title: CD34+ (SLX.19173.i711_i508)

tag: tissue

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-150

status: Public on Nov 17 2022

type: RNA

city: Neuherberg

first: Karolina

last: Worf

address: Ingolstaedter Landstr. 1

department: Computational Health

country: Germany

institute: Helmholtz Zentrum Muenchen

description: DLPFC expression case sample

hyb_protocol: Hybridization was conducted by the Australian Genome Research Facility (AGRF; Melbourne, Australia), which prepared samples for hybridization with a standard probe cocktail and hybridized them overnight in an Affymetrix Human Exon 1.0 ST v2 Array.

scan_protocol: Scanning of the arrays was carried out by the Australian Genome Research Facility (AGRF; Melbourne, Australia) according to the protocol provided by Affymetrix.

data_processing:
Data were processed using the oligo package version 1.50.0 in R 3.6.1. Oligo’s Robust Multichip Average (RMA) algorithm was used for background adjustment, quantile normalisation and summarization (using median-polish) at the probeset level. Probesets that did not contain start or stop information, were labelled as controls in the current NetAffx annotation for Affymetrix’s HuEx 1.0 ST v2 array, were cross-hybridized (number_cross_hyb_probes ≥ 1), or were located on X, Y and M chromosomes were removed from the data set. The SVA package version 3.34.0 in R was used for batch correction of known and hidden batches.
HuEx-1_0-st-v2.r2.pgf

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: postmortem dorsolateral prefrontal cortex tissue

label_protocol: Labeling was performed by the Australian Genome Research Facility (AGRF; Melbourne, Australia), which performed cRNA labeling of the samples with biotin using the Affymetrix Synthesis and Labeling Kit.

growth_protocol: Subjects were refrigerated within 5 hours of being found. Brodmann area 9 (BA 9) was taken from the lateral surface of the frontal lobe from an area comprising the middle frontal superior gyrus to the inferior frontal sulcus of the left hemisphere. After removal at autopsy, brain tissue was rapidly processed and frozen at -70°C using a standardized procedure that minimizes autolytic effects.

extract_protocol: Total RNA was isolated from ∼100 mg frozen gray matter using 1.0 ml TRIzol reagent (Life Technologies). After homogenization and phase separation, an equal volume of 70% ethanol was added to the aqueous phase. RNA isolation was performed using RNeasy minikits (Qiagen), and all samples were treated with DNase by column digestion. RNA quantity and quality were analyzed by spectrophotometry with NanoDrop (Thermo Fischer Science) and by determination of RNA integrity numbers (RINs) using an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples with RIN ⩾ 6.00 were used for further analysis with Affymetrix Human Exon 1.0 ST v2 arrays (Affymetrix).

treatment_protocol: not applicable

tag: sample

tag: diagnosis

value: SCZ

tag: dx

value: case

tag: age

tag: Sex

value: M

tag: ph

tag: pmi

tag: rin

tag: suicide

value: N

tag: type of death

value: Natural

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs

tag: t2d prs

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: CD34+ (SLX.19173.i702_i508)

type: SRA

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
Reads were mapped to the Homo sapiens genome (EMSEMBL GRCh38 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Assembly: GRCh38
Supplementary files format and content: HTSeq counts/gene counts (.txt)

molecule: polyA RNA

source_name: mobilised peripheral blood

growth_protocol: LT-HSCs (CD34+/CD38-/CD45RA-/CD90+/CD49f+), ST-HSCs( CD34+/CD38-/CD45RA-/CD90-/CD49f-) or CD34+ were cultured for 62 h in media mimicking gene therapy conditions: GMP grade SCGM (CellGenix) supplemented with L-Glutamine (1%) (Thermo Fisher Scientific), Pen/Strep (1%) (Thermo Fisher Scientific) in addition to the following cytokines: SCF (300ng/ml), Flt-3L (300ng/ml), IL-3 (60ng/ml) and TPO (100ng/ml).  Flow-sorted cells were cultured in this medium in a 96 well flat bottom plate coated with 33.3ug/ml of Retronectin (Takara). The 62 hr protocol consisted of pre-stimulation in gene therapy media (24 hr) followed by transduction with a lentiviral vector containing GFP (14 hr), an interim incubation in gene therapy media without the vector (10 hr) and a second hit of transduction (14 hr).

extract_protocol:
Single cells were directly sorted in lysis buffer according to Smart-Seq2 protocol (Picelli et al., Nat protocol, 2014). A lysis buffer was prepared of 20U/l SUPER-In RNase inhibitor (Thermo Fisher Scientific) and 0.4% Triton-X100 (ratio of 1:19). The lysis buffer was added to a mix of DTT (Thermo Fisher Scientific) (final concentration of 0.57mM), dNTPs (Invitrogen) (final concentration 0.11mM) and nuclease free water (Thermo Fisher Scientific) and 4ul aliquoted per well in a 96 well PCR plate and stored at -80°C.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For 62 h culture durations a separate condition was included where cells were cultured with 200nM Palbociclib (PD033299).

tag: tissue

value: mobilised peripheral blood

tag: cell type

tag: time

tag: condition

value: GFP+PD-

tag: batch

tag: donor

tag: sample type

value: Single cell


title: CD34+ (SLX.19173.i703_i508)


title: CD34+ (SLX.19173.i701_i508)


title: DLPFC expression from sample 9-152

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

tag: ph

tag: pmi

tag: rin

tag: suicide

value: Y

value: Violent


title: DLPFC expression from sample 9-129

description: DLPFC expression control sample

value: CTL

value: control

tag: type of death

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs

tag: t2d prs


title: LT-HSC (SLX.19173.i712_i507)

tag: tissue

tag: cell type

value: LT-HSC

tag: time

tag: condition

value: GFP+PD+

tag: batch

tag: donor

tag: sample type


title: LT-HSC (SLX.19173.i710_i507)


title: LT-HSC (SLX.19173.i709_i507)


title: LT-HSC (SLX.19173.i711_i507)


title: LT-HSC (SLX.19173.i708_i507)


title: LT-HSC (SLX.19173.i707_i507)


title: DLPFC expression from sample 9-128

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

tag: ph

tag: pmi

tag: rin

tag: suicide


title: DLPFC expression from sample 9-151

description: DLPFC expression control sample

tag: type of death

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-127

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: tissue


title: DLPFC expression from sample 9-122

description: DLPFC expression case sample

tag: dx

tag: age

tag: Sex

value: F

value: Non-violent


title: DLPFC expression from sample 9-119

description: DLPFC expression control sample

tag: ph

tag: pmi

tag: rin


title: LT-HSC (SLX.19173.i706_i507)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: LT-HSC (SLX.19173.i705_i507)


title: DLPFC expression from sample 9-115

description: DLPFC expression case sample

value: MDD

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs


title: DLPFC expression from sample 9-124

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: SCZ

tag: dx

value: case

tag: age

tag: Sex

tag: ph

tag: pmi

tag: t2d prs

tag: tissue


title: LT-HSC (SLX.19173.i703_i507)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-117

description: DLPFC expression case sample

tag: rin

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: LT-HSC (SLX.19173.i704_i507)


title: LT-HSC (SLX.19173.i701_i507)


title: ST-HSC (SLX.19173.i712_i506)

value: ST-HSC


title: LT-HSC (SLX.19173.i702_i507)


title: DLPFC expression from sample 9-113

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

value: M

tag: ph

tag: pmi

value: N

value: Natural

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-094

description: DLPFC expression case sample

tag: rin

tag: suicide

tag: tissue

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: DLPFC expression from sample 9-112

description: DLPFC expression case sample

tag: type of death

tag: adhd prs

tag: bd prs


title: ST-HSC (SLX.19173.i711_i506)

value: mobilised peripheral blood

tag: cell type

tag: time

tag: condition

value: GFP+PD-

tag: batch

tag: donor

tag: sample type

value: Single cell


title: DLPFC expression from sample 9-109

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

value: Y

value: Violent

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: ST-HSC (SLX.19173.i710_i506)

tag: tissue


title: DLPFC expression from sample 9-089

description: DLPFC expression control sample

value: CTL

value: control

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-086

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: dx


title: DLPFC expression from sample 9-134

description: DLPFC expression case sample

tag: age

tag: Sex

tag: cdg prs


title: DLPFC expression from sample 9-116

description: DLPFC expression control sample

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: ST-HSC (SLX.19173.i709_i506)

tag: tissue

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: ST-HSC (SLX.19173.i708_i506)


title: DLPFC expression from sample 9-126

description: DLPFC expression case sample

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: ST-HSC (SLX.19173.i707_i506)


title: ST-HSC (SLX.19173.i706_i506)


title: DLPFC expression from sample 9-105

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: ST-HSC (SLX.19173.i705_i506)

tag: tissue

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-096

description: DLPFC expression case sample

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-085

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

value: F

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: DLPFC expression from sample 9-087

description: DLPFC expression case sample

tag: ph

tag: pmi

tag: tissue


title: DLPFC expression from sample 9-083

description: DLPFC expression control sample

tag: rin

tag: suicide

tag: type of death


title: ST-HSC (SLX.19173.i702_i506)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-088

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: ST-HSC (SLX.19173.i701_i506)

tag: tissue


title: DLPFC expression from sample 9-078

description: DLPFC expression case sample

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: DLPFC expression from sample 9-077

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: dx


title: LT-HSC (SLX.19173.i712_i505)

tag: cell type

value: LT-HSC

tag: time

tag: condition

value: NT

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-079

description: DLPFC expression case sample

value: MDD

tag: age

tag: Sex

tag: ph

tag: pmi

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs

tag: tissue


title: LT-HSC (SLX.19173.i709_i505)


title: DLPFC expression from sample 9-069

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: rin

tag: suicide

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: ST-HSC (SLX.19173.i703_i506)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: ST-HSC (SLX.19173.i704_i506)


title: DLPFC expression from sample 9-061

description: DLPFC expression control sample

tag: dx

tag: age

tag: Sex

tag: ph

tag: pmi

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: LT-HSC (SLX.19173.i710_i505)

tag: tissue


title: DLPFC expression from sample 9-073

description: DLPFC expression control sample

tag: sample

tag: diagnosis

tag: rin

tag: suicide

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: LT-HSC (SLX.19173.i707_i505)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: DLPFC expression from sample 9-064

description: DLPFC expression case sample

value: BPD

tag: dx

value: case

tag: age

tag: Sex

tag: ph

tag: pmi

value: Non-violent

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: LT-HSC (SLX.19173.i706_i505)

tag: tissue


title: LT-HSC (SLX.19173.i711_i505)


title: DLPFC expression from sample 9-060

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: M

tag: rin

tag: suicide

value: N

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: DLPFC expression from sample 9-053

description: DLPFC expression control sample

tag: dx

tag: age

tag: Sex

value: Natural

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: LT-HSC (SLX.19173.i704_i505)

value: mobilised peripheral blood

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: LT-HSC (SLX.19173.i705_i505)

tag: tissue

value: Single cell


title: DLPFC expression from sample 9-048

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: ph

tag: pmi

tag: rin

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-065

description: DLPFC expression control sample

tag: dx

tag: age

tag: Sex

tag: suicide

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: DLPFC expression from sample 9-068

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: tissue


title: LT-HSC (SLX.19173.i703_i505)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: LT-HSC (SLX.19173.i701_i505)


title: Nip-scATAC-HS-Rep2

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

country: China

institute: Chinese Academy of Agricultrual Sciences

library_source: genomic

data_processing:
FASTQ files of each sample were firstly processed by using cellranger-atac (v.1.2.0) count pipeline coupled with Oryza sativa Nip genome to generate fragment and cell files, respectively.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: cell ranger format

molecule: genomic DNA

organism: Oryza sativa

source_name: nuclei

growth_protocol: Rice Nip seeds were soaked in water in the dark until germination, and then cultured in Hoagland’s Complete Nutrient Solution for 3 days (28℃, 10-h-light/14-h dark cycles, 300 lux).

