12_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient


title: Non-classical monocytes from recovered patient 30969

description:
30969_monosNC
30969_S1_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient

source_name: Non-classical monocytes from peripheral blood


title: Non-classical monocytes from recovered patient 30943

description:
30943_monosNC
30943_S17_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Neutrophils from recovered patient 30916

description:
30916_neutros
30916_S4_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient


title: Classical monocytes from recovered patient 30969

description:
30969_monos
30969_S6_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient

source_name: Classical monocytes from peripheral blood


title: Classical monocytes from recovered patient 30969 (resequenced)

description:
30969_monos_reseq
30969_reseq411_S25_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Classical monocytes from recovered patient 30946

description:
30946_monos
30946_S4_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Classical monocytes from recovered patient 30915

description:
30915_monos
30915_S23_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Regorafenib, 133_09 (RNA-seq)

tag: tissue


title: Neutrophils from recovered patient 30915

description:
30915_neutros
30915_S19_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient


title: Classical monocytes from recovered patient 30913

description:
30913_monos
30913_S16_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Classical monocytes from recovered patient 30943

description:
30943_monos
30943_S3_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30917

description:
30917_monosNC
30917_S14_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30946 (resequenced)

description:
30946_dendM_reseq420
30946_reseq418_S20_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient

source_name: Myeloid dendritic cells from peripheral blood


title: Myeloid dendritic cells from recovered patient 30946

description:
30946_dendM
30946_S2_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Classical monocytes from recovered patient 30918

description:
30918_monos
30918_S15_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient

value: Monoclonal B-cell lymphocytosis


title: Neutrophils from recovered patient 30943 (resequenced)

description:
30943_neutros_reseq416
30943_reseq413_S25_R*_001.neutros
mRNA-3' from neutrophils sorted from recovered patient


title: Non-classical monocytes from recovered patient 30913 (resequenced)

description:
30913_monosNC_reseq417
30913_reseq412_S30_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Classical monocytes from recovered patient 30916

description:
30916_monos
30916_S24_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30969

description:
30969_dendM
30969_S5_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30969 (resequenced)

description:
30969_dendM_reseq420
30969_reseq418_S23_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Basophils from recovered patient 30969

description:
30969_basos
30969_S16_R*_001.basos
mRNA-3' from basophils sorted from recovered patient

source_name: Basophils from peripheral blood


title: Non-classical monocytes from recovered patient 30916

description:
30916_monosNC
30916_S19_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30916 (resequenced420)

description:
30916_monosNC_reseq420
30916_reseq412_S3_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30916 (resequenced417)

description:
30916_monosNC_reseq417
30916_reseq412_S33_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30915

description:
30915_dendM
30915_S19_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30917

description:
30917_dendM
30917_S20_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Non-classical monocytes from recovered patient 30915

description:
30915_monosNC
30915_S22_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30918

description:
30918_monosNC
30918_S20_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30918 (resequenced420)

description:
30918_monosNC_reseq420
30918_reseq412_S4_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Classical monocytes from recovered patient 30917

description:
30917_monos
30917_S20_R*_001.monos
mRNA-3' from classical monocytes sorted from recovered patient


title: Non-classical monocytes from recovered patient 30918 (resequenced417)

description:
30918_monosNC_reseq417
30918_reseq412_S34_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30943

description:
30943_dendM
30943_S3_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30913

description:
30913_dendM
30913_S16_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30916

description:
30916_dendM
30916_S22_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Basophils from recovered patient 30918

description:
30918_basos
30918_S18_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30918

description:
30918_dendM
30918_S17_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30943

description:
30943_dendP
30943_S20_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient

source_name: Plasmacytoid dendritic cells from peripheral blood


title: Basophils from recovered patient 30943

description:
30943_basos
30943_S19_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Myeloid dendritic cells from recovered patient 30943 (resequenced)

description:
30943_dendM_reseq420
30943_reseq418_S21_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from recovered patient


title: Basophils from recovered patient 30913

description:
30913_basos
30913_S8_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Non-classical monocytes from recovered patient 30913

description:
30913_monosNC
30913_S11_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from recovered patient


title: Basophils from recovered patient 30916

description:
30916_basos
30916_S13_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30916

description:
30916_dendP
30916_S19_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30946

description:
30946_dendP
30946_S3_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Basophils from recovered patient 30946

description:
30946_basos
30946_S9_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30913

description:
30913_dendP
30913_S14_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30918

description:
30918_dendP
30918_S22_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30913 (resequenced)

description:
30913_dendP_reseq420
30913_reseq417_S14_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Basophils from recovered patient 30917