extract_protocol:
Primary root tips with 5 mm in length from the 3-day-old rice seedlings were harvested and fixed with cold paraformaldehyde solution (2%) for 30 min. Then the root tips were transferred to Dounce grinder (kimble), which was filled with cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 1 mM MgCl2, 1% BSA) and 0.2% Tween 20, 0.2% NP-40, 0.0075% Digitonin. 0.5% 2-ME (v/v) were added and then the roots were grinded completely. The homogenate was filtered with a 20 μm mesh (Sysmex) following by centrifuge at 480 rcf for 5 min at 4℃. After removing supernatant, 1% BSA buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA (v/v)) was added to resuspend pellet. Then, the mixture was placed on 80% percoll and following by centrifuge at 300 rcf for 25 min at 4℃. After removing 150 μl supernatant, nuclei were transferred to a new eppendorf tube and washed twice with 1% BSA buffer. The nuclei were resuspended in chilled Diluted Nuclei Buffer (10x Genomics, PN-2000153). The nuclei were stained by DAPI and trypan to check the quality and quantity.
The isolated nuclei were processed immediately through the 10x Chromium Single Cell Platform according to the manufacturer’s instructions (10x Genomics). Briefly, 16,000 resuspended nuclei (concentration 3,000-7,000 nuclei/μl) were combined with ATAC Buffer and ATAC Tn5 transposase (10x Genomics) to form a transposition mix. After incubation for 30 min at 37 °C, barcoding reagent and enzyme (10x Genomics) were added, and the resulting mix were loaded onto a single-cell chip, which was subsequently placed into a Chromium Single Cell Controller instrument for library construction. Quantification of DNA library was done by Agilent 2100 Bioanalyzer, then sequenced with an Illumina Hiseq2000 sequencer.

value: 5mm root tip

tag: Stage

tag: cultivar

value: Nipponbare


title: DLPFC expression from sample 9-047

description: DLPFC expression case sample

tag: dx

tag: age

tag: Sex

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: CD34+ (SLX.19173.i712_i504)

tag: tissue

tag: cell type

tag: time

tag: condition


title: LT-HSC (SLX.19173.i702_i505)

tag: batch

tag: donor

tag: sample type


title: Nip-scATAC-Normal-Rep2

tag: Stage

tag: cultivar


title: DLPFC expression from sample 9-037

description: DLPFC expression control sample

tag: sample

tag: diagnosis

value: CTL

tag: dx

tag: age

tag: Sex

tag: ph

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: Nip-scATAC-Normal-Rep1

tag: tissue


title: CD34+ (SLX.19173.i710_i504)

tag: cell type

tag: time

tag: condition

tag: batch


title: Nip-ATAC-HS-Rep2

data_processing:
FASTQ files were mapped to Oryza sativa Nip genome by using Bowtie2  with “-N 1 -X 2000” parameters. MACS2 software was used to call peaks with -q 0.05 --nomodel --extsize 150. We defined differential peaks between two groups with MAnorm software  by using abs(Mvalue)>=1, M value is the log2foldchange of normalization chromatin accessibility signal between two Normal and HS samples.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: Bigwig file format containing peak information

extract_protocol:
Primary root tips with 5 mm in length from the 3-day-old rice seedlings were harvested and fixed with cold paraformaldehyde solution (2%) for 30 min. Then the root tips were transferred to Dounce grinder (kimble), which was filled with cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 1 mM MgCl2, 1% BSA) and 0.2% Tween 20, 0.2% NP-40, 0.0075% Digitonin. 0.5% 2-ME (v/v) were added and then the roots were grinded completely. The homogenate was filtered with a 20 μm mesh (Sysmex) following by centrifuge at 480 rcf for 5 min at 4℃. After removing supernatant, 1% BSA buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA (v/v)) was added to resuspend pellet. Then, the mixture was placed on 80% percoll and following by centrifuge at 300 rcf for 25 min at 4℃. After removing 150 μl supernatant, nuclei were transferred to a new eppendorf tube and washed twice with 1% BSA buffer.
Bulk ATAC-seq was performed as described previously (Liang et al., 2021 BMC biology. PMID: 33740972)

tag: Stage

tag: cultivar


title: DLPFC expression from sample 9-039

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: pmi

tag: rin

tag: suicide

value: Y

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: CD34+ (SLX.19173.i708_i504)

tag: donor

tag: sample type


title: Nip-ATAC-Normal-Rep2

tag: tissue


title: CD34+ (SLX.19173.i709_i504)

tag: cell type

tag: time


title: Nip-ATAC-HS-Rep1


title: Nip-ATAC-Normal-Rep1


title: DLPFC expression from sample 9-029

description: DLPFC expression control sample

tag: dx

value: control

tag: age

tag: Sex

tag: ph

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: CD34+ (SLX.19173.i707_i504)

tag: condition

tag: batch


title: CD34+ (SLX.19173.i706_i504)


title: CD34+ (SLX.19173.i711_i504)


title: DLPFC expression from sample 9-052

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: pmi

tag: rin

tag: suicide

value: Violent

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: LT-HSC (SLX.19173.i708_i505)

tag: tissue

tag: cell type

value: LT-HSC

tag: time

value: NT

tag: donor

tag: sample type


title: CD34+ (SLX.19173.i705_i504)


title: DLPFC expression from sample 9-032

description: DLPFC expression case sample

value: BPD

tag: dx

tag: age

tag: Sex

tag: ph

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: DLPFC expression from sample 9-031

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: MDD

value: case

value: F

tag: pmi

tag: rin

tag: suicide

tag: adhd prs

tag: bd prs


title: DLPFC expression from sample 9-120

description: DLPFC expression case sample

value: SCZ

tag: ea prs

tag: t2d prs

tag: tissue


title: CD34+ (SLX.19173.i703_i504)

tag: cell type

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: HEK293T, SARS2 nsp1 Induced, R B3

city: Amherst

first: Mandy

last: Muller

state: MA

address: 639 North Pleasant Street

department: Microbiology

country: USA

institute: Univ of Massachusetts Amherst

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS2 nsp1 protein under a doxycycline inducible promoter, induced, B is second set of triplicates
Mock vs SARS2.xlsx

data_processing:
Using the Galaxy Server (Galaxy Version 2.4.5+galaxy1) all processing was done using default parameters, reads wre aligned to human genome (hg38) using Bowtie2
After alignment transcripts were assembled and differential expression analysis were performed sing Cufflink and Cuffdiff. Data normalization was done using FPKM methodology using gene length and total number of mapped reads.
Analysis was performed between induced conditions vs the uninduced conditions.
Assembly: UCSC Human Genome Hg38
Supplementary files format and content: Excel Sheets, tabular data with FPKM, log2(fold_change), p_value, and q_value, additional calulcations for the -log10(p_value)

source_name: kidney; Embryo

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

extract_protocol:
RNA was harvested using TRIzol Reagent and RNA was harvested following manufacturer's protocol
RNA libraries were prepared using NextSeq500 Mid-150 cycle kit by genomic resources lab at University of Massachusetts Amherst

treatment_protocol: Samples were either induced with 1ul/ml doxycycline or left in an uninduced state and collected 24hrs (Uninduced samples were collected at same time as first group of induced replicates)

value: kidney; Embryo

tag: cell line

value: epithelial

tag: genotype

value: nsp1 Induced

tag: treatment

value: Lentiviral Transduced nsp1, 1ul/ml Doxycycline


title: HEK293T, SARS2 nsp1 Induced, R B1


title: HEK293T, SARS2 nsp1 Induced, R A3

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS2 nsp1 protein under a doxycycline inducible promoter, induced, A is first set of triplicates
Mock vs SARS2.xlsx


title: HEK293T, SARS2 nsp1 Induced, R A2


title: DLPFC expression from sample 9-015

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

value: M

tag: ph

tag: pmi

tag: type of death

value: Non-violent

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: HEK293T, SARS2 nsp1 Induced, R A1

tag: tissue

tag: cell type


title: Nip-scATAC-HS-Rep1

value: 5mm root tip

tag: Stage

tag: cultivar

value: Nipponbare


title: CD34+ (SLX.19173.i702_i504)

value: mobilised peripheral blood

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type

value: Single cell


title: DLPFC expression from sample 9-030

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

tag: rin

tag: suicide

value: Y

value: Violent

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: CD34+ (SLX.19173.i701_i504)

tag: tissue

tag: cell type

value: NT


title: HEK293T, SARS2 nsp1 Uninduced, R3

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS2 nsp1 protein under a doxycycline inducible promoter, uninduced
Mock vs SARS2.xlsx

tag: cell line

tag: genotype

value: nsp1 uninduced

tag: treatment

value: Lentiviral Transduced nsp1


title: LT-HSC (SLX.19173.i711_i503)

value: LT-HSC

tag: time

tag: condition

value: GFP-PD-

tag: batch

tag: donor

tag: sample type


title: HEK293T, SARS2 nsp1 Uninduced, R2

value: kidney; Embryo

value: epithelial


title: DLPFC expression from sample 9-026

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: SCZ

tag: dx

value: case

tag: age

tag: Sex

tag: ph

tag: pmi

tag: type of death

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs


title: LT-HSC (SLX.19173.i710_i503)

tag: tissue

tag: cell type

tag: time


title: DLPFC expression from sample 9-098

description: DLPFC expression control sample

value: CTL

value: control

value: M

tag: rin

tag: suicide

value: N

value: Natural

tag: adhd prs

tag: bd prs

tag: ea prs

tag: t2d prs


title: DLPFC expression from sample 9-012

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: BPD

tag: dx

tag: age

tag: Sex

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: LT-HSC (SLX.19173.i709_i503)

value: mobilised peripheral blood

tag: condition

tag: batch

tag: donor

tag: sample type

value: Single cell


title: LT-HSC (SLX.19173.i708_i503)

tag: tissue

tag: cell type


title: HEK293T, SARS1 nsp1 Induced, R B3

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS1 nsp1 protein under a doxycycline inducible promoter, induced, B is second set of triplicates
Mock vs SARS1.xlsx

tag: cell line

tag: genotype

value: nsp1 Induced

tag: treatment

value: Lentiviral Transduced nsp1, 1ul/ml Doxycycline


title: HEK293T, SARS1 nsp1 Induced, R B2


title: LT-HSC (SLX.19173.i707_i503)

value: LT-HSC

tag: time


title: HEK293T, SARS1 nsp1 Induced, R B1


title: HEK293T, SARS2 nsp1 Uninduced, R1

value: nsp1 uninduced

value: Lentiviral Transduced nsp1


title: DLPFC expression from sample 9-022

description: DLPFC expression case sample

value: F

tag: ph

tag: pmi

tag: rin

tag: suicide

value: Y

tag: type of death

value: Non-violent

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs


title: HEK293T, SARS1 nsp1 Induced, R A3

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS1 nsp1 protein under a doxycycline inducible promoter, induced, A is first set of triplicates
Mock vs SARS1.xlsx

tag: tissue

value: kidney; Embryo

tag: cell type

value: epithelial


title: LT-HSC (SLX.19173.i706_i503)

tag: condition

value: GFP-PD-

tag: batch

tag: donor

tag: sample type


title: LT-HSC (SLX.19173.i705_i503)

tag: time


title: HEK293T, SARS1 nsp1 Induced, R A2

tag: cell line

tag: genotype

tag: treatment


title: LT-HSC (SLX.19173.i704_i503)


title: HEK293T, SARS1 nsp1 Uninduced, R3

description:
HEK 293T cells lentivirally transduced with beta coronavirus SARS1 nsp1 protein under a doxycycline inducible promoter, uninduced
Mock vs SARS1.xlsx


title: HEK293T, SARS1 nsp1 Induced, R A1


title: LT-HSC (SLX.19173.i703_i503)


title: LT-HSC (SLX.19173.i702_i503)


title: DLPFC expression from sample 9-034

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: SCZ

tag: dx

value: case

tag: age

tag: Sex

value: M

tag: ph

tag: pmi

tag: rin

tag: suicide

value: N

tag: type of death

tag: adhd prs

tag: t2d prs


title: DLPFC expression from sample 9-006

description: DLPFC expression case sample

value: Violent

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs

tag: tissue

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: HEK293T, SARS1 nsp1 Uninduced, R2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: LT-HSC (SLX.19173.i701_i503)

value: mobilised peripheral blood

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type

value: Single cell


title: HEK293T, MERS nsp1 Induced, R B3

description:
HEK 293T cells lentivirally transduced with beta coronavirus MERS nsp1 protein under a doxycycline inducible promoter, induced, B is second set of triplicates
Mock vs MERS.xlsx

value: nsp1 Induced

value: Lentiviral Transduced nsp1, 1ul/ml Doxycycline


title: ST-HSC (SLX.19173.i711_i502)

value: ST-HSC

value: NT


title: HEK293T, MERS nsp1 Induced, R B2


title: ST-HSC (SLX.19173.i710_i502)


title: DLPFC expression from sample 9-003

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: MDD

tag: dx

tag: age

tag: Sex

tag: ph

tag: pmi

tag: rin

tag: suicide

value: Y

tag: type of death

tag: adhd prs

tag: t2d prs


title: HEK293T, MERS nsp1 Induced, R A3

description:
HEK 293T cells lentivirally transduced with beta coronavirus MERS nsp1 protein under a doxycycline inducible promoter, induced, A is first set of triplicates
Mock vs MERS.xlsx

tag: tissue

value: kidney; Embryo

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ST-HSC (SLX.19173.i709_i502)

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type


title: ST-HSC (SLX.19173.i708_i502)


title: HEK293T, MERS nsp1 Induced, R A2

value: epithelial


title: ST-HSC (SLX.19173.i707_i502)


title: HEK293T, MERS nsp1 Induced, R A1


title: HEK293T, MERS nsp1 Uninduced, R3

description:
HEK 293T cells lentivirally transduced with beta coronavirus MERS nsp1 protein under a doxycycline inducible promoter, uninduced
Mock vs MERS.xlsx

value: nsp1 uninduced

value: Lentiviral Transduced nsp1


title: ST-HSC (SLX.19173.i706_i502)


title: ST-HSC (SLX.19173.i705_i502)


title: HEK293T, MERS nsp1 Induced, R B1


title: HEK293T, MERS nsp1 Uninduced, R2


title: ST-HSC (SLX.19173.i704_i502)


title: ST-HSC (SLX.19173.i703_i502)


title: HEK293T, MERS nsp1 Uninduced, R1


title: HEK293T, 229E nsp1 Induced, R B3

description:
HEK 293T cells lentivirally transduced with alpha coronavirus 229E nsp1 protein under a doxycycline inducible promoter, induced, B is second set of triplicates
Mock vs 229E.xlsx


title: HEK293T, 229E nsp1 Induced, R B1


title: HEK293T, 229E nsp1 Induced, R A3

description:
HEK 293T cells lentivirally transduced with alpha coronavirus 229E nsp1 protein under a doxycycline inducible promoter, induced, A is first set of triplicates
Mock vs 229E.xlsx


title: LT-HSC (SLX.19173.i729_i522)

value: LT-HSC


title: HEK293T, 229E nsp1 Induced, R A2


title: LT-HSC (SLX.19173.i727_i522)


title: HEK293T, SARS1 nsp1 Uninduced, R1


title: HEK293T, 229E nsp1 Induced, R A1


title: HEK293T, 229E nsp1 Uninduced, R3

description:
HEK 293T cells lentivirally transduced with alpha coronavirus 229E nsp1 protein under a doxycycline inducible promoter, uninduced
Mock vs 229E.xlsx


title: CD34+ (SLX.19173.i724_i522)


title: LT-HSC (SLX.19173.i726_i522)


title: HEK293T, 229E nsp1 Induced, R B2


title: HEK293T, 229E nsp1 Uninduced, R1


title: HEK293T, 229E nsp1 Uninduced, R2


title: CD34+ (SLX.19173.i722_i522)


title: DLPFC expression from sample 9-001

description: DLPFC expression control sample

tag: sample

tag: diagnosis

value: CTL

tag: dx

value: control

tag: age

tag: Sex

value: M

tag: ph

value: Natural

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs


title: cutnrun-HSA-V5-Rep2

city: RTP

first: Nicholas

last: Dietrich

state: NC

address: 111 TW Alexander

department: ESCBL

institute: NIH

data_processing:
Library strategy: CUT&RUN
Adapter sequences were trimmed from reads using Cutadapt (Martin 2011) and low quality reads were removed from analysis using Sickle 1.33 (Joshi et al 2011).
CUT&RUN reads were aligned to the hg19 genome assembly using Bowtie2. Reads were deduplicated with Picard and processed with Samtools.
Peaks were called using MACS2 version 2.2 with the following setting: p-value cutoff 0.0001 and minimum score greater than 5.
bigwig files were generated…
Genome_build: hg19
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: bigwig files

source_name: SW-13 cells

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
CUT&RUN was performed as described by Skene et al 2017). 300,000 cells per sample were isolated and anti-V5 antibody (Invitrogen) was used for all samples. pAG-Mnase was added to each sample to a final concentration of 700ng/ml. Chromatin digestion was performed after addition of CaCl2 and DNA digestion was halted Digestion was allowed to proceed on ice for 30 minutes and halted by the addition of 2X Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50 micrograms/ml RNase A, 50 micrograms/ml glycogen). DNA was extracted by the addition of SDS (final concentration 0.1%) and proteinase K (final 10 micrograms/ml) and incubating at 55 degrees for 1 hour. The material was extracted with one equivalent volume of Phenol/Chloroform/Isoamyl Alcohol 25:24:1 (ThermoFisher Scientific), precipitated and washed with 100% ethanol. DNA was resuspended in 150 microliters of water followed by the addition of 75 microliters of AMPure XP beads (Beckmann Agencourt). Beads were mixed and incubated for 5 minutes, added to a magnet for 2 minutes and the supernatant was collected as size selected fragments. The DNA was precipitated by adding 700 microliters of ethanol and 1 ul of 20 mg/ml glycogen and spun at 16000xg for 10 minutes. The pellet was washed with 70% ethanol and resuspended in 20 microliters of 10mM Tris-HCl, 1mM EDTA.
Libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit according to manufacturer's instructions. Libraries were PCR amplified for 12 cycles according to the manufacturer's instructions.

treatment_protocol: All replicates were treated with Doxycycline for 24 hours.

tag: cell type

value: adrenacorticoid carcinoma cell line

tag: chip antibody

value: Anti-V5 (Invitrogen, R96025)

tag: treatment

value: treated with Dox for 24 hours

tag: cell line


title: ST-HSC (SLX.19173.i720_i522)

tag: tissue

value: mobilised peripheral blood

tag: time

tag: condition

tag: batch

tag: donor

tag: sample type

value: Single cell


title: DLPFC expression from sample 9-002

description: DLPFC expression case sample

tag: sample

tag: diagnosis

value: SCZ

tag: dx

value: case

tag: age

tag: Sex

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

value: Violent

tag: adhd prs

tag: t2d prs

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: ST-HSC (SLX.19173.i712_i502)

tag: tissue

tag: cell type

value: ST-HSC

tag: time

value: NT


title: DLPFC expression from sample 9-008

description: DLPFC expression case sample

value: BPD

value: F

value: N

value: Non-violent

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: ea prs


title: DLPFC expression from sample 9-038

description: DLPFC expression case sample

tag: sample

tag: diagnosis

tag: dx

tag: age

tag: Sex

value: M

value: Y


title: cutnrun-HSA-V5-Rep1

value: adrenacorticoid carcinoma cell line

tag: chip antibody

tag: treatment

tag: cell line


title: ST-HSC (SLX.19173.i701_i502)

tag: tissue

tag: condition

tag: batch

tag: donor

tag: sample type


title: ST-HSC (SLX.19173.i719_i522)

tag: cell type

tag: time


title: cutnrun-BRG1-V5-Rep2

value: Anti-V5 (Invitrogen, R96025)


title: CD34+ (SLX.19173.i723_i522)


title: LT-HSC (SLX.19173.i729_i521)

value: LT-HSC


title: LT-HSC (SLX.19173.i728_i521)

value: mobilised peripheral blood


title: ST-HSC (SLX.19173.i716_i522)

value: Single cell


title: BCL7-siABC-Dox-A

description: Individual SW13 cell line expressing iBRG1-V5 construct after continuous selection of G418.

data_processing:
Adapter sequences were trimmed from reads using Cutadapt (Martin 2011) and low quality reads were removed from analysis using Sickle 1.33 (Joshi et al 2011).
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) with default parameters.
Gene counts were generated using Salmon (Patro et al 2017).
Differential expression analysis was performed on aggregated gene pseudocounts using limma-voom 3.42.2 (Law et al 2014).
Genome_build: hg19
Supplementary_files_format_and_content: raw Salmon gene pseudocounts

extract_protocol:
All RNA was produced using TRIzol (Invitrogen) followed by the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Qiagen).
All libraries were sequenced 75x75 base pairs, paired-end on Illumina NextSeq 500.
Libraries were generated using the TruSeq RNA Sample Prep Kit v2 according to manufacturer's instructions (Illumina).

value: Transfected with siRNAs against BCL7A, BCL7B, and BCL7C

value: treated with Dox for 24 hours


title: BCL7-siABC-Dox-B


title: BCL7-siABC-Dox-C


title: ST-HSC (SLX.19173.i718_i522)


title: LT-HSC (SLX.19173.i712_i503)

value: GFP-PD-


title: LT-HSC (SLX.19173.i726_i521)


title: cutnrun-BRG1-V5-Rep1


title: BCL7-siABC-Cont-C

value: untreated


title: LT-HSC (SLX.19173.i727_i521)


title: DLPFC expression from sample 9-056

description: DLPFC expression case sample

value: case

tag: ph

tag: pmi

tag: rin

tag: suicide

tag: type of death

tag: adhd prs

tag: bd prs

tag: cdg prs

tag: mdd-2018 prs

tag: mdd-2019 prs

tag: scz prs

tag: t2d prs

value: postmortem dorsolateral prefrontal cortex (DLPFC)


title: BCL7-siABC-Cont-A

tag: treatment

tag: cell line


title: BCL7-siNTC-Dox-C

value: Transfected with negative control siRNA


title: LT-HSC (SLX.19173.i728_i522)

tag: tissue

tag: condition

value: NT

tag: batch

tag: donor

tag: sample type


title: CD34+ (SLX.19173.i723_i521)

tag: cell type

tag: time


title: BCL7-siABC-Cont-B


title: CD34+ (SLX.19173.i724_i521)


title: BCL7-siNTC-Dox-B


title: CD34+ (SLX.19173.i721_i521)


title: CD34+ (SLX.19173.i722_i521)


title: BCL7-siNTC-Dox-A

value: treated with Dox for 14 days


title: ST-HSC (SLX.19173.i719_i521)

value: ST-HSC


title: BCL7-siNTC-Cont-C


title: BCL7-siNTC-Cont-B


title: LT-HSC (SLX.19173.i729_i520)


title: ST-HSC (SLX.19173.i716_i521)


title: ST-HSC (SLX.19173.i718_i521)


title: BCL7-siNTC-Cont-A


title: LongTerm-HSA-Dox-A

description: Individual SW13 cell line expressing iHSA-V5 construct after continuous selection of G418.