description:
30917_basos
30917_S12_R*_001.basos
mRNA-3' from basophils sorted from recovered patient


title: Neutrophils from infected patient 30894

description:
30894_neutros
30894_S18_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient

value: Infected


title: Neutrophils from infected patient 31037

description:
31037_neutros
31037_S5_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Plasmacytoid dendritic cells from recovered patient 30915

description:
30915_dendP
30915_S17_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Classical monocytes from infected patient 30947

description:
30947_monos
30947_S2_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient

value: Diffuse large B-cell lymphoma


title: Neutrophils from infected patient 30878

description:
30878_neutros
30878_S14_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Plasmacytoid dendritic cells from recovered patient 30969

description:
30969_dendP
30969_S11_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Plasmacytoid dendritic cells from recovered patient 30918 (resequenced)

description:
30918_dendP_reseq420
30918_reseq417_S17_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Neutrophils from infected patient 30872

description:
30872_neutros
30872_S13_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Neutrophils from infected patient 30947

description:
30947_neutros
30947_S21_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Classical monocytes from infected patient 30879

description:
30879_monos
30879_S18_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Plasmacytoid dendritic cells from recovered patient 30917

description:
30917_dendP
30917_S15_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from recovered patient


title: Classical monocytes from infected patient 31037

description:
31037_monos
31037_S8_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Classical monocytes from infected patient 30878

description:
30878_monos
30878_S17_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Neutrophils from infected patient 30879

description:
30879_neutros
30879_S3_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Neutrophils from infected patient 30874

description:
30874_neutros
30874_S1_R*_001.neutros
mRNA-3' from neutrophils sorted from infected patient


title: Classical monocytes from infected patient 30894

description:
30894_monos
30894_S19_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Non-classical monocytes from infected patient 30894

description:
30894_monosNC
30894_S9_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Myeloid dendritic cells from infected patient 30947

description:
30947_dendM
30947_S7_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Non-classical monocytes from infected patient 30878

description:
30878_monosNC
30878_S12_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Myeloid dendritic cells from infected patient 30894

description:
30894_dendM
30894_S1_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Non-classical monocytes from infected patient 31037

description:
31037_monosNC
31037_S7_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Non-classical monocytes from infected patient 30879

description:
30879_monosNC
30879_S15_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Classical monocytes from infected patient 30872

description:
30872_monos
30872_S22_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Myeloid dendritic cells from infected patient 31037

description:
31037_dendM
31037_S14_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Classical monocytes from infected patient 30872 (resequenced)

description:
30872_monos_reseq
30872_reseq411_S33_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Myeloid dendritic cells from infected patient 30878

description:
30878_dendM
30878_S12_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Non-classical monocytes from infected patient 30874

description:
30874_monosNC
30874_S13_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Myeloid dendritic cells from infected patient 30874

description:
30874_dendM
30874_S13_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Basophils from infected patient 30947

description:
30947_basos
30947_S3_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Plasmacytoid dendritic cells from infected patient 30947

description:
30947_dendP
30947_S2_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Plasmacytoid dendritic cells from infected patient 30947 (resequenced)

description:
30947_dendP_reseq420
30947_reseq417_S8_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Basophils from infected patient 31037

description:
31037_basos
31037_S17_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Basophils from infected patient 30874

description:
30874_basos
30874_S6_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Basophils from infected patient 30878

description:
30878_basos
30878_S2_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Myeloid dendritic cells from infected patient 30879

description:
30879_dendM
30879_S15_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Plasmacytoid dendritic cells from infected patient 30894

description:
30894_dendP
30894_S1_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Basophils from infected patient 30878 (resequenced)

description:
30878_basos_reseq420
30878_reseq416_S6_R*_001.basos
mRNA-3' from basophils sorted from infected patient


title: Myeloid dendritic cells from infected patient 30872

description:
30872_dendM
30872_S23_R*_001.dendM
mRNA-3' from myeloid dendritic cells sorted from infected patient


title: Classical monocytes from infected patient 30874

description:
30874_monos
30874_S11_R*_001.monos
mRNA-3' from classical monocytes sorted from infected patient


title: Non-classical monocytes from infected patient 30872

description:
30872_monosNC
30872_S21_R*_001.monosNC
mRNA-3' from non-classical monocytes sorted from infected patient


title: Plasmacytoid dendritic cells from infected patient 30879

description:
30879_dendP
30879_S9_R*_001.dendP
mRNA-3' from plasmacytoid dendritic cells sorted from infected patient


title: Basophils from infected patient 30879

description:
30879_basos
30879_S7_R*_001.basos
mRNA-3' from basophils sorted from infected patient