extract_protocol:
All RNA was produced using TRIzol (Invitrogen) followed by the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Qiagen).
Libraries were generated using the Ribo-Zero Gold and the TruSeq Stranded Total RNA library kit according to manufacturer's instructions (Illumina).


title: LongTerm-HSA-Dox-B


title: LongTerm-HSA-Cont-C


title: LT-HSC (SLX.19173.i728_i520)


title: LT-HSC (SLX.19173.i727_i520)


title: CD34+ (SLX.19173.i724_i520)


title: LT-HSC (SLX.19173.i726_i520)


title: LongTerm-HSA-Cont-A


title: CD34+ (SLX.19173.i723_i520)


title: LongTerm-HSA-Cont-B


title: LongTerm-BRG1-Dox-A


title: LongTerm-BRG1-Dox-B


title: CD34+ (SLX.19173.i722_i520)


title: ST-HSC (SLX.19173.i720_i520)


title: LongTerm-BRG1-Cont-C


title: HEK293T, SARS2 nsp1 Induced, R B2

value: kidney; Embryo

value: epithelial

tag: genotype

value: nsp1 Induced

value: Lentiviral Transduced nsp1, 1ul/ml Doxycycline


title: CD34+ (SLX.19173.i704_i504)


title: ST-HSC (SLX.19173.i719_i520)


title: ST-HSC (SLX.19173.i720_i521)


title: LongTerm-HSA-Dox-C

value: adrenacorticoid carcinoma cell line


title: LongTerm-BRG1-Cont-B


title: ST-HSC (SLX.19173.i718_i520)

value: mobilised peripheral blood


title: ST-HSC (SLX.19173.i716_i520)

value: Single cell


title: LT-HSC (SLX.19173.i729_i518)

value: LT-HSC


title: CD34+ (SLX.19173.i721_i520)


title: LT-HSC (SLX.19173.i728_i518)


title: LongTerm-BRG1-Dox-C

value: treated with Dox for 24 hours


title: CD34+ (SLX.19173.i723_i518)


title: CD34+ (SLX.19173.i724_i518)


title: CD34+ (SLX.19173.i722_i518)


title: 24hr-SW13-Dox-C_rep2

description: Individual SW13 cell line.


title: 24hr-SW13-Cont-A_rep2

description: Individual SW13 cell line.


title: 24hr-SW13-Dox-B_rep2

description: Individual SW13 cell line.


title: 24hr-SW13-Dox-B_rep1

description: Individual SW13 cell line.


title: 24hr-SW13-Dox-A_rep2

description: Individual SW13 cell line.


title: 24hr-SW13-Cont-C_rep2

description: Individual SW13 cell line.


title: LongTerm-BRG1-Cont-A


title: 24hr-SW13-Dox-C_rep1

description: Individual SW13 cell line.


title: 24hr-SW13-Dox-A_rep1

description: Individual SW13 cell line.


title: 24hr-SW13-Cont-C_rep1

description: Individual SW13 cell line.


title: ST-HSC (SLX.19173.i719_i518)


title: 24hr-SW13-Cont-B_rep2

description: Individual SW13 cell line.


title: ST-HSC (SLX.19173.i720_i518)


title: 24hr-SW13-Cont-B_rep1

description: Individual SW13 cell line.


title: ST-HSC (SLX.19173.i718_i518)


title: 24hr-SW13-Cont-A_rep1

description: Individual SW13 cell line.


title: 24hr-HSA-Dox-C_rep2


title: LT-HSC (SLX.19173.i727_i518)


title: LT-HSC (SLX.19173.i726_i518)


title: 24hr-HSA-Dox-B_rep2


title: 24hr-HSA-Dox-A_rep2


title: LT-HSC (SLX.19173.i729_i517)


title: CD34+ (SLX.19173.i721_i518)


title: LT-HSC (SLX.19173.i728_i517)


title: LT-HSC (SLX.19173.i727_i517)


title: 24hr-HSA-Cont-C_rep2


title: 24hr-HSA-Cont-B_rep2


title: CD34+ (SLX.19173.i723_i517)


title: 24hr-HSA-Dox-C_rep1


title: CD34+ (SLX.19173.i721_i517)


title: CD34+ (SLX.19173.i722_i517)


title: ST-HSC (SLX.19173.i720_i517)


title: ST-HSC (SLX.19173.i719_i517)


title: ST-HSC (SLX.19173.i718_i517)


title: 24hr-HSA-Dox-A_rep1


title: 24hr-HSA-Cont-C_rep1


title: 24hr-HSA-Dox-B_rep1


title: 24hr-HSA-Cont-B_rep1


title: ST-HSC (SLX.19173.i716_i518)


title: ST-HSC (SLX.19173.i716_i517)


title: 24hr-HSA-Cont-A_rep1


title: LT-HSC (SLX.19173.i729_i516)


title: 24hr-BRG1-Dox-C_rep2


title: 24hr-BRG1-Dox-B_rep2


title: LT-HSC (SLX.19173.i728_i516)


title: 24hr-BRG1-Dox-A_rep2


title: LT-HSC (SLX.19173.i726_i517)


title: ST-HSC (SLX.19173.i702_i502)


title: LT-HSC (SLX.19173.i727_i516)


title: LT-HSC (SLX.19173.i726_i516)


title: CD34+ (SLX.19173.i724_i517)


title: 24hr-BRG1-Cont-B_rep2


title: 24hr-HSA-Cont-A_rep2


title: 24hr-BRG1-Cont-A_rep2


title: CD34+ (SLX.19173.i724_i516)


title: CD34+ (SLX.19173.i723_i516)


title: 24hr-BRG1-Dox-B_rep1


title: 24hr-BRG1-Dox-C_rep1


title: 24hr-BRG1-Dox-A_rep1


title: CD34+ (SLX.19173.i721_i516)


title: ST-HSC (SLX.19173.i719_i516)


title: ST-HSC (SLX.19173.i720_i516)


title: 24hr-BRG1-Cont-A_rep1


title: ST-HSC (SLX.19173.i716_i516)


title: P300_P300ifKO_rep3

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

description:
Ep300_flox;Camk2a_creERT2
RSP300KO5_20958_GTTTCG

data_processing:
Fastqc (v 0.11.8) was used for quality control of NGS data and adapter trimming was performed with trim_galore (v 0.6.4_dev).
Alignment was done with STAR (v 2.6.1) to mm10 (GRCm38) genome and only reads with mapq > 10 were considered for further analysis. Counts were quantified to exons using Rsubread and Mus_musculus.GRCm38.99.gtf from Ensembl. Differential expression analysis was performed with Deseq2 (v 1.30.1).
Assembly: mm10(GRCm38)
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
RNA-seq was performed as detailed in (Lipinski et al., 2020) with minimal modifications. Extraction of RNA from the hippocampal tissue was performed using TRI-reagent (MERCK). Total RNA was treated with DNase I (Qiagen) and its quality was confirmed using nanodrop, Bioanalyzer and RT-qPCR assays.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing parameters were single-end with a length of 50 pb using a illumina Hiseq2500.

treatment_protocol: In adult (3- to 6-month-old) mice, recombination of floxed alleles was induced by 5 intragastrical administrations of tamoxifen (Sigma Aldrich, 20 mg/mL dissolved in corn oil) on alternate days (Fiorenza et al., 2016). In all our experiments with ifKOs, we used CaMKIIα-creERT2- littermates treated with tamoxifen as controls.

tag: strain

value: hippocampus

tag: age

value: 3-6 months old


title: LT-HSC (SLX.19173.i729_i515)


title: LT-HSC (SLX.19173.i728_i515)


title: 24hr-BRG1-Cont-C_rep2

value: untreated


title: LT-HSC (SLX.19173.i727_i515)


title: LT-HSC (SLX.19173.i726_i515)


title: CD34+ (SLX.19173.i724_i515)


title: P300_Control_rep3

description:
Camk2a_creERT2
RSP300WT5_20955_CAGATC

value: Control


title: P300_P300ifKO_rep1

description:
Ep300_flox;Camk2a_creERT2
RSP300KO1_20956_ATGTCA


title: P300_Control_rep2

description:
Camk2a_creERT2
RSP300WT2_20954_TGACCA


title: CD34+ (SLX.19173.i722_i515)


title: CBP_CBPifKO_PTZ45_rep3

description:
Crebbp_flox;Camk2a_creERT2
KOKind45_mm_totalrna_sr_Mlipinski_F_3_S30_L005

extract_protocol:
RNA-seq was performed as detailed in (Lipinski et al., 2020) with minimal modifications. Extraction of RNA from the hippocampal tissue was performed using TRI-reagent (MERCK). Total RNA was treated with DNase I (Qiagen) and its quality was confirmed using nanodrop, Bioanalyzer and RT-qPCR assays.
RNA libraries were prepared for sequencing using standard Illumina protocols . Sequencing parameters were single-end with a length of 50 pb using a illumina Hiseq2500.

treatment_protocol: Saline, Kindling + Saline, Kindling + PTZ

value: Kindling + PTZ

value: CBP-ifKO


title: CBP_CBPifKO_PTZ45_rep2

description:
Crebbp_flox;Camk2a_creERT2
KOKind45_mm_totalrna_sr_Mlipinski_F_2_S29_L005


title: CD34+ (SLX.19173.i722_i516)

value: NT


title: CD34+ (SLX.19173.i721_i515)


title: P300_Control_rep1

description:
Camk2a_creERT2
RSP300WT1_20953_CGATGT


title: CD34+ (SLX.19173.i723_i515)


title: 24hr-BRG1-Cont-C_rep1


title: CBP_Control_PTZ45_rep2

description:
Camk2a_creERT2
WTKind45_mm_totalrna_sr_Mlipinski_C_3_S21_L004


title: 24hr-BRG1-Cont-B_rep1


title: ST-HSC (SLX.19173.i718_i516)

value: ST-HSC


title: ST-HSC (SLX.19173.i719_i515)


title: ST-HSC (SLX.19173.i720_i515)


title: P300_P300ifKO_rep2

description:
Ep300_flox;Camk2a_creERT2
RSP300KO2_20957_CCGTCC


title: ST-HSC (SLX.19173.i718_i515)


title: CBP_CBPifKO_PTZ45_rep1

description:
Crebbp_flox;Camk2a_creERT2
KOKind45_mm_totalrna_sr_Mlipinski_F_1_S28_L005


title: LT-HSC (SLX.19173.i729_i513)


title: CBP_Control_PTZ45_rep1

description:
Camk2a_creERT2
WTKind45_mm_totalrna_sr_Mlipinski_C_1_S19_L004


title: CBP_CBPifKO_PTZ0_rep2

description:
Crebbp_flox;Camk2a_creERT2
KOKind0_mm_totalrna_sr_Mlipinski_E_2_S26_L005

value: Kindling + Saline


title: ST-HSC (SLX.19173.i716_i515)


title: CBP_CBPifKO_PTZ0_rep3

description:
Crebbp_flox;Camk2a_creERT2
KOKind0_mm_totalrna_sr_Mlipinski_E_3_S27_L005


title: LT-HSC (SLX.19173.i728_i513)


title: CBP_Control_PTZ0_rep3

description:
Camk2a_creERT2
WTKind0_mm_totalrna_sr_Mlipinski_B_3_S18_L003


title: LT-HSC (SLX.19173.i727_i513)


title: CBP_Control_PTZ0_rep2

description:
Camk2a_creERT2
WTKind0_mm_totalrna_sr_Mlipinski_B_2_S17_L003


title: CBP_CBPifKO_PTZ0_rep1

description:
Crebbp_flox;Camk2a_creERT2
KOKind0_mm_totalrna_sr_Mlipinski_E_1_S25_L005


title: CD34+ (SLX.19173.i724_i513)


title: CBP_Control_PTZ0_rep1

description:
Camk2a_creERT2
WTKind0_mm_totalrna_sr_Mlipinski_B_1_S16_L003


title: LT-HSC (SLX.19173.i726_i513)


title: CD34+ (SLX.19173.i723_i513)


title: CBP_CBPifKO_Sal_rep3

description:
Crebbp_flox;Camk2a_creERT2
KOSal0_mm_totalrna_sr_Mlipinski_D_3_S24_L004

value: Saline


title: CBP_CBPifKO_Sal_rep2

description:
Crebbp_flox;Camk2a_creERT2
KOSal0_mm_totalrna_sr_Mlipinski_D_2_S23_L004


title: CD34+ (SLX.19173.i722_i513)


title: CBP_CBPifKO_Sal_rep1

description:
Crebbp_flox;Camk2a_creERT2
KOSal0_mm_totalrna_sr_Mlipinski_D_1_S22_L004


title: CBP_Control_Sal_rep1

description:
Camk2a_creERT2
WTSal0_mm_totalrna_sr_Mlipinski_A_1_S13_L003


title: CBP_Control_Sal_rep2

description:
Camk2a_creERT2
WTSal0_mm_totalrna_sr_Mlipinski_A_2_S14_L003


title: ST-HSC (SLX.19173.i720_i513)


title: ST-HSC (SLX.19173.i718_i513)


title: ST-HSC (SLX.19173.i716_i513)


title: CD34+ (SLX.19173.i721_i513)


title: CBP_Control_Sal_rep3

description:
Camk2a_creERT2
WTSal0_mm_totalrna_sr_Mlipinski_A_3_S15_L003


title: H3K27ac_Neurons_Control_SC

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie2, bam files were filtered by removing blacklist regions, non nuclear reads and with mapq > 30 using samtools and bedtools
peaks were called using macs2
Assembly: mm10
Supplementary files format and content: BigWigs normalized using Deeptools and 1/scalefactor(Deseq2)  for those files with more than 5% differences in the scalefactor. In the other cases RPGC from Deeptools was used

extract_protocol:
ChIP-seq were performed as detailed in (Lipinski et al., 2020; Lopez-Atalaya et al., 2013; Valor et al., 2011)
ChIP-seq libraries were single-end, 50 bp of length and sequenced in a HiSeq 2000 or 2500 apparatus

tag: tissue/cell type

value: Camk2a hippocampal neurons

tag: chip antibody

value: H3K27ac (ab4729, Abcam)

value: Standard Cage


title: ST-HSC (SLX.19172.i710_i517)

value: mobilised peripheral blood

value: GFP+PD-


title: TFIIBac_Control

value: Hippocampus

value: TFIIBac(ab5210, Abcam)


title: ST-HSC (SLX.19172.i711_i517)

value: Single cell


title: ST-HSC (SLX.19172.i712_i517)


title: TFIIBac_CBPifKO

value: CBPifKO


title: H3K27ac_Neurons_Control_EE

value: Environmental Enrichment


title: RNAPII_CBPifKO

value: RNAPII(sc-9001 , Santacruz)


title: ST-HSC (SLX.19172.i709_i517)


title: RNAPII_Control

value: Control


title: H3K27ac_EE_CBPifKO_rep2


title: ST-HSC (SLX.19172.i707_i517)


title: ST-HSC (SLX.19172.i708_i517)


title: H3K27ac_EE_CBPifKO_rep1


title: ST-HSC (SLX.19172.i706_i517)


title: H3K27ac_SC_CBPifKO_rep2


title: ST-HSC (SLX.19172.i705_i517)


title: H3K27ac_EE_Control_rep1


title: ST-HSC (SLX.19172.i703_i517)


title: H3K27ac_SC_CBPifKO_rep1


title: ST-HSC (SLX.19172.i704_i517)


title: ST-HSC (SLX.19173.i719_i513)


title: ST-HSC (SLX.19172.i702_i517)


title: H3K27ac_SC_Control_rep2


title: LT-HSC (SLX.19172.i711_i508)

value: LT-HSC


title: H3K27ac_exp1_CBPifKO_rep2


title: H3K27ac_SC_Control_rep1


title: LT-HSC (SLX.19172.i712_i508)


title: H3K27ac_exp1_CBPifKO_rep1


title: ST-HSC (SLX.19172.i701_i517)


title: LT-HSC (SLX.19172.i710_i508)


title: H3K27ac_exp1_Control_rep1


title: LT-HSC (SLX.19172.i709_i508)


title: LT-HSC (SLX.19172.i706_i508)


title: LT-HSC (SLX.19172.i707_i508)


title: H3K27ac_exp1_Control_rep2


title: LT-HSC (SLX.19172.i708_i508)


title: H3K27ac_EE_Control_rep2


title: CBP_CBPifKO_EE_rep3 [KEE3_26030_GGCTAC]

data_processing:
Fastqc (v 0.11.8) was used for quality control of NGS data and adapter trimming was performed with trim_galore (v 0.6.4_dev).
Alignment was done with STAR (v 2.6.1) to mm10 (GRCm38) genome and only reads with mapq > 10 were considered for further analysis. Counts were quantified to exons using Rsubread and Mus_musculus.GRCm38.99.gtf from Ensembl. Differential expression analysis was performed with Deseq2 (v 1.30.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts for each  sample as provided by Rsubread
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: hippocampus

value: 3-6 months old

value: CBP-ifKO


title: CBP_CBPifKO_EE_rep3 [KEE3_26030_GGCTAC_re]


title: CBP_CBPifKO_EE_rep2 [KEE2_26029_TAGCTT_re]


title: LT-HSC (SLX.19172.i704_i508)


title: CBP_CBPifKO_EE_rep2 [KEE2_26029_TAGCTT]


title: LT-HSC (SLX.19172.i703_i508)


title: CBP_CBPifKO_EE_rep1 [KEE1_26028_ACTTGA_re]


title: LT-HSC (SLX.19172.i702_i508)


title: CBP_CBPifKO_EE_rep1 [KEE1_26028_ACTTGA]


title: LT-HSC (SLX.19172.i705_i508)


title: CD34+ (SLX.19172.i711_i507)


title: CBP_Control_EE_rep3 [WEE3_26027_ATCACG]

description: Control


title: LT-HSC (SLX.19172.i701_i508)


title: CBP_Control_EE_rep2 [WEE2_26026_ACTGAT_re]

description: Control


title: CD34+ (SLX.19172.i710_i507)


title: CBP_Control_EE_rep1 [WEE1_26025_GTTTCG_re]

description: Control


title: CD34+ (SLX.19172.i709_i507)


title: CBP_Control_EE_rep2 [WEE2_26026_ACTGAT]

description: Control


title: CD34+ (SLX.19172.i708_i507)


title: CD34+ (SLX.19172.i707_i507)


title: CBP_CBPifKO_SC_rep3 [KHC3_26024_GTCCGC_re]


title: CD34+ (SLX.19172.i706_i507)


title: CD34+ (SLX.19172.i705_i507)


title: CD34+ (SLX.19172.i704_i507)


title: CBP_CBPifKO_SC_rep2 [KHC2_26023_CCGTCC_re]


title: CBP_CBPifKO_SC_rep3 [KHC3_26024_GTCCGC]


title: CBP_CBPifKO_SC_rep2 [KHC2_26023_CCGTCC]


title: CD34+ (SLX.19172.i703_i507)


title: CBP_CBPifKO_SC_rep1 [KHC1_26022_ATGTCA]


title: CBP_Control_SC_rep3 [WHC3_26021_CAGATC_re]

description: Control


title: CBP_CBPifKO_SC_rep1 [KHC1_26022_ATGTCA_re]


title: CD34+ (SLX.19172.i701_i507)


title: CBP_Control_EE_rep3 [WEE3_26027_ATCACG_re]

description: Control


title: LT-HSC (SLX.19172.i712_i506)

value: GFP+PD+


title: LT-HSC (SLX.19172.i711_i506)


title: CD34+ (SLX.19172.i702_i507)


title: CBP_Control_SC_rep3 [WHC3_26021_CAGATC]

description: Control


title: LT-HSC (SLX.19172.i710_i506)


title: LT-HSC (SLX.19172.i708_i506)


title: LT-HSC (SLX.19172.i709_i506)


title: CBP_Control_SC_rep2 [WHC2_26020_TGACCA]

description: Control


title: CBP_Control_SC_rep1 [WHC1_26019_CGATGT_re]

description: Control


title: CBP_Control_SC_rep1 [WHC1_26019_CGATGT]

description: Control


title: LT-HSC (SLX.19172.i707_i506)


title: CBP_CBPifKO_rep3

source_name: Exp


title: CBP_Control_EE_rep1 [WEE1_26025_GTTTCG]

description: Control


title: LT_6h (SLX.12561.N721_S505)

data_processing:
Reads were mapped to the Homo sapiens genome (EMSEMBL GRCh38 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Assembly: GRCh38
Supplementary files format and content: HT-Seq counts / gene counts (.txt)

source_name: cord blood

growth_protocol: LT-HSCs (CD34+/CD38-/CD45RA-/CD90+/CD49f+)  were cultured for 6, 24 h or 72 h in media promoting HSC differentiation: StemPro base media supplemented with Nutrients , Pen/Strep (1%), L-Glu (1%), human LDL (50ng/ml)  in addition to the following cytokines: SCF (100ng/ml), Flt-3L (20ng/ml), TPO (100ng/ml), EPO (3 units/ml), IL-6 (50ng/ml), IL-3 (10ng/ml) and GM-CSF (20ng/ml).

treatment_protocol: For 24 or 72 h culture durations a separate condition was included where LT-HSCs were cultured in differentiation facilitating media with 200nM Palbociclib (PD033299).

value: cord blood

value: LT-HSCs

tag: experimental batch

tag: incubation time

value: UNTR

tag: Sex

value: male

value: pool 1


title: LT-HSC (SLX.19172.i706_i506)

value: mobilised peripheral blood


title: CBP_CBPifKO_rep2


title: CBP_CBPifKO_rep1


title: CBP_Control_rep3


title: LT_6h (SLX.12561.N721_S504)

tag: treatment


title: LT_6h (SLX.12561.N721_S503)


title: CBP_Control_rep1


title: CBP_Control_SC_rep2 [WHC2_26020_TGACCA_re]

description: Control

value: Standard Cage


title: LT_6h (SLX.12561.N719_S507)


title: LT_6h (SLX.12561.N719_S508)


title: LT_6h (SLX.12561.N721_S502)


title: LT_6h (SLX.12561.N719_S505)


title: LT_6h (SLX.12561.N719_S504)


title: LT_6h (SLX.12561.N719_S506)


title: LT_6h (SLX.12561.N719_S503)


title: LT_6h (SLX.12561.N718_S507)


title: LT_6h (SLX.12561.N718_S506)


title: LT_6h (SLX.12561.N718_S508)


title: CBP_Control_rep2


title: LT_6h (SLX.12561.N718_S505)


title: LT_6h (SLX.12561.N718_S504)


title: LT_6h (SLX.12561.N716_S506)


title: LT_6h (SLX.12561.N716_S507)


title: LT_6h (SLX.12561.N716_S508)


title: LT_6h (SLX.12561.N719_S502)


title: Plasma exosome-MDD patient with NSSI 040

city: Taiyuan

first: Yifan

last: Xu

address: 85# of Jie Fang Road

institute: First Hospital of Shanxi Medical University

description: lncRNA and mRNA expression in MDD with NSSI patients

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was incubated at 60°C for exactly 30 minutes to fragment RNA with a reaction volume of 250ul containing 10X Blocking Agent and 25X Fragmentation Buffer following the manufacturers instructions. 250ul of 2x GEx Hybridization Buffer HI-RPM was added to the array to stop the fragmentation reaction and hybridized to Agilent Arraystar Human lncRNA V5 Microarrays at 65°C for 17 hours in Hybridization oven (Agilent p/n G2545A). After hybridization, microarrays were washed with Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326) at 37°C for 5 minutes and Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) at room temperature for 1 minute.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan and setting the parameters to Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was Green and Green PMT was XDR Hi 100%, XDR Lo 10%.

data_processing: Agilent Feature Extraction software was used to analyze scan images.

source_name: Plasma exosome, MDD patient with NSSI

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plasma and total RNA was frozen in -80℃ refrigerator before further experiment.

extract_protocol: An exoRNeasy Midi and Maxi Kits (Qiagen, Cat. NO: 77144, Germany) were used to isolate the plasma exosome and extract exosomal RNA per the manufacturer’s instruction

value: Plasma exosome

value: Male

tag: individual

value: MDD patient with NSSI


title: LT_6h (SLX.12561.N718_S503)

tag: tissue


title: Plasma exosome-MDD patient with NSSI 035

value: Female


title: Plasma exosome-MDD patient with NSSI 036


title: Plasma exosome-MDD patient with NSSI 037


title: LT_6h (SLX.12561.N718_S502)


title: LT_6h (SLX.12561.N716_S504)


title: Plasma exosome-MDD patient with NSSI 029


title: Plasma exosome-MDD patient with NSSI 034


title: Plasma exosome-MDD patient with NSSI 031


title: Plasma exosome-Healthy control 007

description: lncRNA and mRNA expression in HC

source_name: Plasma exosome, Healthy control

value: Healthy control


title: Plasma exosome-Healthy control 011

description: lncRNA and mRNA expression in HC


title: Plasma exosome-Healthy control 009

description: lncRNA and mRNA expression in HC


title: Plasma exosome-Healthy control 012

description: lncRNA and mRNA expression in HC


title: Plasma exosome-MDD patient with NSSI 038


title: Plasma exosome-MDD patient with NSSI 039


title: LT_6h (SLX.12561.N716_S503)


title: Plasma exosome-Healthy control 010

description: lncRNA and mRNA expression in HC


title: LT_6h (SLX.12561.N716_S502)


title: LT_6h (SLX.12561.N727_S517)


title: LT_6h (SLX.12561.N728_S517)


title: Plasma exosome-MDD patient with NSSI 030


title: Plasma exosome-Healthy control 008

description: lncRNA and mRNA expression in HC


title: LT_6h (SLX.12561.N726_S517)


title: LT_6h (SLX.12561.N722_S517)


title: LT_6h (SLX.12561.N723_S517)


title: LT_6h (SLX.12561.N718_S517)


title: LT_6h (SLX.12561.N721_S517)


title: LT_6h (SLX.12561.N719_S517)


title: Plasma exosome-Healthy control 004

description: lncRNA and mRNA expression in HC


title: LT_6h (SLX.12561.N716_S517)


title: LT_0h (SLX.12561.N711_S517)


title: Plasma exosome-Healthy control 006

description: lncRNA and mRNA expression in HC


title: LT_0h (SLX.12561.N711_S508)


title: Plasma exosome-Healthy control 002

description: lncRNA and mRNA expression in HC


title: LT_0h (SLX.12561.N711_S507)


title: LT_0h (SLX.12561.N711_S506)


title: WT3_GFP

city: nanjing

first: tengxiao

last: guo

address: nanjing road

institute: State Key Laboratory of Experimental Hematology

data_processing:
illimina casava1.7 software used for basecalling.
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
After harvesting cells, add trizol and freeze them in - 80 ° refrigerator
RNA libranries were prepared for sequencing using stanard illumina protocols

value: bone marrow

tag: strain background

value: GFP+ cell

value: CELF2 WT


title: WT2_GFP


title: LT_0h (SLX.12561.N711_S505)


title: WT1_GFP


title: WT_KG

value: K+G- cell in GFP+


title: KO3_GFP

value: CELF2 KO


title: KO_KG


title: LT_0h (SLX.12561.N711_S504)

value: cord blood


title: LT_0h (SLX.12561.N711_S503)

value: LT-HSCs


title: KO2_GFP


title: Plasma exosome-Healthy control 001

description: lncRNA and mRNA expression in HC


title: LT_0h (SLX.12561.N710_S517)

value: UNTR


title: LT_0h (SLX.12561.N711_S502)

value: male


title: liver, Arid2 LKO, rep2

city: Shanghai

first: Jing-Jing

last: Li

email: tide7@163.com, jjli@sinh.ac.cn

address: No. 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Heath, Chinese Academy of Science

data_processing:
Quality control-The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reads mapping to the reference genome-Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Quantification of gene expression level-featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis-Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Assembly: mm10

source_name: liver

extract_protocol:
Total RNA was isolated from liver tissues of WT and Arid2 LKO mice using TRIzol reagent (Invitrogen). RNA was harvested using Rneasy mini plus kit (Qiagen). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: liver

value: Arid2 liver specific KO

value: No treatment


title: liver, Arid2 WT, rep3

value: WT


title: liver, Arid2 LKO, rep1


title: LT_0h (SLX.12561.N710_S508)

value: pool 1


title: liver, Arid2 LKO, rep3


title: liver, Arid2 WT, rep1


title: liver, Arid2 WT, rep2


title: LT_0h (SLX.12561.N710_S507)


title: TCR_sequencing

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

description: TCR sequencing data for lymph node samples

library_source: transcriptomic single cell

data_processing:
Raw read processing of scRNA-seq reads was performed as previously described (Macosko et al., 2015).
Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Then, cells with less than 700 unique genes detected and genes detected in fewer than 5 cells were filtered out.
Cell hashing data was aligned to HTO barcodes using CITE-seq-Count v1.4.2 (Roelli et al., 2019).
Briefly, reads were aggregated by cell barcode and UMI, and UMI with under 10 reads were discarded. ClusterSets.py was used to divide sequences for each UMI into sets of similar sequences. Only sets of sequences that comprised greater than 90% of the sequences obtained for that UMI were considered further. Consensus sequences for each UMI were determined using the BuildConsensus.py function. Consensus sequences were then mapped against TCRV and TCRJ IMGT references sequences with IgBlast.
Paired TCR sequencing and read alignment was performed as previously described (Tu et al., 2019).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: Lymph node

extract_protocol:
For scRNA-seq of ex vivo-primed T cells, CD8+ OT-I T cells and ZsG+ DC1 sorted from tumor-draining mLN were cultured alone or in the presence of Tregs sorted from tumor-draining mLN (added at the 1:8 Treg:OT-I ratio) as described above. After the 3 day co-culture, cells were collected for sequencing. For scRNA-seq of Tregs, LN were mashed through a 70 μm filter into RPMI (GIBCO), then incubated with αCD16/CD32 (clone 93, BioLegend) in FACS buffer (PBS (GIBCO) with 1% FBS (Atlanta Biologicals) and 2 mM EDTA (Invitrogen)) for 15 min at 4°C, washed with FACS buffer and stained with a mix of αCD45-APC (1:200, clone 30-F11, Biolegend) and Total-seq A mouse hashtag antibody (1:100, clone 30-F11, Biolegend) in FACS buffer to label individual mice (hashtag labeling was only performed for tdLN, not naïve LN). Cells were then washed twice in FACS buffer and tdLN cells from multiple mice were pooled together for subsequent CD4+ T cell enrichment sing the mouse CD4+ T cell isolation kit (Miltenyi Biotec), following manufacturer’s instructions. Next, cells were stained for FACS and Tregs were sorted as previously described.
Seq-Well

value: Lymph node

value: T cell


title: Coculture_Treg

description: DC1+CD8+Treg coculture

value: PlusTreg


title: LT_0h (SLX.12561.N710_S506)


title: Flank_naive_rep2

description: Inguinal lymph node from non-tumor-bearing mice


title: LT_0h (SLX.12561.N710_S505)


title: Coculture_NoTreg_rep1

description: DC1+CD8 coculture

value: NoTreg


title: Coculture_NoTreg_rep2

description: DC1+CD8 coculture


title: KO1_GFP

value: bone marrow

value: GFP+ cell


title: LT_0h (SLX.12561.N710_S504)


title: Flank_naive_rep1


title: LT_0h (SLX.12561.N710_S503)


title: Flank_tdLN_rep2

description: Inguinal lymph node from flank tumor-bearing mice


title: LT_0h (SLX.12561.N710_S502)


title: LT_0h (SLX.12561.N709_S517)


title: Lung_tdLN_rep1

description: Mediastinal lymph node from lung tumor-bearing mice


title: Lung_tdLN_rep2


title: LT_0h (SLX.12561.N709_S508)


title: C2C12,FHL3-KO,rep2

city: wuhan

first: wei

last: bai

address: hongshan District

institute: Huazhong Agricultural University

data_processing:
The clustering of the index-coded samples was performed using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
The library preparations were sequenced and 150 bp paired-end reads were generated
After adaptor trimming and low-quality reads removing by Trim Galore (v 0.6.6), the high-quality clean reads were aligned to the reference genome (UCSC MM10) with Hisat2 (v2.2.1)
The numbers of reads mapped to each gene were counted using FeatureCounts(v2.0.1)
Diferential expression analysis of the genes was performed using the R package DESeq2(v1.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: C2C12 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C and 5% CO2.

extract_protocol:
Total RNAs were isolated using Trizol (ThermoFisher, 10296028). Genomic DNA was removed using Turbo DNA-Free Kit (ThermoFisher, AM1907). Total RNA integrity was determined using RNA 6000 Nano Kit (Agilent, 5067–1511)
Libraries of amplified RNA were prepared in accordance with the Illumina protocol.

treatment_protocol: For myogenic differentiation, cells were transferred to DMEM containing 2% horse serum (HS).

tag: cell line

value: myoblasts

value: KO

value: myogenic differentiation

value: Day 4


title: C2C12,FHL3-KO,rep3


title: C2C12,WT,rep3


title: C2C12,FHL3-KO,rep1


title: LT_0h (SLX.12561.N709_S507)

value: cord blood

value: LT-HSCs

value: UNTR

tag: donor


title: C2C12,WT,rep2


title: C2C12,WT,rep1


title: LT_0h (SLX.12561.N709_S506)

value: male


title: LT_0h (SLX.12561.N709_S505)


title: LT_0h (SLX.12561.N709_S502)


title: Lung_naive_rep2

description: Mediastinal lymph node from non-tumor-bearing mice


title: LT_0h (SLX.12561.N709_S503)


title: Lung_naive_rep1


title: LT_0h (SLX.12561.N707_S507)


title: Flank_tdLN_rep1


title: SalPreIP-3

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Sequencing results were quality-tested using FastQC (version 0.11.7)
Illumina sequencing adaptors were removed using Trimmomatic (version 0.38), and reads aligning to the mouse rRNA were removed using bowtie2
Surviving reads were then aligned, using STAR (version 2.7.0d), to the mouse transcriptome (Ensembl Release 97)
The number of reads mapped to each feature were counted using htseq-count (version 0.9.1)
Genome_build: Mouse: Ensembl 97
Supplementary_files_format_and_content: Gene counts

source_name: Brain

extract_protocol:
RNA was extracted from the input and TRAP samples using Trizol LS (Life Technologies) and a purification kit (Zymo Research, R1014) and quality-tested using RNA Pico Chips and BioAnalyzer 2100 (Agilent Technologies).
Libraries were prepared from 1 ug RNA using a library prep kit (NEB #7770), rRNA depletion kit (NEB #E6310), and Ampure XP beads (Beckman #A63881), and following manufacturer’s instructions. Prior to sequencing, quality was tested using a High Sensitivity D1000 ScreenTape (Agilent Technologies). Each library was sequenced as 2X150 bp fragments to about 30 million reads of depth using Illumina HiSeq3000 machines.

treatment_protocol: Three week old Astrocyte-TRAP mice of both sexes were intraperitoneally injected with PTZ at 60 mg/kg (Sigma P6500, 5 mg/ml stock solution in normal saline). Mice showing persistent convulsions at 8-10 minutes were subjected to rapid decapitation using decapicones (Braintree Scientific) for harvesting the brains. Control mice were injected with 110 μl normal saline (Sal) and decapitated similarly after 10 minutes. The harvested brains were snap-frozen in liquid nitrogen and stored at −80°C for TRAP.

tag: sample group

value: Input

value: Saline

value: Astrocytes


title: LT_0h (SLX.12561.N707_S506)

tag: cell type

value: pool 1


title: SalPreIP-2


title: LT_0h (SLX.12561.N709_S504)


title: SalPreIP-1


title: LT_0h (SLX.12561.N707_S508)


title: SalIP-3

value: TRAP


title: LT_0h (SLX.12561.N707_S505)


title: LT_0h (SLX.12561.N707_S504)


title: SalIP-1


title: SalIP-2


title: LT_0h (SLX.12561.N707_S502)


title: LT_0h (SLX.12561.N706_S517)


title: PtzPreIP-3

value: Ptz


title: LT_0h (SLX.12561.N706_S508)


title: PtzIP-3


title: LT_0h (SLX.12561.N706_S506)


title: PtzIP-2


title: LT_0h (SLX.12561.N706_S505)


title: PtzIP-1


title: LT_0h (SLX.12561.N706_S504)


title: input

source_name: input

value: Hippocampus


title: LT_0h (SLX.12561.N706_S503)


title: H2Bac_Het

description: CBP+/-

value: H2Bac (Sanchiz-Segura et al, 2009)

value: CBPhet


title: LT_0h (SLX.12561.N706_S502)


title: H3K914ac_CBPifKO

value: CBPifKO


title: LT_0h (SLX.12561.N705_S508)


title: H2Bac_Controlhet

description: WT

value: Control


title: LT_0h (SLX.12561.N707_S503)


title: H3K914ac_Control


title: LT_0h (SLX.12561.N705_S517)


title: H2Bac_CBPifKO


title: LT_0h (SLX.12561.N705_S506)


title: LT_0h (SLX.12561.N705_S507)


title: PtzPreIP-2


title: H2Bac_Control


title: D1 H3K27me3 Active Motif rep2

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
D1_27me3_Active_merged-W200-G600-FDR0.01-island.bed
D1_27me3_Active_merged_CPM.bw

data_processing:
Library strategy: CUT&RUN
Base call files were demultiplexed and converted into Fastq files using bcl2fastq (version v2.20.0.422)
Fastq files were aligned to mm10 reference genome with bowtie2 (version 2.1.0) with options: -q --local --no-mixed --no-unal --dovetail --phred33. Uniquely mapped reads (mapping quality score >= 20) were selected using samtools (version 0.1.19, samtools view -q 20).
Duplicates were removed using Picard MarksDuplicates function. Deduplicated mapped reads with insert size between 150 and 500 bp using samtools for downstream analyses
Read alignments were normalized to total mapped reads using deepTools with command: bamCoverage –bam inbam -o outbw –normalizaUsing CPM and visualized by deepTools pyGenomeTracks
H3K4me3 peaks were called using MACS2 with parameters: -f BAM -g mm -B --keep-dup all -q 0.01. H3K27me3 peaks were called using SICER with the command: sicer -t inbam -c control -s mm10. H3K27me3 peaks with false discovery rate less than 0.01 were selected.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and peak files

source_name: INTACT-isolated MSN A2a cells

growth_protocol: Neuro2a cells (ATCC CCL-131) were cultured in EMEM medium with 10% FBS in 6-well plates

extract_protocol:
INTACT (Mo et al., 2015)
NEB Ultra II library preparation kit (protocol from Liu, N. et al. 2018)
CUT&RUN (Skene & Henikoff, 2017)

treatment_protocol: N2a cells were first lysed to isolate the nuclei. The nuclei were then centrifuged and washed.

value: MSN D1

value: H3K27me3 Active Motif


title: PtzPreIP-1


title: LT_0h (SLX.12561.N706_S507)

extract_protocol:
Single cells were directly sorted in lysis buffer according to Smart-Seq2 protocol (Picelli et al., Nat protocol, 2014). A lysis buffer was prepared of 20U/l SUPER-In RNase inhibitor (Thermo Fisher Scientific) and 0.4% Triton-X100 (ratio of 1:19). The lysis buffer was added to a mix of DTT (Thermo Fisher Scientific) (final concentration of 0.57mM), dNTPs (Invitrogen) (final concentration 0.11mM) and nuclease free water (Thermo Fisher Scientific) and 4ul aliquoted per well in a 96 well PCR plate and stored at -80°C.
libraries were prepared for sequencing using standard Illumina protocols

value: cord blood


title: D1 H3K27me3 Active Motif rep1


title: LT_0h (SLX.12561.N705_S502)

value: LT-HSCs


title: LT_0h (SLX.12561.N705_S503)

value: UNTR


title: D1 H3K27me3 Thermo Fisher rep2

value: H3K27me3 Thermo Fisher


title: LT_0h (SLX.12561.N703_S517)

value: male


title: D1 H3K27me3 Thermo Fisher rep1


title: A2a H3K27me3 Thermo Fisher rep1

value: MSN A2a


title: LT_0h (SLX.12561.N703_S507)


title: A2a H3K27me3 Thermo Fisher rep2


title: A2a H3K27me3 Active Motif rep2

description:
A2a_27me3_Active_merged-W200-G600-FDR0.01-island.bed
A2a_27me3_Active_merged_CPM.bw


title: LT_0h (SLX.12561.N703_S506)


title: LT_0h (SLX.12561.N705_S505)


title: LT_0h (SLX.12561.N703_S505)


title: LT_0h (SLX.12561.N705_S504)


title: A2a H3K4me3 Active Motif rep2

value: H3K4me3 Active Motif


title: A2a H3K27me3 Active Motif rep1


title: A2a H3K4me3 Active Motif rep1


title: LT_0h (SLX.12561.N703_S504)

value: pool 1


title: LT_0h (SLX.12561.N703_S502)


title: LT_0h (SLX.12561.N703_S503)


title: serum-control-77707

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Data processing
Matrix non-normalized: Assays with multiple melting curve peaks or inconsistent with the specifications (more details in label protocol) or differing by less than 5 Cq from negative control were removed. Data from two batches of assays were included in a single table. Otherwise data are unprocessed.
Matrix normalized: For further analysis, miRNAs were filtered so that the final set contains miRNAs with Cq<37 in at least half of the samples in each of the four groups (ALMS, BBS, control, obesity). Batch effect was removed using ComBat run in R with batch marked as A or B as indicated in samples’ characteristics. Finally, Cq values were normalized by subtracting each Cq value from mean Cq for 80 miRNAs detected in all samples. As a result, higher normalized values indicate higher expression (contrary to raw Cq). All above-described steps, except ComBat, were implemented in Python.
Fold Change: Data in this sheet were generated using limma algorithm in R.
Data description
Matrix non-normalized: Data as provided by laboratory after background filtration. Values within 5 Cq from negative control were considered as noise and removed. No further processing was applied.
Matrix normalized: Data filtered and normalized as described in “data processing” section.
Fold Change: Presented fold-changes (FC) were calculated on preprocessed data (matrix normalized) using limma in R. The limma model included only one explanatory variable: group, taking one of the following values for each patient: ALMS, BBS, obesity, control as indicated in samples’ characteristics. Single model was developed including all four groups. FC values were calculated for pairwise comparisons of the groups.

label: SYBR green

source_name: Serum

label_protocol: 19 µl RNA was reverse transcribed in 95 µl reactions using the miRCURY LNA RT Kit (QIAGEN). cDNA was diluted 50 x and assayed in 10 µl PCR reactions according to the protocol for miRCURY LNA miRNA PCR; each miRNA was assayed once by qPCR on the miRNA Ready-to-Use PCR, Human panel I+II using miRCURY LNA SYBR Green master mix. Negative controls excluding template from the reverse transcription reaction were performed and profiled like the samples. The amplification was performed in a LightCycler 480 Real-Time PCR System (Roche) in 384 well plates. The amplification curves were analyzed using the Roche LC software, both for determination of Cq (by the 2nd derivative method) and for melting curve analysis.

extract_protocol: The serum was thawed on ice and centrifuged at 3000 x g for 5 min in a 4°C. An aliquot of 200 μL per sample was transferred to a FluidX tube and 60 μl of Lysis solution BF containing 1μg carrier-RNA per 60μl Lysis Solution BF and RNA spike-in template mixture was added to the sample and mixed for 1 min and incubated for 7 min at room temperature, followed by addition of 20 μL Protein Precipitation solution BF. Total RNA was extracted from the samples using miRCURY RNA isolation Kit – Biofuids; high-throughput bead-based protocol (Hilden, Germany) in an automated 96 well format. The purified total RNA was eluted in a final volume of 50 μl.

tag: group

tag: gender

value: female

tag: batch

value: B

value: serum from blood


title: LT_0h (SLX.12561.N703_S508)


title: A2a H3K4me3 Abcam rep1

description:
A2a_H3K4me3_peaks.narrowPeak
A2a_K4_ABCAM_merged_CPM.bw

tag: strain

value: H3K4me3 Abcam


title: LT_0h (SLX.12561.N702_S517)


title: M2

city: Daegu

first: Byungheon

last: Lee

state: Outside U.S. & Canada

address: 680 Guckchaebosang-ro, Jung-gu

department: School of Medicine

country: South Korea

institute: Kyungpook National University

description: miR expression in M2 macrophages

hyb_protocol: Hybridization was done using GeneChip hybridization oven, followed by washing and staining using Genechip fluidics station.The labeled RNA was heated to 99°C for 5 minutes and then to 45°C for 5 minutes.  RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 hours at 48°C on an Affymetrix® 450 Fluidics Station.  The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, California, United States).

scan_protocol: The chips were then scanned with an Affymetrix GCS 3000 canner (Affymetrix, Santa Clara, California, United States).

data_processing:
Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species.  The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.   All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2
The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species.The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2.

label: FlashTag Biotin HSR RNA label

label_protocol: poly*(A) tailing and ligation were done using FlashTag Biotin HSR RNA labelling kit

growth_protocol: Bone marrow cells were isolated from tibias and femurs of Balb/c mice and cultured in DMEM supplemented with 10 ng/mL of colony-stimulating factor-1 (CSF-1; Gibco, Carlsbad, CA, USA) and 10% FBS for 7 d. The culture medium was changed every other day.

extract_protocol: RNAs for miRNA profiling were isolated using the miRNeasy® Mini Kit. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Next, the cells were incubated with  20 ng/mL of recombinant mouse IL4 for 24–48 h to achieve M2 polarization.

value: Balb/c

tag: genotype

value: WT

value: M2 macrophage


title: M2 treated with Aza and TSA, biological rep 1

description: miR expression in M2 macrophages after treatment with epigenetic modifiers

source_name: M2 treated with Aza and TSA

treatment_protocol: Next, the cells were incubated with  20 ng/mL of recombinant mouse IL4 for 24–48 h to achieve M2 polarization.Then,macrophages were treated with 5-aza-dC for 24 h followed by treatment with 5-aza-dC and TSA for 48 h.

value: Aza and TSA


title: M2 treated with Aza and TSA, biological rep 2


title: D1 H3K4me3 Active Motif rep2

source_name: INTACT-isolated MSN D1 cells

value: MSN D1

tag: chip antibody


title: LT_0h (SLX.12561.N702_S508)

value: cord blood

tag: experimental batch


title: M1 treated with Aza and TSA

description: miR expression in M1 macrophages after treatment with epigenetic modifiers

source_name: M1 treated with Aza and TSA

treatment_protocol: Next, the cells were incubated with 100 ng/mL of lipopolysaccharide and 20 ng/mL of recombinant mouse IFN-γ (R&D Systems, Minneapolis, MN, USA), for 24–48 h to achieve M1 polarization.Then,macrophages were treated with 5-aza-dC for 24 h followed by treatment with 5-aza-dC and TSA for 48 h.

value: M1 macrophage


title: D1 H3K4me3 Active Motif rep1


title: Control BMDM

description: miR expression in bone marrow derived macrophage from mouse

source_name: Control BMDM

value: BMDM

value: Control


title: M1, biological rep 1

description: miR expression in M1 macrophages

treatment_protocol: Next, the cells were incubated with 100 ng/mL of lipopolysaccharide and 20 ng/mL of recombinant mouse IFN-γ (R&D Systems, Minneapolis, MN, USA), for 24–48 h to achieve M1 polarization.


title: serum-control-77705

tag: age


title: serum-control-77704

value: male


title: M1, biological rep 2

description: miR expression in M1 macrophages

tag: Sex


title: serum-control-77703


title: LT_0h (SLX.12561.N702_S507)

value: LT-HSCs

tag: incubation time

tag: treatment

value: UNTR


title: D1 H3K4me3 Abcam rep2

description:
D1_H3K4me3_peaks.narrowPeak
D1_K4_abcam_merged_CPM.bw


title: A2a H3K4me3 Abcam rep2

value: MSN A2a


title: serum-control-77706

value: female

tag: tissue


title: serum-control-77702

value: B


title: D1 H3K4me3 Abcam rep1


title: LT_0h (SLX.12561.N702_S506)

value: pool 1


title: LT_0h (SLX.12561.N707_S517)


title: D1 H3K4me3 Epicyphr

value: H3K4me3 Epicyphr


title: LT_0h (SLX.12561.N702_S504)


title: LT_0h (SLX.12561.N702_S505)


title: D1 no antibody control

value: no antibody


title: LT_0h (SLX.12561.N702_S503)


title: A2a IgG control

value: IgG Epicyphr


title: A2a H3K4me3 Epicyphr rep2


title: LT_0h (SLX.12561.N701_S508)


title: serum-control-77701

value: serum from blood


title: serum-control-77700


title: serum-obesity-77697

value: Obesity


title: serum-control-77699


title: serum-control-77698


title: N2a H3K27me3 500K

value: neuroblastoma cell

value: H3K27me3 Active Motif


title: serum-obesity-77695


title: LT_0h (SLX.12561.N701_S507)

value: cord blood


title: A2a H3K4me3 Epicyphr rep1


title: serum-obesity-77696


title: serum-obesity-77694


title: LT_0h (SLX.12561.N701_S506)


title: N2a H3K27me3 50K


title: D1 IgG control

value: MSN D1


title: LT_0h (SLX.12561.N701_S504)


title: N2a H3K4me3 500K


title: serum-obesity-77693


title: N2a H3K4me3 50K


title: LT_0h (SLX.12561.N701_S503)


title: LT_0h (SLX.12561.N701_S505)


title: serum-obesity-77692


title: serum-obesity-77691


title: serum-obesity-77690


title: LT_0h (SLX.12561.N702_S502)


title: LT_0h (SLX.12561.N701_S517)


title: N2a IgG 500K


title: LT_0h (SLX.12561.N701_S502)


title: N2a IgG 50K


title: serum-obesity-77689


title: Tubular epithelial cells_baseline_rep4

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

data_processing:
RNA-sequencing data was processed as previously described in Chothani et al, 20191. Raw sequencing data (.bcl files) were demultiplexed into fastq files with Illumina’s bcl2fastq v2.16.0.10 based on unique index pairs. Adaptors and low quality reads were trimmed using Trimmomatic V0.362, retaining reads >20 nucleotides. Read mapping was carried out using STAR v2.5.2b3 to the Ensembl Human GRCh38 v86 reference genome using standard parameters for full-length RNA-seq in the ENCODE project. Read counting was carried out using featureCounts4 to get gene-level quantification of genomic features: featureCounts -t exon -g gene_id -O -s 2 -J -p -R -G. Quality check for sequencing data and mapping data was carried out using FastQC v0.11.55 and MultiQC6. Differential expression (DE) was performed with DESeq2 v1.14.17 by using raw reads count from featureCounts. Baseline samples were used as the reference level for each paired two-group comparison with 1h, 6h and 24h samples.
Assembly: hg38

source_name: Renal tubular epithelial cells

extract_protocol: Primary human renal proximal tubular epithelial cells (TECs, 4100, lot 19754, ScienCell) isolated from healthy human kidney (20 year old female) were grown and maintained in complete renal epithelial cell growth medium (4101, ScienCell) containing fetal bovine serum (FBS, 0010, ScienCell), epithelial cell growth supplement (EpiCGS, 4152, ScienCell) and antibiotic solution (P/S, 0503, ScienCell).

value: Renal tubular epithelial cells

value: baseline


title: Tubular epithelial cells_baseline_rep1


title: Tubular epithelial cells_baseline_rep2


title: Tubular epithelial cells_baseline_rep3


title: Liver HFD 335

city: Qingdao

first: Chen

address: Hefei Road 758

institute: Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University

description: mRNA

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using HISAT2.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with count and annotation for every sample and every gene

source_name: Liver

extract_protocol:
Liver were homogenized on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols by NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: source

value: liver

value: HFD


title: Liver I3A 303

description: mRNA


title: serum-obesity-77688


title: Liver HFD 334

description: mRNA


title: serum-obesity-77687


title: siPARP1_Input_BR2_2

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
ChIP-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. H4K20me1 enriched regions were identified by calling broad peaks (target over input) using MACS2. Signal tracks were generated using deeptools bamCoverage with the parameters, -normalizeUsing RPKM -of bigwig. H4K20me1 peaks were annotated using HOMER annotatePeaks.pl.  Transcription factor binding motifs enrichment near H4K20me1peaks was searched using the HOMER tool findMotifsGenome.pl with default parameters
NicE-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. Open chromatin regions were identified by callingnarrow peaks using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: HeLa

growth_protocol: HeLa cells were grown according to ATCC ‘s recommendations.

extract_protocol: ChiP-seq, One-pot UniNicE-seq

treatment_protocol: For PARP1 overexpression and knockdown study, HeLa cells were cultured in a 6 well plate format. After FLAG-PARP1 plasmid (control used as FLAG-plasmid) or esiRNA PARP1 (control used as esiRNA GFP) transfections for 48hrs, chromatin and DNA was extracted according to New England Biolabs's recommendations and submitted to ChIP-seq and NicE-seq respectively.

value: Cervical cancer cells

tag: condition

value: Input

tag: antibody


title: Liver I3A 305

description: mRNA


title: Hashtagged_scVDJ_sample_2

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: 10X Genomics VDJ

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v3.1.0).
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scVDJ-seq

extract_protocol:
Fresh human biospecimens were initially digested into a single cell suspension and cryopreserved in Bambanker Freezing Medium. On the day of the 10X Genomics protocol, cryopreserved samples were thawed, sorted for DAPI- CD45+ CD3+ T cells, hashtagged, stained with TotalSeq C v.1.0 cocktail from Biolegend.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Briefly, cDNA amplification included 14-16 cycles and 5.8 ng-20 ng of the material was used to prepare sequencing libraries with 16 cycles of PCR. An aliquot of cDNA generated was used to enrich for V(D)J regions using the Chromium Single Cell V(D)J Enrichment Kit Human T Cell according to the manufacturer’s protocol with 10 cycles of PCR during enrichment and 9 cycles during library preparation. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE150 or PE26/91 run using the NovaSeq 6000 SP or S4 Reagent Kit. An average of 24 million paired reads was generated per sample.

value: T cells


title: Tubular epithelial cells_stimulated_6 hour_rep3

value: stimulated 6 hour


title: Tubular epithelial cells_stimulated_6 hour_rep2


title: Tubular epithelial cells_stimulated_6 hour_rep4


title: Hashtagged_scVDJ_sample_1

description: 10X Genomics VDJ


title: serum-ALMS-77685

value: Alström syndrome (ALMS)

value: male

value: B


title: serum-BBS-77684

value: Bardet-Biedl syndrome (BBS)

value: female

value: serum from blood


title: siGFP_Input_BR2_2


title: serum-BBS-77686


title: Tubular epithelial cells_stimulated_6 hour_rep1


title: Hashtagged_scCITEseq_sample_2

description: 10X Genomics HTO and CITEseq

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v3.1.0).
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

extract_protocol:
Fresh human biospecimens were initially digested into a single cell suspension and cryopreserved in Bambanker Freezing Medium. On the day of the 10X Genomics protocol, cryopreserved samples were thawed, sorted for DAPI- CD45+ CD3+ T cells, hashtagged, stained with TotalSeq C v.1.0 cocktail from Biolegend.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Briefly, cDNA amplification included 14-16 cycles and 5.8 ng-20 ng of the material was used to prepare sequencing libraries with 16 cycles of PCR. Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup with aMPure XP beads. Libraries were constructed using the Chromium Single Cell 5’ Feature Barcode Library Kit according to the manufacturer’s protocol with 9 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE26/91 or PE28/91 run using the NovaSeq 6000 SP or S2 Reagent Kit. An average of 60 million paired reads was generated per sample.


title: siPARP1_Input_BR2_1


title: serum-BBS-77682


title: serum-BBS-77681


title: Hashtagged_scCITEseq_sample_1

description: 10X Genomics HTO and CITEseq


title: siGFP_Input_BR2_1


title: siPARP1_Knockdown_H4K20me1_ChIP_BR2_2


title: Tubular epithelial cells_stimulated_24 hour_rep3

value: stimulated 24 hour


title: serum-BBS-77680


title: siPARP1_Knockdown_H4K20me1_ChIP_BR2_1


title: Tubular epithelial cells_stimulated_24 hour_rep2


title: serum-ALMS-77683


title: serum-ALMS-77679


title: Hashtagged_scRNA_sample_1

description: 10X Genomics scRNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v3.1.0).
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Fresh human biospecimens were initially digested into a single cell suspension and cryopreserved in Bambanker Freezing Medium. On the day of the 10X Genomics protocol, cryopreserved samples were thawed, sorted for DAPI- CD45+ CD3+ T cells, hashtagged, stained with TotalSeq C v.1.0 cocktail from Biolegend.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Briefly, cDNA amplification included 14-16 cycles and 5.8 ng-20 ng of the material was used to prepare sequencing libraries with 16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE26/91 or PE28/91 run using the NovaSeq 6000 SP or S1 Reagent Kit. An average of 108 million reads were generated per sample.


title: LT_6h (SLX.12561.N716_S505)

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

source_name: cord blood

value: cord blood

value: LT-HSCs

value: UNTR

tag: donor

value: pool 1


title: Hashtagged_scRNA_sample_2

description: 10X Genomics scRNA

tag: cell type


title: serum-ALMS-77677

tag: group


title: Tubular epithelial cells_stimulated_1 hour_rep4

value: Renal tubular epithelial cells

value: stimulated 1 hour